FastSurfer Singularity #28
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| name: FastSurfer Singularity | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| # Checkout repo | |
| checkout: | |
| runs-on: ci-gpu | |
| steps: | |
| - uses: actions/checkout@v2 | |
| # Prepare job: Set up Python, Go, Singularity | |
| prepare-job: | |
| runs-on: ci-gpu | |
| needs: checkout | |
| steps: | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| - name: Set up Go | |
| uses: actions/setup-go@v5 | |
| with: | |
| go-version: '^1.13.1' # The Go version to download (if necessary) and use. | |
| - name: Set up Singularity | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.3 | |
| # Build Docker Image and convert it to Singularity | |
| build-singularity-image: | |
| runs-on: ci-gpu | |
| needs: prepare-job | |
| steps: | |
| - name: Build Docker Image and conver to Singularity | |
| run: | | |
| cd $RUNNER_SINGULARITY_IMGS | |
| FILE="fastsurfer-gpu.sif" | |
| if [ ! -f "$FILE" ]; then | |
| # If the file does not exist, build the file | |
| echo "SIF File does not exist. Building file." | |
| PYTHONPATH=$PYTHONPATH | |
| cd $PYTHONPATH | |
| python3 Docker/build.py --device cuda --dry_run --tag fastsurfer_gpu:cuda | bash | |
| cd $RUNNER_SINGULARITY_IMGS | |
| singularity build --force fastsurfer-gpu.sif docker-daemon://fastsurfer_gpu:cuda | |
| else | |
| echo "File already exists" | |
| cd $PYTHONPATH | |
| fi | |
| # Run FastSurfer on MRI data | |
| run-fastsurfer: | |
| runs-on: ci-gpu | |
| needs: build-singularity-image | |
| steps: | |
| - name: Run FastSurfer | |
| run: | | |
| singularity exec --nv \ | |
| --no-home \ | |
| --bind $GITHUB_WORKSPACE:/fastsurfer-dev \ | |
| --env FASTSURFER_HOME=/fastsurfer-dev \ | |
| -B $RUNNER_FS_MRI_DATA:/data \ | |
| -B $RUNNER_FS_OUTPUT:/output \ | |
| -B $RUNNER_FS_LICENSE:/fs_license \ | |
| $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \ | |
| /fastsurfer/run_fastsurfer.sh \ | |
| --fs_license /fs_license/.license \ | |
| --t1 /data/subjectx/orig.mgz \ | |
| --sid subjectX --sd /output \ | |
| --parallel --3T | |
| # Test file existence | |
| test-file-existence: | |
| runs-on: ci-gpu | |
| needs: run-fastsurfer | |
| steps: | |
| - name: Test File Existence | |
| run: | | |
| singularity exec --bind $GITHUB_WORKSPACE:/fastsurfer-dev --env FASTSURFER_HOME=/fastsurfer-dev my_fastsurfer.sif python3 test/test_file_existence.py $RUNNER_FS_OUTPUT_FILES | |
| # Test for errors in log files | |
| test-error-messages: | |
| runs-on: ci-gpu | |
| needs: [run-fastsurfer, test-file-existence] | |
| steps: | |
| - name: Test Log Files For Error Messages | |
| run: | | |
| singularity exec --bind $GITHUB_WORKSPACE:/fastsurfer-dev --env FASTSURFER_HOME=/fastsurfer-dev my_fastsurfer.sif python3 test/test_error_messages.py $RUNNER_FS_OUTPUT_LOGS |