Singularity/warp の変更点

• 追加された行はこの色です。
• 削除された行はこの色です。
• Singularity/warp へ行く。
• Singularity/warp の差分を削除

#author("2026-07-07T12:20:01+00:00","default:sysosa","sysosa")
#author("2026-07-07T12:21:20+00:00","default:sysosa","sysosa")
CentOS7でwarpが動かなかったので作った

定義ファイルを下記のようにしてます

「warp=2.0.0dev36」とバージョン指定を行ってます。
ほかのversionらは [[https://anaconda.org/channels/warpem/packages/warp/overview>+https://anaconda.org/channels/warpem/packages/warp/overview]] で確認できます

#code(nonumber){{
Bootstrap: docker
From: nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04

%post
    apt-get update
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
        wget bzip2 ca-certificates git \
        libglib2.0-0 libxext6 libsm6 libxrender1 \
        libgl1 libgomp1 \
        && apt-get clean

    wget -O /tmp/Miniforge3.sh \
        https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
    bash /tmp/Miniforge3.sh -b -p /opt/conda
    . /opt/conda/etc/profile.d/conda.sh

    conda create -y -n warp \
        warp=2.0.0dev36 \
        -c warpem \
        -c nvidia/label/cuda-11.8.0 \
        -c pytorch \
        -c conda-forge

    conda clean -afy

%environment
    export PATH=/opt/conda/envs/warp/bin:/opt/conda/bin:$PATH
    export LD_LIBRARY_PATH=/opt/conda/envs/warp/lib:$LD_LIBRARY_PATH

%runscript
    exec "$@"
}}


っで
#code(nonumber){{
[root@centos7 ~]# apptainer build warp.sif warp.def
 :
 :
[root@centos7 ~]# ls -lh warp.*
-rw-r--r--. 1 root root 865 Jul  4 02:27 warp.def
-rwxr-xr-x. 1 root root 10G Jul  4 02:58 warp.sif

[root@centos7 ~]#
}}
と「warp.sif」を得ました

使いかとしては
#code(nonumber){{
[saber@centos7 ~]$ apptainer exec --nv /apps/warp.sif WarpTools --help

[saber@centos7 ~]$ apptainer exec --nv /apps/warp.sif MTools --help
}}


***imodとaretomo3も加える [#j845009e]

AreTomo3に既に構築版があったのでそれを採用した
IMODは今時点での最新を取得

コンテナはcuda12.4にしてます。恐らくは前述のcuda-11.8でもいいのかなと思いますが.

#code(nonumber){{
Bootstrap: docker
From: nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04

%post
    apt-get update
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
        wget bzip2 ca-certificates git \
        libglib2.0-0 libxext6 libsm6 libxrender1 \
        libgl1 libgomp1 default-jre libtiff-dev unzip tar \
        && apt-get clean

    wget -O /tmp/Miniforge3.sh \
        https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
    bash /tmp/Miniforge3.sh -b -p /opt/conda
    . /opt/conda/etc/profile.d/conda.sh

    conda create -y -n warp \
        warp=2.0.0dev36 \
        -c warpem \
        -c nvidia/label/cuda-11.8.0 \
        -c pytorch \
        -c conda-forge

    #conda clean -afy
    wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_5.1.12_RHEL7-64_CUDA12.0.sh --no-check-certificate
    bash imod_5.1.12_RHEL7-64_CUDA12.0.sh -dir /opt -script /opt -yes
    rm -f imod_5.1.12_RHEL7-64_CUDA12.0.sh

    wget -O /tmp/aretomo3.zip \
        https://github.com/czimaginginstitute/AreTomo3/releases/download/v2.2.2/AreTomo3_2.2.2_07-11-2025.zip
    mkdir /opt/AreTomo3
    cd /opt/AreTomo3
    unzip /tmp/aretomo3.zip
    ln -s AreTomo3_2.2.2_07-11-2025 AreTomo3
    ln -s AreTomo3_2.2.2_07-11-2025 aretomo3
    ln -s AreTomo3_2.2.2_07-11-2025 aretomo

    rm -f /tmp/Miniforge3.sh /tmp/imod.sh /tmp/aretomo3.zip
    rm -f /tmp/Miniforge3.sh /tmp/aretomo3.zip

%environment
    export PATH=/opt/conda/envs/warp/bin:/opt/conda/bin:/opt/imod_5.1.12/bin:/opt/AreTomo3:$PATH
    export LD_LIBRARY_PATH=/opt/conda/envs/warp/lib:/opt/imod_5.1.12/lib:$LD_LIBRARY_PATH
    export IMOD_DIR=/opt/imod_5.1.12
    export IMOD_QTLIBDIR=/opt/imod_5.1.12/qtlib
    export IMOD_PLUGIN_DIR=/opt/imod_5.1.12/lib/imodplug
    export IMOD_CALIB_DIR=/opt/imod_5.1.12/autodoc

%runscript
    exec "$@"
}}