include tool in default message_property_mappings

* fix: run deduplication before saving dataset during preprocessing

Move deduplicate_and_log_datasets call before save_preprocessed_dataset
in both SFT and RL data loading pipelines. This ensures the saved
preprocessed dataset is already de-duplicated, so subsequent loads
from cache don't contain duplicates.

Fixes #2719

* fix: include deduplication flag in dataset hash and warn on skip_prepare_dataset+dedup

- Add dataset_exact_deduplication to the hash string in
  generate_dataset_hash_from_config so cached datasets are invalidated
  when the dedup setting changes.
- Log a warning when skip_prepare_dataset=True and
  dataset_exact_deduplication=True, since dedup will be silently
  skipped in that configuration (both SFT and RL paths).

* fix: add ValueError for skip_prepare+dedup, fix test mock target and formatting

- Add config validator (check_deduplication_with_skip_prepare) that raises
  ValueError when skip_prepare_dataset=True and dataset_exact_deduplication=True
- Replace runtime warnings in sft.py/rl.py with the validator check
- Fix RL test: patch axolotl.utils.data.rl.load_tokenizer instead of
  axolotl.loaders.load_tokenizer to properly mock the imported reference
- Fix ruff lint (remove unused imports) and formatting issues

* refactor: inline deduplicate function per review feedback

* fix test fixture, lint

---------

Co-authored-by: ManasVardhan <manasvardhan@users.noreply.github.com>
Co-authored-by: Wing Lian <wing@axolotl.ai>

.github/workflows/base.yml

@@ -51,14 +51,22 @@ jobs:
             torch_cuda_arch_list: "7.0 7.5 8.0 8.6 8.7 8.9 9.0+PTX"
             dockerfile: "Dockerfile-base"
             platforms: "linux/amd64,linux/arm64"
-          - cuda: "129"
-            cuda_version: 12.9.1
+          - cuda: "128"
+            cuda_version: 12.8.1
             cudnn_version: ""
             python_version: "3.12"
-            pytorch: 2.9.1
+            pytorch: 2.10.0
             torch_cuda_arch_list: "7.0 7.5 8.0 8.6 8.7 8.9 9.0+PTX"
             dockerfile: "Dockerfile-base"
             platforms: "linux/amd64,linux/arm64"
+#          - cuda: "129"
+#            cuda_version: 12.9.1
+#            cudnn_version: ""
+#            python_version: "3.12"
+#            pytorch: 2.9.1
+#            torch_cuda_arch_list: "7.0 7.5 8.0 8.6 8.7 8.9 9.0+PTX"
+#            dockerfile: "Dockerfile-base"
+#            platforms: "linux/amd64,linux/arm64"
           - cuda: "130"
             cuda_version: 13.0.0
             cudnn_version: ""
@@ -75,6 +83,14 @@ jobs:
             torch_cuda_arch_list: "9.0+PTX"
             dockerfile: "Dockerfile-base"
             platforms: "linux/amd64,linux/arm64"
+          - cuda: "130"
+            cuda_version: 13.0.0
+            cudnn_version: ""
+            python_version: "3.12"
+            pytorch: 2.10.0
+            torch_cuda_arch_list: "9.0+PTX"
+            dockerfile: "Dockerfile-base"
+            platforms: "linux/amd64,linux/arm64"
 #          - cuda: "128"
 #            cuda_version: 12.8.1
 #            cudnn_version: ""
@@ -157,14 +173,22 @@ jobs:
             torch_cuda_arch_list: "7.0 7.5 8.0 8.6 8.7 8.9 9.0+PTX"
             dockerfile: "Dockerfile-uv-base"
             platforms: "linux/amd64,linux/arm64"
-          - cuda: "129"
-            cuda_version: 12.9.1
+          - cuda: "128"
+            cuda_version: 12.8.1
             cudnn_version: ""
             python_version: "3.12"
-            pytorch: 2.9.1
+            pytorch: 2.10.0
             torch_cuda_arch_list: "7.0 7.5 8.0 8.6 8.7 8.9 9.0+PTX"
             dockerfile: "Dockerfile-uv-base"
             platforms: "linux/amd64,linux/arm64"
+#          - cuda: "129"
+#            cuda_version: 12.9.1
+#            cudnn_version: ""
+#            python_version: "3.12"
+#            pytorch: 2.9.1
+#            torch_cuda_arch_list: "7.0 7.5 8.0 8.6 8.7 8.9 9.0+PTX"
+#            dockerfile: "Dockerfile-uv-base"
+#            platforms: "linux/amd64,linux/arm64"
           - cuda: "130"
             cuda_version: 13.0.0
             cudnn_version: ""
@@ -181,6 +205,14 @@ jobs:
             torch_cuda_arch_list: "9.0+PTX"
             dockerfile: "Dockerfile-uv-base"
             platforms: "linux/amd64,linux/arm64"
+          - cuda: "130"
+            cuda_version: 13.0.0
+            cudnn_version: ""
+            python_version: "3.12"
+            pytorch: 2.10.0
+            torch_cuda_arch_list: "9.0+PTX"
+            dockerfile: "Dockerfile-uv-base"
+            platforms: "linux/amd64,linux/arm64"
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.github/workflows/main.yml

@@ -34,16 +34,28 @@ jobs:
             axolotl_extras:
             platforms: "linux/amd64,linux/arm64"
             is_latest: true
-          - cuda: 129
-            cuda_version: 12.9.1
+          - cuda: 128
+            cuda_version: 12.8.1
             python_version: "3.12"
+            pytorch: 2.10.0
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+#          - cuda: 129
+#            cuda_version: 12.9.1
+#            python_version: "3.12"
+#            pytorch: 2.9.1
+#            axolotl_extras:
+#            platforms: "linux/amd64,linux/arm64"
+          - cuda: 130
+            cuda_version: 13.0.0
+            python_version: "3.11"
             pytorch: 2.9.1
             axolotl_extras:
             platforms: "linux/amd64,linux/arm64"
           - cuda: 130
             cuda_version: 13.0.0
-            python_version: "3.11"
-            pytorch: 2.9.1
+            python_version: "3.12"
+            pytorch: 2.10.0
             axolotl_extras:
             platforms: "linux/amd64,linux/arm64"
     runs-on: axolotl-gpu-runner
@@ -86,6 +98,77 @@ jobs:
             ${{ (matrix.is_latest) && format('{0}-latest', steps.metadata.outputs.tags) || '' }}
           labels: ${{ steps.metadata.outputs.labels }}
 
+  build-axolotl-uv:
+    if: ${{ ! contains(github.event.commits[0].message, '[skip docker]') && github.repository_owner == 'axolotl-ai-cloud' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - cuda: 128
+            cuda_version: 12.8.1
+            python_version: "3.11"
+            pytorch: 2.9.1
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+            is_latest: true
+          - cuda: 128
+            cuda_version: 12.8.1
+            python_version: "3.12"
+            pytorch: 2.10.0
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+          - cuda: 130
+            cuda_version: 13.0.0
+            python_version: "3.11"
+            pytorch: 2.9.1
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+          - cuda: 130
+            cuda_version: 13.0.0
+            python_version: "3.12"
+            pytorch: 2.10.0
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+    runs-on: axolotl-gpu-runner
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Docker metadata
+        id: metadata
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            axolotlai/axolotl-uv
+          tags: |
+            type=ref,event=branch
+            type=pep440,pattern={{version}}
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      # guidance for testing before pushing: https://docs.docker.com/build/ci/github-actions/test-before-push/
+      - name: Build and export to Docker
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: ${{ matrix.platforms }}
+          build-args: |
+            BASE_TAG=${{ github.ref_type == 'tag' && 'main' || github.ref_name }}-base-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}
+            CUDA=${{ matrix.cuda }}
+            PYTORCH_VERSION=${{ matrix.pytorch }}
+            AXOLOTL_ARGS=${{ matrix.axolotl_args }}
+            AXOLOTL_EXTRAS=${{ matrix.axolotl_extras}}
+          file: ./docker/Dockerfile-uv
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: |
+            ${{ steps.metadata.outputs.tags }}-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}${{ matrix.axolotl_extras != '' && '-' || '' }}${{ matrix.axolotl_extras }}
+            ${{ steps.metadata.outputs.tags }}-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}
+            ${{ (matrix.is_latest) && format('{0}-latest', steps.metadata.outputs.tags) || '' }}
+          labels: ${{ steps.metadata.outputs.labels }}
+
   build-axolotl-cloud:
     needs: build-axolotl
     if: ${{ ! contains(github.event.commits[0].message, '[skip docker]') && github.repository_owner == 'axolotl-ai-cloud' }}
@@ -112,16 +195,28 @@ jobs:
             axolotl_extras:
             is_latest: true
             platforms: "linux/amd64,linux/arm64"
-          - cuda: 129
-            cuda_version: 12.9.1
+          - cuda: 128
+            cuda_version: 12.8.1
             python_version: "3.12"
+            pytorch: 2.10.0
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+#          - cuda: 129
+#            cuda_version: 12.9.1
+#            python_version: "3.12"
+#            pytorch: 2.9.1
+#            axolotl_extras:
+#            platforms: "linux/amd64,linux/arm64"
+          - cuda: 130
+            cuda_version: 13.0.0
+            python_version: "3.11"
             pytorch: 2.9.1
             axolotl_extras:
             platforms: "linux/amd64,linux/arm64"
           - cuda: 130
             cuda_version: 13.0.0
-            python_version: "3.11"
-            pytorch: 2.9.1
+            python_version: "3.12"
+            pytorch: 2.10.0
             axolotl_extras:
             platforms: "linux/amd64,linux/arm64"
     runs-on: axolotl-gpu-runner
@@ -159,6 +254,73 @@ jobs:
              ${{ (matrix.is_latest) && format('{0}-latest', steps.metadata.outputs.tags) || '' }}
           labels: ${{ steps.metadata.outputs.labels }}
 
+  build-axolotl-cloud-uv:
+    needs: build-axolotl-uv
+    if: ${{ ! contains(github.event.commits[0].message, '[skip docker]') && github.repository_owner == 'axolotl-ai-cloud' }}
+    # this job needs to be run on self-hosted GPU runners...
+    strategy:
+      matrix:
+        include:
+          - cuda: 128
+            cuda_version: 12.8.1
+            python_version: "3.11"
+            pytorch: 2.9.1
+            axolotl_extras:
+            is_latest: true
+            platforms: "linux/amd64,linux/arm64"
+          - cuda: 128
+            cuda_version: 12.8.1
+            python_version: "3.12"
+            pytorch: 2.10.0
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+          - cuda: 130
+            cuda_version: 13.0.0
+            python_version: "3.11"
+            pytorch: 2.9.1
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+          - cuda: 130
+            cuda_version: 13.0.0
+            python_version: "3.12"
+            pytorch: 2.10.0
+            axolotl_extras:
+            platforms: "linux/amd64,linux/arm64"
+    runs-on: axolotl-gpu-runner
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Docker metadata
+        id: metadata
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            axolotlai/axolotl-cloud-uv
+          tags: |
+            type=ref,event=branch
+            type=pep440,pattern={{version}}
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Build
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: ${{ matrix.platforms }}
+          build-args: |
+            BASE_TAG=${{ github.ref_type == 'tag' && 'main' || github.ref_name }}-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}${{ matrix.axolotl_extras != '' && '-' || '' }}${{ matrix.axolotl_extras }}
+            CUDA=${{ matrix.cuda }}
+          file: ./docker/Dockerfile-cloud-uv
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: |
+             ${{ steps.metadata.outputs.tags }}-py${{ matrix.python_version }}-cu${{ matrix.cuda }}-${{ matrix.pytorch }}${{ matrix.axolotl_extras != '' && '-' || '' }}${{ matrix.axolotl_extras }}
+             ${{ (matrix.is_latest) && format('{0}-latest', steps.metadata.outputs.tags) || '' }}
+          labels: ${{ steps.metadata.outputs.labels }}
+
   build-axolotl-cloud-no-tmux:
     needs: build-axolotl
     if: ${{ ! contains(github.event.commits[0].message, '[skip docker]') && github.repository_owner == 'axolotl-ai-cloud' }}

.github/workflows/tests-nightly.yml

@@ -37,7 +37,7 @@ jobs:
         id: hf-cache-restore-s3
         run: |
           mkdir -p /home/runner/.cache/huggingface/hub
-          curl -L https://d1dttdx32dkk5p.cloudfront.net/hf-cache.tar.zst | tar -xf - -C /home/runner/.cache/huggingface/hub/  --use-compress-program unzstd
+          curl -L https://axolotl-ci.b-cdn.net/hf-cache.tar.zst | tar -xf - -C /home/runner/.cache/huggingface/hub/  --use-compress-program unzstd
 
       - name: Setup Python
         uses: actions/setup-python@v5

.github/workflows/tests.yml

@@ -75,7 +75,7 @@ jobs:
         id: hf-cache-restore-s3
         run: |
           mkdir -p ~/.cache/huggingface/hub
-          curl -L https://d1dttdx32dkk5p.cloudfront.net/hf-cache.tar.zst | tar -xpf - -C ~/.cache/huggingface/hub/  --use-compress-program unzstd --strip-components=1
+          curl -L https://axolotl-ci.b-cdn.net/hf-cache.tar.zst | tar -xpf - -C ~/.cache/huggingface/hub/  --use-compress-program unzstd --strip-components=1
           ls -ltr ~/.cache/huggingface/hub/
 
       - name: Setup Python
@@ -170,7 +170,7 @@ jobs:
         id: hf-cache-restore-s3
         run: |
           mkdir -p ~/.cache/huggingface/hub
-          curl -L https://d1dttdx32dkk5p.cloudfront.net/hf-cache.tar.zst | tar -xpf - -C ~/.cache/huggingface/hub/  --use-compress-program unzstd --strip-components=1
+          curl -L https://axolotl-ci.b-cdn.net/hf-cache.tar.zst | tar -xpf - -C ~/.cache/huggingface/hub/  --use-compress-program unzstd --strip-components=1
           ls -ltr ~/.cache/huggingface/hub/
 
       - name: Setup Python
@@ -264,8 +264,8 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - cuda: 129
-            cuda_version: 12.9.1
+          - cuda: 130
+            cuda_version: 13.0.0
             python_version: "3.12"
             pytorch: 2.9.1
             num_gpus: 1

.gitignore

@@ -193,6 +193,3 @@ out/
 
 # scm auto-versioning
 src/axolotl/_version.py
-
-# macOS
-.DS_Store

docker/Dockerfile-base

@@ -59,34 +59,18 @@ RUN git lfs install --skip-repo && \
     pip3 install -U --no-cache-dir pydantic==1.10.10 && \
     pip3 cache purge
 
-RUN case "$PYTORCH_VERSION" in \
-        2.9.[0-9]*) \
-            if [ "$CUDA" = "128" ]; then \
-                if [ "$TARGETARCH" = "amd64" ]; then \
-                    WHL_FILE="flash_attn-2.8.3+cu128torch2.9-cp311-cp311-linux_x86_64.whl"; \
-                    WHL_VERSION="v0.5.4"; \
-                elif [ "$TARGETARCH" = "arm64" ]; then \
-                    WHL_FILE="flash_attn-2.8.3+cu128torch2.9-cp311-cp311-linux_aarch64.whl"; \
-                    WHL_VERSION="v0.6.4"; \
-                else \
-                    echo "Unsupported architecture: $TARGETARCH"; exit 1; \
-                fi; \
-                wget -nv https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/${WHL_VERSION}/${WHL_FILE}; \
-                pip3 install --no-cache-dir ${WHL_FILE}; \
-                rm ${WHL_FILE}; \
-            elif [ "$CUDA" = "130" ]; then \
-                if [ "$TARGETARCH" = "amd64" ]; then \
-                    WHL_FILE="flash_attn-2.8.3+cu130torch2.9-cp311-cp311-linux_x86_64.whl"; \
-                    WHL_VERSION="v0.5.4"; \
-                elif [ "$TARGETARCH" = "arm64" ]; then \
-                    WHL_FILE="flash_attn-2.8.3+cu130torch2.9-cp311-cp311-linux_aarch64.whl"; \
-                    WHL_VERSION="v0.6.4"; \
-                else \
-                    echo "Unsupported architecture: $TARGETARCH"; exit 1; \
-                fi; \
-                wget -nv https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/${WHL_VERSION}/${WHL_FILE}; \
-                pip3 install --no-cache-dir ${WHL_FILE}; \
-                rm ${WHL_FILE}; \
-            fi \
-            ;; \
-    esac
+# Map Python version (e.g., 3.12 -> cp312)
+RUN PYTHON_CP="cp$(echo $PYTHON_VERSION | tr -d '.')" && \
+    # Map PyTorch version (e.g., 2.9.1 -> torch2.9, 2.10.0 -> torch2.10)
+    TORCH_TAG="torch$(echo $PYTORCH_VERSION | grep -oP '^\d+\.\d+')" && \
+    # Map architecture
+    case "$TARGETARCH" in \
+        amd64) ARCH_TAG="x86_64" ;; \
+        arm64) ARCH_TAG="aarch64" ;; \
+        *) echo "Unsupported architecture: $TARGETARCH"; exit 1 ;; \
+    esac && \
+    WHL_VERSION="v0.7.16" && \
+    WHL_FILE="flash_attn-2.8.3+cu${CUDA}${TORCH_TAG}-${PYTHON_CP}-${PYTHON_CP}-linux_${ARCH_TAG}.whl" && \
+    wget -nv "https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/${WHL_VERSION}/${WHL_FILE}" && \
+    pip3 install --no-cache-dir "${WHL_FILE}" && \
+    rm "${WHL_FILE}"

docker/Dockerfile-cloud-uv

@@ -0,0 +1,30 @@
+ARG BASE_TAG=main
+FROM axolotlai/axolotl-uv:$BASE_TAG
+
+ENV HF_DATASETS_CACHE="/workspace/data/huggingface-cache/datasets"
+ENV HF_HUB_CACHE="/workspace/data/huggingface-cache/hub"
+ENV HF_HOME="/workspace/data/huggingface-cache/hub"
+ENV HF_HUB_ENABLE_HF_TRANSFER="1"
+
+EXPOSE 8888
+EXPOSE 22
+
+COPY scripts/cloud-entrypoint.sh /root/cloud-entrypoint.sh
+COPY scripts/motd /etc/motd
+
+RUN uv pip install jupyterlab notebook ipywidgets && \
+    jupyter lab clean
+RUN apt update && \
+    apt install --yes --no-install-recommends openssh-server tmux iproute2 nvtop && \
+    rm -rf /var/cache/apt/archives && \
+    rm -rf /var/lib/apt/lists/* && \
+    mkdir -p ~/.ssh && \
+    chmod 700 ~/.ssh && \
+    printf "\n[[ -z \"\$TMUX\"  ]] && { tmux attach-session -t ssh_tmux || tmux new-session -s ssh_tmux; exit; }\n" >> ~/.bashrc && \
+    printf "[ ! -z \"\$TERM\" -a -r /etc/motd ] && cat /etc/motd\n" >> ~/.bashrc && \
+    chmod +x /workspace/axolotl/scripts/cloud-entrypoint.sh && \
+    chmod +x /root/cloud-entrypoint.sh && \
+    echo 'set-option -g history-limit 5000' >> ~/.tmux.conf
+
+ENTRYPOINT ["/root/cloud-entrypoint.sh"]
+CMD ["sleep", "infinity"]

docker/Dockerfile-uv

@@ -0,0 +1,47 @@
+ARG BASE_TAG=main-base
+FROM axolotlai/axolotl-base-uv:$BASE_TAG
+
+ARG TORCH_CUDA_ARCH_LIST="7.0 7.5 8.0 8.6+PTX"
+ARG AXOLOTL_EXTRAS=""
+ARG AXOLOTL_ARGS=""
+ARG CUDA="118"
+ARG PYTORCH_VERSION="2.1.2"
+ARG TARGETARCH
+
+ENV PYTORCH_VERSION=$PYTORCH_VERSION
+
+RUN apt-get update && \
+    apt-get install -y --allow-change-held-packages vim curl nano libnccl2 libnccl-dev rsync s3fs && \
+    rm -rf /var/cache/apt/archives && \
+    rm -rf /var/lib/apt/lists/*
+
+WORKDIR /workspace
+
+RUN git clone --depth=1 https://github.com/axolotl-ai-cloud/axolotl.git
+
+WORKDIR /workspace/axolotl
+
+# If AXOLOTL_EXTRAS is set, append it in brackets; don't install deepspeed with arm64
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+        BASE_EXTRAS="flash-attn,ring-flash-attn,optimizers,ray"; \
+    else \
+        BASE_EXTRAS="deepspeed,flash-attn,ring-flash-attn,optimizers,ray"; \
+    fi && \
+    if [ "$AXOLOTL_EXTRAS" != "" ]; then \
+        uv pip install --no-build-isolation -e .[$BASE_EXTRAS,$AXOLOTL_EXTRAS] $AXOLOTL_ARGS; \
+    else \
+        uv pip install --no-build-isolation -e .[$BASE_EXTRAS] $AXOLOTL_ARGS; \
+    fi && \
+    python scripts/unsloth_install.py --uv | sh && \
+    python scripts/cutcrossentropy_install.py --uv | sh && \
+    uv pip install pytest && \
+    uv cache clean
+
+# fix so that git fetch/pull from remote works with shallow clone
+RUN git config remote.origin.fetch "+refs/heads/*:refs/remotes/origin/*" && \
+    git config --get remote.origin.fetch && \
+    git config --global credential.helper store
+
+COPY .axolotl-complete.bash /root/.axolotl-complete.bash
+RUN chmod +x /root/.axolotl-complete.bash && \
+    echo 'source /root/.axolotl-complete.bash' >> ~/.bashrc

docker/Dockerfile-uv-base

@@ -6,6 +6,7 @@ ARG TARGETARCH
 
 FROM nvidia/cuda:$CUDA_VERSION-cudnn$CUDNN_VERSION-devel-ubuntu$UBUNTU_VERSION AS base-builder
 
+ARG TARGETARCH
 ARG PYTHON_VERSION="3.11"
 ARG PYTORCH_VERSION="2.6.0"
 ARG CUDA="126"
@@ -39,28 +40,18 @@ RUN if [ "$TARGETARCH" = "amd64" ]; then \
         uv pip install "mamba_ssm @ git+https://github.com/state-spaces/mamba.git@main"; \
     fi
 
-RUN case "$PYTORCH_VERSION" in \
-        2.9.[0-9]*) \
-            if [ "$TARGETARCH" = "amd64" ]; then \
-                if [ "$CUDA" = "128" ]; then \
-                    wget -nv https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/v0.5.4/flash_attn-2.8.3+cu128torch2.9-cp311-cp311-linux_x86_64.whl; \
-                    uv pip install --no-cache-dir flash_attn-2.8.3+cu128torch2.9-cp311-cp311-linux_x86_64.whl; \
-                    rm flash_attn-2.8.3+cu128torch2.9-cp311-cp311-linux_x86_64.whl; \
-                elif [ "$CUDA" = "130" ]; then \
-                    wget -nv https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/v0.5.4/flash_attn-2.8.3+cu130torch2.9-cp311-cp311-linux_x86_64.whl; \
-                    uv pip install --no-cache-dir flash_attn-2.8.3+cu130torch2.9-cp311-cp311-linux_x86_64.whl; \
-                    rm flash_attn-2.8.3+cu130torch2.9-cp311-cp311-linux_x86_64.whl; \
-                fi \
-            elif [ "$TARGETARCH" = "arm64" ]; then \
-                if [ "$CUDA" = "128" ]; then \
-                    wget -nv https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/v0.6.4/flash_attn-2.8.3+cu128torch2.9-cp311-cp311-linux_aarch64.whl; \
-                    uv pip install --no-cache-dir flash_attn-2.8.3+cu128torch2.9-cp311-cp311-linux_aarch64.whl; \
-                    rm flash_attn-2.8.3+cu128torch2.9-cp311-cp311-linux_aarch64.whl; \
-                elif [ "$CUDA" = "130" ]; then \
-                    wget -nv https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/v0.6.4/flash_attn-2.8.3+cu130torch2.9-cp311-cp311-linux_aarch64.whl; \
-                    uv pip install --no-cache-dir flash_attn-2.8.3+cu130torch2.9-cp311-cp311-linux_aarch64.whl; \
-                    rm flash_attn-2.8.3+cu130torch2.9-cp311-cp311-linux_aarch64.whl; \
-                fi \
-            fi \
-            ;; \
-    esac
+# Map Python version (e.g., 3.12 -> cp312)
+RUN PYTHON_CP="cp$(echo $PYTHON_VERSION | tr -d '.')" && \
+    # Map PyTorch version (e.g., 2.9.1 -> torch2.9, 2.10.0 -> torch2.10)
+    TORCH_TAG="torch$(echo $PYTORCH_VERSION | grep -oP '^\d+\.\d+')" && \
+    # Map architecture
+    case "$TARGETARCH" in \
+        amd64) ARCH_TAG="x86_64" ;; \
+        arm64) ARCH_TAG="aarch64" ;; \
+        *) echo "Unsupported architecture: $TARGETARCH"; exit 1 ;; \
+    esac && \
+    WHL_VERSION="v0.7.16" && \
+    WHL_FILE="flash_attn-2.8.3+cu${CUDA}${TORCH_TAG}-${PYTHON_CP}-${PYTHON_CP}-linux_${ARCH_TAG}.whl" && \
+    wget -nv "https://github.com/mjun0812/flash-attention-prebuild-wheels/releases/download/${WHL_VERSION}/${WHL_FILE}" && \
+    uv pip install --no-cache-dir "${WHL_FILE}" && \
+    rm "${WHL_FILE}"

docs/cli.qmd

@@ -210,6 +210,8 @@ axolotl lm-eval config.yml
 Configuration options:
 
 ```yaml
+lm_eval_model: # model to evaluate (local or hf path)
+
 # List of tasks to evaluate
 lm_eval_tasks:
   - arc_challenge
@@ -218,7 +220,7 @@ lm_eval_batch_size: # Batch size for evaluation
 output_dir: # Directory to save evaluation results
 ```
 
-See [LM Eval Harness](https://github.com/EleutherAI/lm-evaluation-harness) for more details.
+See [LM Eval Harness integration docs](https://docs.axolotl.ai/docs/custom_integrations.html#language-model-evaluation-harness-lm-eval) for full configuration details.
 
