From 7f508750556b06de34d79de4343f5f8bddaf5cf8 Mon Sep 17 00:00:00 2001 From: svdenhau Date: Tue, 14 Nov 2023 16:38:59 +0100 Subject: [PATCH] stuff --- configs/csc_mahti.yaml | 40 ------------------ configs/csc_puhti.yaml | 40 ------------------ configs/vsc_hortense.yaml | 44 -------------------- container/Dockerfile_py310_cuda | 72 --------------------------------- container/Dockerfile_py39_cuda | 72 --------------------------------- 5 files changed, 268 deletions(-) delete mode 100644 configs/csc_mahti.yaml delete mode 100644 configs/csc_puhti.yaml delete mode 100644 configs/vsc_hortense.yaml delete mode 100644 container/Dockerfile_py310_cuda delete mode 100644 container/Dockerfile_py39_cuda diff --git a/configs/csc_mahti.yaml b/configs/csc_mahti.yaml deleted file mode 100644 index ec4714e..0000000 --- a/configs/csc_mahti.yaml +++ /dev/null @@ -1,40 +0,0 @@ ---- -container: - engine: "apptainer" - uri: "oras://ghcr.io/molmod/psiflow:3.0.0-cuda" -ModelEvaluation: - cores_per_worker: 1 - simulation_engine: 'openmm' - SlurmProvider: - partition: "interactive" - account: "project_2008666" - nodes_per_block: 1 # each block fits on (less than) one node - cores_per_node: 4 # number of cores per slurm job - init_blocks: 0 - max_blocks: 1 # do not use more than one block - walltime: "01:00:00" # walltime per block -ModelTraining: - cores_per_worker: 32 - gpu: true - SlurmProvider: - partition: "gputest" - account: "project_2008666" - nodes_per_block: 1 - cores_per_node: 32 - init_blocks: 0 - max_blocks: 1 - walltime: "00:15:00" - scheduler_options: "#SBATCH --gres=gpu:a100:1" -ReferenceEvaluation: - cores_per_worker: 4 - max_walltime: 20 - cpu_affinity: 'alternating' - SlurmProvider: - partition: "interactive" - account: "project_2008666" - nodes_per_block: 1 # each block fits on (less than) one node - cores_per_node: 16 # number of cores per slurm job - init_blocks: 0 - max_blocks: 1 # do not use more than one block - walltime: "01:00:00" # walltime per block -... diff --git a/configs/csc_puhti.yaml b/configs/csc_puhti.yaml deleted file mode 100644 index 76df0e4..0000000 --- a/configs/csc_puhti.yaml +++ /dev/null @@ -1,40 +0,0 @@ ---- -container: - engine: "apptainer" - uri: "oras://ghcr.io/molmod/psiflow:3.0.0-cuda" -ModelEvaluation: - cores_per_worker: 1 - simulation_engine: 'openmm' - SlurmProvider: - partition: "small" - account: "project_2008666" - nodes_per_block: 1 # each block fits on (less than) one node - cores_per_node: 40 # number of cores per slurm job - init_blocks: 0 - max_blocks: 1 # do not use more than one block - walltime: "01:00:00" # walltime per block -ModelTraining: - cores_per_worker: 10 - gpu: true - SlurmProvider: - partition: "gpu" - account: "project_2008666" - nodes_per_block: 1 - cores_per_node: 10 - init_blocks: 0 - max_blocks: 1 - walltime: "02:00:00" - scheduler_options: "#SBATCH --gres=gpu:v100:1" -ReferenceEvaluation: - cores_per_worker: 4 - max_walltime: 20 - cpu_affinity: 'alternating' - SlurmProvider: - partition: "small" - account: "project_2008666" - nodes_per_block: 1 # each block fits on (less than) one node - cores_per_node: 40 # number of cores per slurm job - init_blocks: 0 - max_blocks: 1 # do not use more than one block - walltime: "01:00:00" # walltime per block -... diff --git a/configs/vsc_hortense.yaml b/configs/vsc_hortense.yaml deleted file mode 100644 index d78abf2..0000000 --- a/configs/vsc_hortense.yaml +++ /dev/null @@ -1,44 +0,0 @@ ---- -container: - engine: "apptainer" - uri: "oras://ghcr.io/molmod/psiflow:2.0.0-cuda" -ModelEvaluation: - cores_per_worker: 1 - simulation_engine: 'openmm' - SlurmProvider: - partition: "cpu_rome" - account: "2022_069" - nodes_per_block: 1 # each block fits on (less than) one node - cores_per_node: 8 # number of cores per slurm job - init_blocks: 1 # initialize a block at the start of the workflow - max_blocks: 1 # do not use more than one block - walltime: "01:00:00" # walltime per block - exclusive: false # rest of compute node free to use - scheduler_options: "#SBATCH --clusters=dodrio\n" -ModelTraining: - cores_per_worker: 12 - gpu: true - SlurmProvider: - partition: "gpu_rome_a100" - account: "2022_069" - nodes_per_block: 1 - cores_per_node: 12 - init_blocks: 1 - max_blocks: 1 - walltime: "01:00:00" - exclusive: false - scheduler_options: "#SBATCH --clusters=dodrio\n#SBATCH --gpus=1\n" -ReferenceEvaluation: - max_walltime: 20 - SlurmProvider: - partition: "cpu_rome" - account: "2022_069" - nodes_per_block: 1 - cores_per_node: 64 - init_blocks: 1 - min_blocks: 0 - max_blocks: 10 - walltime: "01:00:00" - exclusive: false - scheduler_options: "#SBATCH --clusters=dodrio\n" -... diff --git a/container/Dockerfile_py310_cuda b/container/Dockerfile_py310_cuda deleted file mode 100644 index 863025b..0000000 --- a/container/Dockerfile_py310_cuda +++ /dev/null @@ -1,72 +0,0 @@ -# bring in the micromamba image so we can copy files from it -FROM mambaorg/micromamba:1.4.2 as micromamba - -# This is the image we are going add micromaba to: -FROM svandenhaute/cp2k:2023.1 -#FROM nvidia/cuda:11.8.0-runtime-ubuntu22.04 - -USER root - -# if your image defaults to a non-root user, then you may want to make the -# next 3 ARG commands match the values in your image. You can get the values -# by running: docker run --rm -it my/image id -a -ARG MAMBA_USER=mamba -ARG MAMBA_USER_ID=1000 -ARG MAMBA_USER_GID=1000 -ENV MAMBA_USER=$MAMBA_USER -ENV MAMBA_ROOT_PREFIX="/opt/conda" -ENV MAMBA_EXE="/bin/micromamba" - -COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE" -COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh -COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh -COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh - -RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \ - /usr/local/bin/_dockerfile_setup_root_prefix.sh - -# modify entrypoint to also activate cp2k -RUN head -n -1 /usr/local/bin/_entrypoint.sh > /usr/local/bin/entry.sh -RUN echo "source /opt/cp2k-toolchain/install/setup\n" >> /usr/local/bin/entry.sh -RUN echo "export PATH=\"/opt/cp2k/exe/local:\${PATH}\"\n" >> /usr/local/bin/entry.sh -RUN echo "export PATH=\"/opt/cp2k-toolchain/install/mpich-4.0.3/bin:\${PATH}\"\n" >> /usr/local/bin/entry.sh -RUN echo "exec \"\$@\"" >> /usr/local/bin/entry.sh -RUN chmod +x /usr/local/bin/entry.sh - -USER $MAMBA_USER - -SHELL ["/usr/local/bin/_dockerfile_shell.sh"] - -RUN micromamba install --yes --name base --channel conda-forge \ - jq && \ - micromamba clean --all --yes - -RUN CONDA_OVERRIDE_CUDA="11.8" micromamba install -n base --yes -c conda-forge \ - python=3.10 pip \ - openmm-plumed openmm-torch pytorch=1.13.1=cuda* \ - py-plumed && \ - micromamba clean -af --yes -ARG MAMBA_DOCKERFILE_ACTIVATE=1 # (otherwise python will not be found) - -RUN pip install cython==0.29.36 matscipy prettytable && \ - pip install git+https://github.com/molmod/molmod && \ - pip install git+https://github.com/molmod/yaff && \ - pip install e3nn==0.4.4 -RUN pip install numpy ase tqdm pyyaml 'torch-runstats>=0.2.0' 