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ljwoods2ljwoods2
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Merge pull request #21 from Becksteinlab/develop
Workshop dry run prep
2 parents 254a6a8 + ede73dc commit 7acff3e

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-35
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6 files changed

+35
-35
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‎.github/workflows/ci.yaml‎

Lines changed: 14 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ jobs:
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strategy:
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matrix:
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arch: [amd64]
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tag_suffix: [GPU, GPU-Thread-MPI, GPU-Node-MPI]
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build: [GPU, GPU-Thread-MPI, GPU-Node-MPI]
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# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
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permissions:
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contents: read
@@ -31,13 +31,13 @@ jobs:
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uses: actions/checkout@v4
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- name: Convert compiler options to simple tag suffix
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id: GMX_OPTS
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id: option
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run: |
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if [[ "${{ matrix.tag_suffix }}" == "GPU-Thread-MPI" ]]; then
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if [ "${{ matrix.build }}" == "GPU-Thread-MPI" ]; then
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echo GMX_OPTS="-DGMX_GPU=CUDA -DGMX_THREAD_MPI=ON" >> $GITHUB_ENV
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elif [[ "${{ matrix.tag_suffix }}" == "GPU-Node-MPI" ]]; then
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elif [ "${{ matrix.build }}" == "GPU-Node-MPI" ]; then
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echo GMX_OPTS="-DGMX_GPU=CUDA -DGMX_MPI=ON" >> $GITHUB_ENV
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elif [[ "${{ matrix.tag_suffix }}" == "GPU" ]]; then
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elif [ "${{ matrix.build }}" == "GPU" ]; then
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echo GMX_OPTS="-DGMX_GPU=CUDA -DGMX_MPI=OFF" >> $GITHUB_ENV
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fi
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@@ -47,14 +47,14 @@ jobs:
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context: ./docker/gromacs
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push: false
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build-args:
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GMX_OPTS=${{ matrix.GMX_OPTS }}
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GMX_OPTS="${{ env.GMX_OPTS }}"
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build-lammps-image:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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arch: [amd64]
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tag_suffix: ["GPU-Node-MPI", "GPU"]
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build: ["GPU-Node-MPI", "GPU"]
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# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
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permissions:
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contents: read
@@ -73,11 +73,11 @@ jobs:
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uses: actions/checkout@v4
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- name: Convert compiler options to simple tag suffix
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id: LMP_OPTS
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id: option
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run: |
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if [[ "${{ matrix.tag_suffix }}" == "GPU-Node-MPI" ]]; then
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if [ "${{ matrix.build }}" == "GPU-Node-MPI" ]; then
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echo LMP_OPTS="-D PKG_GPU=on -D GPU_API=cuda -D BUILD_MPI=yes" >> $GITHUB_ENV
80-
elif [[ "${{ matrix.tag_suffix }}" == "GPU" ]]; then
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elif [ "${{ matrix.build }}" == "GPU" ]; then
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echo LMP_OPTS="-D PKG_GPU=on -D GPU_API=cuda -D BUILD_MI=no" >> $GITHUB_ENV
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fi
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@@ -87,14 +87,14 @@ jobs:
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context: ./docker/lammps
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push: false
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build-args: |
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LMP_OPTS=${{ matrix.LMP_OPTS }}
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LMP_OPTS="${{ env.LMP_OPTS }}"
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build-common-image:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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arch: [amd64]
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build: ["Common-CPU", "Common-GPU"]
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build: ["Common-CPU"] #, "Common-GPU"]
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permissions:
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contents: read
@@ -132,5 +132,5 @@ jobs:
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push: false
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file: ./docker/common/${{ env.DOCKERFILE }}
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build-args: |
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GMX_OPTS=${{ env.GMX_OPTS }}
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LMP_OPTS=${{ env.LMP_OPTS }}
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GMX_OPTS="${{ env.GMX_OPTS }}"
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LMP_OPTS="${{ env.LMP_OPTS }}"

‎.github/workflows/deploy_docker.yaml‎

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ jobs:
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strategy:
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matrix:
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arch: [amd64]
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tag_suffix: [GPU, GPU-Thread-MPI, GPU-Node-MPI]
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build: [GPU, GPU-Thread-MPI, GPU-Node-MPI]
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# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
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permissions:
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contents: read
@@ -44,13 +44,13 @@ jobs:
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Convert compiler options to simple tag suffix
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id: GMX_OPTS
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id: option
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run: |
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if [[ "${{ matrix.tag_suffix }}" == "GPU-Thread-MPI" ]]; then
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if [ "${{ matrix.build }}" == "GPU-Thread-MPI" ]; then
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echo GMX_OPTS="-DGMX_GPU=CUDA -DGMX_THREAD_MPI=ON" >> $GITHUB_ENV
51-
elif [[ "${{ matrix.tag_suffix }}" == "GPU-Node-MPI" ]]; then
51+
elif [ "${{ matrix.build }}" == "GPU-Node-MPI" ]; then
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echo GMX_OPTS="-DGMX_GPU=CUDA -DGMX_MPI=ON" >> $GITHUB_ENV
53-
elif [[ "${{ matrix.tag_suffix }}" == "GPU" ]]; then
53+
elif [ "${{ matrix.build }}" == "GPU" ]; then
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echo GMX_OPTS="-DGMX_GPU=CUDA -DGMX_MPI=OFF" >> $GITHUB_ENV
5555
fi
5656
# This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
@@ -67,17 +67,17 @@ jobs:
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with:
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context: ./docker/gromacs
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push: true
70-
tags: "${{ steps.meta.outputs.tags }}-GROMACS-${{ matrix.tag_suffix }}"
70+
tags: "${{ steps.meta.outputs.tags }}-GROMACS-${{ matrix.build }}"
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
73-
GMX_OPTS=${{ env.GMX_OPTS }}
73+
GMX_OPTS="${{ env.GMX_OPTS }}"
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build-and-push-lammps-image:
7676
runs-on: ubuntu-latest
7777
strategy:
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matrix:
7979
arch: [amd64]
80-
tag_suffix: ["GPU-Node-MPI", "GPU"]
80+
build: ["GPU-Node-MPI", "GPU"]
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8282
# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
8383
permissions:
@@ -105,11 +105,11 @@ jobs:
105105
password: ${{ secrets.GITHUB_TOKEN }}
106106