 ### delinearize-llama4
 

examples/colab-notebooks/colab-axolotl-example.ipynb

@@ -40,7 +40,7 @@
     "%%capture\n",
     "# This step can take ~5-10 minutes to install dependencies\n",
     "!pip install --no-build-isolation axolotl[flash-attn]>=0.9.1\n",
-    "!pip install \"cut-cross-entropy[transformers] @ git+https://github.com/axolotl-ai-cloud/ml-cross-entropy.git@0d4ce4b\""
+    "!pip install \"cut-cross-entropy[transformers] @ git+https://github.com/axolotl-ai-cloud/ml-cross-entropy.git@58d6572\""
    ]
   },
   {

examples/gemma3/gemma-3-4b-qlora.yml

@@ -1,7 +1,8 @@
 base_model: google/gemma-3-4b-it
 
-plugins:
-  - axolotl.integrations.gemma3.Gemma3TextFromMultimodalPlugin
+# Need to set else transformers tries to load vision too
+model_type: Gemma3ForCausalLM
+cls_model_config: Gemma3TextConfig
 
 load_in_4bit: true
 
@@ -29,6 +30,7 @@ lora_model_dir:
 sequence_len: 2048
 sample_packing: true
 
+
 lora_r: 32
 lora_alpha: 16
 lora_dropout: 0

examples/qat_nvfp4/Gemma3-12B_baseline.yml

@@ -1,11 +1,12 @@
 base_model: google/gemma-3-12b-it
+# Automatically upload checkpoint and final model to HF
 # hub_model_id: username/custom_model_name
+
 load_in_8bit: false
 load_in_4bit: false
 strict: false
 
 plugins:
-  - axolotl.integrations.gemma3.Gemma3TextFromMultimodalPlugin
   - axolotl.integrations.liger.LigerPlugin
 
 liger_rope: true

examples/qat_nvfp4/Gemma3-12B_qat.yml

@@ -7,7 +7,6 @@ load_in_4bit: false
 strict: false
 
 plugins:
-  - axolotl.integrations.gemma3.Gemma3TextFromMultimodalPlugin
   - axolotl.integrations.liger.LigerPlugin
 
 liger_rope: true

examples/qat_nvfp4/Math-Gemma3-12B_baseline.yml

@@ -1,11 +1,12 @@
 base_model: google/gemma-3-12b-it
+# Math finetuning configuration for Gemma3-12B
 # hub_model_id: username/custom_model_name
+
 load_in_8bit: false
 load_in_4bit: false
 strict: false
 
 plugins:
-  - axolotl.integrations.gemma3.Gemma3TextFromMultimodalPlugin
   - axolotl.integrations.liger.LigerPlugin
 
 liger_rope: true

examples/qat_nvfp4/Math-Gemma3-12B_qat.yml

@@ -7,7 +7,6 @@ load_in_4bit: false
 strict: false
 
 plugins:
-  - axolotl.integrations.gemma3.Gemma3TextFromMultimodalPlugin
   - axolotl.integrations.liger.LigerPlugin
 
 liger_rope: true

examples/qat_nvfp4/Math-Gemma3-27B_baseline.yml

@@ -1,11 +1,12 @@
 base_model: google/gemma-3-27b-it
+# Math finetuning configuration for Gemma3-27B
 # hub_model_id: username/custom_model_name
+
 load_in_8bit: false
 load_in_4bit: false
 strict: false
 
 plugins:
-  - axolotl.integrations.gemma3.Gemma3TextFromMultimodalPlugin
   - axolotl.integrations.liger.LigerPlugin
 
 liger_rope: true

examples/qat_nvfp4/Math-Gemma3-27B_qat.yml

@@ -7,7 +7,6 @@ load_in_4bit: false
 strict: false
 
 plugins:
-  - axolotl.integrations.gemma3.Gemma3TextFromMultimodalPlugin
   - axolotl.integrations.liger.LigerPlugin
 
 liger_rope: true

requirements.txt

@@ -2,25 +2,25 @@
 
 # START section of dependencies that don't install on Darwin/MacOS
 bitsandbytes==0.49.1
-triton>=3.0.0
+triton>=3.4.0
 mamba-ssm==1.2.0.post1
 xformers>=0.0.23.post1
-liger-kernel==0.6.4
+liger-kernel==0.7.0
 # END section
 
 packaging==26.0
 huggingface_hub>=1.1.7
 peft>=0.18.1
 tokenizers>=0.22.1
-transformers==5.0.0
+transformers==5.2.0
 accelerate==1.12.0
 datasets==4.5.0
 deepspeed>=0.18.3
-trl==0.27.1
+trl==0.28.0
 hf_xet==1.2.0
-kernels==0.11.5
+kernels==0.12.1
 
-trackio>=0.13.0
+trackio>=0.16.1
 typing-extensions>=4.15.0
 
 optimum==1.16.2
@@ -63,7 +63,7 @@ langdetect==1.0.9
 immutabledict==4.2.0
 antlr4-python3-runtime==4.13.2
 
-torchao==0.13.0
+torchao==0.16.0
 openenv-core==0.1.0
 schedulefree==1.4.1
 

scripts/cutcrossentropy_install.py

@@ -29,5 +29,5 @@ UV_PREFIX = "uv " if USE_UV else ""
 
 print(
     UNINSTALL_PREFIX
-    + f'{UV_PREFIX}pip install "cut-cross-entropy[transformers] @ git+https://github.com/axolotl-ai-cloud/ml-cross-entropy.git@0d4ce4b"'
+    + f'{UV_PREFIX}pip install "cut-cross-entropy[transformers] @ git+https://github.com/axolotl-ai-cloud/ml-cross-entropy.git@58d6572"'
 )

scripts/merge_gemma3_multimodal_weights.py

@@ -1,225 +0,0 @@
-"""Merge trained text-only Gemma3 weights back into a full multimodal checkpoint.
-
-After training with the Gemma3TextFromMultimodalPlugin, the saved checkpoint
-contains only the language model weights (with ``model.language_model.*``
-prefix, reversed by transformers v5's key_mapping on save).
-
-This script reconstructs a full ``Gemma3ForConditionalGeneration`` checkpoint by
-combining the trained language model weights with the original vision tower and
-projector weights from the base multimodal model.
-
-Usage::
-
-    python scripts/merge_gemma3_multimodal_weights.py \\
-        --original-model google/gemma-3-4b-it \\
-        --trained-model /path/to/trained/output \\
-        --output-dir /path/to/merged
-"""
-
-import argparse
-import json
-import logging
-from pathlib import Path
-
-import torch
-from huggingface_hub import split_torch_state_dict_into_shards
-from safetensors.torch import load_file, save_file
-from transformers import AutoConfig
-
-LOG = logging.getLogger(__name__)
-
-
-def collect_safetensors(model_dir: Path) -> dict[str, torch.Tensor]:
-    """Load and merge all safetensors shard files in a directory."""
-    shard_files = sorted(model_dir.glob("*.safetensors"))
-    if not shard_files:
-        raise FileNotFoundError(f"No safetensors files found in {model_dir}")
-
-    state_dict: dict[str, torch.Tensor] = {}
-    for shard in shard_files:
-        LOG.info("Loading %s", shard.name)
-        state_dict.update(load_file(str(shard)))
-    return state_dict
-
-
-def merge(
-    original_model: str,
-    trained_model: str,
-    output_dir: str,
-    *,
-    trust_remote_code: bool = False,
-) -> None:
-    original_path = Path(original_model)
-    trained_path = Path(trained_model)
-    out_path = Path(output_dir)
-    out_path.mkdir(parents=True, exist_ok=True)
-
-    # 1. Load the original multimodal checkpoint
-    LOG.info("Loading original multimodal weights from %s", original_model)
-    if original_path.is_dir():
-        original_sd = collect_safetensors(original_path)
-    else:
-        from huggingface_hub import snapshot_download
-
-        cached = Path(
-            snapshot_download(original_model, allow_patterns=["*.safetensors"])
-        )
-        original_sd = collect_safetensors(cached)
-
-    # 2. Load trained text-only weights (already reversed to model.language_model.* by
-    #    transformers v5 key_mapping on save)
-    LOG.info("Loading trained text-only weights from %s", trained_model)
-    trained_sd = collect_safetensors(trained_path)
-
-    # 3. Classify original keys
-    lang_keys = {k for k in original_sd if k.startswith("model.language_model.")}
-    vision_keys = {k for k in original_sd if k.startswith("model.vision_tower.")}
-    projector_keys = {
-        k for k in original_sd if k.startswith("model.multi_modal_projector.")
-    }
-    other_keys = set(original_sd.keys()) - lang_keys - vision_keys - projector_keys
-
-    LOG.info(
-        "Original checkpoint: %d language, %d vision, %d projector, %d other keys",
-        len(lang_keys),
-        len(vision_keys),
-        len(projector_keys),
-        len(other_keys),
-    )
-
-    # 4. Classify trained keys (reverse mapping on save gives model.language_model.* prefix)
-    trained_lang_keys = {k for k in trained_sd if k.startswith("model.language_model.")}
-    trained_other = set(trained_sd.keys()) - trained_lang_keys
-
-    LOG.info(
-        "Trained checkpoint: %d language keys, %d other keys",
-        len(trained_lang_keys),
-        len(trained_other),
-    )
-
-    # 5. Build merged state dict
-    merged: dict[str, torch.Tensor] = {}
-
-    # Keep vision tower and projector from original
-    for key in vision_keys | projector_keys:
-        merged[key] = original_sd[key]
-
-    # Use trained language model weights (overwrite original)
-    for key in trained_lang_keys:
-        merged[key] = trained_sd[key]
-
-    # For other trained keys (like lm_head.weight), use trained version
-    for key in trained_other:
-        merged[key] = trained_sd[key]
-
-    # For any original other keys not covered by trained (shouldn't usually happen),
-    # keep original
-    for key in other_keys:
-        if key not in merged:
-            merged[key] = original_sd[key]
-
-    # Check for missing language keys that were in original but not in trained
-    missing_lang = lang_keys - trained_lang_keys
-    if missing_lang:
-        LOG.warning(
-            "%d language keys in original but not in trained; keeping original: %s",
-            len(missing_lang),
-            list(missing_lang)[:5],
-        )
-        for key in missing_lang:
-            merged[key] = original_sd[key]
-
-    LOG.info("Merged checkpoint: %d total keys", len(merged))
-
-    # 6. Save merged weights (sharded at 50GB, matching transformers default)
-    LOG.info("Saving merged weights to %s", out_path)
-    state_dict_split = split_torch_state_dict_into_shards(merged, max_shard_size="50GB")
-
-    for filename, tensors in state_dict_split.filename_to_tensors.items():
-        shard = {name: merged[name] for name in tensors}
-        save_file(shard, str(out_path / filename))
-
-    if state_dict_split.is_sharded:
-        index = {
-            "metadata": {
-                "total_size": sum(t.numel() * t.element_size() for t in merged.values())
-            },
-            "weight_map": state_dict_split.tensor_to_filename,
-        }
-        with open(out_path / "model.safetensors.index.json", "w") as f:
-            json.dump(index, f, indent=2)
-        LOG.info("Saved %d shards", len(state_dict_split.filename_to_tensors))
-
-    # 7. Copy/update config
-    LOG.info("Writing config.json")
-    original_config = AutoConfig.from_pretrained(
-        original_model, trust_remote_code=trust_remote_code
-    )
-
-    # Update text_config fields from trained model's config if available
-    trained_config_path = trained_path / "config.json"
-    if trained_config_path.exists():
-        with open(trained_config_path) as f:
-            trained_config_dict = json.load(f)
-
-        # The trained config is the text sub-config; merge its fields into
-        # the original composite config's text_config
-        if hasattr(original_config, "text_config"):
-            for key, val in trained_config_dict.items():
-                if key not in ("model_type", "_name_or_path", "architectures"):
-                    if hasattr(original_config.text_config, key):
-                        setattr(original_config.text_config, key, val)
-
-    original_config.save_pretrained(out_path)
-
-    # 8. Copy tokenizer files from trained model if present
-    tokenizer_files = list(trained_path.glob("tokenizer*")) + list(
-        trained_path.glob("special_tokens_map*")
-    )
-    if tokenizer_files:
-        import shutil
-
-        for tok_file in tokenizer_files:
-            shutil.copy2(tok_file, out_path / tok_file.name)
-        LOG.info("Copied %d tokenizer files", len(tokenizer_files))
-
-    LOG.info("Merge complete. Output saved to %s", out_path)
-
-
-def main():
-    parser = argparse.ArgumentParser(
-        description="Merge trained text-only Gemma3 weights back into a multimodal checkpoint."
-    )
-    parser.add_argument(
-        "--original-model",
-        required=True,
-        help="HuggingFace model ID or local path to the original multimodal model",
-    )
-    parser.add_argument(
-        "--trained-model",
-        required=True,
-        help="Local path to the trained text-only model output directory",
-    )
-    parser.add_argument(
-        "--output-dir",
-        required=True,
-        help="Directory to save the merged multimodal checkpoint",
-    )
-    parser.add_argument(
-        "--trust-remote-code",
-        action="store_true",
-        default=False,
-        help="Trust remote code when loading model config",
-    )
-    args = parser.parse_args()
-
-    merge(
-        original_model=args.original_model,
-        trained_model=args.trained_model,
-        output_dir=args.output_dir,
-        trust_remote_code=args.trust_remote_code,
-    )
-
-
-if __name__ == "__main__":
-    main()

setup.py

@@ -26,6 +26,11 @@ def parse_requirements(extras_require_map):
     try:
         xformers_version = [req for req in _install_requires if "xformers" in req][0]
         install_xformers = platform.machine() != "aarch64"
+        if platform.machine() == "aarch64":
+            # skip torchao on ARM64
+            _install_requires = [
+                req for req in _install_requires if "torchao" not in req
+            ]
         if "Darwin" in platform.system():
             # skip packages not compatible with OSX
             skip_packages = [

src/axolotl/cli/config.py

@@ -5,7 +5,7 @@ import os
 import tempfile
 from pathlib import Path
 from tempfile import NamedTemporaryFile
-from typing import Union
+from typing import Any, Optional, Union
 from urllib.parse import urlparse
 
 import requests
@@ -32,6 +32,63 @@ from axolotl.utils.wandb_ import setup_wandb_env_vars
 
 LOG = get_logger(__name__)
 
+
+def _coerce_value(value: Any, existing: Optional[Any] = None) -> Any:
+    """Coerce a string CLI value to its most likely Python type.
+
+    If an existing value is present in the config, its type is used to guide
+    casting.  Otherwise, YAML-style inference is applied: booleans, ints,
+    floats, and None literals are recognised automatically.
+
+    Args:
+        value: The raw value (typically a string from the CLI).
+        existing: An optional existing config value whose type guides coercion.
+
+    Returns:
+        The value cast to the inferred or expected type.
+    """
+    if not isinstance(value, str):
+        return value
+
+    # If the config already has a typed value, cast to match
+    if existing is not None:
+        if isinstance(existing, bool):
+            return value.lower() in ("true", "1", "yes")
+        if isinstance(existing, int):
+            try:
+                return int(value)
+            except (ValueError, TypeError):
+                return value
+        if isinstance(existing, float):
+            try:
+                return float(value)
+            except (ValueError, TypeError):
+                return value
+        # For other types (str, list, dict, etc.), return as-is
+        return value
+
+    # No existing value -- use YAML-style inference
+    lower = value.lower()
+    if lower in ("true", "yes"):
+        return True
+    if lower in ("false", "no"):
+        return False
+    if lower in ("null", "none", "~"):
+        return None
+
+    # Try int then float
+    try:
+        return int(value)
+    except ValueError:
+        pass
+    try:
+        return float(value)
+    except ValueError:
+        pass
+
+    return value
+
+
 API_KEY_FIELDS = {"comet_api_key"}
 
 TELEMETRY_MANAGER = TelemetryManager.get_instance()
@@ -208,13 +265,37 @@ def load_cfg(
     # If there are any options passed in the cli, if it is something that seems valid
     # from the yaml, then overwrite the value
     cfg_keys = cfg.keys()
+
+    # Separate nested (dot-notation) kwargs from flat kwargs
+    nested_kwargs: dict[str, dict[str, Any]] = {}
+    flat_kwargs: dict[str, Any] = {}
     for key, value in kwargs.items():
+        if "__" in key:
+            parent, child = key.split("__", 1)
+            nested_kwargs.setdefault(parent, {})[child] = value
+        else:
+            flat_kwargs[key] = value
+
+    # Apply flat kwargs
+    for key, value in flat_kwargs.items():
         # If not strict, allow writing to cfg even if it's not in the yml already
         if key in cfg_keys or not cfg.strict:
-            if isinstance(cfg[key], bool):
-                cfg[key] = bool(value)
-            else:
-                cfg[key] = value
+            cfg[key] = _coerce_value(value, cfg.get(key))
+
+    # Apply nested kwargs (e.g., trl__beta -> cfg.trl.beta)
+    for parent, children in nested_kwargs.items():
+        if parent not in cfg_keys and cfg.strict:
+            continue
+        if cfg[parent] is None:
+            cfg[parent] = {}
+        if not isinstance(cfg[parent], dict):
+            LOG.warning(
+                "Overwriting non-dict value for '%s' with nested CLI overrides", parent
+            )
+            cfg[parent] = {}
+        for child_key, child_value in children.items():
+            existing_child = cfg[parent].get(child_key)
+            cfg[parent][child_key] = _coerce_value(child_value, existing_child)
 
     try:
         device_props = torch.cuda.get_device_properties("cuda")

src/axolotl/cli/utils/args.py

@@ -2,7 +2,7 @@
 
 import dataclasses
 from functools import wraps
-from types import NoneType
+from types import NoneType, UnionType
 from typing import Any, Callable, Type, Union, get_args, get_origin
 
 import click
@@ -20,7 +20,8 @@ def _strip_optional_type(field_type: type | str | None):
         If the input type is `Union[T, None]` or `Optional[T]`, returns `T`. Otherwise
             returns the input type unchanged.
     """
-    if get_origin(field_type) is Union and type(None) in get_args(field_type):
+    is_union = get_origin(field_type) is Union or isinstance(field_type, UnionType)
+    if is_union and type(None) in get_args(field_type):
         field_type = next(
             t for t in get_args(field_type) if not isinstance(t, NoneType)
         )
@@ -87,10 +88,70 @@ def add_options_from_dataclass(config_class: Type[Any]) -> Callable:
     return decorator
 
 
+def _is_pydantic_model(field_type: type) -> bool:
+    """Check if a type is a Pydantic BaseModel subclass."""
+    try:
+        return isinstance(field_type, type) and issubclass(field_type, BaseModel)
+    except TypeError:
+        return False
+
+
+def _get_field_description(field) -> str | None:
+    """Get description from a Pydantic field, checking both .description and json_schema_extra."""
+    if field.description:
+        return field.description
+    if field.json_schema_extra and isinstance(field.json_schema_extra, dict):
+        return field.json_schema_extra.get("description")
+    return None
+
+
+def _add_nested_model_options(
+    function: Callable, parent_name: str, model_class: Type[BaseModel]
+) -> Callable:
+    """
+    Add Click options for all fields of a nested Pydantic model using dot-notation.
+
+    Note: Only single-level nesting is supported (e.g., ``--trl.beta``).
+    Deeper nesting (e.g., ``--trl.scheduler.warmup``) is not handled.
+
+    Args:
+        function: Click command function to add options to.
+        parent_name: Parent field name (e.g., "trl").
+        model_class: Nested Pydantic model class.
+
+    Returns:
+        Function with added Click options.
+    """
+    for sub_name, sub_field in reversed(model_class.model_fields.items()):
+        sub_type = _strip_optional_type(sub_field.annotation)
+        # Use dot notation: --parent.sub_field
+        cli_name = f"{parent_name}.{sub_name}".replace("_", "-")
+        # The kwarg name uses double-underscore as separator
+        param_name = f"{parent_name}__{sub_name}"
+        description = _get_field_description(sub_field)
+
+        if sub_type is bool:
+            option_name = f"--{cli_name}/--no-{cli_name}"
+            function = click.option(
+                option_name, param_name, default=None, help=description
+            )(function)
+        else:
+            option_name = f"--{cli_name}"
+            click_type = {str: str, int: int, float: float}.get(sub_type)
+            function = click.option(
+                option_name, param_name, default=None, type=click_type, help=description
+            )(function)
+
+    return function
+
+
 def add_options_from_config(config_class: Type[BaseModel]) -> Callable:
     """
     Create Click options from the fields of a Pydantic model.
 
+    For fields whose type is itself a Pydantic BaseModel, dot-notation CLI options are
+    generated for each sub-field (e.g., ``--trl.beta=0.1``).
+
     Args:
         config_class: PyDantic model with fields to parse from the CLI
 
@@ -103,6 +164,11 @@ def add_options_from_config(config_class: Type[BaseModel]) -> Callable:
         for name, field in reversed(config_class.model_fields.items()):
             field_type = _strip_optional_type(field.annotation)
 
+            # Handle nested Pydantic models with dot-notation options
+            if _is_pydantic_model(field_type):
+                function = _add_nested_model_options(function, name, field_type)
+                continue
+
             if field_type is bool:
                 field_name = name.replace("_", "-")
                 option_name = f"--{field_name}/--no-{field_name}"

src/axolotl/core/builders/causal.py

@@ -122,6 +122,12 @@ class HFCausalTrainerBuilder(TrainerBuilderBase):
             ColabCallback = colab_inference_post_train_callback(trainer)
             callbacks.append(ColabCallback(self.cfg))
 
+        if getattr(self.cfg, "generate_samples", False):
+            from axolotl.utils.callbacks.generation import SFTGenerationCallback
+
+            callbacks.append(SFTGenerationCallback(trainer))
+            LOG.info("SFT sample generation enabled")
+
         callbacks.extend(super().get_post_trainer_create_callbacks(trainer=trainer))
         return callbacks
 
@@ -246,7 +252,8 @@ class HFCausalTrainerBuilder(TrainerBuilderBase):
             ddp_find_unused_parameters
         )
 
-        training_arguments_kwargs["group_by_length"] = self.cfg.group_by_length
+        if self.cfg.group_by_length:
+            training_arguments_kwargs["train_sampling_strategy"] = "group_by_length"
         training_arguments_kwargs["curriculum_sampling"] = self.cfg.curriculum_sampling
 
         training_arguments_kwargs["sample_packing"] = bool(self.cfg.sample_packing)

src/axolotl/core/builders/rl.py

@@ -11,7 +11,6 @@ from axolotl.core.trainers import (
 )
 from axolotl.core.trainers.dpo import DPOStrategy
 from axolotl.core.trainers.dpo.args import AxolotlDPOConfig
-from axolotl.core.trainers.grpo import GRPOStrategy
 from axolotl.integrations.base import PluginManager
 from axolotl.loaders.utils import ensure_dtype
 from axolotl.utils.callbacks.qat import QATCallback
@@ -53,6 +52,8 @@ class HFRLTrainerBuilder(TrainerBuilderBase):
         trainer_cls_args = [self.model]
 
         if self.cfg.rl in {RLType.GRPO, RLType.GDPO}:
+            from axolotl.core.trainers.grpo import GRPOStrategy
+
             trainer_cls = GRPOStrategy.get_trainer_class(
                 sequence_parallel=self.cfg.context_parallel_size > 1
             )
@@ -133,21 +134,17 @@ class HFRLTrainerBuilder(TrainerBuilderBase):
             if self.cfg.cpo_alpha is not None:
                 training_args_kwargs["cpo_alpha"] = self.cfg.cpo_alpha
 
-            # Handle when max_prompt_length == max_length from defaults
-            # CPOTrainer requires strictly less than
-            if (
-                training_args_kwargs["max_prompt_length"]
-                == training_args_kwargs["max_length"]
-            ):
-                training_args_kwargs["max_prompt_length"] -= 1
+            blocklist_args_kwargs.append("max_prompt_length")
 
         elif self.cfg.rl is RLType.ORPO:
             training_args_cls = AxolotlORPOConfig
 
+            blocklist_args_kwargs.append("max_prompt_length")
+
         elif self.cfg.rl is RLType.KTO:
             training_args_cls = AxolotlKTOConfig
             # KTOConfig in TRL >= 0.27.0 no longer accepts max_prompt_length
-            blocklist_args_kwargs = ["max_prompt_length"]
+            blocklist_args_kwargs.append("max_prompt_length")
 
             training_args_kwargs["desirable_weight"] = (
                 self.cfg.kto_desirable_weight or 1.0
@@ -157,6 +154,8 @@ class HFRLTrainerBuilder(TrainerBuilderBase):
             )
 
         elif self.cfg.rl in {RLType.GRPO, RLType.GDPO}:
+            from axolotl.core.trainers.grpo import GRPOStrategy
+
             training_args_cls = GRPOStrategy.get_training_args_class()
             training_args_kwargs.update(GRPOStrategy.set_training_args_kwargs(self.cfg))
             blocklist_args_kwargs = GRPOStrategy.get_blocklist_args_kwargs()

src/axolotl/core/trainers/base.py

@@ -719,6 +719,8 @@ class AxolotlTrainer(
         output_dir = output_dir if output_dir is not None else self.args.output_dir
         os.makedirs(output_dir, exist_ok=True)
         LOG.info(f"Saving model checkpoint to {output_dir}")
+
+        # fix for Context Parallel save
         if state_dict is None:
             state_dict = self.accelerator.get_state_dict(self.model)
         if state_dict is not None:
@@ -726,6 +728,7 @@ class AxolotlTrainer(
                 k: v.clone() if isinstance(v, torch.Tensor) else v
                 for k, v in state_dict.items()
             }
+
         supported_classes = (
             (PreTrainedModel,)
             if not is_peft_available()
@@ -736,6 +739,7 @@ class AxolotlTrainer(
         if not isinstance(self.model, supported_classes):
             if state_dict is None:
                 state_dict = self.model.state_dict()
+
             if isinstance(
                 self.accelerator.unwrap_model(self.model, keep_torch_compile=False),
                 supported_classes,
@@ -745,6 +749,7 @@ class AxolotlTrainer(
                 ).save_pretrained(
                     output_dir,
                     state_dict=state_dict,
+                    is_main_process=self.accelerator.is_main_process,
                 )
             else:
                 LOG.info(
@@ -756,11 +761,7 @@ class AxolotlTrainer(
                     metadata={"format": "pt"},
                 )
         else:
-            self.model.save_pretrained(
-                output_dir,
-                state_dict=state_dict,
-                is_main_process=self.accelerator.is_main_process,
-            )
+            self.model.save_pretrained(output_dir, state_dict=state_dict)
 
         if self.processing_class is not None:
             self.processing_class.save_pretrained(output_dir)
@@ -772,11 +773,7 @@ class AxolotlTrainer(
             LOG.info(
                 "Saving Trainer.data_collator.tokenizer by default as Trainer.processing_class is `None`"
             )
-            save_jinja_files = True
-            if self.axolotl_cfg:
-                save_jinja_files = self.axolotl_cfg.tokenizer_save_jinja_files
-            self.data_collator.tokenizer.save_pretrained(
-                output_dir, save_jinja_files=save_jinja_files
-            )
+            self.data_collator.tokenizer.save_pretrained(output_dir)
+
         # Good practice: save your training arguments together with the trained model
         torch.save(self.args, os.path.join(output_dir, TRAINING_ARGS_NAME))

src/axolotl/core/trainers/dpo/trainer.py

@@ -57,16 +57,18 @@ class AxolotlDPOTrainer(
     def tokenize_row(
         features,
         processing_class,
-        max_prompt_length,
-        max_completion_length,
-        add_special_tokens,
+        max_prompt_length: int | None = None,
+        max_completion_length: int | None = None,
+        add_special_tokens: bool = True,
+        is_chat: bool = False,
     ) -> Dict:
         res = DPOTrainer.tokenize_row(
             features,
             processing_class,
-            max_prompt_length,
-            max_completion_length,
-            add_special_tokens,
+            max_prompt_length=max_prompt_length,
+            max_completion_length=max_completion_length,
+            add_special_tokens=add_special_tokens,
+            is_chat=is_chat,
         )
         # fix when the tokenizer doesn't have a bos_token_id, e.g. Qwen
         if processing_class.bos_token is None and res["prompt_input_ids"][0] is None:

src/axolotl/core/trainers/mixins/scheduler.py

@@ -25,7 +25,7 @@ class SchedulerMixin(Trainer):
     args = None  # type: "AxolotlTrainingArguments"  # type: ignore[name-defined]
 
     def create_scheduler(
-        self, num_training_steps: int, optimizer: torch.optim.Optimizer = None
+        self, num_training_steps: int, optimizer: None | torch.optim.Optimizer = None
     ) -> LRScheduler:
         """
         Set up the scheduler. The optimizer of the trainer must have been set up either before this method is called or
@@ -45,6 +45,13 @@ class SchedulerMixin(Trainer):
             and self.args.cosine_min_lr_ratio is not None
         )
 
+        if optimizer is None:
+            if self.optimizer is None:
+                raise ValueError(
+                    "Optimizer must be set before calling create_scheduler or passed as an argument."
+                )
+            optimizer = self.optimizer
+
         # fmt: off
         if self.lr_scheduler is None:  # type: ignore
             # fmt: on

src/axolotl/integrations/cut_cross_entropy/README.md

@@ -19,7 +19,7 @@ python scripts/cutcrossentropy_install.py | sh
 
 - If you are installing from pip
 ```bash
-pip3 uninstall -y cut-cross-entropy && pip3 install "cut-cross-entropy[transformers] @ git+https://github.com/axolotl-ai-cloud/ml-cross-entropy.git@0d4ce4b"
+pip3 uninstall -y cut-cross-entropy && pip3 install "cut-cross-entropy[transformers] @ git+https://github.com/axolotl-ai-cloud/ml-cross-entropy.git@58d6572"
 ```
 
 ## Usage
@@ -31,6 +31,7 @@ plugins:
 
 ## Supported Models
 
+- afmoe
 - apertus
 - arcee
 - cohere
@@ -51,6 +52,7 @@ plugins:
 - glm4v
 - glm4v_moe
 - glm_image
+- glm_moe_dsa
 - gpt_oss
 - granite
 - granitemoe
@@ -76,14 +78,19 @@ plugins:
 - olmo
 - olmo2
 - olmo3
+- olmoe
 - phi
 - phi3
 - phi4_multimodal
 - qwen2
+- qwen2_5_vl
 - qwen2_moe
 - qwen2_vl
-- qwen2_5_vl
 - qwen3
+- qwen3_5
+- qwen3_5_moe
+- qwen3_5_moe_vl
+- qwen3_5_vl
 - qwen3_moe
 - qwen3_next
 - qwen3_vl

src/axolotl/integrations/cut_cross_entropy/__init__.py

@@ -35,7 +35,7 @@ LOG = get_logger(__name__)
 
 _CCE_INSTALL_MESSAGE = (
     "Please install Axolotl's fork of cut_cross_entropy with transformers support using "
-    '`pip install "cut-cross-entropy[transformers] @ git+https://github.com/axolotl-ai-cloud/ml-cross-entropy.git@0d4ce4b"`'
+    '`pip install "cut-cross-entropy[transformers] @ git+https://github.com/axolotl-ai-cloud/ml-cross-entropy.git@58d6572"`'
 )
 
 
@@ -104,7 +104,7 @@ class CutCrossEntropyPlugin(BasePlugin):
 
     def patch_llama_like(
         self,
-        model_type: str,
+        model_type_to_patch: str,
     ) -> None:
         """
         Generic patch for model architectures with causal lm similar to llama
@@ -112,7 +112,10 @@ class CutCrossEntropyPlugin(BasePlugin):
         from cut_cross_entropy.transformers.patch import PATCH_FNS
 
         def patch_generic(
-            maybe_model, patch_options, model_type: str, remote_model_id: str | None
+            maybe_model,
+            patch_options,
+            remote_model_id: str | None,
+            model_type: str,
         ):
             import cut_cross_entropy.transformers.llama
             from cut_cross_entropy.transformers.llama import cce_forward
@@ -136,11 +139,13 @@ class CutCrossEntropyPlugin(BasePlugin):
                     f"Error: {str(e)}"
                 ) from e
 
-        if model_type not in PATCH_FNS:
+        if model_type_to_patch not in PATCH_FNS:
             LOG.warning_once(
-                "Setting up generic cce patch for model type: %s", model_type
+                "Setting up generic cce patch for model type: %s", model_type_to_patch
             )
             LOG.warning_once(
-                f"Generic Cut Cross Entropy + {model_type} support is experimental and may not work as expected."
+                f"Generic Cut Cross Entropy + {model_type_to_patch} support is experimental and may not work as expected."
+            )
+            PATCH_FNS[model_type_to_patch] = partial(
+                patch_generic, model_type=model_type_to_patch
             )
-            PATCH_FNS[model_type] = partial(patch_generic, model_type=model_type)

src/axolotl/integrations/gemma3/README.md

@@ -1,37 +0,0 @@
-# Gemma3 Text-from-Multimodal Plugin
-
-Load a Gemma3 multimodal checkpoint (e.g. `google/gemma-3-4b-it`) directly into `Gemma3ForCausalLM` for text-only training. This bypasses the multimodal trainer path and enables sample packing and other text-specific optimizations.
-
-## How it works
-
-The plugin uses transformers v5's `key_mapping` parameter on `from_pretrained` to remap `model.language_model.*` checkpoint keys to `model.*`, matching what `Gemma3ForCausalLM` expects. Vision tower and projector weights are automatically discarded. On save, transformers reverses the mapping so checkpoints retain the original `model.language_model.*` prefix.
-
-## Usage
-
-Add the plugin to your YAML config:
-
-```yaml
-base_model: google/gemma-3-4b-it
-
-plugins:
-  - axolotl.integrations.gemma3.Gemma3TextFromMultimodalPlugin
-```
-
-See `examples/gemma3/gemma-3-4b-qlora.yml` for a complete example.
-
-## Merging weights back into a multimodal checkpoint
-
-After training, the saved checkpoint contains only the language model weights. To reconstruct a full `Gemma3ForConditionalGeneration` checkpoint (with the original vision tower and projector), use the merge script:
-
-```bash
-python scripts/merge_gemma3_multimodal_weights.py \
-    --original-model google/gemma-3-4b-it \
-    --trained-model /path/to/trained/output \
-    --output-dir /path/to/merged
-```
-
-This combines:
-- **Trained language model weights** from your output checkpoint
-- **Original vision tower + projector weights** from the base multimodal model
-
-The merged checkpoint can be loaded as `Gemma3ForConditionalGeneration` for multimodal inference or further training.

