Singularity/warp をテンプレートにして作成
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開始行:
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/...
#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...
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:$...
export LD_LIBRARY_PATH=/opt/conda/envs/warp/lib:$LD_L...
%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 War...
[saber@centos7 ~]$ apptainer exec --nv /apps/warp.sif MTo...
}}
***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...
#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...
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...
bash imod_5.1.12_RHEL7-64_CUDA12.0.sh -dir /opt -scri...
rm -f imod_5.1.12_RHEL7-64_CUDA12.0.sh
wget -O /tmp/aretomo3.zip \
https://github.com/czimaginginstitute/AreTomo3/re...
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/aretomo3.zip
%environment
export PATH=/opt/conda/envs/warp/bin:/opt/conda/bin:/...
export LD_LIBRARY_PATH=/opt/conda/envs/warp/lib:/opt/...
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 "$@"
}}
終了行:
CentOS7でwarpが動かなかったので作った
定義ファイルを下記のようにしてます
「warp=2.0.0dev36」とバージョン指定を行ってます。
ほかのversionらは [[https://anaconda.org/channels/warpem/...
#code(nonumber){{
Bootstrap: docker
From: nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04
%post
apt-get update
DEBIAN_FRONTEND=noninteractive apt-get install -y \
wget bzip2 ca-certificates git \
libglib2.0-0 libxext6 libsm6 libxrender1 \
libgl1 libgomp1 \
&& apt-get clean
wget -O /tmp/Miniforge3.sh \
https://github.com/conda-forge/miniforge/releases...
bash /tmp/Miniforge3.sh -b -p /opt/conda
. /opt/conda/etc/profile.d/conda.sh
conda create -y -n warp \
warp=2.0.0dev36 \
-c warpem \
-c nvidia/label/cuda-11.8.0 \
-c pytorch \
-c conda-forge
conda clean -afy
%environment
export PATH=/opt/conda/envs/warp/bin:/opt/conda/bin:$...
export LD_LIBRARY_PATH=/opt/conda/envs/warp/lib:$LD_L...
%runscript
exec "$@"
}}
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 War...
[saber@centos7 ~]$ apptainer exec --nv /apps/warp.sif MTo...
}}
***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...
#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...
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...
bash imod_5.1.12_RHEL7-64_CUDA12.0.sh -dir /opt -scri...
rm -f imod_5.1.12_RHEL7-64_CUDA12.0.sh
wget -O /tmp/aretomo3.zip \
https://github.com/czimaginginstitute/AreTomo3/re...
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/aretomo3.zip
%environment
export PATH=/opt/conda/envs/warp/bin:/opt/conda/bin:/...
export LD_LIBRARY_PATH=/opt/conda/envs/warp/lib:/opt/...
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 "$@"
}}
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