diff --git a/Dockerfile b/Dockerfile index 7703c548ed45c035e9d9d5c78b539cb297fd6102..23324f726545e13e8bc3e5b3878e2488fa283d79 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,19 +1,19 @@ -From mambaorg/micromamba:bullseye +From mambaorg/micromamba:1-bullseye # update conda and the OS -RUN conda update conda && \ - conda upgrade --all -y && \ +RUN micromamba update micromamba && \ + micromamba upgrade --all -y && \ apt-get update && \ apt-get -y install curl && \ DEBIAN_FRONTEND=noninteractive apt-get -y upgrade && \ DEBIAN_FRONTEND=noninteractive apt-get -y autoremove && \ DEBIAN_FRONTEND=noninteractive apt-get -y clean autoclean -RUN curl https://gitlab.pasteur.fr/tru/micromamba-py310-pytorch-cuda11.7/-/raw/main/conda-list--explicit.yml > conda-list--explicit.yml && \ - conda create --name py310-pytorch-1.13.1 --file conda-list--explicit.yml && \ - eval "$(conda shell.bash hook)" && \ - conda activate py310-pytorch-1.13.1 && \ - conda list --explicit > /conda-list--explicit.yml +RUN curl https://gitlab.pasteur.fr/tru/micromamba-py310-pytorch-cuda11.7/-/raw/main/conda-env-export.yml > conda-env-export.yml && \ + micromamba create --name py310-pytorch-1.13.1 --file conda-env-export.yml && \ + eval "$(micromamba shell hook -s posix )" && \ + micromamba activate py310-pytorch-1.13.1 && \ + micromamba env export > /conda-env-export.yml ADD https://gitlab.pasteur.fr/tru/micromamba-py310-pytorch-cuda11.7/-/raw/main/runscript.sh /runscript.sh RUN chmod 755 /runscript.sh diff --git a/Singularity b/Singularity index 1ca964324410ba3a723fef5a74d870131030fb6c..decd1b3cc30d7228b64abf6acbaa5163d3fd2694 100644 --- a/Singularity +++ b/Singularity @@ -1,23 +1,23 @@ Bootstrap: docker -From: docker pull mambaorg/micromamba:bullseye +From: docker pull mambaorg/micromamba:1-bullseye %post # update conda and the OS -conda update conda && \ -conda upgrade --all -y && \ +micromamba update micromamba && \ +micromamba upgrade --all -y && \ apt-get update && \ apt-get -y install curl && \ DEBIAN_FRONTEND=noninteractive apt-get -y upgrade && \ DEBIAN_FRONTEND=noninteractive apt-get -y autoremove && \ DEBIAN_FRONTEND=noninteractive apt-get -y clean autoclean -curl https://gitlab.pasteur.fr/tru/micromamba-py310-pytorch-cuda11.7/-/raw/main/conda-list--explicit.yml > conda-list--explicit.yml && \ - conda create --name py310-pytorch-1.13.1 --file conda-list--explicit.yml && \ - eval "$(conda shell.bash hook)" && \ - conda activate py310-pytorch-1.13.1 && \ - conda list --explicit > /conda-list--explicit.yml +curl https://gitlab.pasteur.fr/tru/micromamba-py310-pytorch-cuda11.7/-/raw/main/conda-env-export.yml > conda-env-export.yml && \ +micromamba create --name py310-pytorch-1.13.1 --file conda-env-export.yml && \ +eval "$(micromamba shell hook -s posix )" && \ +micromamba activate py310-pytorch-1.13.1 && \ +micromamba env export > /conda-env-export.yml %post -eval "$(conda shell.bash hook)" && \ -conda activate py310-pytorch-1.13.1 && \ +eval "$(micromamba shell hook -s posix )" && \ +micromamba activate py310-pytorch-1.13.1 && \ "$@" diff --git a/conda-env-export.yml b/conda-env-export.yml new file mode 100644 index 0000000000000000000000000000000000000000..689c65e7cdc74bc77d173d2a6725cf6b97bfbc66 --- /dev/null +++ b/conda-env-export.yml @@ -0,0 +1,70 @@ +name: py310-pytorch +channels: + - pytorch + - nvidia + - conda-forge +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_kmp_llvm + - blas=2.116=mkl + - blas-devel=3.9.0=16_linux64_mkl + - bzip2=1.0.8=h7f98852_4 + - ca-certificates=2022.12.7=ha878542_0 + - cuda=11.7.1=0 + - cuda-cudart=11.7.99=0 + - cuda-cupti=11.7.101=0 + - cuda-libraries=11.7.1=0 + - cuda-nvrtc=11.7.99=0 + - cuda-nvtx=11.7.91=0 + - cuda-runtime=11.7.1=0 + - cuda-toolkit=11.7.1=0 + - cuda-tools=11.7.1=0 + - gds-tools=1.6.0.25=0 + - icu=70.1=h27087fc_0 + - ld_impl_linux-64=2.40=h41732ed_0 + - libblas=3.9.0=16_linux64_mkl + - libcblas=3.9.0=16_linux64_mkl + - libcublas=11.10.3.66=0 + - libcufft=10.7.2.124=h4fbf590_0 + - libcufile=1.6.0.25=0 + - libcurand=10.3.2.56=0 + - libcusolver=11.4.0.1=0 + - libcusparse=11.7.4.91=0 + - libffi=3.4.2=h7f98852_5 + - libgcc-ng=12.2.0=h65d4601_19 + - libgfortran-ng=12.2.0=h69a702a_19 + - libgfortran5=12.2.0=h337968e_19 + - libgomp=12.2.0=h65d4601_19 + - libhwloc=2.9.0=hd6dc26d_0 + - libiconv=1.17=h166bdaf_0 + - liblapack=3.9.0=16_linux64_mkl + - liblapacke=3.9.0=16_linux64_mkl + - libnpp=11.7.4.75=0 + - libnsl=2.0.0=h7f98852_0 + - libnvjpeg=11.8.0.2=0 + - libsqlite=3.40.0=h753d276_0 + - libstdcxx-ng=12.2.0=h46fd767_19 + - libuuid=2.32.1=h7f98852_1000 + - libxml2=2.10.3=h7463322_0 + - libzlib=1.2.13=h166bdaf_4 + - llvm-openmp=15.0.7=h0cdce71_0 + - micromamba=1.3.1=0 + - mkl=2022.1.0=h84fe81f_915 + - mkl-devel=2022.1.0=ha770c72_916 + - mkl-include=2022.1.0=h84fe81f_915 + - ncurses=6.3=h27087fc_1 + - openssl=3.0.8=h0b41bf4_0 + - pip=23.0.1=pyhd8ed1ab_0 + - python=3.10.9=he550d4f_0_cpython + - pytorch=1.13.1=py3.10_cuda11.7_cudnn8.5.0_0 + - pytorch-cuda=11.7=h67b0de4_1 + - pytorch-mutex=1.0=cuda + - readline=8.1.2=h0f457ee_0 + - setuptools=67.4.0=pyhd8ed1ab_0 + - tbb=2021.8.0=hf52228f_0 + - tk=8.6.12=h27826a3_0 + - typing_extensions=4.4.0=pyha770c72_0 + - tzdata=2022g=h191b570_0 + - wheel=0.38.4=pyhd8ed1ab_0 + - xz=5.2.6=h166bdaf_0 +prefix: /pasteur/appa/scratch/mambaforge/2023-03-02/envs/py310-pytorch diff --git a/conda-list--explicit.yml b/conda-list--explicit.yml deleted file mode 100644 index 1cddfcaed772a476e7d58b67a6fd094ae33e7451..0000000000000000000000000000000000000000 --- a/conda-list--explicit.yml +++ /dev/null @@ -1,67 +0,0 @@ -# This file may be used to create an environment using: -# $ conda create --name <env> --file <this file> -# platform: linux-64 -@EXPLICIT -https://conda.anaconda.org/nvidia/linux-64/cuda-cupti-11.7.101-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/cuda-nvtx-11.7.91-0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/micromamba-1.3.1-0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda -https://conda.anaconda.org/nvidia/linux-64/cuda-cudart-11.7.99-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/cuda-nvrtc-11.7.99-0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda -https://conda.anaconda.org/nvidia/linux-64/libcublas-11.10.3.66-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/libcufft-10.7.2.124-h4fbf590_0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/libcufile-1.6.0.25-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/libcurand-10.3.2.56-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/libcusolver-11.4.0.1-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/libcusparse-11.7.4.91-0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-12.2.0-h337968e_19.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/libnpp-11.7.4.75-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/libnvjpeg-11.8.0.2-0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/mkl-include-2022.1.0-h84fe81f_915.tar.bz2 -https://conda.anaconda.org/pytorch/noarch/pytorch-mutex-1.0-cuda.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda -https://conda.anaconda.org/nvidia/linux-64/cuda-libraries-11.7.1-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/gds-tools-1.6.0.25-0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-12.2.0-h69a702a_19.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/cuda-runtime-11.7.1-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/cuda-tools-11.7.1-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/cuda-toolkit-11.7.1-0.tar.bz2 -https://conda.anaconda.org/nvidia/linux-64/cuda-11.7.1-0.tar.bz2 -https://conda.anaconda.org/pytorch/noarch/pytorch-cuda-11.7-h67b0de4_1.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_kmp_llvm.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.8-h0b41bf4_0.conda -https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.10.3-h7463322_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-15.0.7-h0cdce71_0.conda -https://conda.anaconda.org/conda-forge/linux-64/readline-8.1.2-h0f457ee_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.9.0-hd6dc26d_0.conda -https://conda.anaconda.org/conda-forge/linux-64/python-3.10.9-he550d4f_0_cpython.conda -https://conda.anaconda.org/conda-forge/noarch/setuptools-67.4.0-pyhd8ed1ab_0.conda -https://conda.anaconda.org/conda-forge/linux-64/tbb-2021.8.0-hf52228f_0.conda -https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.4.0-pyha770c72_0.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/wheel-0.38.4-pyhd8ed1ab_0.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/mkl-2022.1.0-h84fe81f_915.tar.bz2 -https://conda.anaconda.org/conda-forge/noarch/pip-23.0.1-pyhd8ed1ab_0.conda -https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-16_linux64_mkl.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/mkl-devel-2022.1.0-ha770c72_916.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-16_linux64_mkl.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-16_linux64_mkl.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/liblapacke-3.9.0-16_linux64_mkl.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/blas-devel-3.9.0-16_linux64_mkl.tar.bz2 -https://conda.anaconda.org/conda-forge/linux-64/blas-2.116-mkl.tar.bz2 -https://conda.anaconda.org/pytorch/linux-64/pytorch-1.13.1-py3.10_cuda11.7_cudnn8.5.0_0.tar.bz2 diff --git a/runscript.sh b/runscript.sh index ce3b3a9663c2fbae14b3bc7561bd16b6fc938ae8..46158ad91da760a3e0573d470a9a715fb45ffa29 100644 --- a/runscript.sh +++ b/runscript.sh @@ -1,5 +1,4 @@ #!/bin/bash -eval "$(conda shell.bash hook)" && \ -conda activate py310-pytorch-1.13.1 && \ +eval "$(micromamba shell hook -s posix)" && \ +micromamba activate py310-pytorch-1.13.1 && \ "$@" -