src/axolotl/integrations/gemma3/__init__.py

@@ -1,9 +0,0 @@
-"""Gemma3 integration for loading multimodal checkpoints as text-only models."""
-
-from .args import Gemma3TextFromMultimodalArgs
-from .plugin import Gemma3TextFromMultimodalPlugin
-
-__all__ = [
-    "Gemma3TextFromMultimodalArgs",
-    "Gemma3TextFromMultimodalPlugin",
-]

src/axolotl/integrations/gemma3/args.py

@@ -1,31 +0,0 @@
-"""Pydantic input args for the Gemma3 text-from-multimodal plugin."""
-
-from pydantic import BaseModel, model_validator
-
-from axolotl.utils.logging import get_logger
-
-LOG = get_logger(__name__)
-
-
-class Gemma3TextFromMultimodalArgs(BaseModel):
-    """Configuration args for loading a Gemma3 multimodal checkpoint as text-only."""
-
-    gemma3_text_from_multimodal: bool = True
-    extract_text_config: bool = False
-
-    @model_validator(mode="before")
-    @classmethod
-    def set_model_type(cls, data):
-        if not isinstance(data, dict):
-            return data
-
-        if not data.get("gemma3_text_from_multimodal", True):
-            return data
-
-        if not data.get("model_type"):
-            LOG.info(
-                "Gemma3TextFromMultimodalPlugin: auto-setting model_type to Gemma3ForCausalLM"
-            )
-            data["model_type"] = "Gemma3ForCausalLM"
-
-        return data

src/axolotl/integrations/gemma3/plugin.py

@@ -1,107 +0,0 @@
-"""Plugin for loading Gemma3 multimodal checkpoints into Gemma3ForCausalLM (text-only).
-
-Uses transformers v5's ``key_mapping`` parameter on ``from_pretrained`` to remap
-``model.language_model.*`` keys to ``model.*``, discarding vision tower and projector
-weights.  On save, transformers automatically reverses the mapping so saved
-checkpoints retain the original ``model.language_model.*`` prefix.
-"""
-
-from axolotl.integrations.base import BasePlugin
-from axolotl.utils.logging import get_logger
-
-LOG = get_logger(__name__)
-
-# key_mapping for transformers from_pretrained:
-# Remap checkpoint keys matching ^model.language_model -> model
-# Vision tower / projector keys won't match any model parameter and are discarded.
-GEMMA3_KEY_MAPPING = {"^model.language_model": "model"}
-
-
-class Gemma3TextFromMultimodalPlugin(BasePlugin):
-    """Load a Gemma3 multimodal checkpoint as a text-only Gemma3ForCausalLM.
-
-    Hooks
-    -----
-    register(cfg)
-        Runs before config validation.  Sets the ``_extract_text_config`` flag,
-        ensures ``model_type`` is ``Gemma3ForCausalLM``, and injects
-        ``key_mapping`` into ``model_kwargs`` so that ``from_pretrained`` remaps
-        ``model.language_model.*`` → ``model.*``.
-
-    pre_model_load(cfg)
-        Runs after config validation/normalization but before model instantiation.
-        Validates that ``model_config_type`` is ``gemma3_text`` and
-        ``is_multimodal`` is False (confirming that ``_extract_text_config``
-        worked correctly).
-    """
-
-    def get_input_args(self) -> str:
-        return "axolotl.integrations.gemma3.Gemma3TextFromMultimodalArgs"
-
-    def register(self, cfg: dict):
-        """Set up config for multimodal → text-only loading.
-
-        This runs before Pydantic validation, so ``cfg`` is a raw dict.
-        """
-        if not cfg.get("gemma3_text_from_multimodal", True):
-            raise ValueError(
-                "Gemma3TextFromMultimodalPlugin: disabled via config, but plugin selected"
-            )
-
-        # Flag for load_model_config() to extract the text sub-config
-        cfg["extract_text_config"] = True
-
-        # Ensure model_type is set for the text-only model class
-        if not cfg.get("model_type"):
-            cfg["model_type"] = "Gemma3ForCausalLM"
-
-        # Inject key_mapping into model_kwargs so from_pretrained remaps weights
-        model_kwargs = cfg.setdefault("model_kwargs", {})
-        model_kwargs["key_mapping"] = GEMMA3_KEY_MAPPING
-
-    def pre_model_load(self, cfg):
-        """Validate that config extraction worked before model instantiation."""
-        if not getattr(cfg, "gemma3_text_from_multimodal", True):
-            return
-
-        if cfg.model_config_type != "gemma3_text":
-            LOG.warning(
-                "Gemma3TextFromMultimodalPlugin: expected model_config_type='gemma3_text' "
-                "but got '%s'. The text config extraction may not have worked.",
-                cfg.model_config_type,
-            )
-
-        if cfg.is_multimodal or cfg.processor_type:
-            raise ValueError(
-                "Multimodal mode is enabled (processor_type set), but "
-                "Gemma3TextFromMultimodalPlugin enabled. "
-                "Please disable one of the two."
-            )
-
-    def post_train(self, cfg, model):
-        """Log merge command after training completes."""
-        if cfg.adapter:
-            LOG.info(
-                "Adapter training detected. To reconstruct the multimodal checkpoint:\n"
-                "  1. Merge adapter weights into the text-only base model:\n"
-                "       axolotl merge_lora <your_config.yml>\n"
-                "  2. Then merge the resulting full model back into the multimodal checkpoint:\n"
-                "       python scripts/merge_gemma3_multimodal_weights.py \\\n"
-                "         --original-model %s \\\n"
-                "         --trained-model %s/merged \\\n"
-                "         --output-dir %s/multi-modal/merged",
-                cfg.base_model,
-                cfg.output_dir,
-                cfg.output_dir,
-            )
-        else:
-            LOG.info(
-                "To merge trained weights back into the multimodal checkpoint, run:\n"
-                "  python scripts/merge_gemma3_multimodal_weights.py \\\n"
-                "    --original-model %s \\\n"
-                "    --trained-model %s \\\n"
-                "    --output-dir %s/multi-modal/merged",
-                cfg.base_model,
-                cfg.output_dir,
-                cfg.output_dir,
-            )

src/axolotl/integrations/kernels/README.md

@@ -0,0 +1,44 @@
+# Kernels Integration
+
+MoE (Mixture of Experts) kernels speed up training for MoE layers and reduce VRAM costs. In transformers v5, `batched_mm` and `grouped_mm` were integrated as built-in options via the `experts_implementation` config kwarg:
+
+```python
+class ExpertsInterface(GeneralInterface):
+    _global_mapping = {
+        "batched_mm": batched_mm_experts_forward,
+        "grouped_mm": grouped_mm_experts_forward,
+    }
+```
+
+In our custom integration, we add support for **ScatterMoE**, which is even more efficient and faster than `grouped_mm`.
+
+## Usage
+
+Add the following to your axolotl YAML config:
+
+```yaml
+plugins:
+  - axolotl.integrations.kernels.KernelsPlugin
+
+use_kernels: true
+use_scattermoe: true
+```
+
+**Important:** Setting `experts_implementation` is incompatible with `use_scattermoe`.
+
+## How It Works
+
+The `KernelsPlugin` runs before model loading and:
+
+1. Registers the ScatterMoE kernel from the [`axolotl-ai-co/scattermoe`](https://huggingface.co/axolotl-ai-co/scattermoe) Hub repo.
+2. Patches the model's `SparseMoeBlock` forward method with the optimized ScatterMoE implementation.
+
+This works for any MoE model in transformers that uses a `SparseMoeBlock` class (Mixtral, Qwen2-MoE, OLMoE, etc.).
+
+## Limitations
+
+ScatterMoE uses a softmax -> topk routing, so results may be different for some model arch as baseline (GPT-OSS, GLM_MOE_DSA).
+
+## Note on MegaBlocks
+
+We tested [MegaBlocks](https://huggingface.co/kernels-community/megablocks) but were unable to ensure numerical accuracy, so we did not integrate it. It was also incompatible with many newer model architectures in transformers.

src/axolotl/integrations/kernels/args.py

@@ -33,3 +33,16 @@ class KernelsArgs(BaseModel):
             data["experts_implementation"] = "eager"
 
         return data
+
+    @model_validator(mode="before")
+    @classmethod
+    def disable_mlp_kernel_scattermoe(cls, data):
+        if data.get("use_scattermoe") is True:
+            if data.get("lora_mlp_kernel") is True:
+                LOG.warning(
+                    "Disabling lora_mlp_kernel when using scattermoe due to compatibility issues."
+                )
+                data["lora_mlp_kernel"] = False
+            data["mlp_kernel"] = False
+
+        return data

src/axolotl/integrations/kernels/libs/scattermoe_lora/__init__.py

@@ -0,0 +1,18 @@
+# SPDX-License-Identifier: Apache-2.0
+# Copyright (c) Axolotl AI
+# Licensed under the Apache License, Version 2.0
+
+from . import layers
+from .lora_ops import ParallelExperts
+from .parallel_experts import flatten_sort_count, parallel_linear
+from .parallel_linear_lora import ScatterMoELoRA, parallel_linear_lora
+
+__all__ = [
+    "layers",
+    "ParallelExperts",
+    "flatten_sort_count",
+    "parallel_linear",
+    "ScatterMoELoRA",
+    "parallel_linear_lora",
+    "lora_ops",
+]

src/axolotl/integrations/kernels/libs/scattermoe_lora/kernels/__init__.py

@@ -0,0 +1,12 @@
+# SPDX-License-Identifier: Apache-2.0
+#
+# Original work Copyright (c) Shawn Tan and ScatterMoE Contributors
+# Adapted from https://github.com/shawntan/scattermoe
+# See https://github.com/shawntan/scattermoe/blob/main/LICENSE
+#
+# Modifications and LoRA adaptation Copyright (c) Axolotl AI
+# Licensed under the Apache License, Version 2.0
+
+from . import lora_ops, ops
+
+__all__ = ["ops", "lora_ops"]

src/axolotl/integrations/kernels/libs/scattermoe_lora/kernels/ops.py

@@ -0,0 +1,645 @@
+# SPDX-License-Identifier: Apache-2.0
+# Adapted from https://github.com/shawntan/scattermoe
+# Copyright (c) Shawn Tan and ScatterMoE Contributors
+# Licensed under the Apache License, Version 2.0
+# See https://github.com/shawntan/scattermoe/blob/main/LICENSE
+
+from typing import Optional
+
+import torch
+import triton
+import triton.language as tl
+
+BLOCK_M = 128
+ALLOW_TF32 = True
+
+
+@triton.jit
+def _compute_expert_block(
+    E_idx,
+    E_mask,
+    M_in_idx,
+    N_block,
+    N_mask,
+    X_ptr,
+    stride_xm,
+    stride_xk,
+    W_ptr,
+    stride_we,
+    stride_wk,
+    stride_wn,
+    K,
+    acc,
+    no_k_mask,
+    BLOCK_K,
+    allow_tf32=True,
+):
+    K_block = tl.arange(0, BLOCK_K)
+    X_blk_ptrs = X_ptr + M_in_idx[:, None] * stride_xm + K_block[None, :] * stride_xk
+    W_blk_ptrs = (
+        W_ptr
+        + K_block[:, None] * stride_wk
+        + N_block[None, :] * stride_wn
+        + E_idx * stride_we
+    )
+    iters = tl.cdiv(K, BLOCK_K)
+
+    for K_block_id in range(iters):
+        if no_k_mask:
+            x = tl.load(X_blk_ptrs, mask=E_mask[:, None])
+            w = tl.load(W_blk_ptrs, mask=N_mask[None, :])
+        else:
+            K_mask = (K_block_id * BLOCK_K + K_block) < K
+            x = tl.load(X_blk_ptrs, mask=E_mask[:, None] & K_mask[None, :])
+            w = tl.load(W_blk_ptrs, mask=K_mask[:, None] & N_mask[None, :])
+
+        X_blk_ptrs += BLOCK_K * stride_xk
+        W_blk_ptrs += BLOCK_K * stride_wk
+        acc = tl.dot(x, w, acc, allow_tf32=allow_tf32)
+    return acc
+
+
+def _scatter2scatter_configs():
+    return [
+        triton.Config({"BLOCK_N": 128, "BLOCK_K": 32}, num_stages=4, num_warps=4),
+    ]
+
+
+@triton.autotune(
+    configs=_scatter2scatter_configs(),
+    key=["M", "N", "K"],
+)
+@triton.heuristics(
+    {
+        "NO_K_MASK": lambda args: (args["K"] % args["BLOCK_K"]) == 0,
+        "NO_N_MASK": lambda args: (args["N"] % args["BLOCK_N"]) == 0,
+    }
+)
+@triton.jit
+def _scatter2scatter(
+    X_ptr,
+    stride_xm: tl.constexpr,
+    stride_xk: tl.constexpr,
+    W_ptr,
+    stride_we,
+    stride_wk: tl.constexpr,
+    stride_wn: tl.constexpr,
+    Y_ptr,
+    stride_ym: tl.constexpr,
+    stride_yn: tl.constexpr,
+    B_ptr,
+    stride_be: tl.constexpr,
+    stride_bn: tl.constexpr,
+    grouped_idx_ptr,
+    expert_idxs_ptr,
+    # block_start_idx_ptr,
+    FAN_OUT: tl.constexpr,
+    M,
+    K: tl.constexpr,
+    N: tl.constexpr,
+    E: tl.constexpr,
+    BLOCK_M: tl.constexpr,
+    BLOCK_N: tl.constexpr,
+    BLOCK_K: tl.constexpr,
+    ACC_TYPE: tl.constexpr,
+    # OUT_M,
+    allow_tf32: tl.constexpr,
+    x_grouped: tl.constexpr,
+    y_grouped: tl.constexpr,
+    NO_K_MASK: tl.constexpr,
+    NO_N_MASK: tl.constexpr,
+):
+    pid = tl.program_id(axis=0)
+
+    N_BLOCK_COUNT = tl.cdiv(N, BLOCK_N)
+    M_block_id = pid // N_BLOCK_COUNT
+    N_block_id = pid % N_BLOCK_COUNT
+
+    M_block = M_block_id * BLOCK_M + tl.arange(0, BLOCK_M)
+    N_block = N_block_id * BLOCK_N + tl.arange(0, BLOCK_N)
+    N_mask = N_block < N
+    M_boundary_mask = M_block < (FAN_OUT * M)
+    E_idxs = tl.load(expert_idxs_ptr + M_block, mask=M_boundary_mask, other=E)
+
+    no_k_mask = K % BLOCK_K == 0
+
+    acc = tl.zeros((BLOCK_M, BLOCK_N), dtype=ACC_TYPE)
+    E_first_idx = tl.min(E_idxs)
+    E_last_idx = tl.minimum(tl.max(E_idxs), E - 1)
+    M_idx = tl.load(grouped_idx_ptr + M_block, mask=M_boundary_mask).to(tl.int32)
+    for E_idx in range(E_first_idx, E_last_idx + 1):
+        E_mask = E_idxs == E_idx
+        E_M_idx = M_idx
+        if x_grouped:
+            M_in_idx = M_block
+        else:
+            M_in_idx = E_M_idx // FAN_OUT
+        acc = _compute_expert_block(
+            E_idx,
+            E_mask,
+            M_in_idx,
+            N_block,
+            N_mask,
+            X_ptr,
+            stride_xm,
+            stride_xk,
+            W_ptr,
+            stride_we,
+            stride_wk,
+            stride_wn,
+            K,
+            acc,
+            no_k_mask,
+            BLOCK_K,
+            allow_tf32=allow_tf32,
+        )
+
+    if B_ptr is not None:
+        B_blk_ptrs = B_ptr + E_idxs[:, None] * stride_be + N_block[None, :] * stride_bn
+        acc += tl.load(B_blk_ptrs, mask=M_boundary_mask[:, None] & N_mask[None, :])
+
+    if y_grouped:
+        M_out_idx = M_block
+    else:
+        M_out_idx = M_idx
+    Y_blk_ptrs = Y_ptr + (M_out_idx[:, None] * stride_ym + N_block[None, :] * stride_yn)
+    tl.store(Y_blk_ptrs, acc, mask=M_boundary_mask[:, None] & N_mask[None, :])
+
+
+def scatter2scatter(
+    X,
+    W,
+    sorted_expert_idxs,
+    sorted_scattered_idxs,
+    k,
+    b=None,
+    x_grouped=False,
+    y_grouped=False,
+    out=None,
+):
+    assert sorted_scattered_idxs.size(0) == sorted_expert_idxs.size(0)
+    assert sorted_scattered_idxs.size(0) == X.size(0) * k
+    # Pre-kernel setup
+    y_dim = W.size(-1)
+    L_scattered = sorted_expert_idxs.size(0)
+    if out is None:
+        output = torch.empty((L_scattered, y_dim), device=X.device, dtype=X.dtype)
+    else:
+        assert out.size(0) == L_scattered and out.size(1) == y_dim
+        output = out
+
+    scatter2scatter_compileable(
+        output,
+        W,
+        X,
+        k,
+        sorted_expert_idxs,
+        sorted_scattered_idxs,
+        b,
+        x_grouped,
+        y_grouped,
+    )
+    return output
+
+
+@torch.library.custom_op("scattermoe::scatter2scatter", mutates_args={"output"})
+def scatter2scatter_compileable(
+    output: torch.Tensor,
+    W: torch.Tensor,
+    X: torch.Tensor,
+    k: int,
+    sorted_expert_idxs: torch.Tensor,
+    sorted_scattered_idxs: torch.Tensor,
+    b: Optional[torch.Tensor],
+    x_grouped: bool,
+    y_grouped: bool,
+) -> None:
+    def grid(META):
+        grid_num = (
+            triton.cdiv(sorted_expert_idxs.size(0), META["BLOCK_M"])
+            * triton.cdiv(META["N"], META["BLOCK_N"]),
+        )
+        return grid_num
+
+    if b is None:
+        b = None
+        stride_be = stride_bn = 0
+    else:
+        stride_be, stride_bn = b.stride()
+
+    _scatter2scatter[grid](
+        # X_ptr, stride_xm, stride_xk,
+        X,
+        X.stride(0),
+        X.stride(1),
+        # W_ptr, stride_we, stride_wk, stride_wn,
+        W,
+        W.stride(0),
+        W.stride(1),
+        W.stride(2),
+        # Y_ptr, stride_ym, stride_yn,
+        output,
+        output.stride(0),
+        output.stride(1),
+        # B_ptr, stride_be, stride_bn
+        b,
+        stride_be,
+        stride_bn,
+        grouped_idx_ptr=sorted_scattered_idxs,
+        expert_idxs_ptr=sorted_expert_idxs,
+        # block_start_idx_ptr=padded_block_idxs,
+        FAN_OUT=k,
+        M=X.size(0),
+        K=X.size(1),
+        N=output.size(1),
+        E=W.size(0),
+        BLOCK_M=BLOCK_M,
+        ACC_TYPE=tl.float32,
+        allow_tf32=ALLOW_TF32,
+        x_grouped=x_grouped,
+        y_grouped=y_grouped,
+    )
+
+
+def _config_XtY():
+    return [
+        triton.Config(
+            {"BLOCK_N": 128, "BLOCK_K": 128, "BLOCK_M": 32}, num_stages=4, num_warps=4
+        ),
+    ]
+
+
+def group_bwd_W(DY, X, expert_offsets, E, has_bias=False):
+    DWt = torch.zeros((E, DY.size(-1), X.size(-1)), device=DY.device, dtype=DY.dtype)
+    DW = DWt.permute(0, 2, 1)
+    if has_bias:
+        Db = torch.zeros((E, DY.size(-1)), device=DY.device, dtype=DY.dtype)
+    else:
+        Db = None
+    groupXtY_compileable(E, DW, Db, DY, X, expert_offsets)
+    return DW, Db
+
+
+@torch.library.custom_op("scattermoe::groupXtY", mutates_args={"DW", "Db"})
+def groupXtY_compileable(
+    E: int,
+    DW: torch.Tensor,
+    Db: Optional[torch.Tensor],
+    DY: torch.Tensor,
+    X: torch.Tensor,
+    expert_offsets: torch.Tensor,
+) -> None:
+    def grid(META):
+        grid = (
+            E * triton.cdiv(META["K"], META["BLOCK_K"]),
+            triton.cdiv(META["N"], META["BLOCK_N"]),
+        )
+        return grid
+
+    if Db is None:
+        stride_dbe = 0
+        stride_dbn = 0
+    else:
+        stride_dbe, stride_dbn = Db.stride()
+
+    _groupXtY[grid](
+        # DY_ptr, stride_dym, stride_dyk,
+        DY,
+        DY.stride(0),
+        DY.stride(1),
+        # X_ptr, stride_xm, stride_xn,
+        X,
+        X.stride(0),
+        X.stride(1),
+        # DW_ptr, stride_dwe, stride_dwk, stride_dwn,
+        DW,
+        DW.stride(0),
+        DW.stride(1),
+        DW.stride(2),
+        # Db_ptr, stride_dwe, stride_dbn,
+        Db,
+        stride_dbe,
+        stride_dbn,
+        # expert_offsets_ptr,
+        expert_offsets,
+        # K: tl.constexpr, N: tl.constexpr,
+        M=DY.size(0),
+        N=DY.size(-1),
+        K=X.size(-1),
+        # ACC_TYPE: tl.constexpr,
+        ACC_TYPE=tl.float32,
+        allow_tf32=ALLOW_TF32,
+    )
+
+
+@triton.autotune(
+    configs=_config_XtY(),
+    key=["M", "N", "K"],
+)
+@triton.heuristics(
+    {
+        "NO_K_MASK": lambda args: (args["K"] % args["BLOCK_K"]) == 0,
+        "NO_N_MASK": lambda args: (args["N"] % args["BLOCK_N"]) == 0,
+    }
+)
+@triton.jit
+def _groupXtY(
+    DY_ptr,
+    stride_dym,
+    stride_dyk,
+    X_ptr,
+    stride_xm,
+    stride_xn,
+    DW_ptr,
+    stride_dwe,
+    stride_dwk,
+    stride_dwn,
+    Db_ptr,
+    stride_dbe,
+    stride_dbn,
+    expert_offsets_ptr,
+    M,
+    K: tl.constexpr,
+    N: tl.constexpr,
+    BLOCK_M: tl.constexpr,
+    BLOCK_N: tl.constexpr,
+    BLOCK_K: tl.constexpr,
+    ACC_TYPE: tl.constexpr,
+    allow_tf32: tl.constexpr,
+    NO_K_MASK: tl.constexpr,
+    NO_N_MASK: tl.constexpr,
+):
+    pid0 = tl.program_id(axis=0)
+    pid1 = tl.program_id(axis=1)
+    num0 = tl.num_programs(0)
+    num1 = tl.num_programs(1)
+    # pid1, pid0 = tl.swizzle2d(pid1, pid0, num1, num0, 128)
+    pid0, pid1 = tl.swizzle2d(pid0, pid1, num0, num1, 4)
+
+    K_BLOCK_COUNT = tl.cdiv(K, BLOCK_K)
+    E_idx = pid0 // K_BLOCK_COUNT
+    K_block_id = pid0 % K_BLOCK_COUNT
+    N_block_id = pid1
+
+    if E_idx == 0:
+        start_idx = 0
+    else:
+        start_idx = tl.load(expert_offsets_ptr + E_idx - 1).to(tl.int32)
+    end_idx = tl.load(expert_offsets_ptr + E_idx).to(tl.int32)
+
+    if end_idx > start_idx:
+        M_block = tl.max_contiguous(start_idx + tl.arange(0, BLOCK_M), BLOCK_M)
+
+        K_block = K_block_id * BLOCK_K + tl.arange(0, BLOCK_K)
+        K_mask = K_block < K
+        K_block = tl.max_contiguous(tl.multiple_of(K_block % K, BLOCK_K), BLOCK_K)
+
+        N_block = N_block_id * BLOCK_N + tl.arange(0, BLOCK_N)
+        N_mask = N_block < N
+        N_block = tl.max_contiguous(tl.multiple_of(N_block % N, BLOCK_N), BLOCK_N)
+
+        M_idxs = M_block
+        xt_blk_ptrs = X_ptr + K_block[:, None] * stride_xn + M_idxs[None, :] * stride_xm
+        dy_blk_ptrs = (
+            DY_ptr + M_idxs[:, None] * stride_dym + N_block[None, :] * stride_dyk
+        )
+        if (Db_ptr is not None) and (K_block_id == 0):
+            _xty_and_bias(
+                E_idx,
+                start_idx,
+                end_idx,
+                M_block,
+                K_block,
+                K_mask,
+                N_block,
+                N_mask,
+                dy_blk_ptrs,
+                stride_dym,
+                xt_blk_ptrs,
+                stride_xm,
+                DW_ptr,
+                stride_dwe,
+                stride_dwk,
+                stride_dwn,
+                Db_ptr,
+                stride_dbe,
+                stride_dbn,
+                BLOCK_M,
+                BLOCK_N,
+                BLOCK_K,
+                ACC_TYPE,
+                allow_tf32,
+                NO_K_MASK,
+                NO_N_MASK,
+                compute_bias=True,
+            )
+        else:
+            _xty_and_bias(
+                E_idx,
+                start_idx,
+                end_idx,
+                M_block,
+                K_block,
+                K_mask,
+                N_block,
+                N_mask,
+                dy_blk_ptrs,
+                stride_dym,
+                xt_blk_ptrs,
+                stride_xm,
+                DW_ptr,
+                stride_dwe,
+                stride_dwk,
+                stride_dwn,
+                Db_ptr,
+                stride_dbe,
+                stride_dbn,
+                BLOCK_M,
+                BLOCK_N,
+                BLOCK_K,
+                ACC_TYPE,
+                allow_tf32,
+                NO_K_MASK,
+                NO_N_MASK,
+                compute_bias=False,
+            )
+
+
+@triton.jit
+def _xty_and_bias(
+    E_idx,
+    start_idx,
+    end_idx,
+    M_block,
+    K_block,
+    K_mask,
+    N_block,
+    N_mask,
+    dy_blk_ptrs,
+    stride_dym,
+    xt_blk_ptrs,
+    stride_xm,
+    DW_ptr,
+    stride_dwe,
+    stride_dwk,
+    stride_dwn,
+    Db_ptr,
+    stride_dbe,
+    stride_dbn,
+    BLOCK_M,
+    BLOCK_N,
+    BLOCK_K,
+    ACC_TYPE,
+    allow_tf32,
+    NO_K_MASK,
+    NO_N_MASK,
+    compute_bias: tl.constexpr,
+):
+    if compute_bias:
+        db_acc = tl.zeros((BLOCK_N,), dtype=ACC_TYPE)
+    else:
+        db_acc = None
+
+    acc = tl.zeros((BLOCK_K, BLOCK_N), dtype=ACC_TYPE)
+    iters = tl.cdiv(end_idx - start_idx, BLOCK_M)
+    for i in range(0, iters):
+        M_mask = (i * BLOCK_M + M_block) < end_idx
+        if NO_K_MASK:
+            xt = tl.load(xt_blk_ptrs, mask=M_mask[None, :])
+        else:
+            xt = tl.load(xt_blk_ptrs, mask=K_mask[:, None] & M_mask[None, :])
+        if NO_N_MASK:
+            dy = tl.load(dy_blk_ptrs, mask=M_mask[:, None])
+        else:
+            dy = tl.load(dy_blk_ptrs, mask=M_mask[:, None] & N_mask[None, :])
+
+        acc += tl.dot(xt, dy, out_dtype=ACC_TYPE, allow_tf32=allow_tf32)
+
+        xt_blk_ptrs += BLOCK_M * stride_xm
+        dy_blk_ptrs += BLOCK_M * stride_dym
+
+        if compute_bias:
+            db_acc += tl.sum(dy, axis=0)
+
+    DW_blk_ptrs = (
+        DW_ptr
+        + E_idx * stride_dwe
+        + K_block[:, None] * stride_dwk
+        + N_block[None, :] * stride_dwn
+    )
+    acc = acc.to(DW_blk_ptrs.dtype.element_ty)
+    tl.store(DW_blk_ptrs, acc, mask=K_mask[:, None] & N_mask[None, :])
+    if compute_bias:
+        Db_blk_ptrs = Db_ptr + E_idx * stride_dbe + N_block * stride_dbn
+        tl.store(Db_blk_ptrs, db_acc, mask=N_mask)
+
+
+def _config_grouping():
+    return [
+        triton.Config({"BLOCK_N": 256, "BLOCK_K": 128}, num_stages=4, num_warps=4),
+        # triton.Config({'BLOCK_N': 128, 'BLOCK_K': 64}, num_stages=4, num_warps=4),
+        # triton.Config({'BLOCK_N': 64, 'BLOCK_K': 32}, num_stages=4, num_warps=4),
+    ]
+
+
+def group(A, sorted_expert_idxs, coeff=None, fan_out=1, out=None):
+    N = sorted_expert_idxs.size(0)
+    K = A.size(1)
+    assert A.size(0) * fan_out == N
+    if out is not None:
+        Y = out
+    else:
+        Y = torch.empty((N, K), dtype=A.dtype, device=A.device)
+    group_compileable(A, K, N, Y, coeff, coeff is not None, fan_out, sorted_expert_idxs)
+    return Y
+
+
+@torch.library.custom_op("scattermoe::group", mutates_args={"Y"})
+def group_compileable(
+    A: torch.Tensor,
+    K: int,
+    N: int,
+    Y: torch.Tensor,
+    coeff: Optional[torch.Tensor],
+    has_coeff: bool,
+    fan_out: int,
+    sorted_expert_idxs: torch.Tensor,
+) -> None:
+    def grid(META):
+        grid_num = (triton.cdiv(META["N"], META["BLOCK_N"]),)
+        return grid_num
+
+    _group[grid](
+        # A_ptr, stride_an, stride_ai,
+        A,
+        A.stride(0),
+        A.stride(1),
+        has_coeff,
+        coeff,
+        fan_out,
+        # Y_ptr, stride_yn, stride_yk,
+        Y,
+        Y.stride(0),
+        Y.stride(1),
+        # grouped_idx_ptr,
+        sorted_expert_idxs,
+        # N: tl.constexpr, K: tl.constexpr,
+        N,
+        K,
+    )
+
+
+@triton.autotune(configs=_config_grouping(), key=["K"])
+@triton.heuristics({"NO_K_MASK": lambda args: (args["K"] % args["BLOCK_K"]) == 0})
+@triton.jit
+def _group(
+    src_ptr,
+    stride_sn,
+    stride_sk,
+    has_coeff: tl.constexpr,
+    coeff_ptr,
+    FAN_OUT: tl.constexpr,
+    tgt_ptr,
+    stride_tn,
+    stride_ti,
+    grouped_idx_ptr,
+    N,
+    K: tl.constexpr,
+    BLOCK_N: tl.constexpr,
+    BLOCK_K: tl.constexpr,
+    NO_K_MASK: tl.constexpr,
+):
+    pid = tl.program_id(axis=0)
+
+    N_block_id = pid
+    N_blk = N_block_id * BLOCK_N + tl.arange(0, BLOCK_N)
+    N_mask = N_blk < N
+    N_blk = tl.max_contiguous(tl.multiple_of(N_blk % N, BLOCK_N), BLOCK_N)
+    N_idx = tl.load(grouped_idx_ptr + N_blk, mask=N_mask, other=0)
+
+    K_blk = tl.arange(0, BLOCK_K)
+    src_blk_ptrs = (
+        src_ptr + (N_idx // FAN_OUT)[:, None] * stride_sn + K_blk[None, :] * stride_sk
+    )
+    tgt_blk_ptrs = tgt_ptr + N_blk[:, None] * stride_tn + K_blk[None, :] * stride_ti
+
+    if has_coeff:
+        c = tl.load(coeff_ptr + N_idx, mask=N_mask)[:, None]
+
+    iters = tl.cdiv(K, BLOCK_K)
+    for i in range(0, iters):
+        if NO_K_MASK or i < iters - 1:
+            block = tl.load(src_blk_ptrs, mask=N_mask[:, None])
+            if has_coeff:
+                block *= c
+            tl.store(tgt_blk_ptrs, block, mask=N_mask[:, None])
+
+        else:
+            K_mask = (i * BLOCK_K + K_blk) < K
+            mask = N_mask[:, None] & K_mask[None, :]
+            block = tl.load(src_blk_ptrs, mask=mask)
+            if has_coeff:
+                block *= c
+            tl.store(tgt_blk_ptrs, block, mask=mask)
+        src_blk_ptrs += BLOCK_K * stride_sk
+        tgt_blk_ptrs += BLOCK_K * stride_ti

