permissions, namd opts

Becksteinlab · Dec 17, 2024 · 79118cc · 79118cc
1 parent ab3f82e
commit 79118cc
Show file tree

Hide file tree

Showing 5 changed files with 47 additions and 38 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -13,7 +13,7 @@ jobs:
         strategy:
           matrix:
             arch: [amd64]
-            build: ["Common-CPU", "Common-GPU"]
+            build: ["common-cpu", "common-gpu"]
 
         permissions:
           contents: read
@@ -34,7 +34,7 @@ jobs:
           - name: Option
             id: option
             run: |
-              if [ "${{ matrix.build }}" == "Common-CPU" ]; then
+              if [ "${{ matrix.build }}" == "common-cpu" ]; then
                 echo GMX_OPTS= >> $GITHUB_ENV
                 echo LMP_OPTS= >> $GITHUB_ENV
                 echo NAMD_OPTS= >> $GITHUB_ENV
@@ -46,19 +46,19 @@ jobs:
                 echo DOCKERFILE="GPU.Dockerfile" >> $GITHUB_ENV
               fi
 
-          - name: Build and push Docker image
-            uses: docker/build-push-action@v5
-            with:
-              context: ./docker/common
-              push: false
-              file: ./docker/common/${{ env.DOCKERFILE }}
-              build-args: |
-                GMX_OPTS="${{ env.GMX_OPTS }}"
-                LMP_OPTS="${{ env.LMP_OPTS }}"
-                CUDA_VER=12.4.1
-                DISTRO_ARCH=${{ matrix.arch }}
-                DISTRO_VER=22.04
-                DISTRO_NAME=ubuntu
+          # - name: Build and push Docker image
+          #   uses: docker/build-push-action@v5
+          #   with:
+          #     context: ./docker/common
+          #     push: false
+          #     file: ./docker/common/${{ env.DOCKERFILE }}
+          #     build-args: |
+          #       GMX_OPTS="${{ env.GMX_OPTS }}"
+          #       LMP_OPTS="${{ env.LMP_OPTS }}"
+          #       CUDA_VER=12.4.1
+          #       DISTRO_ARCH=${{ matrix.arch }}
+          #       DISTRO_VER=22.04
+          #       DISTRO_NAME=ubuntu
 
           - name: Build and push private NAMD Docker image
             uses: docker/build-push-action@v5

diff --git a/.github/workflows/deploy_docker.yaml b/.github/workflows/deploy_docker.yaml
@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         arch: [amd64]
-        build: ["Common-CPU", "Common-GPU"]
+        build: ["common-cpu", "common-gpu"]
 
     permissions:
       contents: read
@@ -47,7 +47,7 @@ jobs:
       - name: Option
         id: option
         run: |
-          if [ "${{ matrix.build }}" == "Common-CPU" ]; then
+          if [ "${{ matrix.build }}" == "common-cpu" ]; then
             echo GMX_OPTS= >> $GITHUB_ENV
             echo LMP_OPTS= >> $GITHUB_ENV
             echo NAMD_OPTS= >> $GITHUB_ENV
@@ -65,29 +65,29 @@ jobs:
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v5
-        with:
-          context: ./docker/common
-          file: ./docker/common/${{ env.DOCKERFILE }}
-          push: true
-          tags: ${{ steps.meta.outputs.tags }}-${{ matrix.build }}
-          labels: ${{ steps.meta.outputs.labels }}
-          build-args: |
-            GMX_OPTS="${{ env.GMX_OPTS }}"
-            LMP_OPTS="${{ env.LMP_OPTS }}"
-            CUDA_VER=12.4.1
-            DISTRO_ARCH=${{ matrix.arch }}
-            DISTRO_VER=22.04
-            DISTRO_NAME=ubuntu
+      # - name: Build and push Docker image
+      #   uses: docker/build-push-action@v5
+      #   with:
+      #     context: ./docker/common
+      #     file: ./docker/common/${{ env.DOCKERFILE }}
+      #     push: true
+      #     tags: ${{ steps.meta.outputs.tags }}-${{ matrix.build }}
+      #     labels: ${{ steps.meta.outputs.labels }}
+      #     build-args: |
+      #       GMX_OPTS="${{ env.GMX_OPTS }}"
+      #       LMP_OPTS="${{ env.LMP_OPTS }}"
+      #       CUDA_VER=12.4.1
+      #       DISTRO_ARCH=${{ matrix.arch }}
+      #       DISTRO_VER=22.04
+      #       DISTRO_NAME=ubuntu
 
