Singularity/eman をテンプレートにして作成
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開始行:
EMAN-1.9をSingularityで用意してみる
EMANは既に[[EMAN2.91>EMAN2]]とか進んでいるのですが、昔のE...
っが、そのための計算機を用意すするのは微妙で、コンテナ技...
#code(nonumber){{
[illya@rockylinux ~]$ sudo singularity build --sandbox em...
[illya@rockylinux ~]$ sudo singularity shell --writable e...
Singularity> yum install fftw2-devel cmake gsl-devel libp...
Singularity> mkdir -p /apps/src
Singularity> cd /apps/src/
Singularity> tar xf ~/eman-src-1.9.tar2.gz
Singularity> cd eman/
Singularity> mkdir build
Singularity> cd build
Singularity> cmake -DEMAN_INSTALL_PREFIX=/apps/eman ..
Singularity> make
Singularity> make install
[illya@rockylinux ~]$ sudo vi eman/environment
#!/bin/sh
# Custom environment shell code should follow
export PATH=/apps/eman/bin:$PATH
export EMANDIR=/apps/eman
export LD_LIBRARY_PATH=/apps/eman/lib
[illya@rockylinux ~]$
}}
使ってみる
#code(nonumber){{
[illya@rockylinux ~]$ singularity shell eman
Singularity>
Singularity> eman
}}
sifを作ってみる
#code(nonumber){{
[illya@rockylinux ~]$ cat eman.def
BootStrap: docker
From: spack/centos6:latest
%files
/Public/em/eman-src-1.9.tar2.gz /usr/src
%post
yum install fftw2-devel cmake gsl-devel libpng-devel li...
mkdir -p /apps/src
cd /apps/src
tar xf /usr/src/eman-src-1.9.tar2.gz
cd eman
mkdir build
cd build
cmake -DEMAN_INSTALL_PREFIX=/apps/EMAN ..
make
make install
%environment
export PATH=/apps/EMAN/bin:$PATH
export LD_LIBRARY_PATH=/apps/EMAN/lib:$LD_LIBRARY_PATH
export EMANDIR=/apps/EMAN
[illya@rockylinux ~]$
[illya@rockylinux ~]$ singularity build -f eman-1.9.sif e...
[illya@rockylinux ~]$ ls -lh eman-1.9.sif
-rwxr-xr-x. 1 illya illya 300M Jul 8 05:50 eman-1.9.sif ...
[illya@rockylinux ~]$
[illya@rockylinux ~]$ singularity shell eman-1.9.sif
Singularity> eman
EMAN 1.9 ($Date: 2009/02/18 05:12:22 $).
Run 'eman help' for detailed help.
Singularity>
}}
&ref(2022y07m08d_055211977.png,nolink);
終了行:
EMAN-1.9をSingularityで用意してみる
EMANは既に[[EMAN2.91>EMAN2]]とか進んでいるのですが、昔のE...
っが、そのための計算機を用意すするのは微妙で、コンテナ技...
#code(nonumber){{
[illya@rockylinux ~]$ sudo singularity build --sandbox em...
[illya@rockylinux ~]$ sudo singularity shell --writable e...
Singularity> yum install fftw2-devel cmake gsl-devel libp...
Singularity> mkdir -p /apps/src
Singularity> cd /apps/src/
Singularity> tar xf ~/eman-src-1.9.tar2.gz
Singularity> cd eman/
Singularity> mkdir build
Singularity> cd build
Singularity> cmake -DEMAN_INSTALL_PREFIX=/apps/eman ..
Singularity> make
Singularity> make install
[illya@rockylinux ~]$ sudo vi eman/environment
#!/bin/sh
# Custom environment shell code should follow
export PATH=/apps/eman/bin:$PATH
export EMANDIR=/apps/eman
export LD_LIBRARY_PATH=/apps/eman/lib
[illya@rockylinux ~]$
}}
使ってみる
#code(nonumber){{
[illya@rockylinux ~]$ singularity shell eman
Singularity>
Singularity> eman
}}
sifを作ってみる
#code(nonumber){{
[illya@rockylinux ~]$ cat eman.def
BootStrap: docker
From: spack/centos6:latest
%files
/Public/em/eman-src-1.9.tar2.gz /usr/src
%post
yum install fftw2-devel cmake gsl-devel libpng-devel li...
mkdir -p /apps/src
cd /apps/src
tar xf /usr/src/eman-src-1.9.tar2.gz
cd eman
mkdir build
cd build
cmake -DEMAN_INSTALL_PREFIX=/apps/EMAN ..
make
make install
%environment
export PATH=/apps/EMAN/bin:$PATH
export LD_LIBRARY_PATH=/apps/EMAN/lib:$LD_LIBRARY_PATH
export EMANDIR=/apps/EMAN
[illya@rockylinux ~]$
[illya@rockylinux ~]$ singularity build -f eman-1.9.sif e...
[illya@rockylinux ~]$ ls -lh eman-1.9.sif
-rwxr-xr-x. 1 illya illya 300M Jul 8 05:50 eman-1.9.sif ...
[illya@rockylinux ~]$
[illya@rockylinux ~]$ singularity shell eman-1.9.sif
Singularity> eman
EMAN 1.9 ($Date: 2009/02/18 05:12:22 $).
Run 'eman help' for detailed help.
Singularity>
}}
&ref(2022y07m08d_055211977.png,nolink);
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