src/axolotl/integrations/kernels/libs/scattermoe_lora/kernels/single.py

@@ -0,0 +1,98 @@
+# SPDX-License-Identifier: Apache-2.0
+# Adapted from https://github.com/shawntan/scattermoe
+# Copyright (c) Shawn Tan and ScatterMoE Contributors
+# Licensed under the Apache License, Version 2.0
+# See https://github.com/shawntan/scattermoe/blob/main/LICENSE
+
+import torch
+import triton
+import triton.language as tl
+
+
+@triton.jit
+def _single2scatter(
+    X_ptr,
+    stride_xm,
+    stride_xk,
+    W_ptr,
+    stride_we,
+    stride_wk,
+    stride_wn,
+    Y_ptr,
+    stride_ym,
+    stride_yn,
+    expert_idxs_ptr,
+    FAN_OUT: tl.constexpr,
+    K: tl.constexpr,
+    N: tl.constexpr,
+    E: tl.constexpr,
+    BLOCK_N: tl.constexpr,
+    BLOCK_K: tl.constexpr,
+    ACC_TYPE: tl.constexpr,
+):
+    pid0 = tl.program_id(axis=0)
+    pid1 = tl.program_id(axis=1)
+
+    N_block_id = pid0
+    if FAN_OUT == 1:
+        in_idx = pid1
+    else:
+        in_idx = 0
+    out_idx = pid1
+
+    K_block = tl.arange(0, BLOCK_K)
+    N_block = tl.max_contiguous(
+        tl.multiple_of((N_block_id * BLOCK_N + tl.arange(0, BLOCK_N)) % N, BLOCK_N),
+        BLOCK_N,
+    )
+    E_idx = tl.load(expert_idxs_ptr + pid1)
+    X_blk_ptrs = X_ptr + in_idx * stride_xm + K_block[:, None] * stride_xk
+    W_blk_ptrs = (
+        W_ptr
+        + E_idx * stride_we
+        + K_block[:, None] * stride_wk
+        + N_block[None, :] * stride_wn
+    )
+    N_mask = N_block < N
+    acc = tl.zeros((1, BLOCK_N), dtype=ACC_TYPE)
+    for _K_block_id in range(0, tl.cdiv(K, BLOCK_K)):
+        K_mask = K_block < K
+        x = tl.load(X_blk_ptrs, mask=K_mask[:, None], other=0.0)
+        w = tl.load(W_blk_ptrs, mask=K_mask[:, None] & N_mask[None, :], other=0.0)
+        acc += tl.sum(x * w, axis=0)[None, :]
+        X_blk_ptrs += BLOCK_K * stride_xk
+        W_blk_ptrs += BLOCK_K * stride_wk
+        K_block += BLOCK_K
+    Y_blk_ptrs = Y_ptr + out_idx * stride_ym + N_block[None, :] * stride_yn
+    tl.store(Y_blk_ptrs, acc, mask=N_mask[None, :])
+
+
+def single2scatter(X, W, expert_idxs):
+    E, xdim, ydim = W.size()
+    k = expert_idxs.size(1)
+    assert X.size(0) == k or X.size(0) == 1
+    Y = torch.empty((k, ydim), device=X.device, dtype=X.dtype)
+    BLOCK_N = 128
+    BLOCK_K = 128
+    grid = triton.cdiv(ydim, BLOCK_N), k
+    _single2scatter[grid](
+        X,
+        X.stride(0),
+        X.stride(1),
+        W,
+        W.stride(0),
+        W.stride(1),
+        W.stride(2),
+        Y,
+        Y.stride(0),
+        Y.stride(1),
+        expert_idxs,
+        FAN_OUT=Y.size(0) // X.size(0),
+        K=xdim,
+        N=ydim,
+        E=E,
+        BLOCK_N=BLOCK_N,
+        BLOCK_K=BLOCK_K,
+        ACC_TYPE=tl.float32,
+    )
+    return Y

src/axolotl/integrations/kernels/libs/scattermoe_lora/layers.py

@@ -0,0 +1,439 @@
+# SPDX-License-Identifier: Apache-2.0
+#
+# Original work Copyright (c) Shawn Tan and ScatterMoE Contributors
+# Adapted from https://github.com/shawntan/scattermoe
+# See https://github.com/shawntan/scattermoe/blob/main/LICENSE
+#
+# Modifications and LoRA adaptation Copyright (c) Axolotl AI
+# Licensed under the Apache License, Version 2.0
+
+"""
+ScatterMoE layer replacements for HuggingFace MoE architectures.
+
+Provides drop-in forward replacements that use ScatterMoE kernels for
+acceleration. When used via the HF ``kernels`` library
+(``replace_kernel_forward_from_hub``), these classes replace the forward
+method of the original MoE block.
+
+LoRA support
+------------
+When peft wraps parameters via ``target_parameters``, the ``self.experts``
+submodule becomes a chain of ``ParamWrapper`` objects and the ``self.gate``
+router may also become a ``ParamWrapper``.  The ``HFScatterMoEGatedMLP``
+forward detects this and automatically:
+
+1. Unwraps ``self.gate`` to the base router, applying gate LoRA delta
+2. Unwraps ``self.experts`` to the base ``OlmoeExperts`` module
+3. Extracts LoRA A/B weights and scaling from each wrapper
+4. Converts B layout from peft rank-major to scattermoe expert-major
+5. Routes to ``parallel_linear_lora`` for fused LoRA computation
+6. Passes through ``self.shared_expert`` / ``self.shared_expert_gate``
+   (peft wraps their linear layers with standard LoRA, no special handling)
+"""
+
+import torch
+from torch import nn
+from torch.nn import functional as F
+
+from .parallel_experts import flatten_sort_count, parallel_linear
+from .parallel_linear_lora import get_lora_params_from_wrapper, parallel_linear_lora
+
+# =============================================================================
+# LoRA layout conversion utilities (peft <-> scattermoe)
+# =============================================================================
+
+
+def peft_lora_B_to_scattermoe(peft_B, num_experts, rank):
+    """Convert peft rank-major lora_B ``[out, E*r]`` to scattermoe
+    expert-major ``[N, r*E]``.
+
+    peft reshapes B to ``[out, r, E]`` (rank-major).
+    scattermoe slices B as ``[:, e*r:(e+1)*r]`` (expert-major).
+    """
+    N = peft_B.shape[0]
+    return (
+        peft_B.reshape(N, rank, num_experts)
+        .permute(0, 2, 1)
+        .contiguous()
+        .reshape(N, num_experts * rank)
+    )
+
+
+def peft_lora_to_scattermoe(peft_A, peft_B, num_experts, rank):
+    """Convert peft LoRA weights to scattermoe layout (with A<->B swap).
+
+    peft operates on the parameter in its native storage layout ``[E, dim1, dim2]``
+    where ``in_features=dim1, out_features=dim2``.  ScatterMoE transposes the
+    parameter (``W = param.transpose(2, 1)``) giving ``[E, dim2, dim1]`` with
+    ``K=dim2, N=dim1``.  Because of this transposition, peft's A and B roles
+    are swapped relative to scattermoe's convention.
+
+    peft gives:
+        lora_A ``[r*E, dim1]``, lora_B ``[dim2, r*E]``
+
+    scattermoe needs:
+        lora_A ``[r*E, K=dim2]``, lora_B ``[N=dim1, r*E]``
+
+    This function swaps A<->B and converts B from rank-major to expert-major.
+    Uses vectorized tensor operations (no Python loop over experts).
+
+    Works for **both** gate_up_proj and down_proj since the transposition
+    issue is the same for any parameter.
+    """
+    peft_B_em = peft_lora_B_to_scattermoe(peft_B, num_experts, rank)
+
+    dim1 = peft_A.shape[1]  # peft in_features -> scattermoe N
+    dim2 = peft_B_em.shape[0]  # peft out_features -> scattermoe K
+
+    # smoe_A: per expert, transpose B_e [dim2, r] -> [r, dim2]
+    # [dim2, E*r] -> [dim2, E, r] -> [E, r, dim2] -> [E*r, dim2]
+    smoe_A = (
+        peft_B_em.reshape(dim2, num_experts, rank)
+        .permute(1, 2, 0)
+        .contiguous()
+        .reshape(rank * num_experts, dim2)
+    )
+
+    # smoe_B: per expert, transpose A_e [r, dim1] -> [dim1, r]
+    # [E*r, dim1] -> [E, r, dim1] -> [dim1, E, r] -> [dim1, E*r]
+    smoe_B = (
+        peft_A.reshape(num_experts, rank, dim1)
+        .permute(2, 0, 1)
+        .contiguous()
+        .reshape(dim1, num_experts * rank)
+    )
+
+    return smoe_A, smoe_B
+
+
+def peft_down_proj_lora_to_scattermoe(peft_A, peft_B, num_experts, rank):
+    """Deprecated alias for :func:`peft_lora_to_scattermoe`."""
+    return peft_lora_to_scattermoe(peft_A, peft_B, num_experts, rank)
+
+
+# =============================================================================
+# ParamWrapper unwrapping
+# =============================================================================
+
+
+def _unwrap_gate_lora(gate_module):
+    """Unwrap peft ``ParamWrapper`` on the router gate.
+
+    When peft targets ``gate.weight``, ``self.gate`` becomes::
+
+        ParamWrapper(weight)
+          -> base_layer: OlmoeTopKRouter (the real module)
+
+    This function detects the wrapping and returns the base router, its
+    weight tensor, and an optional LoRA delta tensor.
+
+    Returns:
+        (base_gate, gate_weight, gate_lora_delta_or_None)
+
+        ``base_gate`` is the original router module (with ``.top_k``,
+        ``.num_experts``, ``.norm_topk_prob``).
+        ``gate_weight`` is the base router weight (may be a DTensor under FSDP).
+        ``gate_lora_delta_or_None`` is the LoRA delta tensor if LoRA is active,
+        else ``None``.  Kept separate to avoid mixing DTensor + Tensor in an add.
+    """
+    if hasattr(gate_module, "base_layer") and hasattr(gate_module, "lora_A"):
+        base_gate = gate_module.base_layer
+        lora_A, lora_B, scaling = get_lora_params_from_wrapper(gate_module)
+        if lora_A is not None:
+            # gate weight: [num_experts, hidden_size]
+            # lora_A: [r, hidden_size], lora_B: [num_experts, r]
+            # delta = scaling * B @ A = [num_experts, hidden_size]
+            delta = scaling * (lora_B @ lora_A)
+            return base_gate, base_gate.weight, delta
+        else:
+            return base_gate, base_gate.weight, None
+    else:
+        # No wrapping — gate is the original module
+        return gate_module, gate_module.weight, None
+
+
+def _convert_smoe_lora(lora_A, lora_B, num_experts, rank, scaling):
+    """Convert peft LoRA weights to scattermoe layout."""
+    smoe_A, smoe_B = peft_lora_to_scattermoe(lora_A, lora_B, num_experts, rank)
+    return (smoe_A, smoe_B, scaling)
+
+
+def _unwrap_experts_lora(experts_module):
+    """Walk a peft ``ParamWrapper`` chain on ``self.experts``.
+
+    When peft targets ``experts.gate_up_proj`` and ``experts.down_proj`` via
+    ``target_parameters``, ``self.experts`` becomes a nested chain::
+
+        ParamWrapper(down_proj)
+          -> base_layer: ParamWrapper(gate_up_proj)
+              -> base_layer: OlmoeExperts (the real module)
+
+    This function walks the chain, collects LoRA params keyed by
+    ``parameter_name``, and returns the base experts module.
+
+    Returns:
+        (base_experts, gup_lora, down_lora)
+
+        Each ``*_lora`` is either ``(smoe_A, smoe_B, scaling)`` or ``None``.
+        A/B are already in scattermoe layout.
+    """
+    # Collect ParamWrapper layers by their parameter_name
+    wrappers = {}
+    module = experts_module
+    while hasattr(module, "base_layer") and hasattr(module, "lora_A"):
+        param_name = getattr(module, "parameter_name", None)
+        if param_name is not None:
+            wrappers[param_name] = module
+        module = module.base_layer
+
+    base_experts = module
+
+    if not wrappers:
+        return base_experts, None, None
+
+    # Determine num_experts from base module
+    num_experts = getattr(base_experts, "num_experts", None)
+    if num_experts is None:
+        # Fallback: infer from parameter shape
+        gup = getattr(base_experts, "gate_up_proj", None)
+        if gup is not None:
+            num_experts = gup.shape[0]
+
+    # Extract gate_up_proj LoRA (needs A<->B swap due to transposition)
+    gup_lora = None
+    gup_wrapper = wrappers.get("gate_up_proj")
+    if gup_wrapper is not None:
+        lora_A, lora_B, scaling = get_lora_params_from_wrapper(gup_wrapper)
+        if lora_A is not None:
+            rank = lora_A.shape[0] // num_experts
+            gup_lora = _convert_smoe_lora(lora_A, lora_B, num_experts, rank, scaling)
+
+    # Extract down_proj LoRA (needs A<->B swap due to transposition)
+    down_lora = None
+    down_wrapper = wrappers.get("down_proj")
+    if down_wrapper is not None:
+        lora_A, lora_B, scaling = get_lora_params_from_wrapper(down_wrapper)
+        if lora_A is not None:
+            rank = lora_A.shape[0] // num_experts
+            down_lora = _convert_smoe_lora(lora_A, lora_B, num_experts, rank, scaling)
+
+    return base_experts, gup_lora, down_lora
+
+
+# =============================================================================
+# Layer classes
+# =============================================================================
+
+
+class ScatterMoEGatedMLP(nn.Module):
+    def forward(self, layer_input):
+        """
+        Forward pass of the mixture of experts layer.
+
+        Args:
+            layer_input (Tensor):
+                Input tensor.
+
+        Returns:
+            Tensor:
+                Output tensor.
+        """
+        bsz, length, emb_size = layer_input.size()
+        layer_input = layer_input.reshape(-1, emb_size)
+        # compute the top_k routing decision
+        router_logits = self.router.layer(layer_input)
+        routing_weights = F.softmax(router_logits, dim=1, dtype=torch.float)
+        routing_weights, selected_experts = torch.topk(
+            routing_weights, self.router.top_k, dim=-1
+        )
+        routing_weights /= routing_weights.sum(dim=-1, keepdim=True)
+        routing_weights = routing_weights.to(layer_input.dtype)
+        sorted_expert_idxs, sorted_scattered_idxs, expert_offsets = flatten_sort_count(
+            selected_experts, num_experts=self.router.num_experts
+        )
+
+        # compute experts
+        gates, h = parallel_linear(
+            layer_input,
+            self.input_linear.weight.transpose(2, 1),
+            self.router.top_k,
+            sorted_expert_idxs,
+            sorted_scattered_idxs,
+            expert_offsets,
+            grouped_in=False,
+            grouped_out=True,
+        ).chunk(2, dim=-1)
+        h = self.activation(gates) * h
+        layer_output = parallel_linear(
+            h,
+            self.output_linear.weight.transpose(2, 1),
+            1,
+            sorted_expert_idxs,
+            sorted_scattered_idxs,
+            expert_offsets,
+            grouped_in=True,
+            grouped_out=False,
+            gates=routing_weights,
+        )
+        layer_output = layer_output.view(bsz, length, emb_size)
+        return layer_output
+
+
+class HFScatterMoEGatedMLP(nn.Module):
+    """
+    ScatterMoE-accelerated forward pass for HF MoEs (OLMoE / Qwen2MoE).
+
+    Used as a kernel layer via the HF ``kernels`` library.  The ``forward``
+    method replaces the original ``OlmoeSparseMoeBlock.forward``.
+
+    Supports both full-parameter training and LoRA fine-tuning:
+
+    * **Full-param**: uses ``parallel_linear`` (base ScatterMoE kernel)
+    * **LoRA**: detects peft ``ParamWrapper`` on ``self.experts``, extracts
+      adapter weights, and uses ``parallel_linear_lora`` (fused kernel)
+    """
+
+    @staticmethod
+    def forward(self: nn.Module, layer_input: torch.Tensor):
+        """
+        Forward pass using ScatterMoE kernels.
+
+        Args:
+            self: The MoeSparseMoeBlock module containing:
+                - self.gate: Router (or peft ParamWrapper wrapping it)
+                - self.experts: Experts module (or peft ParamWrapper chain)
+                - self.shared_expert: Optional shared expert (e.g. Qwen2MoE)
+                - self.shared_expert_gate: Optional shared expert gate
+            layer_input: Input tensor [batch_size, seq_len, hidden_size]
+
+        Returns:
+            Tensor: [batch_size, seq_len, hidden_size]
+        """
+        batch_size, sequence_length, hidden_dim = layer_input.shape
+        hidden_states_flat = layer_input.view(-1, hidden_dim)
+
+        # ====================================================================
+        # Shared Expert (if present, e.g. Qwen2MoE)
+        # ====================================================================
+        # peft wraps individual linear layers inside shared_expert with
+        # standard LoRA — calling forward() handles this transparently.
+        if hasattr(self, "shared_expert") and self.shared_expert is not None:
+            shared_expert_output = self.shared_expert(hidden_states_flat)
+            # shared_expert_gate may also be peft-wrapped (standard LoRA
+            # on nn.Linear), its forward() applies LoRA automatically.
+            shared_expert_gate_output = F.sigmoid(
+                self.shared_expert_gate(hidden_states_flat)
+            )
+            shared_expert_output = shared_expert_output * shared_expert_gate_output
+        else:
+            shared_expert_output = None
+
+        # ====================================================================
+        # Router Computation (with optional gate LoRA)
+        # ====================================================================
+        base_gate, gate_weight, gate_lora_delta = _unwrap_gate_lora(self.gate)
+        router_logits = F.linear(hidden_states_flat, gate_weight)
+        if gate_lora_delta is not None:
+            router_logits = router_logits + F.linear(
+                hidden_states_flat, gate_lora_delta
+            )
+        routing_weights = F.softmax(router_logits, dim=1, dtype=torch.float)
+
+        top_k = base_gate.top_k
+        num_experts = base_gate.num_experts
+        routing_weights, selected_experts = torch.topk(routing_weights, top_k, dim=-1)
+
+        if base_gate.norm_topk_prob:
+            routing_weights /= routing_weights.sum(dim=-1, keepdim=True)
+        routing_weights = routing_weights.to(hidden_states_flat.dtype)
+
+        sorted_expert_idxs, sorted_scattered_idxs, expert_offsets = flatten_sort_count(
+            selected_experts, num_experts=num_experts
+        )
+
+        # ====================================================================
+        # Detect LoRA (peft ParamWrapper) and extract adapter weights
+        # ====================================================================
+        experts, gup_lora, down_lora = _unwrap_experts_lora(self.experts)
+
+        # ====================================================================
+        # Gate + Up projection
+        # ====================================================================
+        gate_up_W = experts.gate_up_proj.transpose(2, 1)  # [E, hidden, 2*inter]
+
+        if gup_lora is not None:
+            gup_A, gup_B, gup_scaling = gup_lora
+            gup = parallel_linear_lora(
+                hidden_states_flat,
+                gate_up_W,
+                top_k,
+                sorted_expert_idxs,
+                sorted_scattered_idxs,
+                expert_offsets,
+                lora_A=gup_A,
+                lora_B=gup_B,
+                scaling=gup_scaling,
+                grouped_in=False,
+                grouped_out=True,
+                use_fused_dX=True,
+                use_fused_gather=True,
+            )
+        else:
+            gup = parallel_linear(
+                hidden_states_flat,
+                gate_up_W,
+                top_k,
+                sorted_expert_idxs,
+                sorted_scattered_idxs,
+                expert_offsets,
+                grouped_in=False,
+                grouped_out=True,
+            )
+
+        gates, h = gup.chunk(2, dim=-1)
+        h = experts.act_fn(gates) * h
+
+        # ====================================================================
+        # Down projection
+        # ====================================================================
+        down_W = experts.down_proj.transpose(2, 1)  # [E, inter, hidden]
+
+        if down_lora is not None:
+            down_A, down_B, down_scaling = down_lora
+            expert_output = parallel_linear_lora(
+                h,
+                down_W,
+                1,
+                sorted_expert_idxs,
+                sorted_scattered_idxs,
+                expert_offsets,
+                lora_A=down_A,
+                lora_B=down_B,
+                scaling=down_scaling,
+                gates=routing_weights,
+                grouped_in=True,
+                grouped_out=False,
+                use_fused_dX=True,
+                use_fused_gather=True,
+            )
+        else:
+            expert_output = parallel_linear(
+                h,
+                down_W,
+                1,
+                sorted_expert_idxs,
+                sorted_scattered_idxs,
+                expert_offsets,
+                grouped_in=True,
+                grouped_out=False,
+                gates=routing_weights,
+            )
+
+        # ====================================================================
+        # Combine with shared expert and reshape
+        # ====================================================================
+        if shared_expert_output is not None:
+            expert_output = expert_output + shared_expert_output
+
+        expert_output = expert_output.view(batch_size, sequence_length, hidden_dim)
+        return expert_output

src/axolotl/integrations/kernels/libs/scattermoe_lora/lora_ops.py

@@ -0,0 +1,99 @@
+# SPDX-License-Identifier: Apache-2.0
+# Copyright (c) Axolotl AI
+# Licensed under the Apache License, Version 2.0
+
+"""
+ParallelExperts module with LoRA support.
+
+Provides a drop-in replacement for ScatterMoE's ParallelExperts that
+uses the fused LoRA kernel when adapter weights are attached.
+"""
+
+from typing import Optional
+
+import torch
+import torch.nn as nn
+
+from .parallel_linear_lora import parallel_linear_lora
+
+
+class ParallelExperts(nn.Module):
+    """
+    Parallel Experts with fused LoRA support.
+
+    Drop-in replacement for the original ParallelExperts. When LoRA parameters
+    are attached via set_lora(), the forward pass uses a fused kernel:
+        Y = X @ W + scaling * (X @ A^T) @ B^T
+    """
+
+    def __init__(
+        self,
+        num_experts: int,
+        input_size: int,
+        output_size: int,
+        bias: bool = False,
+    ) -> None:
+        super().__init__()
+        self.weight = nn.Parameter(torch.empty(num_experts, output_size, input_size))
+        if bias:
+            self.bias = nn.Parameter(torch.empty(num_experts, output_size))
+        else:
+            self.bias = None
+        self.num_experts = num_experts
+        self.input_size = input_size
+        self.output_size = output_size
+        self._lora_A: torch.Tensor | None = None
+        self._lora_B: torch.Tensor | None = None
+        self._lora_scaling: float | None = None
+        self.reset_parameters()
+
+    def reset_parameters(self) -> None:
+        nn.init.normal_(self.weight, std=0.02)
+        if self.bias is not None:
+            nn.init.zeros_(self.bias)
+
+    def extra_repr(self) -> str:
+        return (
+            f"num_experts={self.num_experts}, "
+            f"input_size={self.input_size}, "
+            f"output_size={self.output_size}"
+        )
+
+    def set_lora(self, lora_A: torch.Tensor, lora_B: torch.Tensor, scaling: float):
+        """Attach LoRA parameters for fused computation."""
+        self._lora_A = lora_A
+        self._lora_B = lora_B
+        self._lora_scaling = scaling
+
+    def clear_lora(self):
+        """Remove LoRA parameters."""
+        self._lora_A = None
+        self._lora_B = None
+        self._lora_scaling = None
+
+    def forward(
+        self,
+        inputs: torch.Tensor,
+        k: int,
+        sorted_expert_idxs: torch.Tensor,
+        sorted_scattered_idxs: torch.Tensor,
+        expert_offsets: torch.Tensor,
+        gates: Optional[torch.Tensor] = None,
+        grouped_in: bool = False,
+        grouped_out: bool = False,
+    ) -> torch.Tensor:
+        return parallel_linear_lora(
+            inputs,
+            self.weight.permute(0, 2, 1),  # [E, input, output]
+            k,
+            sorted_expert_idxs,
+            sorted_scattered_idxs,
+            expert_offsets,
+            lora_A=self._lora_A,
+            lora_B=self._lora_B,
+            scaling=self._lora_scaling if self._lora_scaling is not None else 1.0,
+            expert_biases=self.bias,
+            gates=gates,
+            grouped_in=grouped_in,
+            grouped_out=grouped_out,
+        )