'torch-ema>=0.3.0' mdtraj tables -RUN pip install git+https://github.com/acesuit/MACE.git@55f7411 && \ - pip install git+https://github.com/mir-group/nequip.git@develop --no-deps && \ - pip install git+https://github.com/mir-group/allegro --no-deps && \ - pip install git+https://github.com/svandenhaute/openmm-ml.git@triclinic -RUN pip install pyscf - -ARG GIT_COMMIT_SHA -RUN pip install 'psiflow[parsl] @ git+https://github.com/molmod/psiflow' -RUN pip cache purge - -ENV OMPI_MCA_plm_rsh_agent= -ENV OMP_PROC_BIND=TRUE - -ENTRYPOINT ["/usr/local/bin/entry.sh"] diff --git a/container/Dockerfile_py39_cuda b/container/Dockerfile_py39_cuda deleted file mode 100644 index 8c3937a..0000000 --- a/container/Dockerfile_py39_cuda +++ /dev/null @@ -1,72 +0,0 @@ -# bring in the micromamba image so we can copy files from it -FROM mambaorg/micromamba:1.4.2 as micromamba - -# This is the image we are going add micromaba to: -FROM svandenhaute/cp2k:2023.1 -#FROM nvidia/cuda:11.8.0-runtime-ubuntu22.04 - -USER root - -# if your image defaults to a non-root user, then you may want to make the -# next 3 ARG commands match the values in your image. You can get the values -# by running: docker run --rm -it my/image id -a -ARG MAMBA_USER=mamba -ARG MAMBA_USER_ID=1000 -ARG MAMBA_USER_GID=1000 -ENV MAMBA_USER=$MAMBA_USER -ENV MAMBA_ROOT_PREFIX="/opt/conda" -ENV MAMBA_EXE="/bin/micromamba" - -COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE" -COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh -COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh -COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh - -RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \ - /usr/local/bin/_dockerfile_setup_root_prefix.sh - -# modify entrypoint to also activate cp2k -RUN head -n -1 /usr/local/bin/_entrypoint.sh > /usr/local/bin/entry.sh -RUN echo "source /opt/cp2k-toolchain/install/setup\n" >> /usr/local/bin/entry.sh -RUN echo "export PATH=\"/opt/cp2k/exe/local:\${PATH}\"\n" >> /usr/local/bin/entry.sh -RUN echo "export PATH=\"/opt/cp2k-toolchain/install/mpich-4.0.3/bin:\${PATH}\"\n" >> /usr/local/bin/entry.sh -RUN echo "exec \"\$@\"" >> /usr/local/bin/entry.sh -RUN chmod +x /usr/local/bin/entry.sh - -USER $MAMBA_USER - -SHELL ["/usr/local/bin/_dockerfile_shell.sh"] - -RUN micromamba install --yes --name base --channel conda-forge \ - jq && \ - micromamba clean --all --yes - -RUN CONDA_OVERRIDE_CUDA="11.8" micromamba install -n base --yes -c conda-forge \ - python=3.9 pip \ - openmm-plumed openmm-torch pytorch=1.13.1=cuda* \ - py-plumed && \ - micromamba clean -af --yes -ARG MAMBA_DOCKERFILE_ACTIVATE=1 # (otherwise python will not be found) - -RUN pip install cython==0.29.36 matscipy prettytable && \ - pip install git+https://github.com/molmod/molmod && \ - pip install git+https://github.com/molmod/yaff && \ - pip install e3nn==0.4.4 -RUN pip install numpy ase tqdm pyyaml 'torch-runstats>=0.2.0' 'torch-ema>=0.3.0' mdtraj tables -RUN pip install git+https://github.com/acesuit/MACE.git@55f7411 && \ - pip install git+https://github.com/mir-group/nequip.git@develop --no-deps && \ - pip install git+https://github.com/mir-group/allegro --no-deps && \ - pip install git+https://github.com/svandenhaute/openmm-ml.git@triclinic -RUN pip install pyscf - -ARG GIT_COMMIT_SHA -RUN pip install 'psiflow[parsl] @ git+https://github.com/molmod/psiflow' -RUN pip cache purge - -ENV OMPI_MCA_plm_rsh_agent= -ENV OMP_PROC_BIND=TRUE - -ENTRYPOINT ["/usr/local/bin/entry.sh"]