From 00122d9289049c7150f9fc8b65e80e30145ad0b2 Mon Sep 17 00:00:00 2001 From: Tru Huynh <tru@pasteur.fr> Date: Thu, 2 Mar 2023 18:11:53 +0100 Subject: [PATCH] fix micromamna --no-deps --- Dockerfile | 10 ++++++---- Singularity | 9 ++++++--- runscript.sh | 1 + 3 files changed, 13 insertions(+), 7 deletions(-) diff --git a/Dockerfile b/Dockerfile index b190ef0..3732d49 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,11 +7,13 @@ RUN apt-get update && \ DEBIAN_FRONTEND=noninteractive apt-get -y autoremove && \ DEBIAN_FRONTEND=noninteractive apt-get -y clean autoclean -RUN eval "$(micromamba shell hook -s posix )" && \ - micromamba update micromamba && \ - micromamba upgrade --all -y && \ +RUN export MAMBA_ROOT_PREFIX=/opt/conda && \ + eval "$(micromamba shell hook -s posix )" && \ + micromamba update -q -y micromamba -c conda-forge -p ${MAMBA_ROOT_PREFIX} && \ + micromamba update -q -y --all -c conda-forge -p ${MAMBA_ROOT_PREFIX} && \ + mkdir -p ${MAMBA_ROOT_PREFIX}/envs && \ curl https://gitlab.pasteur.fr/tru/micromamba-py310-pytorch-cuda11.7/-/raw/main/conda-env-export.yml > conda-env-export.yml && \ - micromamba create --name py310-pytorch-1.13.1 --file conda-env-export.yml && \ + micromamba create -y --no-deps --name py310-pytorch-1.13.1 --file conda-env-export.yml && \ micromamba activate py310-pytorch-1.13.1 && \ micromamba env export > /conda-env-export.yml diff --git a/Singularity b/Singularity index 07413fe..38d72cc 100644 --- a/Singularity +++ b/Singularity @@ -9,15 +9,18 @@ DEBIAN_FRONTEND=noninteractive apt-get -y upgrade && \ DEBIAN_FRONTEND=noninteractive apt-get -y autoremove && \ DEBIAN_FRONTEND=noninteractive apt-get -y clean autoclean +export MAMBA_ROOT_PREFIX=/opt/conda && \ eval "$(micromamba shell hook -s posix )" && \ -micromamba update micromamba && \ -micromamba upgrade --all -y && \ +micromamba update -q -y micromamba -c conda-forge -p ${MAMBA_ROOT_PREFIX} && \ +micromamba update -q -y --all -c conda-forge -p ${MAMBA_ROOT_PREFIX} && \ +mkdir -p ${MAMBA_ROOT_PREFIX}/envs && \ curl https://gitlab.pasteur.fr/tru/micromamba-py310-pytorch-cuda11.7/-/raw/main/conda-env-export.yml > conda-env-export.yml && \ -micromamba create --name py310-pytorch-1.13.1 --file conda-env-export.yml && \ +micromamba create -y --no-deps --name py310-pytorch-1.13.1 --file conda-env-export.yml && \ micromamba activate py310-pytorch-1.13.1 && \ micromamba env export > /conda-env-export.yml %post +export MAMBA_ROOT_PREFIX=/opt/conda && \ eval "$(micromamba shell hook -s posix )" && \ micromamba activate py310-pytorch-1.13.1 && \ "$@" diff --git a/runscript.sh b/runscript.sh index 46158ad..4bff4d0 100644 --- a/runscript.sh +++ b/runscript.sh @@ -1,4 +1,5 @@ #!/bin/bash +export MAMBA_ROOT_PREFIX=/opt/conda && \ eval "$(micromamba shell hook -s posix)" && \ micromamba activate py310-pytorch-1.13.1 && \ "$@" -- GitLab