src/axolotl/integrations/kernels/libs/scattermoe_lora/parallel_experts.py

@@ -0,0 +1,253 @@
+# SPDX-License-Identifier: Apache-2.0
+# Adapted from https://github.com/shawntan/scattermoe
+# Copyright (c) Shawn Tan and ScatterMoE Contributors
+# Licensed under the Apache License, Version 2.0
+# See https://github.com/shawntan/scattermoe/blob/main/LICENSE
+
+from typing import Optional
+
+import torch
+import torch.nn as nn
+
+from . import kernels
+
+
+@torch.library.custom_op("scattermoe::bincount", mutates_args={})
+def compileable_bincount(x: torch.Tensor, minlength: int) -> torch.Tensor:
+    return x.bincount(minlength=minlength)
+
+
+@compileable_bincount.register_fake
+def _(x: torch.Tensor, minlength: int) -> torch.Tensor:
+    return torch.empty(minlength, dtype=torch.long, device=x.device)
+
+
+@torch.compile
+def flatten_sort_count(expert_idxs: torch.Tensor, num_experts: int):
+    with torch.no_grad():
+        flattened_expert_idxs = expert_idxs.flatten()
+        sorted_expert_idxs, sorted_scattered_idxs = torch.sort(flattened_expert_idxs)
+        expert_counts = compileable_bincount(
+            flattened_expert_idxs, minlength=num_experts
+        )
+        expert_offsets = expert_counts.cumsum(-1)
+        return sorted_expert_idxs, sorted_scattered_idxs, expert_offsets
+
+
+class ParallelLinear(torch.autograd.Function):
+    @staticmethod
+    def forward(
+        ctx,
+        x: torch.Tensor,
+        expert_weights: torch.Tensor,
+        k: int,
+        sorted_expert_idxs: torch.Tensor,
+        sorted_scattered_idxs: torch.Tensor,
+        expert_offsets: torch.Tensor,
+        expert_biases: Optional[torch.Tensor] = None,
+        gates: Optional[torch.Tensor] = None,
+        grouped_in: bool = False,
+        grouped_out: bool = False,
+    ):
+        with torch.device(x.device):
+            output = kernels.ops.scatter2scatter(
+                X=x,
+                W=expert_weights,
+                b=expert_biases,
+                k=k,
+                sorted_expert_idxs=sorted_expert_idxs,
+                sorted_scattered_idxs=sorted_scattered_idxs,
+                x_grouped=grouped_in,
+                y_grouped=grouped_out,
+            )
+            if gates is not None:
+                output_expanded = output.view(
+                    gates.size(0), gates.size(1), output.size(-1)
+                )
+                output = (gates.unsqueeze(1) @ output_expanded).squeeze(1)
+            else:
+                output_expanded = None
+
+            ctx.save_for_backward(
+                x,
+                expert_weights,
+                expert_biases,
+                sorted_expert_idxs,
+                sorted_scattered_idxs,
+                expert_offsets,
+                gates,
+                output_expanded,
+            )
+            ctx.grouped_in = grouped_in
+            ctx.grouped_out = grouped_out
+            ctx.k = k
+        return output
+
+    @staticmethod
+    def backward(ctx, grad_out: torch.Tensor):
+        with torch.device(grad_out.device):
+            (
+                x,
+                expert_weights,
+                expert_biases,
+                sorted_expert_idxs,
+                sorted_scattered_idxs,
+                expert_offsets,
+                gates,
+                output_expanded,
+            ) = ctx.saved_tensors
+            k = ctx.k
+            grouped_in = ctx.grouped_in
+            grouped_out = ctx.grouped_out
+
+            if gates is not None:
+                # calculate gates gradient
+                # d_gates = torch.bmm(output_expanded, grad_out[:, :, None]).squeeze(-1)
+                d_gates = (output_expanded @ grad_out.unsqueeze(-1)).squeeze(-1)
+                gates_flat = gates.flatten()
+                gate_fan = gates.size(1)
+                grouped_grad_out = output_expanded.flatten(
+                    0, 1
+                )  # reuse expanded buffer later
+            else:
+                d_gates = None
+                gates_flat = None
+                gate_fan = 1
+                grouped_grad_out = None
+
+            if grouped_out:
+                grouped_grad_out = grad_out
+            else:
+                grouped_grad_out = kernels.ops.group(
+                    grad_out,
+                    sorted_scattered_idxs,
+                    fan_out=gate_fan,
+                    coeff=gates_flat,
+                    out=grouped_grad_out,
+                )
+            if grouped_in:
+                grouped_x = x
+                d_expanded_input = None
+            else:
+                grouped_x = kernels.ops.group(x, sorted_scattered_idxs, fan_out=k)
+                d_expanded_input = grouped_x
+
+            d_weights, d_biases = kernels.ops.group_bwd_W(
+                DY=grouped_grad_out,
+                X=grouped_x,
+                expert_offsets=expert_offsets,
+                E=expert_weights.size(0),
+                has_bias=expert_biases is not None,
+            )
+
+            d_expanded_input = kernels.ops.scatter2scatter(
+                X=grouped_grad_out,
+                x_grouped=True,
+                W=expert_weights.permute(0, 2, 1),
+                sorted_expert_idxs=sorted_expert_idxs,
+                sorted_scattered_idxs=sorted_scattered_idxs,
+                k=1,
+                y_grouped=grouped_in,
+                out=d_expanded_input,  # Reuse grouped_x buffer
+            )
+
+            if k == 1:
+                d_input = d_expanded_input
+            else:
+                d_input = d_expanded_input.view(
+                    x.size(0), k, d_expanded_input.size(-1)
+                ).sum(-2)
+        return (
+            # x, expert_weights,
+            d_input,
+            d_weights,
+            # k, sorted_expert_idxs, sorted_scattered_idxs, expert_offsets,
+            None,
+            None,
+            None,
+            None,
+            # bias, gates
+            d_biases,
+            d_gates,
+            # grouped_in, grouped_out,
+            None,
+            None,
+        )
+
+
+def parallel_linear(
+    inputs,
+    expert_weights,
+    k,
+    sorted_expert_idxs,
+    sorted_scattered_idxs,
+    expert_offsets,
+    expert_biases=None,
+    gates=None,
+    grouped_in=False,
+    grouped_out=False,
+):
+    results = ParallelLinear.apply(
+        inputs,
+        expert_weights,
+        k,
+        sorted_expert_idxs,
+        sorted_scattered_idxs,
+        expert_offsets,
+        expert_biases,
+        gates,
+        grouped_in,
+        grouped_out,
+    )
+    return results
+
+
+class ParallelExperts(nn.Module):
+    def __init__(self, num_experts, input_size, output_size, bias=False) -> None:
+        super().__init__()
+        self.weight = nn.Parameter(torch.empty(num_experts, output_size, input_size))
+
+        if bias:
+            self.bias = nn.Parameter(torch.empty(num_experts, output_size))
+        else:
+            self.bias = None
+
+        self.num_experts = num_experts
+        self.input_size = input_size
+        self.output_size = output_size
+        self.reset_parameters()
+
+    def extra_repr(self):
+        return "num_experts={}, input_size={}, output_size={}".format(
+            self.num_experts, self.input_size, self.output_size
+        )
+
+    def reset_parameters(self) -> None:
+        nn.init.normal_(self.weight, std=0.02)
+        if self.bias is not None:
+            nn.init.zeros_(self.bias)
+
+    def forward(
+        self,
+        inputs,
+        k,
+        sorted_expert_idxs,
+        sorted_scattered_idxs,
+        expert_offsets,
+        gates=None,
+        grouped_in=False,
+        grouped_out=False,
+    ):
+        results = parallel_linear(
+            inputs,
+            self.weight.permute(0, 2, 1),
+            k,
+            sorted_expert_idxs,
+            sorted_scattered_idxs,
+            expert_offsets,
+            expert_biases=self.bias,
+            gates=gates,
+            grouped_in=grouped_in,
+            grouped_out=grouped_out,
+        )
+        return results

src/axolotl/integrations/kernels/libs/scattermoe_lora/parallel_linear_lora.py

@@ -0,0 +1,480 @@
+# SPDX-License-Identifier: Apache-2.0
+# Copyright (c) Axolotl AI
+# Licensed under the Apache License, Version 2.0
+
+"""
+ScatterMoE + LoRA Autograd Function
+====================================
+
+Provides the autograd function and Python interface for fused ScatterMoE + LoRA.
+
+Key design for LoRA training:
+  - Expert weights W are FROZEN (no gradient computed for W).
+  - Only LoRA adapter weights (A, B) receive gradients.
+  - The input gradient dX is still computed (needed for upstream layers).
+  - This avoids the expensive group_bwd_W computation entirely.
+
+Forward:
+  Y = X @ W + scaling * (X @ A^T) @ B^T
+
+Backward (W frozen):
+  dX = dY @ W^T + scaling * (dY @ B) @ A          (via scatter2scatter for base, separate for LoRA)
+  dA = scaling * (dY @ B)^T @ X                     (per-expert, on grouped data)
+  dB = scaling * dY^T @ (X @ A^T)                   (per-expert, on grouped data)
+"""
+
+from typing import Optional
+
+import torch
+
+from .kernels import ops as base_ops
+from .kernels.lora_ops import (
+    group_bwd_lora,
+    group_bwd_lora_fused,
+    scatter2scatter_lora,
+    scatter2scatter_lora_dX,
+)
+
+
+class ScatterMoELoRA(torch.autograd.Function):
+    """
+    Autograd function for fused ScatterMoE + LoRA with frozen expert weights.
+
+    This function is optimized for the LoRA fine-tuning scenario where:
+    - Expert weights W are frozen (requires_grad=False)
+    - Only LoRA A and B matrices receive gradients
+    - Input gradients are computed for upstream layer backprop
+    """
+
+    @staticmethod
+    def forward(
+        ctx,
+        x: torch.Tensor,
+        expert_weights: torch.Tensor,
+        k: int,
+        sorted_expert_idxs: torch.Tensor,
+        sorted_scattered_idxs: torch.Tensor,
+        expert_offsets: torch.Tensor,
+        lora_A: torch.Tensor,
+        lora_B: torch.Tensor,
+        scaling: float,
+        expert_biases: Optional[torch.Tensor] = None,
+        gates: Optional[torch.Tensor] = None,
+        grouped_in: bool = False,
+        grouped_out: bool = False,
+        use_fused_dX: bool = False,
+        use_fused_gather: bool = False,
+    ):
+        with torch.device(x.device):
+            # Fused forward: Y = X @ W + scaling * (X @ A^T) @ B^T
+            output = scatter2scatter_lora(
+                X=x,
+                W=expert_weights,
+                sorted_expert_idxs=sorted_expert_idxs,
+                sorted_scattered_idxs=sorted_scattered_idxs,
+                k=k,
+                lora_A=lora_A,
+                lora_B=lora_B,
+                scaling=scaling,
+                b=expert_biases,
+                x_grouped=grouped_in,
+                y_grouped=grouped_out,
+            )
+
+            # Handle gating (weighted combination of top-k expert outputs)
+            if gates is not None:
+                output_expanded = output.view(
+                    gates.size(0), gates.size(1), output.size(-1)
+                )
+                output = (gates.unsqueeze(1) @ output_expanded).squeeze(1)
+            else:
+                output_expanded = None
+
+            ctx.save_for_backward(
+                x,
+                lora_A,
+                lora_B,
+                sorted_expert_idxs,
+                sorted_scattered_idxs,
+                expert_offsets,
+                gates,
+                output_expanded,
+            )
+            # Store frozen weights as plain Python attributes instead of
+            # save_for_backward.  This avoids:
+            # 1. Version-check conflicts with FSDP unshard/reshard
+            # 2. Pinning all-gathered parameters via saved_tensors hooks
+            # 3. Interfering with activation offloading pack/unpack hooks
+            # Safe because expert_weights are frozen (requires_grad=False).
+            ctx.expert_weights = expert_weights
+            ctx.expert_biases = expert_biases
+            ctx.grouped_in = grouped_in
+            ctx.grouped_out = grouped_out
+            ctx.k = k
+            ctx.scaling = scaling
+            ctx.use_fused_dX = use_fused_dX
+            ctx.use_fused_gather = use_fused_gather
+
+        return output
+
+    @staticmethod
+    def backward(ctx, grad_out: torch.Tensor):
+        with torch.device(grad_out.device):
+            (
+                x,
+                lora_A,
+                lora_B,
+                sorted_expert_idxs,
+                sorted_scattered_idxs,
+                expert_offsets,
+                gates,
+                output_expanded,
+            ) = ctx.saved_tensors
+            expert_weights = ctx.expert_weights
+
+            k = ctx.k
+            scaling = ctx.scaling
+            grouped_in = ctx.grouped_in
+            grouped_out = ctx.grouped_out
+            E = expert_weights.size(0)
+
+            # ------------------------------------------------------------------
+            # Gate gradients (if using top-k gating with routing weights)
+            # ------------------------------------------------------------------
+            if gates is not None:
+                # d_gates[t, j] = output_expanded[t, j, :] . grad_out[t, :]
+                d_gates = (output_expanded @ grad_out.unsqueeze(-1)).squeeze(-1)
+                gates_flat = gates.flatten()
+                gate_fan = gates.size(1)
+                # Reuse output_expanded buffer for grouped_grad_out
+                grouped_grad_out = output_expanded.flatten(0, 1)
+            else:
+                d_gates = None
+                gates_flat = None
+                gate_fan = 1
+                grouped_grad_out = None
+
+            # ------------------------------------------------------------------
+            # LoRA gradients (dA, dB) and setup for dX
+            # ------------------------------------------------------------------
+            # Fused gather uses sorted_scattered_idxs for indirect X access
+            # in the Triton kernel, avoiding the group(x) allocation.
+            #
+            # can_fuse_gather: X is ungrouped and not too large for scatter loads
+            #   - When gates is None and grouped_out=False: both DY and X ungrouped
+            #   - When grouped_out=True (gate_up_proj): DY already grouped, X ungrouped
+            #     -> use dy_grouped=True in the fused kernel
+            M_total = sorted_scattered_idxs.size(0)
+            K_dim = x.size(-1)
+            N_dim = expert_weights.size(-1)
+            fuse_gather_workload = M_total * max(K_dim, N_dim)
+            _FUSE_GATHER_THRESHOLD = 2**24  # ~16M elements
+
+            can_fuse_gather = (
+                ctx.use_fused_gather
+                and not grouped_in  # X must be ungrouped for scatter access
+                and gates is None  # gate coeff requires multiplicative gather
+                and fuse_gather_workload < _FUSE_GATHER_THRESHOLD
+            )
+
+            if can_fuse_gather:
+                # ------------------------------------------------------------------
+                # Fused path: skip group(x) entirely
+                # ------------------------------------------------------------------
+                d_expanded_input = None
+
+                d_lora_A, d_lora_B = group_bwd_lora_fused(
+                    DY=grad_out,
+                    X=x,
+                    lora_A=lora_A,
+                    lora_B=lora_B,
+                    expert_offsets=expert_offsets,
+                    sorted_scattered_idxs=sorted_scattered_idxs,
+                    E=E,
+                    k=k,
+                    scaling=scaling,
+                    dy_grouped=grouped_out,
+                )
+
+                # Prepare grouped_grad_out for the dX path (needed by both
+                # the fused dX kernel when grouped_out=True, and the non-fused path)
+                if grouped_out:
+                    grouped_grad_out = grad_out
+                elif not ctx.use_fused_dX:
+                    grouped_grad_out = base_ops.group(
+                        grad_out,
+                        sorted_scattered_idxs,
+                        fan_out=gate_fan,
+                        coeff=gates_flat,
+                        out=grouped_grad_out,
+                    )
+            else:
+                # ------------------------------------------------------------------
+                # Original path: explicit group() calls
+                # ------------------------------------------------------------------
+                if grouped_out:
+                    grouped_grad_out = grad_out
+                else:
+                    grouped_grad_out = base_ops.group(
+                        grad_out,
+                        sorted_scattered_idxs,
+                        fan_out=gate_fan,
+                        coeff=gates_flat,
+                        out=grouped_grad_out,
+                    )
+
+                if grouped_in:
+                    grouped_x = x
+                    d_expanded_input = None
+                else:
+                    grouped_x = base_ops.group(x, sorted_scattered_idxs, fan_out=k)
+                    d_expanded_input = grouped_x  # Will be overwritten; reuse buffer
+
+                d_lora_A, d_lora_B = group_bwd_lora(
+                    DY=grouped_grad_out,
+                    X=grouped_x,
+                    lora_A=lora_A,
+                    lora_B=lora_B,
+                    expert_offsets=expert_offsets,
+                    E=E,
+                    scaling=scaling,
+                )
+
+            # ------------------------------------------------------------------
+            # Input gradient: dX = dY @ W^T + scaling * (dY @ B) @ A
+            # ------------------------------------------------------------------
+            if ctx.use_fused_dX:
+                if can_fuse_gather and not grouped_out:
+                    # Fully fused: read ungrouped DY via scatter pattern
+                    d_expanded_input = scatter2scatter_lora_dX(
+                        DY=grad_out,
+                        W=expert_weights,
+                        sorted_expert_idxs=sorted_expert_idxs,
+                        sorted_scattered_idxs=sorted_scattered_idxs,
+                        k=1,
+                        lora_A=lora_A,
+                        lora_B=lora_B,
+                        scaling=scaling,
+                        dy_grouped=False,
+                        dx_grouped=grouped_in,
+                        out=d_expanded_input,
+                    )
+                else:
+                    # Fused dX only: read from pre-grouped DY
+                    d_expanded_input = scatter2scatter_lora_dX(
+                        DY=grouped_grad_out,
+                        W=expert_weights,
+                        sorted_expert_idxs=sorted_expert_idxs,
+                        sorted_scattered_idxs=sorted_scattered_idxs,
+                        k=1,
+                        lora_A=lora_A,
+                        lora_B=lora_B,
+                        scaling=scaling,
+                        dy_grouped=True,
+                        dx_grouped=grouped_in,
+                        out=d_expanded_input,
+                    )
+            else:
+                # Original path: separate base scatter2scatter + LoRA Python loop
+                d_expanded_input = base_ops.scatter2scatter(
+                    X=grouped_grad_out,
+                    x_grouped=True,
+                    W=expert_weights.permute(0, 2, 1),  # [E, N, K]
+                    sorted_expert_idxs=sorted_expert_idxs,
+                    sorted_scattered_idxs=sorted_scattered_idxs,
+                    k=1,
+                    y_grouped=grouped_in,
+                    out=d_expanded_input,
+                )
+
+                # LoRA part: dX_lora = scaling * (dY @ B) @ A
+                if scaling != 0.0:
+                    d_input_lora_grouped = _compute_lora_input_grad(
+                        grouped_grad_out,
+                        lora_A,
+                        lora_B,
+                        expert_offsets,
+                        E,
+                        scaling,
+                    )
+                    if grouped_in:
+                        d_expanded_input.add_(d_input_lora_grouped)
+                    else:
+                        # Scatter-add LoRA gradient directly into d_expanded_input.
+                        # Avoids allocating a zeros_like + add result
+                        d_expanded_input[sorted_scattered_idxs] += d_input_lora_grouped
+
+            # Reduce over top-k if k > 1
+            if k == 1:
+                d_input = d_expanded_input
+            else:
+                d_input = d_expanded_input.view(
+                    x.size(0), k, d_expanded_input.size(-1)
+                ).sum(-2)
+
+            # W is frozen during LoRA training -- skip weight gradient
+            d_weights = (
+                torch.zeros_like(expert_weights)
+                if expert_weights.requires_grad
+                else None
+            )
+            d_biases = None
+
+        return (
+            d_input,
+            d_weights,
+            None,
+            None,
+            None,
+            None,  # k, sorted indices, offsets
+            d_lora_A,
+            d_lora_B,
+            None,  # lora_A, lora_B, scaling
+            d_biases,
+            d_gates,
+            None,
+            None,  # grouped_in, grouped_out
+            None,  # use_fused_dX
+            None,  # use_fused_gather
+        )
+
+
+def _compute_lora_input_grad(
+    grouped_grad_out: torch.Tensor,
+    lora_A: torch.Tensor,
+    lora_B: torch.Tensor,
+    expert_offsets: torch.Tensor,
+    E: int,
+    scaling: float,
+) -> torch.Tensor:
+    """
+    Compute the LoRA contribution to the input gradient:
+      dX_lora = scaling * (dY @ B) @ A
+
+    Uses PyTorch ops on expert-grouped data.
+    Each expert e: dX_e = scaling * (dY_e @ B_e) @ A_e
+    """
+    R = lora_A.size(0) // E
+    K = lora_A.size(1)
+    M_total = grouped_grad_out.size(0)
+
+    d_input_lora = torch.zeros(
+        (M_total, K), device=grouped_grad_out.device, dtype=grouped_grad_out.dtype
+    )
+
+    compute_dtype = grouped_grad_out.dtype
+
+    prev_offset = 0
+    for e in range(E):
+        curr_offset = expert_offsets[e].item()
+        if curr_offset > prev_offset:
+            dy_e = grouped_grad_out[prev_offset:curr_offset]  # [M_e, N]
+            a_e = lora_A[e * R : (e + 1) * R, :].to(compute_dtype)  # [r, K]
+            b_e = lora_B[:, e * R : (e + 1) * R].to(compute_dtype)  # [N, r]
+
+            # dX_e = scaling * (dY_e @ B_e) @ A_e
+            dy_b = dy_e @ b_e  # [M_e, r]
+            dx_e = scaling * (dy_b @ a_e)  # [M_e, K]
+            d_input_lora[prev_offset:curr_offset] = dx_e
+
+        prev_offset = curr_offset
+
+    return d_input_lora
+
+
+# =============================================================================
+# Helper: Extract LoRA params from PEFT ParamWrapper
+# =============================================================================
+
+
+def get_lora_params_from_wrapper(module) -> tuple:
+    """
+    Extract LoRA parameters from a PEFT ParamWrapper.
+
+    Returns:
+        (lora_A, lora_B, scaling) if LoRA is active, else (None, None, None)
+    """
+    if not hasattr(module, "lora_A") or not hasattr(module, "lora_B"):
+        return None, None, None
+
+    active_adapters = getattr(module, "active_adapters", ["default"])
+    if not active_adapters:
+        return None, None, None
+
+    adapter_name = active_adapters[0]
+
+    lora_A_dict = getattr(module, "lora_A", {})
+    lora_B_dict = getattr(module, "lora_B", {})
+    scaling_dict = getattr(module, "scaling", {})
+
+    if adapter_name not in lora_A_dict:
+        return None, None, None
+
+    lora_A = lora_A_dict[adapter_name].weight
+    lora_B = lora_B_dict[adapter_name].weight
+    scaling = scaling_dict[adapter_name]
+
+    return lora_A, lora_B, scaling
+
+
+# =============================================================================
+# Drop-in replacement for parallel_linear
+# =============================================================================
+
+
+def parallel_linear_lora(
+    inputs: torch.Tensor,
+    expert_weights: torch.Tensor,
+    k: int,
+    sorted_expert_idxs: torch.Tensor,
+    sorted_scattered_idxs: torch.Tensor,
+    expert_offsets: torch.Tensor,
+    lora_A: Optional[torch.Tensor] = None,
+    lora_B: Optional[torch.Tensor] = None,
+    scaling: float = 1.0,
+    expert_biases: Optional[torch.Tensor] = None,
+    gates: Optional[torch.Tensor] = None,
+    grouped_in: bool = False,
+    grouped_out: bool = False,
+    use_fused_dX: bool = False,
+    use_fused_gather: bool = False,
+):
+    """
+    Drop-in replacement for parallel_linear that supports LoRA.
+
+    If lora_A and lora_B are provided, uses fused LoRA kernel.
+    Otherwise falls back to standard scatter2scatter.
+    """
+    if lora_A is not None and lora_B is not None:
+        return ScatterMoELoRA.apply(
+            inputs,
+            expert_weights,
+            k,
+            sorted_expert_idxs,
+            sorted_scattered_idxs,
+            expert_offsets,
+            lora_A,
+            lora_B,
+            scaling,
+            expert_biases,
+            gates,
+            grouped_in,
+            grouped_out,
+            use_fused_dX,
+            use_fused_gather,
+        )
+    else:
+        from .parallel_experts import ParallelLinear
+
+        return ParallelLinear.apply(
+            inputs,
+            expert_weights,
+            k,
+            sorted_expert_idxs,
+            sorted_scattered_idxs,
+            expert_offsets,
+            expert_biases,
+            gates,
+            grouped_in,
+            grouped_out,
+        )

src/axolotl/integrations/kernels/plugin.py

@@ -1,5 +1,7 @@
+from pathlib import Path
+
 from kernels import (
-    LayerRepository,
+    LocalLayerRepository,
     Mode,
     register_kernel_mapping,
     replace_kernel_forward_from_hub,
@@ -19,16 +21,19 @@ class KernelsPlugin(BasePlugin):
             self._kernelize_model(cfg.model_config_type)
 
     def _register_kernels(self):
+        plugin_root = Path(__file__).parent
         register_kernel_mapping(
             {
                 "HFScatterMoEParallelExperts": {
                     "cuda": {
-                        Mode.TRAINING: LayerRepository(
-                            repo_id="axolotl-ai-co/scattermoe",
+                        Mode.TRAINING: LocalLayerRepository(
+                            repo_path=plugin_root / "libs" / "scattermoe_lora",
+                            package_name="scattermoe_lora",
                             layer_name="HFScatterMoEGatedMLP",
                         ),
-                        Mode.INFERENCE: LayerRepository(
-                            repo_id="axolotl-ai-co/scattermoe",
+                        Mode.INFERENCE: LocalLayerRepository(
+                            repo_path=plugin_root / "libs" / "scattermoe_lora",
+                            package_name="scattermoe_lora",
                             layer_name="HFScatterMoEGatedMLP",
                         ),
                     },

src/axolotl/integrations/lm_eval/README.md

@@ -6,6 +6,12 @@ See https://github.com/EleutherAI/lm-evaluation-harness
 
 ## Usage
 
+There are two ways to use the LM Eval integration:
+
+### 1. Post-Training Evaluation
+
+When training with the plugin enabled, evaluation runs automatically after training completes:
+
 ```yaml
 plugins:
   - axolotl.integrations.lm_eval.LMEvalPlugin
@@ -16,9 +22,50 @@ lm_eval_tasks:
   - arc_easy
 
 lm_eval_batch_size: # Batch size for evaluation
-output_dir: # Directory to save evaluation results
+
+# Directory to save evaluation results.
+# The final model is loaded from this directory
+# unless specified otherwise (see below)
+output_dir:
 ```
 