107107
- name: Convert compiler options to simple tag suffix
108-
id: tag_suffix
108+
id: option
109109
run: |
110-
if [[ "${{ matrix.tag_suffix }}" == "GPU-Node-MPI" ]]; then
110+
if [ "${{ matrix.build }}" == "GPU-Node-MPI" ]; then
111111
echo LMP_OPTS="-D PKG_GPU=on -D GPU_API=cuda -D BUILD_MPI=yes" >> $GITHUB_ENV
112-
elif [[ "${{ matrix.tag_suffix }}" == "GPU" ]]; then
112+
elif [ "${{ matrix.build }}" == "GPU" ]; then
113113
echo LMP_OPTS="-D PKG_GPU=on -D GPU_API=cuda -D BUILD_MI=no" >> $GITHUB_ENV
114114
fi
115115
# This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
@@ -126,17 +126,17 @@ jobs:
126126
with:
127127
context: ./docker/lammps
128128
push: true
129-
tags: "${{ steps.meta.outputs.tags }}-LAMMPS-${{ matrix.tag_suffix }}"
129+
tags: "${{ steps.meta.outputs.tags }}-LAMMPS-${{ matrix.build }}"
130130
labels: ${{ steps.meta.outputs.labels }}
131131
build-args: |
132-
LMP_OPTS=${{ env.LMP_OPTS }}
132+
LMP_OPTS="${{ env.LMP_OPTS }}"
133133
134134
build-common-image:
135135
runs-on: ubuntu-latest
136136
strategy:
137137
matrix:
138138
arch: [amd64]
139-
build: ["Common-CPU", "Common-GPU"]
139+
build: ["Common-CPU"] #, "Common-GPU"]
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141141
permissions:
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contents: read
@@ -190,5 +190,5 @@ jobs:
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tags: ${{ steps.meta.outputs.tags }}-${{ matrix.build }}
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labels: ${{ steps.meta.outputs.labels }}
192192
build-args: |
193-
GMX_OPTS=${{ env.GMX_OPTS }}
194-
LMP_OPTS=${{ env.LMP_OPTS }}
193+
GMX_OPTS="${{ env.GMX_OPTS }}"
194+
LMP_OPTS="${{ env.LMP_OPTS }}"

‎docker/common/install_gromacs.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ export NPROC=$(nproc)
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export LIBRARY_PATH=${CONDA_PREFIX}/lib
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export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib
88

9-
git clone https://github.com/hcho38/gromacs.git
9+
git clone https://gitlab.com/ljwoods2/gromacs.git
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cd gromacs
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git checkout imd-v3
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mkdir build

‎docker/common/install_lammps.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ export NPROC=$(nproc)
88
# Setup LAMMPS
99
git clone https://github.com/ljwoods2/lammps.git
1010
cd lammps
11-
git checkout imd-v3
11+
git checkout imd-v3-integration
1212
mkdir build
1313
cd build
1414
cmake ../cmake/ $(echo ${1} | sed 's/"//g') -D PKG_MISC=yes -D PKG_H5MD=yes -DCMAKE_INSTALL_PREFIX=/opt/lammps_build

‎docker/gromacs/install_gromacs.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ export LIBRARY_PATH=${CONDA_PREFIX}/lib
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export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib
99

1010

11-
git clone https://github.com/hcho38/gromacs.git
11+
git clone https://gitlab.com/ljwoods2/gromacs.git
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cd gromacs
1313
git checkout imd-v3
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mkdir build

‎docker/lammps/install_lammps.sh‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,9 +8,9 @@ export NPROC=$(nproc)
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# Setup LAMMPS
99
git clone https://github.com/ljwoods2/lammps.git
1010
cd lammps
11-
git checkout imd-v3
11+
git checkout imd-v3-integration
1212
mkdir build
1313
cd build
1414
cmake ../cmake/ $(echo ${1} | sed 's/"//g') -D PKG_MISC=yes -D PKG_H5MD=yes -DCMAKE_INSTALL_PREFIX=/opt/lammps_build
1515
cmake --build . -j ${NPROC}
16-
make install
16+
make install

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