       - name: Build and push private NAMD Docker image
         uses: docker/build-push-action@v5
         with:
           context: ./docker/namd
           file: ./docker/namd/${{ env.DOCKERFILE }}
-          push: false
-          tags: ${{ steps.meta.outputs.tags }}-${{ matrix.build }}
+          push: true
+          tags: ghcr.io/becksteinlab/streaming-namd-docker:main-${{ matrix.build }}
           labels: ${{ steps.meta.outputs.labels }}
           build-args: |
             NAMD_OPTS="${{ env.NAMD_OPTS }}"

diff --git a/docker/namd/CPU.Dockerfile b/docker/namd/CPU.Dockerfile
@@ -85,6 +85,7 @@ ARG NAMD_OPTS=""
 
 COPY . .
 RUN . /opt/conda/etc/profile.d/conda.sh && conda env create --file env.yaml
+RUN chmod +x install_namd.sh
 RUN --mount=type=secret,id=NAMD_ACCESS_TOKEN \
     . /opt/conda/etc/profile.d/conda.sh && conda activate env && ./install_namd.sh "$NAMD_OPTS"
 

diff --git a/docker/namd/GPU.Dockerfile b/docker/namd/GPU.Dockerfile
@@ -88,6 +88,7 @@ ARG NAMD_OPTS=""
 
 COPY . .
 RUN . /opt/conda/etc/profile.d/conda.sh && conda env create --file env.yaml
+RUN chmod +x install_namd.sh
 RUN --mount=type=secret,id=NAMD_ACCESS_TOKEN \
     . /opt/conda/etc/profile.d/conda.sh && conda activate env && ./install_namd.sh "$NAMD_OPTS"
 

diff --git a/docker/namd/install_namd.sh b/docker/namd/install_namd.sh
@@ -5,8 +5,8 @@ export HOME_DIR=${PWD}
 # set include path to conda
 # export CPATH=${CONDA_PREFIX}/include
 # # set linker path to conda libs
-export LIBRARY_PATH=${CONDA_PREFIX}/lib
-export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib
+export LIBRARY_PATH=${CONDA_PREFIX}/lib:/usr/local/cuda/lib64
+export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib:/usr/local/cuda/lib64
 export NPROC=$(nproc)
 
 # Setup NAMD
@@ -15,9 +15,16 @@ cd namd
 git checkout IMDv3-dev
 tar xf charm-8.0.0.tar
 cd charm-8.0.0
-./build charm++ multicore-linux-x86_64 -j ${NPROC} --with-production --libdir=${CONDA_PREFIX}/lib --incdir=${CONDA_PREFIX}/include
+./build charm++ multicore-linux-x86_64 -j ${NPROC} \
+    --with-production 
 cd ../
-./config Linux-x86_64-g++ $(echo ${1} | sed 's/"//g') --charm-arch multicore-linux-x86_64 --with-fftw3 --tcl-prefix ${CONDA_PREFIX}  --cxx-opts -L${CONDA_PREFIX}/lib  --cc-opts -L${CONDA_PREFIX}/lib
+./config Linux-x86_64-g++ $(echo ${1} | sed 's/"//g') \
+    --charm-arch multicore-linux-x86_64 --with-fftw3 \
+    --tcl-prefix ${CONDA_PREFIX} \
+    --cxx-opts="-I/usr/local/cuda/include -I${CONDA_PREFIX}/include -L/usr/local/cuda/lib64 -L${CONDA_PREFIX}/lib" \
+    --cc-opts="-I/usr/local/cuda/include -I${CONDA_PREFIX}/include -L/usr/local/cuda/lib64 -L${CONDA_PREFIX}/lib" \
+    --cuda-prefix /usr/local/cuda
+
 cd Linux-x86_64-g++
 make -j ${NPROC}