+Run training as usual:
+```bash
+axolotl train config.yml
+```
+
+### 2. Standalone CLI Evaluation
+
+Evaluate any model directly without training:
+
+```yaml
+lm_eval_model: meta-llama/Llama-2-7b-hf
+
+plugins:
+  - axolotl.integrations.lm_eval.LMEvalPlugin
+
+lm_eval_tasks:
+  - gsm8k
+  - hellaswag
+  - arc_easy
+
+lm_eval_batch_size: 8
+output_dir: ./outputs
+```
+
+Run evaluation:
+```bash
+axolotl lm-eval config.yml
+```
+
+## Model Selection Priority
+
+The model to evaluate is selected in the following priority order:
+
+1. **`lm_eval_model`** - Explicit model path or HuggingFace repo (highest priority)
+2. **`hub_model_id`** - Trained model pushed to HuggingFace Hub
+3. **`output_dir`** - Local checkpoint directory containing trained model weights
+
 ## Citation
 
 ```bib

src/axolotl/integrations/lm_eval/__init__.py

@@ -5,7 +5,7 @@ Module for the Plugin for LM Eval Harness
 import subprocess  # nosec
 
 from axolotl.integrations.base import BasePlugin
-from axolotl.integrations.lm_eval.cli import build_lm_eval_command
+from axolotl.integrations.lm_eval.cli import build_lm_eval_command, get_model_path
 
 from .args import LMEvalArgs as LMEvalArgs
 
@@ -29,7 +29,7 @@ class LMEvalPlugin(BasePlugin):
                 wandb_project=cfg.wandb_project,
                 wandb_entity=cfg.wandb_entity,
                 wandb_name=cfg.wandb_name,
-                model=cfg.lm_eval_model or cfg.hub_model_id,
+                model=get_model_path(cfg),
             ):
                 subprocess.run(  # nosec
                     lm_eval_args,

src/axolotl/integrations/lm_eval/cli.py

@@ -13,6 +13,21 @@ import yaml
 from axolotl.utils.dict import DictDefault
 
 
+def get_model_path(cfg: DictDefault) -> str | None:
+    """
+    Determine which model path to use for evaluation.
+
+    Priority order (highest to lowest):
+    1. lm_eval_model - Explicit model path override
+    2. hub_model_id - Model pushed to HuggingFace Hub
+    3. None - Falls back to output_dir in build_lm_eval_command
+
+    Returns:
+        Model path string or None to use output_dir fallback
+    """
+    return cfg.lm_eval_model or cfg.hub_model_id or None
+
+
 def build_lm_eval_command(
     tasks: list[str],
     bfloat16=True,
@@ -108,7 +123,7 @@ def lm_eval(config: str, cloud: Optional[str] = None):
             wandb_project=cfg.wandb_project,
             wandb_entity=cfg.wandb_entity,
             wandb_name=cfg.wandb_name,
-            model=cfg.lm_eval_model or cfg.hub_model_id,
+            model=get_model_path(cfg),
             revision=cfg.revision,
             apply_chat_template=cfg.apply_chat_template,
             fewshot_as_multiturn=cfg.fewshot_as_multiturn,

src/axolotl/loaders/patch_manager.py

@@ -10,6 +10,7 @@ from functools import cached_property
 import addict
 import transformers
 from transformers import PretrainedConfig, PreTrainedModel
+from transformers.modeling_flash_attention_utils import is_flash_attn_available
 
 from axolotl.integrations.base import PluginManager
 from axolotl.monkeypatch.multipack import (
@@ -328,7 +329,7 @@ class PatchManager:
             else:
                 has_remote_code = False
 
-            if has_remote_code and self.cfg.trust_remote_code is False:
+            if has_remote_code and self.cfg.trust_remote_code is not None:
                 # If explicitly set in YAML, prefer that
                 has_remote_code = self.cfg.trust_remote_code
 
@@ -500,6 +501,7 @@ class PatchManager:
             and not self.cfg.trust_remote_code
             and not self.cfg.gptq
             and self.cfg.flash_attention
+            and is_flash_attn_available()
             and not self.inference
         ):
             # TODO(MengqingCao): split these patches separately

src/axolotl/loaders/processor.py

@@ -19,6 +19,11 @@ def load_processor(cfg: DictDefault, tokenizer: PreTrainedTokenizerBase):
     if cfg.processor_type:
         processor_cls = getattr(transformers, cfg.processor_type)
 
+    # Build common kwargs for processor loading
+    processor_kwargs = {}
+    if cfg.revision_of_model:
+        processor_kwargs["revision"] = cfg.revision_of_model
+
     if cfg.tokenizer_use_mistral_common:
 
         def _patch_mistralcommontokenizer():
@@ -40,6 +45,7 @@ def load_processor(cfg: DictDefault, tokenizer: PreTrainedTokenizerBase):
         if processor_cls == VoxtralProcessor:
             return VoxtralProcessor.from_pretrained(
                 cfg.processor_config,
+                **processor_kwargs,
             )
 
         from axolotl.utils.mistral import Mistral3Processor
@@ -48,10 +54,12 @@ def load_processor(cfg: DictDefault, tokenizer: PreTrainedTokenizerBase):
             tokenizer=tokenizer,
         )
 
+    processor_kwargs["trust_remote_code"] = cfg.trust_remote_code or False
+    processor_kwargs["tokenizer"] = tokenizer
+
     processor = processor_cls.from_pretrained(
         cfg.processor_config,
-        trust_remote_code=cfg.trust_remote_code or False,
-        tokenizer=tokenizer,
+        **processor_kwargs,
     )
 
     # Attempt to load image size from processor if available

src/axolotl/loaders/tokenizer.py

@@ -28,7 +28,10 @@ PLUGIN_MANAGER = PluginManager.get_instance()
 
 
 def modify_tokenizer_files(
-    tokenizer_path: str, token_mappings: dict[int, str], output_dir: str
+    tokenizer_path: str,
+    token_mappings: dict[int, str],
+    output_dir: str,
+    revision: str = "main",
 ) -> str:
     """
     Modify tokenizer files to replace added_tokens strings, save to output directory,
@@ -41,6 +44,7 @@ def modify_tokenizer_files(
         tokenizer_path: Path or name of the original tokenizer
         token_mappings: Dict mapping {token_id (int): new_token_string}
         output_dir: Directory to save the modified tokenizer
+        revision: Model revision/branch/tag/commit to load from (HF Hub)
 
     Returns:
         Path to the modified tokenizer directory
@@ -53,7 +57,9 @@ def modify_tokenizer_files(
 
     if is_local_main_process():
         # Load the tokenizer
-        temp_tokenizer = AutoTokenizer.from_pretrained(tokenizer_path, use_fast=True)
+        temp_tokenizer = AutoTokenizer.from_pretrained(
+            tokenizer_path, use_fast=True, revision=revision
+        )
 
         # Save the tokenizer to the output directory
         temp_tokenizer.save_pretrained(tokenizer_dir)
@@ -134,7 +140,10 @@ def load_tokenizer(cfg: DictDefault) -> PreTrainedTokenizer:
         from axolotl.utils.mistral import HFMistralTokenizer
 
         # Load the HF-compatible wrapper around MistralTokenizer
-        tokenizer = HFMistralTokenizer.from_pretrained(cfg.tokenizer_config)
+        kwargs = {}
+        if cfg.revision_of_model:
+            kwargs["revision"] = cfg.revision_of_model
+        tokenizer = HFMistralTokenizer.from_pretrained(cfg.tokenizer_config, **kwargs)
 
         return tokenizer
 
@@ -150,6 +159,8 @@ def load_tokenizer(cfg: DictDefault) -> PreTrainedTokenizer:
     if cfg.tokenizer_legacy is not None:
         # True is the default w/ https://github.com/huggingface/transformers/pull/25224
         tokenizer_kwargs["legacy"] = cfg.tokenizer_legacy
+    if cfg.revision_of_model:
+        tokenizer_kwargs["revision"] = cfg.revision_of_model
 
     tokenizer_cls = AutoTokenizer
     if cfg.tokenizer_type:
@@ -161,8 +172,11 @@ def load_tokenizer(cfg: DictDefault) -> PreTrainedTokenizer:
     # Apply token string overrides if specified
     if cfg.added_tokens_overrides:
         # Modify tokenizer files and get path to modified tokenizer
+        modify_kwargs = {"output_dir": cfg.output_dir}
+        if cfg.revision_of_model:
+            modify_kwargs["revision"] = cfg.revision_of_model
         tokenizer_path = modify_tokenizer_files(
-            tokenizer_path, cfg.added_tokens_overrides, output_dir=cfg.output_dir
+            tokenizer_path, cfg.added_tokens_overrides, **modify_kwargs
         )
 
     tokenizer = tokenizer_cls.from_pretrained(

src/axolotl/loaders/utils.py

@@ -204,13 +204,6 @@ def load_model_config(cfg: DictDefault) -> PretrainedConfig | addict.Dict:
 
     check_model_config(cfg, model_config)
 
-    # Extract text config from composite config when explicitly requested
-    # (set by plugins like Gemma3TextFromMultimodalPlugin)
-    if getattr(cfg, "extract_text_config", False) and hasattr(
-        model_config, "get_text_config"
-    ):
-        model_config = model_config.get_text_config()
-
     return model_config
 
 

src/axolotl/monkeypatch/gradient_checkpointing/offload_cpu.py

@@ -59,7 +59,12 @@ class CPU_Offloaded_Gradient_Checkpointer(torch.autograd.Function):
         hidden_states = hidden_states.to("cuda", non_blocking=True).detach()
         hidden_states.requires_grad = True
         with torch.enable_grad():
-            (output,) = ctx.forward_function(hidden_states, *ctx.args)
+            output = ctx.forward_function(hidden_states, *ctx.args)
+            # Newer HF models (e.g. Qwen3MoE) using GradientCheckpointingLayer
+            # return a plain tensor, not a tuple.  Older models return tuples
+            # like (hidden_states, present_kv, ...).  Unwrap if needed.
+            if isinstance(output, (tuple, list)):
+                (output,) = output
         torch.autograd.backward(output, dY)
         return (
             None,

src/axolotl/monkeypatch/transformers/trainer_loss_calc.py

@@ -28,8 +28,12 @@ PATCHED_EVAL_CODE = {
     "array": 'metrics[f"{metric_key_prefix}_loss"] = np.nanmean(all_losses).item()',
 }
 
-ORIGINAL_MAYBE_CODE = "tr_loss_scalar = self._nested_gather(tr_loss).mean().item()"
-PATCHED_MAYBE_CODE = "tr_loss_scalar = self._nested_gather(tr_loss).nanmean().item()"
+ORIGINAL_MAYBE_CODE = (
+    "tr_loss_scalar = nested_gather(tr_loss, self.args.parallel_mode).mean().item()"
+)
+PATCHED_MAYBE_CODE = (
+    "tr_loss_scalar = nested_gather(tr_loss, self.args.parallel_mode).nanmean().item()"
+)
 
 
 def check_evaluation_loop_is_patchable() -> bool:

src/axolotl/prompt_strategies/chat_template.py

@@ -48,9 +48,9 @@ class ChatTemplatePrompter(Prompter):
     ):
         # check if message_property_mappings is None or empty dict
         if message_property_mappings is None or (not message_property_mappings):
+            default_message_property_mappings_keys = ["role", "content", "tool"]
             message_property_mappings = {
-                "role": "role",
-                "content": "content",
+                prop: prop for prop in default_message_property_mappings_keys
             }
             if template_thinking_key and field_thinking:
                 message_property_mappings[template_thinking_key] = field_thinking

src/axolotl/telemetry/manager.py

@@ -156,6 +156,10 @@ class TelemetryManager:
         Returns:
             Boolean denoting whether telemetry is enabled or not.
         """
+        # Only rank 0 will send telemetry
+        if not is_main_process():
+            return False
+
         # Parse relevant env vars
         axolotl_do_not_track = os.getenv("AXOLOTL_DO_NOT_TRACK")
         do_not_track = os.getenv("DO_NOT_TRACK")
@@ -169,10 +173,6 @@ class TelemetryManager:
         ):
             return True
 
-        # Only rank 0 will send telemetry
-        if not is_main_process():
-            return False
-
         if do_not_track is None:
             do_not_track = "0"
 

src/axolotl/utils/callbacks/generation.py

@@ -0,0 +1,84 @@
+"""Callback for generating samples during SFT/Pretrain training."""
+
+from transformers.trainer_callback import TrainerCallback, TrainerControl, TrainerState
+from transformers.training_args import TrainingArguments
+
+from axolotl.utils.generation.sft import generate_samples
+from axolotl.utils.logging import get_logger
+
+LOG = get_logger(__name__)
+
+
+class SFTGenerationCallback(TrainerCallback):
+    """Callback for generating samples during SFT/Pretrain training."""
+
+    def __init__(self, trainer):
+        self.trainer = trainer
+
+    def on_evaluate(
+        self,
+        args: TrainingArguments,
+        state: TrainerState,
+        control: TrainerControl,
+        **kwargs,
+    ):
+        """Generate samples at specified intervals."""
+        cfg = self.trainer.axolotl_cfg
+
+        if not getattr(cfg, "generate_samples", False):
+            return
+
+            dataloader = None
+            try:
+                if getattr(self.trainer, "eval_dataset", None) is not None:
+                    dataloader = self.trainer.get_eval_dataloader()
+                    LOG.info(
+                        f"Using eval dataloader for generation at step {state.global_step}"
+                    )
+            except Exception as e:
+                LOG.warning(f"Could not get eval dataloader: {e}")
+                dataloader = None
+
+            if dataloader is None:
+                dataloader = self.trainer.get_train_dataloader()
+                LOG.info(
+                    f"Using train dataloader for generation at step {state.global_step}"
+                )
+
+            samples = generate_samples(
+                model=self.trainer.model,
+                tokenizer=self.trainer.processing_class,
+                dataloader=dataloader,
+                num_generation_samples=getattr(cfg, "num_generation_samples", 3),
+                max_new_tokens=getattr(cfg, "generation_max_new_tokens", 50),
+                temperature=getattr(cfg, "generation_temperature", 0.7),
+                top_p=getattr(cfg, "generation_top_p", None),
+                top_k=getattr(cfg, "generation_top_k", None),
+                do_sample=getattr(cfg, "generation_do_sample", True),
+                prompt_ratio=getattr(cfg, "generation_prompt_ratio", 0.5),
+            )
+            self._log_samples(samples, state.global_step)
+
+    def _log_samples(self, samples: list, step: int):
+        """Log generated samples to console and W&B."""
+        from axolotl.utils.generation.sft import format_generation_for_logging
+
+        for i, sample in enumerate(samples):
+            console_text, wandb_text = format_generation_for_logging(sample, i, step)
+
+            LOG.info(console_text)
+
+            try:
+                import wandb
+
+                if wandb.run is not None:
+                    wandb.log(
+                        {
+                            f"samples/sample_{i + 1}": wandb.Html(
+                                f"<pre>{wandb_text}</pre>"
+                            )
+                        },
+                        step=step,
+                    )
+            except (ImportError, Exception):
+                pass

src/axolotl/utils/data/lock.py

@@ -54,15 +54,19 @@ class FileLockLoader:
 
     def cleanup(self):
         """Clean up ready flag when last process is done."""
-        with FileLock(str(self.lock_file_path)):
-            counter_content = self.counter_path.read_text().strip()
-            count = int(counter_content) if counter_content else 0
-            count -= 1
+        try:
+            with FileLock(str(self.lock_file_path)):
+                counter_content = self.counter_path.read_text().strip()
+                count = int(counter_content) if counter_content else 0
+                count -= 1
 
-            if count <= 0:
-                # Last process cleans everything up
-                self.ready_flag_path.unlink(missing_ok=True)
-                self.counter_path.unlink(missing_ok=True)
-            else:
-                # Still have active processes
-                self.counter_path.write_text(str(count))
+                if count <= 0:
+                    # Last process cleans everything up
+                    self.ready_flag_path.unlink(missing_ok=True)
+                    self.counter_path.unlink(missing_ok=True)
+                else:
+                    # Still have active processes
+                    self.counter_path.write_text(str(count))
+        except FileNotFoundError:
+            # Lock file might have already been deleted by another process
+            pass

src/axolotl/utils/data/rl.py

@@ -246,6 +246,10 @@ def _load_split(cfg: DictDefault, split: Literal["train", "test"]) -> Dataset:
     dataset = merge_datasets(split_datasets, cfg)
 
     if not cfg.skip_prepare_dataset:
+        # Deduplicate before saving so the saved dataset is already de-duplicated
+        if cfg.dataset_exact_deduplication:
+            dataset, _ = deduplicate_and_log_datasets(dataset=dataset)
+
         # Save preprocessed dataset
         dataset_hash = generate_dataset_hash_from_config(
             cfg, datasets_configs, tokenizer.name_or_path

src/axolotl/utils/data/sft.py

@@ -351,6 +351,10 @@ def _load_raw_datasets(
         if cfg.sample_packing:
             dataset, _ = process_datasets_for_packing(cfg, dataset, None)
 
+        # Deduplicate before saving so the saved dataset is already de-duplicated
+        if cfg.dataset_exact_deduplication:
+            dataset, _ = deduplicate_and_log_datasets(dataset=dataset)
+
         # Save the prepared dataset
         dataset_hash = generate_dataset_hash_from_config(
             cfg, datasets_configs, tokenizer.name_or_path
@@ -438,25 +442,8 @@ def _handle_train_dataset_split(
         )
         return train_dataset, eval_dataset
 
-    # No validation split - apply deduplication if needed and return as train dataset
-    if cfg.dataset_exact_deduplication:
-        train_dataset, _ = deduplicate_and_log_datasets(dataset=dataset)
-    else:
-        train_dataset = dataset
-
-    return train_dataset, None
-
-
-def _handle_test_dataset_split(
-    dataset: Dataset, cfg: DictDefault
-) -> tuple[None, Dataset | None]:
-    """Handle processing for test split."""
-    if cfg.dataset_exact_deduplication:
-        eval_dataset, _ = deduplicate_and_log_datasets(dataset=dataset)
-    else:
-        eval_dataset = dataset
-
-    return None, eval_dataset
+    # No validation split - deduplication already applied during preprocessing
+    return dataset, None
 
 
 def _apply_dataset_sharding(dataset: Dataset, cfg: DictDefault) -> Dataset:
@@ -515,6 +502,7 @@ def _load_and_prepare_datasets(
     if split == "train":
         train_dataset, eval_dataset = _handle_train_dataset_split(dataset, cfg)
     else:
-        train_dataset, eval_dataset = _handle_test_dataset_split(dataset, cfg)
+        # Deduplication already applied during preprocessing
+        train_dataset, eval_dataset = None, dataset
 
     return train_dataset, eval_dataset, prompters

src/axolotl/utils/data/shared.py

@@ -520,7 +520,8 @@ def generate_dataset_hash_from_config(
     """
     config_str = (
         f"{cfg.sequence_len}@{cfg.sample_packing}@{cfg.eval_sample_packing}@"
-        f"{cfg.group_by_length}@{cfg.kd_temperature or 1.0}|"
+        f"{cfg.group_by_length}@{cfg.kd_temperature or 1.0}@"
+        f"{cfg.dataset_exact_deduplication or False}|"
         f"{'|'.join(sorted([f'{d.path}:{d.type}:{d.shards}:{d.conversation}:{d.split}:{d.temperature or 1.0}' for d in cfg_datasets]))}"
         f"|{tokenizer_name}"
     )

src/axolotl/utils/data/utils.py

@@ -15,7 +15,7 @@ from datasets import Dataset, IterableDataset
 from axolotl.utils.dict import DictDefault
 from axolotl.utils.logging import get_logger
 from axolotl.utils.samplers.utils import get_dataset_lengths
-from axolotl.utils.trainer import drop_long_seq
+from axolotl.utils.trainer import filter_sequences_by_length
 
 LOG = get_logger(__name__)
 
@@ -148,22 +148,33 @@ def deduplicate_and_log_datasets(
     return dataset, other_dataset
 
 
-def truncate_long_seq(sample, sequence_len=2048, min_sequence_len=2):
+def keep_min_len(sample, min_sequence_len=2):
     """
-    Truncate samples whose sequence length is too long (> sequence_len)
-    or drop those too short (< min_sequence_len).
+    Batched filter function that keeps only samples with sequence length >= min_sequence_len.
+    Returns a list of booleans indicating which samples to keep.
     """
     min_sequence_len = min_sequence_len or 2
 
     input_ids = sample["input_ids"]
+
+    # Batched (input_ids is a list of lists)
     results = []
+    for seq in input_ids:
+        results.append(len(seq) >= min_sequence_len)
+    return results
+
+
+def truncate_long_seq(sample, sequence_len=2048):
+    """
+    Truncate samples whose sequence length is too long (> sequence_len).
+    Modifies the sample in-place and returns the modified sample.
+    """
+    input_ids = sample["input_ids"]
 
     # Batched (input_ids is a list of lists)
     for i, seq in enumerate(input_ids):
         length = len(seq)
-        if length < min_sequence_len:
-            results.append(False)
-        elif length > sequence_len:
+        if length > sequence_len:
             sample["input_ids"][i] = seq[:sequence_len]
             if "attention_mask" in sample:
                 sample["attention_mask"][i] = sample["attention_mask"][i][:sequence_len]
@@ -171,10 +182,133 @@ def truncate_long_seq(sample, sequence_len=2048, min_sequence_len=2):
                 sample["labels"][i] = sample["labels"][i][:sequence_len]
             if "position_ids" in sample:
                 sample["position_ids"][i] = sample["position_ids"][i][:sequence_len]
-            results.append(True)
-        else:
-            results.append(True)
-    return results
+    return sample
+
+
+def _should_skip_processing(dataset: Dataset) -> bool:
+    """Check if dataset should skip long sequence handling."""
+    if (
+        hasattr(dataset, "column_names")
+        and dataset.column_names
+        and "input_ids" not in dataset.column_names
+    ):
+        LOG.warning(
+            "Dataset does not contain 'input_ids' column. Skip drop long seq. This is "
+            "expected for reward modeling."
+        )
+        return True
+    elif not hasattr(dataset, "column_names") or dataset.column_names is None:
+        LOG.info(
+            "Dataset is streaming (IterableDataset), skipping long sequence handling"
+        )
+        return True
+    return False
+
+
+def _log_dataset_stats(dataset: Dataset) -> None:
+    """Log min/max sequence lengths for debugging."""
+    with contextlib.suppress(AttributeError, ValueError):
+        ds_lengths = get_dataset_lengths(dataset, from_arrow=True)
+        LOG.info(f"min_input_len: {np.min(ds_lengths)}")
+        LOG.info(f"max_input_len: {np.max(ds_lengths)}")
+
+
+def _build_filter_kwargs(dataset: Dataset, cfg: DictDefault) -> dict:
+    """Build kwargs for dataset filter/map operations."""
+    kwargs = {}
+    if not isinstance(dataset, IterableDataset):
+        kwargs["num_proc"] = cfg.dataset_num_proc
+        kwargs["load_from_cache_file"] = not cfg.is_preprocess
+    return kwargs
+
+
+def _filter_short_sequences(
+    dataset: Dataset, min_len: int, filter_kwargs: dict
+) -> tuple[Dataset, int]:
+    """Filter out sequences shorter than min_len. Returns (dataset, num_dropped)."""
+    prior_len = len(dataset) if hasattr(dataset, "__len__") else None
+
+    desc_kwargs = {}
+    if filter_kwargs:
+        desc_kwargs["desc"] = f"Filtering Short Sequences (<{min_len})"
+
+    dataset = dataset.filter(
+        functools.partial(keep_min_len, min_sequence_len=min_len),
+        batched=True,
+        **filter_kwargs,
+        **desc_kwargs,
+    )
+
+    dropped = 0
+    if prior_len:
+        dropped = prior_len - len(dataset)
+        if dropped > 0:
+            LOG.info(f"Dropped {dropped} short sequences (<{min_len} tokens)")
+
+    return dataset, dropped
+
+
+def _truncate_long_sequences(
+    dataset: Dataset, max_len: int, map_kwargs: dict
+) -> Dataset:
+    """Truncate sequences longer than max_len."""
+    desc_kwargs = {}
+    if map_kwargs:
+        desc_kwargs["desc"] = f"Truncating Sequences (target_len={max_len})"
+
+    dataset = dataset.map(
+        functools.partial(truncate_long_seq, sequence_len=max_len),
+        batched=True,
+        **map_kwargs,
+        **desc_kwargs,
+    )
+    LOG.info(f"Truncated long sequences to max length {max_len}")
+    return dataset
+
+
+def _drop_outside_range(
+    dataset: Dataset,
+    max_len: int,
+    min_len: int,
+    raise_on_long: bool,
+    filter_kwargs: dict,
+) -> tuple[Dataset, int]:
+    """Drop sequences outside valid length range [min_len, max_len].
+
+    Returns (dataset, num_dropped)."""
+    prior_len = len(dataset) if hasattr(dataset, "__len__") else None
+
+    desc_kwargs = {}
+    if filter_kwargs:
+        action = (
+            "Checking Sequence Lengths"
+            if raise_on_long
+            else "Dropping Invalid Sequences"
+        )
+        desc_kwargs["desc"] = f"{action} (<{min_len} or >{max_len})"
+
+    dataset = dataset.filter(
+        functools.partial(
+            filter_sequences_by_length,
+            sequence_len=max_len,
+            min_sequence_len=min_len,
+            raise_on_drop=raise_on_long,
+        ),
+        batched=True,
+        **filter_kwargs,
+        **desc_kwargs,
+    )
+
+    dropped = 0
+    if not raise_on_long and prior_len:
+        dropped = prior_len - len(dataset)
+        if dropped > 0:
+            LOG.info(
+                f"Dropped {dropped} sequences outside valid range "
+                f"([{min_len}, {max_len}])"
+            )
+
+    return dataset, dropped
 
 
 def handle_long_seq_in_dataset(
@@ -193,80 +327,25 @@ def handle_long_seq_in_dataset(
             'truncate'          truncates them down to sequence_len
             'raise'             raises a ValueError if any sequence was found that was longer than sequence_len
     """
-    if (
-        hasattr(dataset, "column_names")
-        and dataset.column_names
-        and "input_ids" not in dataset.column_names
-    ):
-        LOG.warning(
-            "Dataset does not contain 'input_ids' column. Skip drop long seq. This is "
-            "expected for reward modeling."
-        )
-        return dataset
-    elif not hasattr(dataset, "column_names") or dataset.column_names is None:
-        LOG.info(
-            "Dataset is streaming (IterableDataset), skipping long sequence handling"
-        )
+    # Early returns for special cases
+    if _should_skip_processing(dataset):
         return dataset
 
     excess_length_strategy = (cfg.excess_length_strategy or "drop").lower()
 
-    drop_long = functools.partial(
-        drop_long_seq,
-        sequence_len=sequence_len,
-        min_sequence_len=cfg.min_sample_len,
-        raise_on_drop=excess_length_strategy == "raise",
-    )
+    _log_dataset_stats(dataset)
 
-    with contextlib.suppress(AttributeError):
-        ds_lengths = get_dataset_lengths(dataset, from_arrow=True)
-        min_input_len = np.min(ds_lengths)
-        LOG.info(f"min_input_len: {min_input_len}")
-        max_input_len = np.max(ds_lengths)
-        LOG.info(f"max_input_len: {max_input_len}")
-
-    prior_len = len(dataset) if hasattr(dataset, "__len__") else None
-
-    filter_map_kwargs = {}
-    if not isinstance(dataset, IterableDataset):
-        filter_map_kwargs["num_proc"] = cfg.dataset_num_proc
-        filter_map_kwargs["load_from_cache_file"] = not cfg.is_preprocess
-
-    drop_long_kwargs = {}
-    if filter_map_kwargs:
-        action = (
-            "Checking Sequence Lengths"
-            if excess_length_strategy == "raise"
-            else "Dropping Long Sequences"
-        )
-        drop_long_kwargs["desc"] = f"{action} (>{sequence_len})"
+    # Setup kwargs
+    filter_kwargs = _build_filter_kwargs(dataset, cfg)
 
+    # Handle sequences based on strategy
     if excess_length_strategy == "truncate":
-        process_fn = functools.partial(
-            truncate_long_seq,
-            sequence_len=sequence_len,
-            min_sequence_len=cfg.min_sample_len,
-        )
-        drop_long_kwargs["desc"] = (
-            f"Truncating/Filtering Sequences (target_len={sequence_len})"
-        )
+        dataset, _ = _filter_short_sequences(dataset, cfg.min_sample_len, filter_kwargs)
+        dataset = _truncate_long_sequences(dataset, sequence_len, filter_kwargs)
     else:
-        process_fn = drop_long
-
-    dataset = dataset.filter(
-        process_fn,
-        batched=True,
-        **filter_map_kwargs,
-        **drop_long_kwargs,
-    )
-    if prior_len:
-        dropped = prior_len - len(dataset)
-        if dropped:
-            action = (
-                "truncated/filtered"
-                if excess_length_strategy == "truncate"
-                else "dropped"
-            )
-            LOG.warning(f"{action.title()} {dropped} samples from dataset")
+        raise_on_long = excess_length_strategy == "raise"
+        dataset, _ = _drop_outside_range(
+            dataset, sequence_len, cfg.min_sample_len, raise_on_long, filter_kwargs
+        )
 
     return dataset

src/axolotl/utils/generation/__init__.py

@@ -0,0 +1,5 @@
+"""Generation utilities for monitoring during training."""
+
+from .sft import format_generation_for_logging, generate_samples
+
+__all__ = ["generate_samples", "format_generation_for_logging"]

src/axolotl/utils/generation/sft.py

@@ -0,0 +1,174 @@
+"""Sample generation utilities for SFT/Pretrain training."""
+
+from typing import Any, List, Optional
+
+import torch
+from accelerate.utils import extract_model_from_parallel
+from colorama import Fore, Style
+
+from axolotl.utils.logging import get_logger
+
+LOG = get_logger(__name__)
+
+
+def generate_samples(
+    model: torch.nn.Module,
+    tokenizer: Any,
+    dataloader: Any,
+    num_generation_samples: int = 3,
+    max_new_tokens: int = 50,
+    temperature: float = 0.7,
+    top_p: Optional[float] = None,
+    top_k: Optional[int] = None,
+    do_sample: bool = True,
+    prompt_ratio: float = 0.5,
+) -> List[dict]:
+    """
+    Generate samples from the model during training for monitoring.
+
+    Args:
+        model: The model to generate from
+        tokenizer: The tokenizer to use for encoding/decoding
+        dataloader: Dataloader to sample prompts from
+        num_generation_samples: Number of samples to generate
+        max_new_tokens: Maximum new tokens to generate
+        temperature: Sampling temperature (0.0 = greedy)
+        top_p: Nucleus sampling parameter
+        top_k: Top-k sampling parameter
+        do_sample: Whether to use sampling vs greedy decoding
+        prompt_ratio: Ratio of sequence to use as prompt (0.0-1.0)
+
+    Returns:
+        List of dicts with 'prompt', 'generated', and 'full_text' keys
+    """
+    unwrapped_model = extract_model_from_parallel(model)
+
+    training = unwrapped_model.training
+    unwrapped_model.eval()
+
+    device = next(unwrapped_model.parameters()).device
+
+    generations = []
+
+    try:
+        with torch.no_grad():
+            samples_collected = 0
+
+            for batch in dataloader:
+                if samples_collected >= num_generation_samples:
+                    break
+
+                input_ids = batch["input_ids"].to(device)
+                attention_mask = batch.get("attention_mask")
+                if attention_mask is not None:
+                    attention_mask = attention_mask.to(device)
+                batch_size = input_ids.shape[0]
+
+                indices = torch.randperm(batch_size)[
+                    : num_generation_samples - samples_collected
+                ]
+
+                for idx in indices:
+                    if samples_collected >= num_generation_samples:
+                        break
+
+                    sequence = input_ids[idx]
+
+                    if attention_mask is not None:
+                        seq_len = attention_mask[idx].sum().item()
+                    else:
+                        seq_len = sequence.shape[0]
+
+                    if seq_len < 5:
+                        continue
+
+                    prompt_len = max(1, int(seq_len * prompt_ratio))
+                    prompt_ids = sequence[:prompt_len].unsqueeze(0)
+
+                    try:
+                        generation_config = {
+                            "max_new_tokens": max_new_tokens,
+                            "do_sample": do_sample,
+                            "pad_token_id": tokenizer.pad_token_id
+                            if tokenizer.pad_token_id is not None
+                            else tokenizer.eos_token_id,
+                        }
+
+                        if do_sample:
+                            generation_config["temperature"] = temperature
+                            if top_p is not None:
+                                generation_config["top_p"] = top_p
+                            if top_k is not None:
+                                generation_config["top_k"] = top_k
+
+                        generated_ids = unwrapped_model.generate(
+                            prompt_ids, **generation_config
+                        )
+
+                        prompt_text = tokenizer.decode(
+                            prompt_ids[0], skip_special_tokens=True
+                        )
+                        generated_text = tokenizer.decode(
+                            generated_ids[0][prompt_len:], skip_special_tokens=True
+                        )
+                        full_text = tokenizer.decode(
+                            generated_ids[0], skip_special_tokens=True
+                        )
+
+                        generations.append(
+                            {
+                                "prompt": prompt_text,
+                                "generated": generated_text,
+                                "full_text": full_text,
+                            }
+                        )
+
+                        samples_collected += 1
+
+                    except Exception as e:
+                        LOG.warning(f"Failed to generate sample: {e}", exc_info=True)
+                        continue
+
+    except Exception as e:
+        LOG.warning(f"Error during sample generation: {e}", exc_info=True)
+
+    if training:
+        unwrapped_model.train()
+    else:
+        unwrapped_model.eval()
+
+    return generations
+
+
+def format_generation_for_logging(
+    sample: dict, sample_idx: int, step: int
+) -> tuple[str, str]:
+    """
+    Format a generation sample for pretty logging.
+
+    Args:
+        sample: Dict with 'prompt', 'generated', and 'full_text' keys
+        sample_idx: Index of the sample
+        step: Current training step
+
+    Returns:
+        Tuple of (console_text, wandb_text)
+    """
+    console_text = (
+        f"\n{Style.BRIGHT}{Fore.CYAN}{'=' * 80}{Style.RESET_ALL}\n"
+        f"{Style.BRIGHT}{Fore.GREEN}Sample {sample_idx + 1} (Step {step}){Style.RESET_ALL}\n"
+        f"{Style.BRIGHT}{Fore.CYAN}{'=' * 80}{Style.RESET_ALL}\n"
+        f"{Style.BRIGHT}{Fore.YELLOW}[PROMPT]{Style.RESET_ALL}\n{sample['prompt']}\n\n"
+        f"{Style.BRIGHT}{Fore.MAGENTA}[GENERATED]{Style.RESET_ALL}\n{sample['generated']}\n"
+        f"{Style.BRIGHT}{Fore.CYAN}{'=' * 80}{Style.RESET_ALL}\n"
+    )
+    wandb_text = (
+        f"\n{'=' * 80}\n"
+        f"Sample {sample_idx + 1} (Step {step})\n"
+        f"{'=' * 80}\n"
+        f"[PROMPT]\n{sample['prompt']}\n\n"
+        f"[GENERATED]\n{sample['generated']}\n"
+        f"{'=' * 80}\n"
+    )
+
+    return console_text, wandb_text

src/axolotl/utils/mistral/mistral3_processor.py

@@ -30,18 +30,8 @@ class Mistral3Processor(ProcessorMixin):
     Wraps HFMistralTokenizer and adds image processing capabilities.
     """
 
-    # TODO(nano): This should be removed in transformers V5
-    attributes = ["tokenizer"]
-    tokenizer_class = "HFMistralTokenizer"
-
     def __init__(self, tokenizer: HFMistralTokenizer):
-        # Don't call super().__init__ to avoid the class validation issue
-        self.tokenizer = tokenizer
-
-    @property
-    def chat_template(self) -> None:
-        """Chat template is not supported. Dummy method to satisfy HuggingFace API."""
-        return None
+        super().__init__(tokenizer)
 
     @property
     def audio_tokenizer(self) -> None:

src/axolotl/utils/schemas/config.py

@@ -338,18 +338,6 @@ class AxolotlInputConfig(
     )
     ddp_find_unused_parameters: bool | None = None
 
-    eval_table_size: int | None = Field(
-        default=None,
-        json_schema_extra={
-            "description": "Approximate number of predictions sent to wandb depending on batch size. Enabled above 0. Default is 0"
-        },
-    )
-    eval_max_new_tokens: int | None = Field(
-        default=None,
-        json_schema_extra={
-            "description": "Total number of tokens generated for predictions sent to wandb. Default is 128"
-        },
-    )
     do_causal_lm_eval: bool | None = Field(
         default=None,
         json_schema_extra={
@@ -446,7 +434,16 @@ class AxolotlInputConfig(
         },
     )
 
-    unfrozen_parameters: list[str] | None = None
+    unfrozen_parameters: list[str] | None = Field(
+        default=None,
+        json_schema_extra={
+            "description": "List of regex patterns for parameter names to keep unfrozen. "
+            "All other parameters will be frozen via requires_grad=False. "
+            "Note: range-based patterns (e.g. embed_tokens.weight$[:32000]) use gradient "
+            "zeroing rather than a true freeze, so weight decay will still apply to the "
+            "frozen portion and optimizer states are allocated for the full parameter."
+        },
+    )
 
     sequence_len: int = Field(
         default=512,
@@ -1097,6 +1094,46 @@ class AxolotlInputConfig(
             "description": "Add plugins to extend the pipeline. See `src/axolotl/integrations` for the available plugins or doc below for more details. https://docs.axolotl.ai/docs/custom_integrations.html"
         },
     )
+    generate_samples: bool | None = Field(
+        default=False,
+        json_schema_extra={
+            "description": "Enable sample generation during training for monitoring"
+        },
+    )
+    num_generation_samples: int | None = Field(
+        default=3,
+        json_schema_extra={
+            "description": "Number of samples to generate at each interval"
+        },
+    )
+    generation_max_new_tokens: int | None = Field(
+        default=50,
+        json_schema_extra={"description": "Maximum new tokens to generate per sample"},
+    )
+    generation_temperature: float | None = Field(
+        default=0.7,
+        json_schema_extra={
+            "description": "Temperature for sample generation (0.0 = greedy)"
+        },
+    )
+    generation_top_p: float | None = Field(
+        default=None,
+        json_schema_extra={"description": "Nucleus sampling parameter for generation"},
+    )
+    generation_top_k: int | None = Field(
+        default=None,
+        json_schema_extra={"description": "Top-k sampling parameter for generation"},
+    )
+    generation_prompt_ratio: float | None = Field(
+        default=0.5,
+        json_schema_extra={"description": "Ratio of input to use as prompt (0.0-1.0)"},
+    )
+    generation_do_sample: bool | None = Field(
+        default=True,
+        json_schema_extra={
+            "description": "Whether to use sampling (vs greedy decoding)"
+        },
+    )
 
     @field_serializer("datasets")
     def datasets_serializer(
@@ -1472,3 +1509,16 @@ class AxolotlConfigWCapabilities(AxolotlInputConfig):
                 "dataset_exact_deduplication is not available for streaming datasets. "
             )
         return data
+
+    @model_validator(mode="before")
+    @classmethod
+    def check_deduplication_with_skip_prepare(cls, data):
+        if data.get("dataset_exact_deduplication") and data.get("skip_prepare_dataset"):
+            raise ValueError(
+                "dataset_exact_deduplication=True has no effect when "
+                "skip_prepare_dataset=True. Deduplication runs as part of the "
+                "prepare pipeline, which is skipped. Either set "
+                "skip_prepare_dataset: false or disable "
+                "dataset_exact_deduplication."
+            )
+        return data

src/axolotl/utils/schemas/deprecated.py

@@ -17,6 +17,8 @@ class DeprecatedParameters(BaseModel):
     noisy_embedding_alpha: float | None = None
     dpo_beta: float | None = None
     evaluation_strategy: str | None = None
+    eval_table_size: int | None = None
+    eval_max_new_tokens: int | None = None
 
     @field_validator("max_packed_sequence_len")
     @classmethod
@@ -55,6 +57,27 @@ class DeprecatedParameters(BaseModel):
             LOG.warning("evaluation_strategy is deprecated, use eval_strategy instead")
         return evaluation_strategy
 
+    @field_validator("eval_table_size")
+    @classmethod
+    def validate_eval_table_size(cls, eval_table_size):
+        if eval_table_size is not None:
+            LOG.warning(
+                "eval_table_size is deprecated and superseded by generate_samples config. "
+                "Please use generate_samples: true and num_generation_samples instead. "
+                "The LogPredictionCallback is replaced by the new sample generation feature."
+            )
+        return eval_table_size
+
+    @field_validator("eval_max_new_tokens")
+    @classmethod
+    def validate_eval_max_new_tokens(cls, eval_max_new_tokens):
+        if eval_max_new_tokens is not None:
+            LOG.warning(
+                "eval_max_new_tokens is deprecated and superseded by generate_samples config. "
+                "Please use generation_max_new_tokens instead."
+            )
+        return eval_max_new_tokens
+
 
 class RemappedParameters(BaseModel):
     """Parameters that have been remapped to other names"""

src/axolotl/utils/schemas/peft.py

@@ -1,6 +1,6 @@
 """Pydantic models for PEFT-related configuration"""
 
-from typing import Any
+from typing import Any, Literal
 
 from pydantic import BaseModel, Field, field_validator, model_validator
 
@@ -38,10 +38,10 @@ class LoraConfig(BaseModel):
         default=False, json_schema_extra={"description": "Use bitsandbytes 4 bit"}
     )
 
-    adapter: str | None = Field(
+    adapter: Literal["lora", "qlora", "llama-adapter"] | None = Field(
         default=None,
         json_schema_extra={
-            "description": "If you want to use 'lora' or 'qlora' or leave blank to train all parameters in original model"
+            "description": "If you want to use 'lora', 'qlora', or 'llama-adapter', or leave blank to train all parameters in original model"
         },
     )
     lora_model_dir: str | None = Field(

src/axolotl/utils/trainer.py

@@ -205,10 +205,13 @@ def add_length(sample):
     return sample
 
 
-def drop_long_seq(sample, sequence_len=2048, min_sequence_len=2, raise_on_drop=False):
+def filter_sequences_by_length(
+    sample, sequence_len=2048, min_sequence_len=2, raise_on_drop=False
+):
     """
-    Drop samples whose sequence length is either too long (> sequence_len)
-    or too short (< min_sequence_len).
+    Filter sequences outside valid length range [min_sequence_len, sequence_len].
+
+    Drops samples that are either too short (< min_sequence_len) or too long (> sequence_len).
 
     Works for both single-example (list[int]) or batched (list[list[int]]).
 
@@ -247,7 +250,7 @@ def drop_long_seq(sample, sequence_len=2048, min_sequence_len=2, raise_on_drop=F
 
 
 def process_datasets_for_packing(cfg, train_dataset, eval_dataset):
-    drop_attn_mask = cfg.model_config_type in ["mamba", "gemma3", "gemma3_text"]
+    drop_attn_mask = cfg.model_config_type in ["mamba", "gemma3"]
     if drop_attn_mask:
         LOG.info("dropping attention_mask column")
         train_dataset = train_dataset.remove_columns("attention_mask")
@@ -383,10 +386,10 @@ def process_datasets_for_packing(cfg, train_dataset, eval_dataset):
 def process_pretraining_datasets_for_packing(
     train_dataset, sequence_len, skip_position_ids=True, drop_attention_mask=False
 ):
-    drop_long = partial(drop_long_seq, sequence_len=sequence_len)
+    drop_outside_range = partial(filter_sequences_by_length, sequence_len=sequence_len)
 
     train_dataset = train_dataset.filter(
-        drop_long,
+        drop_outside_range,
         desc="Dropping Long Sequences",
         load_from_cache_file=False,
     )
@@ -480,7 +483,7 @@ def calculate_total_num_steps(cfg, train_dataset, update=True):
                 bin_size=cfg.sample_packing_bin_size,
                 sequential=cfg.sample_packing_sequentially,
                 drop_last=True,
-                num_processes=cfg.dataset_prcoesses,
+                num_processes=cfg.dataset_num_proc,
                 mp_start_method=cfg.sample_packing_mp_start_method or "fork",
             )
 

tests/cli/test_nested_options.py

@@ -0,0 +1,227 @@
+"""Tests for nested config option handling via CLI dot-notation."""
+
+import click
+from click.testing import CliRunner
+from pydantic import BaseModel, Field
+
+from axolotl.cli.utils.args import add_options_from_config, filter_none_kwargs
+
+
+class InnerConfig(BaseModel):
+    """A nested config model for testing."""
+
+    beta: float | None = Field(
+        default=None,
+        description="Beta parameter.",
+    )
+    host: str | None = Field(
+        default=None,
+        description="Server host.",
+    )
+    use_feature: bool = Field(
+        default=False,
+        description="Whether to use the feature.",
+    )
+
+
+class OuterConfig(BaseModel):
+    """A top-level config model for testing."""
+
+    learning_rate: float | None = Field(
+        default=None,
+        description="Learning rate.",
+    )
+    inner: InnerConfig | None = Field(
+        default=None,
+        description="Inner config.",
+    )
+    name: str | None = Field(
+        default=None,
+        description="Model name.",
+    )
+
+
+class TestAddOptionsFromConfigNested:
+    """Test that add_options_from_config handles nested BaseModel fields."""
+
+    def setup_method(self):
+        self.runner = CliRunner()
+
+    def test_nested_dot_notation_options_are_registered(self):
+        """Nested model fields should create --parent.child CLI options."""
+
+        @click.command()
+        @add_options_from_config(OuterConfig)
+        @filter_none_kwargs
+        def cmd(**kwargs):
+            for k, v in sorted(kwargs.items()):
+                click.echo(f"{k}={v}")
+
+        result = self.runner.invoke(cmd, ["--inner.beta=0.5", "--inner.host=localhost"])
+        assert result.exit_code == 0, result.output
+        assert "inner__beta=0.5" in result.output
+        assert "inner__host=localhost" in result.output
+
+    def test_nested_bool_option(self):
+        """Nested bool fields should support --parent.field/--no-parent.field."""
+
+        @click.command()
+        @add_options_from_config(OuterConfig)
+        @filter_none_kwargs
+        def cmd(**kwargs):
+            for k, v in sorted(kwargs.items()):
+                click.echo(f"{k}={v}")
+
+        result = self.runner.invoke(cmd, ["--inner.use-feature"])
+        assert result.exit_code == 0, result.output
+        assert "inner__use_feature=True" in result.output
+
+    def test_flat_and_nested_options_together(self):
+        """Flat and nested options should work together."""
+
+        @click.command()
+        @add_options_from_config(OuterConfig)
+        @filter_none_kwargs
+        def cmd(**kwargs):
+            for k, v in sorted(kwargs.items()):
+                click.echo(f"{k}={v}")
+
+        result = self.runner.invoke(
+            cmd, ["--learning-rate=0.001", "--inner.beta=0.1", "--name=test"]
+        )
+        assert result.exit_code == 0, result.output
+        assert "learning_rate=0.001" in result.output
+        assert "inner__beta=0.1" in result.output
+        assert "name=test" in result.output
+
+    def test_no_nested_options_passed(self):
+        """When no nested options are passed, they should not appear in kwargs."""
+
+        @click.command()
+        @add_options_from_config(OuterConfig)
+        @filter_none_kwargs
+        def cmd(**kwargs):
+            click.echo(f"keys={sorted(kwargs.keys())}")
+
+        result = self.runner.invoke(cmd, ["--learning-rate=0.01"])
+        assert result.exit_code == 0, result.output
+        assert "inner__" not in result.output
+
+
+class TestLoadCfgNestedKwargs:
+    """Test that load_cfg correctly applies nested (double-underscore) kwargs."""
+
+    @staticmethod
+    def _apply_nested_kwargs(cfg, kwargs):
+        """Helper that mirrors the nested kwargs handling from load_cfg,
+        including type coercion for string CLI values."""
+        from axolotl.cli.config import _coerce_value
+
+        nested_kwargs: dict = {}
+        flat_kwargs: dict = {}
+        for key, value in kwargs.items():
+            if "__" in key:
+                parent, child = key.split("__", 1)
+                nested_kwargs.setdefault(parent, {})[child] = value
+            else:
+                flat_kwargs[key] = value
+
+        cfg_keys = cfg.keys()
+        for key, value in flat_kwargs.items():
+            if key in cfg_keys:
+                cfg[key] = _coerce_value(value, cfg.get(key))
+
+        for parent, children in nested_kwargs.items():
+            if cfg[parent] is None:
+                cfg[parent] = {}
+            if not isinstance(cfg[parent], dict):
+                cfg[parent] = {}
+            for child_key, child_value in children.items():
+                existing = cfg[parent].get(child_key)
+                cfg[parent][child_key] = _coerce_value(child_value, existing)
+
+        return cfg
+
+    def test_nested_kwargs_applied_to_cfg(self, tmp_path):
+        """Double-underscore kwargs should set nested config values."""
+        from axolotl.utils.dict import DictDefault
+
+        cfg = DictDefault({"trl": {"beta": 0.1}, "learning_rate": 0.01})
+        # CLI passes strings, so simulate that
+        kwargs = {
+            "trl__beta": "0.5",
+            "trl__host": "192.168.1.1",
+            "learning_rate": "0.02",
+        }
+
+        cfg = self._apply_nested_kwargs(cfg, kwargs)
+
+        assert cfg["learning_rate"] == 0.02
+        assert isinstance(cfg["learning_rate"], float)
+        assert cfg["trl"]["beta"] == 0.5
+        assert isinstance(cfg["trl"]["beta"], float)
+        assert cfg["trl"]["host"] == "192.168.1.1"
+
+    def test_nested_kwargs_creates_parent_if_none(self):
+        """If the parent key is None, nested kwargs should create the dict."""
+        from axolotl.utils.dict import DictDefault
+
+        cfg = DictDefault({"trl": None, "learning_rate": 0.01})
+        cfg = self._apply_nested_kwargs(cfg, {"trl__beta": "0.5"})
+
+        # No existing value, YAML-style inference: "0.5" -> 0.5
+        assert cfg["trl"]["beta"] == 0.5
+        assert isinstance(cfg["trl"]["beta"], float)
+
+    def test_nested_kwargs_overwrites_string_parent(self):
+        """If the parent key is a string, it should be replaced with a dict."""
+        from axolotl.utils.dict import DictDefault
+
+        cfg = DictDefault({"trl": "some_string", "learning_rate": 0.01})
+        cfg = self._apply_nested_kwargs(cfg, {"trl__beta": "0.5"})
+
+        assert cfg["trl"]["beta"] == 0.5
+
+
+class TestCoerceValue:
+    """Test YAML-style type coercion for CLI string values."""
+
+    def test_coerce_with_existing_float(self):
+        from axolotl.cli.config import _coerce_value
+
+        assert _coerce_value("0.5", 0.1) == 0.5
+        assert isinstance(_coerce_value("0.5", 0.1), float)
+
+    def test_coerce_with_existing_int(self):
+        from axolotl.cli.config import _coerce_value
+
+        assert _coerce_value("42", 10) == 42
+        assert isinstance(_coerce_value("42", 10), int)
+
+    def test_coerce_with_existing_bool(self):
+        from axolotl.cli.config import _coerce_value
+
+        assert _coerce_value("true", False) is True
+        assert _coerce_value("false", True) is False
+        assert _coerce_value("1", False) is True
+        assert _coerce_value("0", True) is False
+
+    def test_coerce_yaml_inference_no_existing(self):
+        """Without an existing value, use YAML-style inference."""
+        from axolotl.cli.config import _coerce_value
+
+        assert _coerce_value("true", None) is True
+        assert _coerce_value("false", None) is False
+        assert _coerce_value("42", None) == 42
+        assert isinstance(_coerce_value("42", None), int)
+        assert _coerce_value("3.14", None) == 3.14
+        assert isinstance(_coerce_value("3.14", None), float)
+        assert _coerce_value("null", None) is None
+        assert _coerce_value("hello", None) == "hello"
+
+    def test_coerce_non_string_passthrough(self):
+        """Non-string values should pass through unchanged."""
+        from axolotl.cli.config import _coerce_value
+
+        assert _coerce_value(0.5, 0.1) == 0.5
+        assert _coerce_value(True, False) is True

tests/core/test_builders.py

@@ -300,7 +300,6 @@ class TestHFRLTrainerBuilder:
         self._test_common_training_arguments(training_arguments, rl=orpo_cfg.rl)
         # ORPO specific
         assert training_arguments.beta == 0.1  # maps from orpo_alpha
-        assert training_arguments.max_prompt_length == 512
 
     def test_kto_training_arguments(self, kto_cfg, model, tokenizer):
         builder = HFRLTrainerBuilder(kto_cfg, model, tokenizer)

tests/e2e/multigpu/test_fsdp1.py

@@ -186,6 +186,7 @@ class TestFSDP1:
 
         verify_training_success(temp_dir)
 
+    @pytest.mark.skip(reason="slow test, deprecate fsdp1 asap")
     def test_dpo_fft(self, temp_dir):
         cfg = DictDefault(
             {

tests/e2e/multigpu/test_fsdp2.py

@@ -365,6 +365,7 @@ class TestFSDP2:
 
         verify_training_success(temp_dir)
 
+    @pytest.mark.skip(reason="slow test w cu129 + torch 2.9.1 + py3.12")
     @require_torch_2_7_0
     def test_dpo_fft(self, temp_dir):
         cfg = DictDefault(
@@ -422,6 +423,7 @@ class TestFSDP2:
 
         verify_training_success(temp_dir)
 
+    @pytest.mark.skip(reason="slow test w cu129 + torch 2.9.1 + py3.12")
     @require_torch_2_7_0
     def test_dpo_lora(self, temp_dir):
         cfg = DictDefault(

tests/integrations/test_scattermoe_lora.py

@@ -0,0 +1,323 @@
+# SPDX-License-Identifier: Apache-2.0
+# Copyright (c) Axolotl AI
+# Licensed under the Apache License, Version 2.0
+
+"""
+Unit tests for scattermoe-lora code-review fixes.
+
+Tests cover:
+- KernelsArgs validator: disable_mlp_kernel_scattermoe
+- CPU_Offloaded_Gradient_Checkpointer: tuple vs plain tensor backward
+- ParallelExperts: scaling=0.0 not treated as falsy
+- single2scatter: non-aligned K/N dimensions
+- group_compileable: coeff=None accepted
+- HFScatterMoEGatedMLP / ScatterMoEGatedMLP: return value contract
+"""
+
+from unittest.mock import patch
+
+import pytest
+import torch
+
+# ============================================================================
+# 1. KernelsArgs: disable_mlp_kernel_scattermoe validator
+# ============================================================================
+
+
+class TestKernelsArgsValidator:
+    """Test that disable_mlp_kernel_scattermoe sets both flags correctly.
+
+    These tests call the validator classmethod directly on raw dicts,
+    since lora_mlp_kernel / mlp_kernel are not declared model fields.
+    """
+
+    def test_disables_lora_mlp_kernel_when_scattermoe(self):
+        """lora_mlp_kernel=True gets set to False when use_scattermoe=True."""
+        from axolotl.integrations.kernels.args import KernelsArgs
+
+        data = {
+            "use_kernels": True,
+            "use_scattermoe": True,
+            "lora_mlp_kernel": True,
+        }
+        result = KernelsArgs.disable_mlp_kernel_scattermoe(data)
+        assert result["lora_mlp_kernel"] is False
+        assert result["mlp_kernel"] is False
+
+    def test_mlp_kernel_disabled_without_lora(self):
+        """Even without lora_mlp_kernel, mlp_kernel should be disabled."""
+        from axolotl.integrations.kernels.args import KernelsArgs
+
+        data = {
+            "use_kernels": True,
+            "use_scattermoe": True,
+        }
+        result = KernelsArgs.disable_mlp_kernel_scattermoe(data)
+        assert result["mlp_kernel"] is False
+        # lora_mlp_kernel was not in data, should not be added
+        assert "lora_mlp_kernel" not in result
+
+    def test_lora_mlp_kernel_false_unchanged(self):
+        """lora_mlp_kernel=False should stay False (no warning, no change)."""
+        from axolotl.integrations.kernels.args import KernelsArgs
+
+        data = {
+            "use_kernels": True,
+            "use_scattermoe": True,
+            "lora_mlp_kernel": False,
+        }
+        result = KernelsArgs.disable_mlp_kernel_scattermoe(data)
+        assert result["lora_mlp_kernel"] is False
+
+    def test_no_change_when_scattermoe_disabled(self):
+        """When use_scattermoe is not True, nothing should be changed."""
+        from axolotl.integrations.kernels.args import KernelsArgs
+
+        data = {
+            "use_kernels": True,
+            "use_scattermoe": False,
+            "lora_mlp_kernel": True,
+        }
+        result = KernelsArgs.disable_mlp_kernel_scattermoe(data)
+        assert result["lora_mlp_kernel"] is True
+
+
+class TestParallelExpertsScaling:
+    """Test that scaling=0.0 is preserved and not overridden to 1.0."""
+
+    def test_scaling_zero_preserved(self):
+        """scaling=0.0 should be passed as 0.0, not replaced with 1.0."""
+        pytest.importorskip("triton")
+        from axolotl.integrations.kernels.libs.scattermoe_lora.lora_ops import (
+            ParallelExperts,
+        )
+
+        pe = ParallelExperts(num_experts=2, input_size=4, output_size=4)
+        pe.set_lora(
+            lora_A=torch.randn(4, 4),
+            lora_B=torch.randn(4, 4),
+            scaling=0.0,
+        )
+        assert pe._lora_scaling == 0.0
+
+        # Patch parallel_linear_lora to capture the scaling arg
+        with patch(
+            "axolotl.integrations.kernels.libs.scattermoe_lora.lora_ops.parallel_linear_lora"
+        ) as mock_pll:
+            mock_pll.return_value = torch.randn(4, 4)
+            # Create dummy routing tensors
+            pe.forward(
+                inputs=torch.randn(2, 4),
+                k=1,
+                sorted_expert_idxs=torch.tensor([0, 0, 1, 1]),
+                sorted_scattered_idxs=torch.tensor([0, 1, 0, 1]),
+                expert_offsets=torch.tensor([2, 4]),
+            )
+            # Check that scaling=0.0 was passed, not 1.0
+            call_kwargs = mock_pll.call_args
+            assert (
+                call_kwargs.kwargs.get("scaling") == 0.0
+                or call_kwargs[1].get("scaling") == 0.0
+            ), f"Expected scaling=0.0 but got {call_kwargs}"
+
+    def test_scaling_none_defaults_to_one(self):
+        """scaling=None (no LoRA attached) should default to 1.0."""
+        pytest.importorskip("triton")
+        from axolotl.integrations.kernels.libs.scattermoe_lora.lora_ops import (
+            ParallelExperts,
+        )
+
+        pe = ParallelExperts(num_experts=2, input_size=4, output_size=4)
+        # No set_lora called, so _lora_scaling is None
+
+        with patch(
+            "axolotl.integrations.kernels.libs.scattermoe_lora.lora_ops.parallel_linear_lora"
+        ) as mock_pll:
+            mock_pll.return_value = torch.randn(4, 4)
+            pe.forward(
+                inputs=torch.randn(2, 4),
+                k=1,
+                sorted_expert_idxs=torch.tensor([0, 0, 1, 1]),
+                sorted_scattered_idxs=torch.tensor([0, 1, 0, 1]),
+                expert_offsets=torch.tensor([2, 4]),
+            )
+            call_kwargs = mock_pll.call_args
+            scaling_val = call_kwargs.kwargs.get("scaling") or call_kwargs[1].get(
+                "scaling"
+            )
+            assert scaling_val == 1.0, (
+                f"Expected scaling=1.0 for None but got {scaling_val}"
+            )
+
+    def test_scaling_positive_preserved(self):
+        """Normal positive scaling should be preserved."""
+        pytest.importorskip("triton")
+        from axolotl.integrations.kernels.libs.scattermoe_lora.lora_ops import (
+            ParallelExperts,
+        )
+
+        pe = ParallelExperts(num_experts=2, input_size=4, output_size=4)
+        pe.set_lora(
+            lora_A=torch.randn(4, 4),
+            lora_B=torch.randn(4, 4),
+            scaling=0.5,
+        )
+
+        with patch(
+            "axolotl.integrations.kernels.libs.scattermoe_lora.lora_ops.parallel_linear_lora"
+        ) as mock_pll:
+            mock_pll.return_value = torch.randn(4, 4)
+            pe.forward(
+                inputs=torch.randn(2, 4),
+                k=1,
+                sorted_expert_idxs=torch.tensor([0, 0, 1, 1]),
+                sorted_scattered_idxs=torch.tensor([0, 1, 0, 1]),
+                expert_offsets=torch.tensor([2, 4]),
+            )
+            call_kwargs = mock_pll.call_args
+            scaling_val = call_kwargs.kwargs.get("scaling") or call_kwargs[1].get(
+                "scaling"
+            )
+            assert scaling_val == 0.5
+
+
+# ============================================================================
+# 4. single2scatter: non-aligned K/N dimensions (GPU only)
+# ============================================================================
+
+
+@pytest.mark.skipif(not torch.cuda.is_available(), reason="CUDA not available")
+class TestSingle2ScatterBounds:
+    """Test single2scatter with non-aligned dimensions."""
+
+    def test_non_aligned_k(self):
+        """K not a multiple of BLOCK_K should produce correct results."""
+        from axolotl.integrations.kernels.libs.scattermoe_lora.kernels.single import (
+            single2scatter,
+        )
+
+        E, K, N = 2, 100, 128  # K=100 not a multiple of 128
+        W = torch.randn(E, K, N, device="cuda", dtype=torch.float32)
+        X = torch.randn(1, K, device="cuda", dtype=torch.float32)
+        expert_idxs = torch.tensor([[0, 1]], device="cuda", dtype=torch.long)
+
+        Y = single2scatter(X, W, expert_idxs)
+        assert Y.shape == (2, N)
+
+        # Verify against manual computation
+        Y_ref_0 = X[0] @ W[0]
+        Y_ref_1 = X[0] @ W[1]
+        torch.testing.assert_close(Y[0], Y_ref_0, atol=1e-2, rtol=1e-2)
+        torch.testing.assert_close(Y[1], Y_ref_1, atol=1e-2, rtol=1e-2)
+
+    def test_non_aligned_n(self):
+        """N not a multiple of BLOCK_N should produce correct results."""
+        from axolotl.integrations.kernels.libs.scattermoe_lora.kernels.single import (
+            single2scatter,
+        )
+
+        E, K, N = 2, 128, 100  # N=100 not a multiple of 128
+        W = torch.randn(E, K, N, device="cuda", dtype=torch.float32)
+        X = torch.randn(1, K, device="cuda", dtype=torch.float32)
+        expert_idxs = torch.tensor([[0, 1]], device="cuda", dtype=torch.long)
+
+        Y = single2scatter(X, W, expert_idxs)
+        assert Y.shape == (2, N)
+
+        Y_ref_0 = X[0] @ W[0]
+        Y_ref_1 = X[0] @ W[1]
+        torch.testing.assert_close(Y[0], Y_ref_0, atol=1e-2, rtol=1e-2)
+        torch.testing.assert_close(Y[1], Y_ref_1, atol=1e-2, rtol=1e-2)
+
+    def test_non_aligned_both(self):
+        """Both K and N not aligned should produce correct results."""
+        from axolotl.integrations.kernels.libs.scattermoe_lora.kernels.single import (
+            single2scatter,
+        )
+
+        E, K, N = 2, 100, 100  # Neither aligned to 128
+        W = torch.randn(E, K, N, device="cuda", dtype=torch.float32)
+        X = torch.randn(1, K, device="cuda", dtype=torch.float32)
+        expert_idxs = torch.tensor([[0, 1]], device="cuda", dtype=torch.long)
+
+        Y = single2scatter(X, W, expert_idxs)
+        assert Y.shape == (2, N)
+
+        Y_ref_0 = X[0] @ W[0]
+        Y_ref_1 = X[0] @ W[1]
+        torch.testing.assert_close(Y[0], Y_ref_0, atol=1e-2, rtol=1e-2)
+        torch.testing.assert_close(Y[1], Y_ref_1, atol=1e-2, rtol=1e-2)
+
+
+# ============================================================================
+# 5. group_compileable: coeff=None accepted
+# ============================================================================
+
+
+@pytest.mark.skipif(not torch.cuda.is_available(), reason="CUDA not available")
+class TestGroupCoeffNone:
+    """Test that group() works with coeff=None."""
+
+    def test_group_with_none_coeff(self):
+        """group() should accept coeff=None without errors."""
+        from axolotl.integrations.kernels.libs.scattermoe_lora.kernels.ops import group
+
+        M, K = 4, 32
+        A = torch.randn(M, K, device="cuda", dtype=torch.float32)
+        sorted_expert_idxs = torch.tensor([0, 1, 2, 3], device="cuda", dtype=torch.long)
+
+        # This should not raise a TypeError
+        Y = group(A, sorted_expert_idxs, coeff=None, fan_out=1)
+        assert Y.shape == (M, K)
+
+    def test_group_with_coeff(self):
+        """group() should also work with actual coeff values."""
+        from axolotl.integrations.kernels.libs.scattermoe_lora.kernels.ops import group
+
+        M, K = 4, 32
+        A = torch.randn(M, K, device="cuda", dtype=torch.float32)
+        sorted_expert_idxs = torch.tensor([0, 1, 2, 3], device="cuda", dtype=torch.long)
+        coeff = torch.ones(M, device="cuda", dtype=torch.float32) * 0.5
+
+        Y = group(A, sorted_expert_idxs, coeff=coeff, fan_out=1)
+        assert Y.shape == (M, K)
+
+
+# ============================================================================
+# 6. Layer return value contracts
+# ============================================================================
+
+
+class TestLayerReturnValues:
+    """Test that layer forward methods return the correct types."""
+
+    def test_hf_scatter_moe_returns_single_tensor(self):
+        """HFScatterMoEGatedMLP.forward should return a single tensor, not a tuple."""
+        pytest.importorskip("triton")
+        # Verify the forward method signature and return annotation
+        import inspect
+
+        from axolotl.integrations.kernels.libs.scattermoe_lora.layers import (
+            HFScatterMoEGatedMLP,
+        )
+
+        sig = inspect.signature(HFScatterMoEGatedMLP.forward)
+        # It's a staticmethod taking (self, layer_input)
+        params = list(sig.parameters.keys())
+        assert "self" in params
+        assert "layer_input" in params
+
+    def test_scatter_moe_gated_mlp_docstring_no_router_logits(self):
+        """ScatterMoEGatedMLP.forward docstring should not mention router logits as return."""
+        pytest.importorskip("triton")
+        from axolotl.integrations.kernels.libs.scattermoe_lora.layers import (
+            ScatterMoEGatedMLP,
+        )
+
+        docstring = ScatterMoEGatedMLP.forward.__doc__
+        assert docstring is not None
+        # The docstring should mention output tensor but NOT router logits
+        assert "Output tensor" in docstring or "output tensor" in docstring.lower()
+        assert "Router logits" not in docstring, (
+            "Docstring should not mention 'Router logits' in Returns section"
+        )

tests/test_data.py

@@ -7,7 +7,7 @@ import unittest
 from transformers import LlamaTokenizer
 
 from axolotl.utils.data import encode_streaming, md5
-from axolotl.utils.trainer import drop_long_seq
+from axolotl.utils.trainer import filter_sequences_by_length
 
 from tests.hf_offline_utils import enable_hf_offline
 
@@ -70,17 +70,19 @@ class TestEncodePretraining(unittest.TestCase):
         # -- single sequence --
         # This should work
         data = {"input_ids": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16]}
-        drop_long_seq(data, 32, raise_on_drop=True)
+        filter_sequences_by_length(data, 32, raise_on_drop=True)
 
         # This should return True, since data fits
-        dropped = drop_long_seq(data, 32)
+        dropped = filter_sequences_by_length(data, 32)
         self.assertTrue(dropped)
 
         # This should raise
-        self.assertRaises(ValueError, drop_long_seq, data, 15, raise_on_drop=True)
+        self.assertRaises(
+            ValueError, filter_sequences_by_length, data, 15, raise_on_drop=True
+        )
 
         # This should return False, since data doesn't fit
-        dropped = drop_long_seq(data, 15)
+        dropped = filter_sequences_by_length(data, 15)
         self.assertFalse(dropped)
 
         # -- batch sequence --
@@ -91,13 +93,15 @@ class TestEncodePretraining(unittest.TestCase):
                 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16],
             ]
         }
-        drop_long_seq(data, 32, raise_on_drop=True)
+        filter_sequences_by_length(data, 32, raise_on_drop=True)
 
         # This should raise
-        self.assertRaises(ValueError, drop_long_seq, data, 15, raise_on_drop=True)
+        self.assertRaises(
+            ValueError, filter_sequences_by_length, data, 15, raise_on_drop=True
+        )
 
         # This should keep the first but drop the second entry
-        dropped = drop_long_seq(data, 15)
+        dropped = filter_sequences_by_length(data, 15)
         self.assertEqual(dropped, [True, False])
 
 

tests/test_revision_parameter.py

@@ -0,0 +1,135 @@
+"""Tests for revision_of_model being passed to tokenizer and processor loaders."""
+
+from unittest.mock import MagicMock, patch
+
+from transformers import PreTrainedTokenizerBase
+
+from axolotl.utils.dict import DictDefault
+
+
+class TestRevisionParameter:
+    """Tests for revision_of_model being passed to tokenizer and processor loaders."""
+
+    @patch("axolotl.loaders.tokenizer.load_model_config")
+    @patch("axolotl.loaders.tokenizer.AutoTokenizer")
+    @patch(
+        "axolotl.loaders.patch_manager.PatchManager.apply_pre_tokenizer_load_patches"
+    )
+    def test_load_tokenizer_passes_revision(
+        self, _mock_patches, mock_auto_tokenizer, _mock_load_config
+    ):
+        mock_tokenizer = MagicMock()
+        mock_tokenizer.__class__.__name__ = "MockTokenizer"
+        mock_auto_tokenizer.from_pretrained.return_value = mock_tokenizer
+
+        cfg = DictDefault(
+            {
+                "tokenizer_config": "some-model",
+                "revision_of_model": "abc123",
+            }
+        )
+        from axolotl.loaders.tokenizer import load_tokenizer
+
+        load_tokenizer(cfg)
+
+        call_kwargs = mock_auto_tokenizer.from_pretrained.call_args
+        assert call_kwargs.kwargs.get("revision") == "abc123"
+
+    @patch("axolotl.loaders.tokenizer.load_model_config")
+    @patch("axolotl.loaders.tokenizer.AutoTokenizer")
+    @patch(
+        "axolotl.loaders.patch_manager.PatchManager.apply_pre_tokenizer_load_patches"
+    )
+    def test_load_tokenizer_omits_revision_when_unset(
+        self, _mock_patches, mock_auto_tokenizer, _mock_load_config
+    ):
+        mock_tokenizer = MagicMock()
+        mock_tokenizer.__class__.__name__ = "MockTokenizer"
+        mock_auto_tokenizer.from_pretrained.return_value = mock_tokenizer
+
+        cfg = DictDefault(
+            {
+                "tokenizer_config": "some-model",
+            }
+        )
+        from axolotl.loaders.tokenizer import load_tokenizer
+
+        load_tokenizer(cfg)
+
+        call_kwargs = mock_auto_tokenizer.from_pretrained.call_args
+        assert "revision" not in call_kwargs.kwargs
+
+    @patch("axolotl.loaders.tokenizer.AutoTokenizer")
+    @patch("axolotl.loaders.tokenizer.is_local_main_process", return_value=True)
+    @patch("axolotl.loaders.tokenizer.barrier")
+    def test_modify_tokenizer_files_passes_revision(
+        self, _mock_barrier, _mock_main, mock_auto_tokenizer, temp_dir
+    ):
+        mock_tokenizer = MagicMock()
+        mock_auto_tokenizer.from_pretrained.return_value = mock_tokenizer
+
+        from axolotl.loaders.tokenizer import modify_tokenizer_files
+
+        modify_tokenizer_files("some-model", {}, output_dir=temp_dir, revision="abc123")
+
+        call_kwargs = mock_auto_tokenizer.from_pretrained.call_args
+        assert call_kwargs.kwargs.get("revision") == "abc123"
+
+    @patch("axolotl.loaders.tokenizer.AutoTokenizer")
+    @patch("axolotl.loaders.tokenizer.is_local_main_process", return_value=True)
+    @patch("axolotl.loaders.tokenizer.barrier")
+    def test_modify_tokenizer_files_defaults_revision_to_main(
+        self, _mock_barrier, _mock_main, mock_auto_tokenizer, temp_dir
+    ):
+        mock_tokenizer = MagicMock()
+        mock_auto_tokenizer.from_pretrained.return_value = mock_tokenizer
+
+        from axolotl.loaders.tokenizer import modify_tokenizer_files
+
+        modify_tokenizer_files("some-model", {}, output_dir=temp_dir)
+
+        call_kwargs = mock_auto_tokenizer.from_pretrained.call_args
+        assert call_kwargs.kwargs.get("revision") == "main"
+
+    @patch("axolotl.loaders.processor.AutoProcessor")
+    def test_load_processor_passes_revision(self, mock_auto_processor):
+        mock_processor = MagicMock()
+        mock_processor.size = {}
+        mock_auto_processor.from_pretrained.return_value = mock_processor
+
+        cfg = DictDefault(
+            {
+                "processor_config": "some-model",
+                "revision_of_model": "abc123",
+                "trust_remote_code": False,
+            }
+        )
+        tokenizer = MagicMock(spec=PreTrainedTokenizerBase)
+
+        from axolotl.loaders.processor import load_processor
+
+        load_processor(cfg, tokenizer)
+
+        call_kwargs = mock_auto_processor.from_pretrained.call_args
+        assert call_kwargs.kwargs.get("revision") == "abc123"
+
+    @patch("axolotl.loaders.processor.AutoProcessor")
+    def test_load_processor_omits_revision_when_unset(self, mock_auto_processor):
+        mock_processor = MagicMock()
+        mock_processor.size = {}
+        mock_auto_processor.from_pretrained.return_value = mock_processor
+
+        cfg = DictDefault(
+            {
+                "processor_config": "some-model",
+                "trust_remote_code": False,
+            }
+        )
+        tokenizer = MagicMock(spec=PreTrainedTokenizerBase)
+
+        from axolotl.loaders.processor import load_processor
+
+        load_processor(cfg, tokenizer)
+
+        call_kwargs = mock_auto_processor.from_pretrained.call_args
+        assert "revision" not in call_kwargs.kwargs

tests/test_save_deduplicated.py

@@ -0,0 +1,210 @@
+"""Tests to verify that deduplication runs before dataset saving during preprocessing.
+
+This addresses GitHub issue #2719: Save De-duplicated Set During Pre-processing.
+"""
+
+from unittest.mock import MagicMock, patch
+
+from datasets import Dataset
+
+from axolotl.utils.dict import DictDefault
+
+
+class TestSFTSaveDeduplicatedBeforeSave:
+    """Verify that in SFT data loading, deduplication occurs before saving."""
+
+    @patch("axolotl.utils.data.sft.save_preprocessed_dataset")
+    @patch("axolotl.utils.data.sft.generate_dataset_hash_from_config")
+    @patch("axolotl.utils.data.sft.deduplicate_and_log_datasets")
+    @patch("axolotl.utils.data.sft.merge_datasets")
+    @patch("axolotl.utils.data.sft._load_and_process_single_dataset")
+    @patch("axolotl.utils.data.sft.datasets_with_name_generator")
+    def test_dedup_called_before_save_sft(
+        self,
+        mock_datasets_gen,
+        mock_load_single,
+        mock_merge,
+        mock_dedup,
+        mock_gen_hash,
+        mock_save,
+    ):
+        """Deduplication should be called before save_preprocessed_dataset in SFT."""
+        from axolotl.utils.data.sft import _load_raw_datasets
+
+        # Set up mock data
+        dataset = Dataset.from_dict({"text": ["a", "b", "a"], "label": [1, 2, 1]})
+        deduped_dataset = Dataset.from_dict({"text": ["a", "b"], "label": [1, 2]})
+
+        mock_datasets_gen.return_value = [
+            DictDefault({"path": "test", "type": "alpaca"})
+        ]
+        mock_load_single.return_value = (dataset, None)
+        mock_merge.return_value = dataset
+        mock_dedup.return_value = (deduped_dataset, None)
+        mock_gen_hash.return_value = "testhash"
+
+        cfg = DictDefault(
+            {
+                "skip_prepare_dataset": False,
+                "dataset_exact_deduplication": True,
+                "sequence_len": 1024,
+                "eval_sequence_len": None,
+                "sample_packing": False,
+                "is_preprocess": False,
+                "seed": 42,
+                "datasets": [{"path": "test", "type": "alpaca"}],
+            }
+        )
+
+        tokenizer = MagicMock()
+        tokenizer.name_or_path = "test-tokenizer"
+
+        # Track call order
+        call_order = []
+        mock_dedup.side_effect = lambda **kwargs: (
+            call_order.append("dedup") or (deduped_dataset, None)
+        )
+        mock_save.side_effect = lambda *args, **kwargs: call_order.append("save")
+
+        _load_raw_datasets(
+            cfg=cfg,
+            datasets_configs=cfg.datasets,
+            tokenizer=tokenizer,
+            split="train",
+        )
+
+        # Verify dedup was called
+        assert "dedup" in call_order, "Deduplication should have been called"
+        # Verify save was called
+        assert "save" in call_order, "Save should have been called"
+        # Verify dedup happened before save
+        assert call_order.index("dedup") < call_order.index("save"), (
+            "Deduplication must occur before saving the dataset"
+        )
+
+    @patch("axolotl.utils.data.sft.save_preprocessed_dataset")
+    @patch("axolotl.utils.data.sft.generate_dataset_hash_from_config")
+    @patch("axolotl.utils.data.sft.merge_datasets")
+    @patch("axolotl.utils.data.sft._load_and_process_single_dataset")
+    @patch("axolotl.utils.data.sft.datasets_with_name_generator")
+    def test_no_dedup_when_disabled_sft(
+        self,
+        mock_datasets_gen,
+        mock_load_single,
+        mock_merge,
+        mock_gen_hash,
+        mock_save,
+    ):
+        """Deduplication should not be called when dataset_exact_deduplication is False."""
+        from axolotl.utils.data.sft import _load_raw_datasets
+
+        dataset = Dataset.from_dict({"text": ["a", "b", "a"], "label": [1, 2, 1]})
+
+        mock_datasets_gen.return_value = [
+            DictDefault({"path": "test", "type": "alpaca"})
+        ]
+        mock_load_single.return_value = (dataset, None)
+        mock_merge.return_value = dataset
+        mock_gen_hash.return_value = "testhash"
+
+        cfg = DictDefault(
+            {
+                "skip_prepare_dataset": False,
+                "dataset_exact_deduplication": False,
+                "sequence_len": 1024,
+                "eval_sequence_len": None,
+                "sample_packing": False,
+                "is_preprocess": False,
+                "seed": 42,
+                "datasets": [{"path": "test", "type": "alpaca"}],
+            }
+        )
+
+        tokenizer = MagicMock()
+        tokenizer.name_or_path = "test-tokenizer"
+
+        with patch("axolotl.utils.data.sft.deduplicate_and_log_datasets") as mock_dedup:
+            _load_raw_datasets(
+                cfg=cfg,
+                datasets_configs=cfg.datasets,
+                tokenizer=tokenizer,
+                split="train",
+            )
+            mock_dedup.assert_not_called()
+
+
+class TestRLSaveDeduplicatedBeforeSave:
+    """Verify that in RL data loading, deduplication occurs before saving."""
+
+    @patch.object(Dataset, "filter", lambda self, *args, **kwargs: self)
+    @patch("axolotl.utils.data.rl.save_preprocessed_dataset")
+    @patch("axolotl.utils.data.rl.generate_dataset_hash_from_config")
+    @patch("axolotl.utils.data.rl.deduplicate_and_log_datasets")
+    @patch("axolotl.utils.data.rl.merge_datasets")
+    @patch("axolotl.utils.data.rl.load_dataset_with_config")
+    @patch("axolotl.utils.data.rl.datasets_with_name_generator")
+    @patch("axolotl.utils.data.rl.load_tokenizer")
+    def test_dedup_called_before_save_rl(
+        self,
+        mock_load_tokenizer,
+        mock_datasets_gen,
+        mock_load_dataset,
+        mock_merge,
+        mock_dedup,
+        mock_gen_hash,
+        mock_save,
+    ):
+        """Deduplication should be called before save_preprocessed_dataset in RL."""
+        from axolotl.utils.data.rl import _load_split
+
+        dataset = Dataset.from_dict(
+            {
+                "prompt": ["hi", "bye", "hi"],
+                "chosen": ["a", "b", "a"],
+                "rejected": ["c", "d", "c"],
+            }
+        )
+        deduped_dataset = Dataset.from_dict(
+            {
+                "prompt": ["hi", "bye"],
+                "chosen": ["a", "b"],
+                "rejected": ["c", "d"],
+            }
+        )
+
+        mock_datasets_gen.return_value = [DictDefault({"path": "test", "type": None})]
+        mock_load_dataset.return_value = dataset
+        mock_merge.return_value = dataset
+        mock_dedup.return_value = (deduped_dataset, None)
+        mock_gen_hash.return_value = "testhash"
+
+        tokenizer = MagicMock()
+        tokenizer.name_or_path = "test-tokenizer"
+        mock_load_tokenizer.return_value = tokenizer
+
+        cfg = DictDefault(
+            {
+                "skip_prepare_dataset": False,
+                "dataset_exact_deduplication": True,
+                "sequence_len": 1024,
+                "rl": "dpo",
+                "datasets": [{"path": "test", "type": None}],
+                "hf_use_auth_token": False,
+                "dataset_num_proc": 1,
+                "is_preprocess": False,
+            }
+        )
+
+        call_order = []
+        mock_dedup.side_effect = lambda **kwargs: (
+            call_order.append("dedup") or (deduped_dataset, None)
+        )
+        mock_save.side_effect = lambda *args, **kwargs: call_order.append("save")
+
+        _load_split(cfg, split="train")
+
+        assert "dedup" in call_order, "Deduplication should have been called"
+        assert "save" in call_order, "Save should have been called"
+        assert call_order.index("dedup") < call_order.index("save"), (
+            "Deduplication must occur before saving the dataset"
+        )

tests/test_tokenizers.py

@@ -116,6 +116,7 @@ class TestTokenizers:
             tokenizer.decode([128041, 128042]) == "RANDOM_OVERRIDE_1RANDOM_OVERRIDE_2"
         )
 
+    @pytest.mark.skip("FIXME slow test sdist py3.11 + torch2.8.0")
     @enable_hf_offline
     def test_added_tokens_overrides_gemma3(self, temp_dir):
         cfg = DictDefault(

tests/utils/data/test_utils.py

@@ -0,0 +1,545 @@
+"""
+Unit tests for data utility functions
+"""
+
+import unittest
+from unittest.mock import MagicMock
+
+from datasets import Dataset
+
+from axolotl.utils.data.utils import handle_long_seq_in_dataset
+from axolotl.utils.dict import DictDefault
+
+
+class TestHandleLongSeqInDataset(unittest.TestCase):
+    """
+    Test class for handle_long_seq_in_dataset function
+    """
+
+    def test_drop_strategy_removes_long_sequences(self):
+        """Test that 'drop' strategy removes sequences longer than sequence_len"""
+        # Create dataset with mixed length sequences
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3],  # length 3 - keep
+                    [1, 2, 3, 4, 5],  # length 5 - keep
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],  # length 11 - drop
+                    [1, 2],  # length 2 - keep
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "drop",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Should have dropped the sequence with length 11
+        self.assertEqual(len(result), 3)
+        self.assertEqual(len(result[0]["input_ids"]), 3)
+        self.assertEqual(len(result[1]["input_ids"]), 5)
+        self.assertEqual(len(result[2]["input_ids"]), 2)
+
+    def test_drop_strategy_is_default(self):
+        """Test that 'drop' is the default strategy when not specified"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3],
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],  # length 11 - should drop
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Should have dropped the long sequence
+        self.assertEqual(len(result), 1)
+
+    def test_truncate_strategy_truncates_long_sequences(self):
+        """Test that 'truncate' strategy truncates sequences to sequence_len"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3],  # length 3 - keep as is
+                    [
+                        1,
+                        2,
+                        3,
+                        4,
+                        5,
+                        6,
+                        7,
+                        8,
+                        9,
+                        10,
+                        11,
+                        12,
+                    ],  # length 12 - truncate to 10
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "truncate",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Should have 2 samples
+        self.assertEqual(len(result), 2)
+        # First sample unchanged
+        self.assertEqual(len(result[0]["input_ids"]), 3)
+        # Second sample truncated to 10
+        self.assertEqual(len(result[1]["input_ids"]), 10)
+        self.assertEqual(result[1]["input_ids"], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
+
+    def test_truncate_strategy_truncates_all_auxiliary_fields(self):
+        """Test that truncation applies to all auxiliary fields consistently"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12],
+                ],
+                "attention_mask": [
+                    [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
+                ],
+                "labels": [
+                    [-100, -100, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12],
+                ],
+                "position_ids": [
+                    [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],
+                ],
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "truncate",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # All fields should be truncated to 10
+        self.assertEqual(len(result[0]["input_ids"]), 10)
+        self.assertEqual(len(result[0]["attention_mask"]), 10)
+        self.assertEqual(len(result[0]["labels"]), 10)
+        self.assertEqual(len(result[0]["position_ids"]), 10)
+
+        # Verify content is correct
+        self.assertEqual(result[0]["input_ids"], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
+        self.assertEqual(result[0]["attention_mask"], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
+        self.assertEqual(result[0]["labels"], [-100, -100, 3, 4, 5, 6, 7, 8, 9, 10])
+        self.assertEqual(result[0]["position_ids"], [0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
+
+    def test_raise_strategy_raises_on_long_sequences(self):
+        """Test that 'raise' strategy raises ValueError when encountering long sequences"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3],
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],  # length 11 - should raise
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "raise",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        with self.assertRaises(ValueError):
+            handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+    def test_min_sequence_len_filters_short_sequences(self):
+        """Test that sequences shorter than min_sample_len are filtered out"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1],  # length 1 - drop (< min_sample_len=3)
+                    [1, 2],  # length 2 - drop
+                    [1, 2, 3],  # length 3 - keep
+                    [1, 2, 3, 4, 5],  # length 5 - keep
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "drop",
+                "min_sample_len": 3,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Should only keep sequences with length >= 3
+        self.assertEqual(len(result), 2)
+        self.assertEqual(len(result[0]["input_ids"]), 3)
+        self.assertEqual(len(result[1]["input_ids"]), 5)
+
+    def test_dataset_without_input_ids_column(self):
+        """Test that datasets without 'input_ids' column are returned unchanged"""
+        dataset = Dataset.from_dict(
+            {
+                "chosen": [1, 2, 3],
+                "rejected": [4, 5, 6],
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "drop",
+                "min_sample_len": 2,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Dataset should be unchanged
+        self.assertEqual(len(result), len(dataset))
+        self.assertListEqual(list(result.column_names), ["chosen", "rejected"])
+
+    def test_truncate_filters_short_before_truncating(self):
+        """Test that truncate strategy filters short sequences before truncating long ones
+
+        This is important for efficiency - we should not waste time truncating
+        sequences that will be filtered out anyway.
+        """
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1],  # length 1 - filter out first
+                    [1, 2, 3],  # length 3 - keep, no truncation needed
+                    [
+                        1,
+                        2,
+                        3,
+                        4,
+                        5,
+                        6,
+                        7,
+                        8,
+                        9,
+                        10,
+                        11,
+                        12,
+                    ],  # length 12 - keep and truncate
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "truncate",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Should have filtered out the first (short) sequence
+        self.assertEqual(len(result), 2)
+        # Second sample unchanged
+        self.assertEqual(len(result[0]["input_ids"]), 3)
+        # Third sample truncated to 10
+        self.assertEqual(len(result[1]["input_ids"]), 10)
+
+    def test_case_insensitive_strategy(self):
+        """Test that excess_length_strategy is case-insensitive"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12],
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "TRUNCATE",  # uppercase
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Should still truncate
+        self.assertEqual(len(result[0]["input_ids"]), 10)
+
+    def test_raise_strategy_silently_drops_short_sequences(self):
+        """Test that 'raise' strategy drops short sequences without raising"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1],  # length 1 - too short, should be dropped silently
+                    [1, 2, 3, 4, 5],  # length 5 - keep
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "raise",
+                "min_sample_len": 3,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        # Should NOT raise, just silently drop the short sequence
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        self.assertEqual(len(result), 1)
+        self.assertEqual(len(result[0]["input_ids"]), 5)
+
+    def test_drop_boundary_sequence_equal_to_sequence_len(self):
+        """Test that drop strategy keeps sequences with length exactly equal to sequence_len"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10],  # length 10 == sequence_len
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],  # length 11 > sequence_len
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "drop",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Exactly equal should be kept, one over should be dropped
+        self.assertEqual(len(result), 1)
+        self.assertEqual(len(result[0]["input_ids"]), 10)
+
+    def test_truncate_boundary_sequence_equal_to_sequence_len(self):
+        """Test that truncate strategy leaves sequences with length exactly equal to sequence_len unchanged"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10],  # length 10 == sequence_len
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "truncate",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Should be unchanged - not truncated
+        self.assertEqual(len(result), 1)
+        self.assertEqual(result[0]["input_ids"], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
+
+    def test_empty_dataset(self):
+        """Test that an empty dataset is handled gracefully"""
+        dataset = Dataset.from_dict({"input_ids": []})
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "drop",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        self.assertEqual(len(result), 0)
+
+    def test_all_sequences_dropped_returns_empty_dataset(self):
+        """Test that dropping all sequences results in an empty dataset"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1],  # too short
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],  # too long
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "drop",
+                "min_sample_len": 5,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        self.assertEqual(len(result), 0)
+
+    def test_iterable_dataset_skips_processing(self):
+        """Test that streaming datasets (column_names is None) are returned unchanged.
+
+        The skip check in _should_skip_processing triggers when column_names is
+        None, which happens with true streaming datasets loaded via
+        load_dataset(..., streaming=True).
+        """
+        mock_dataset = MagicMock()
+        mock_dataset.column_names = None
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "drop",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(mock_dataset, sequence_len=10, cfg=cfg)
+
+        # Should be returned unchanged (same object)
+        self.assertIs(result, mock_dataset)
+
+    def test_truncate_with_partial_auxiliary_fields(self):
+        """Test truncation when only some auxiliary fields are present"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12],
+                ],
+                "labels": [
+                    [-100, -100, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12],
+                ],
+                # No attention_mask or position_ids
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "truncate",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        self.assertEqual(len(result[0]["input_ids"]), 10)
+        self.assertEqual(len(result[0]["labels"]), 10)
+        self.assertEqual(result[0]["input_ids"], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
+        self.assertEqual(result[0]["labels"], [-100, -100, 3, 4, 5, 6, 7, 8, 9, 10])
+        # Confirm no extra columns were introduced
+        self.assertListEqual(sorted(result.column_names), ["input_ids", "labels"])
+
+    def test_min_sample_len_defaults_to_two_when_not_set(self):
+        """Test that min_sample_len defaults to 2 when not specified in config"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1],  # length 1 - should be dropped (< default 2)
+                    [1, 2],  # length 2 - should be kept (>= default 2)
+                    [1, 2, 3],  # length 3 - should be kept
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "drop",
+                # min_sample_len not set
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        self.assertEqual(len(result), 2)
+        self.assertEqual(len(result[0]["input_ids"]), 2)
+        self.assertEqual(len(result[1]["input_ids"]), 3)
+
+    def test_invalid_strategy_falls_through_to_drop(self):
+        """Test that an unrecognized strategy value falls through to drop behavior"""
+        dataset = Dataset.from_dict(
+            {
+                "input_ids": [
+                    [1, 2, 3],  # keep
+                    [
+                        1,
+                        2,
+                        3,
+                        4,
+                        5,
+                        6,
+                        7,
+                        8,
+                        9,
+                        10,
+                        11,
+                    ],  # length 11 - should be dropped
+                ]
+            }
+        )
+
+        cfg = DictDefault(
+            {
+                "excess_length_strategy": "not_a_real_strategy",
+                "min_sample_len": 2,
+                "dataset_num_proc": None,
+                "is_preprocess": False,
+            }
+        )
+
+        result = handle_long_seq_in_dataset(dataset, sequence_len=10, cfg=cfg)
+
+        # Should behave like 'drop'
+        self.assertEqual(len(result), 1)
+        self.assertEqual(len(result[0]["input_ids"]), 3)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/utils/test_mistral3_processor.py

@@ -0,0 +1,149 @@
+"""Tests for Mistral3Processor with transformers v5 ProcessorMixin integration"""
+
+from unittest.mock import MagicMock
+
+import pytest
+import torch
+from transformers.feature_extraction_utils import BatchFeature
+
+from axolotl.utils.mistral.mistral3_processor import Mistral3Processor
+from axolotl.utils.mistral.mistral_tokenizer import HFMistralTokenizer
+
+
+@pytest.fixture()
+def mock_tokenizer():
+    """Create a mock HFMistralTokenizer that passes v5 ProcessorMixin isinstance checks."""
+    return MagicMock(spec=HFMistralTokenizer)
+
+
+@pytest.fixture()
+def processor(mock_tokenizer):
+    return Mistral3Processor(tokenizer=mock_tokenizer)
+
+
+class TestMistral3ProcessorInit:
+    def test_tokenizer_is_set(self, processor, mock_tokenizer):
+        assert processor.tokenizer is mock_tokenizer
+
+    def test_chat_template_is_none(self, processor):
+        assert processor.chat_template is None
+
+    def test_audio_tokenizer_is_none(self, processor):
+        assert processor.audio_tokenizer is None
+
+
+class TestApplyChatTemplateTokenized:
+    """Test apply_chat_template with tokenize=True, return_dict=True"""
+
+    @pytest.fixture()
+    def batched_conversations(self):
+        return [
+            [
+                {"role": "user", "content": "Describe this image."},
+                {"role": "assistant", "content": "It is red."},
+            ],
+            [
+                {"role": "user", "content": "What is this?"},
+                {"role": "assistant", "content": "A cat."},
+            ],
+        ]
+
+    def test_returns_batch_feature_with_pixel_values(
+        self, processor, mock_tokenizer, batched_conversations
+    ):
+        pixel_values = torch.randn(2, 3, 224, 224, dtype=torch.float64)
+        mock_tokenizer.apply_chat_template.return_value = {
+            "input_ids": torch.tensor([[1, 2, 3], [4, 5, 6]]),
+            "attention_mask": torch.tensor([[1, 1, 1], [1, 1, 1]]),
+            "pixel_values": pixel_values,
+        }
+
+        result = processor.apply_chat_template(
+            batched_conversations, tokenize=True, return_dict=True
+        )
+
+        assert isinstance(result, BatchFeature)
+        assert "pixel_values" in result
+        assert "image_sizes" in result
+        assert result["pixel_values"].dtype == torch.float32
+        assert result["image_sizes"].shape == (2, 2)
+        assert result["image_sizes"][0].tolist() == [224, 224]
+
+    def test_returns_batch_feature_without_pixel_values(
+        self, processor, mock_tokenizer, batched_conversations
+    ):
+        mock_tokenizer.apply_chat_template.return_value = {
+            "input_ids": torch.tensor([[1, 2, 3], [4, 5, 6]]),
+            "attention_mask": torch.tensor([[1, 1, 1], [1, 1, 1]]),
+        }
+
+        result = processor.apply_chat_template(
+            batched_conversations, tokenize=True, return_dict=True
+        )
+
+        assert isinstance(result, BatchFeature)
+        assert "input_ids" in result
+        assert "image_sizes" not in result
+
+
+class TestApplyChatTemplateNotTokenized:
+    def test_single_conversation_returns_unwrapped(self, processor, mock_tokenizer):
+        """Single conversation (not batched) should return unwrapped result."""
+        single_conversation = [
+            {"role": "user", "content": "Hello"},
+            {"role": "assistant", "content": "Hi"},
+        ]
+        mock_tokenizer.apply_chat_template.return_value = [
+            "<s>[INST]Hello[/INST]Hi</s>"
+        ]
+
+        result = processor.apply_chat_template(
+            single_conversation, tokenize=False, return_dict=False
+        )
+
+        assert result == "<s>[INST]Hello[/INST]Hi</s>"
+
+    def test_batched_conversations_returns_list(self, processor, mock_tokenizer):
+        batched = [
+            [
+                {"role": "user", "content": "Hello"},
+                {"role": "assistant", "content": "Hi"},
+            ],
+            [
+                {"role": "user", "content": "Bye"},
+                {"role": "assistant", "content": "Bye"},
+            ],
+        ]
+        mock_tokenizer.apply_chat_template.return_value = ["text1", "text2"]
+
+        result = processor.apply_chat_template(
+            batched, tokenize=False, return_dict=False
+        )
+
+        assert result == ["text1", "text2"]
+
+
+class TestCall:
+    def test_delegates_to_tokenizer(self, processor, mock_tokenizer):
+        mock_tokenizer.return_value = {
+            "input_ids": [1, 2, 3],
+            "attention_mask": [1, 1, 1],
+        }
+
+        result = processor("Hello world")
+
+        mock_tokenizer.assert_called_once()
+        assert isinstance(result, BatchFeature)
+
+
+class TestReturnTensorsValidation:
+    def test_rejects_non_pt_return_tensors(self, processor):
+        conversation = [
+            {"role": "user", "content": "Hello"},
+            {"role": "assistant", "content": "Hi"},
+        ]
+
+        with pytest.raises(ValueError, match=r"only supports.*return_tensors='pt'"):
+            processor.apply_chat_template(
+                conversation, tokenize=True, return_dict=True, return_tensors="np"
+            )