本家様 http://scipion.i2pc.es/
scipionがver3になりました

[root@centos7 ~]# yum groupinstall "Development Tools"
[root@centos7 ~]# yum install epel-release
[root@centos7 ~]# yum install libzstd-devel hdf5-devel
[root@centos7 ~]# yum install python3-devel python3-tkinter openmpi-devel \
                              wget fftw-devel libtiff-devel java-1.8.0-openjdk-devel libjpeg-turbo-devel sqlite-devel 
 
[root@centos7 ~]#  

「pip3 install scipion-installer」は「~/.cache/pip/http」に収まる

[root@centos7 ~]# python3 -m scipioninstaller --help
usage: installscipion [-h] [-conda] [-venv] [-dev] [-noXmipp] [-j J] [-dry]
                      [-httpsClone] [-noAsk] [-n N] [-sciBranch SCIBRANCH]
                      [-xmippBranch XMIPPBRANCH] [-scratchPath SCRATCHPATH]
                      path
 
Installs scipion3 in a conda or virtualenv environment. Check all parameters
bellow for a custom installation. If there are issues initializing conda you
can set CONDA_ACTIVATION_CMD variable and it will be used instead of guessing.
Typical values are . "/path/to/miniconda3/etc/profile.d/conda.sh" or eval
"$(/path/to/miniconda3/bin/conda shell.bash hook)"
 
positional arguments:
  path                  Location where you want scipion to be installed.
 
optional arguments:
  -h, --help            show this help message and exit
  -conda                Force conda as environment manager, otherwise will use
                        conda anyway if found in the path, else: virtualenv.
  -venv                 Force virtualenv as environment manager, otherwise
                        will use conda if found in the path, otherwise:
                        virtualenv.
  -dev                  installs components in devel mode
  -noXmipp              Xmipp is installed in devel mode under xmipp-bundle
                        dir by default. This flag skips the Xmipp
                        installation.
  -j J                  Number of processors, Xmipp may take a while...
  -dry                  Just shows the commands without running them.
  -httpsClone           Only when -dev is active, makes git clones using https
                        instead of ssh
  -noAsk                try to install scipion ignoring some control questions
                        in that process. You must make sure to write the
                        correct path where Scipion will be installed
  -n N                  Name of the virtual environment. By default, if this
                        parameter is not passed, the name will be scipion3
  -sciBranch SCIBRANCH  Name of the branch of scipion repos to clone when -dev
                        is passed.
  -xmippBranch XMIPPBRANCH
                        Name of the branch of xmipp repos to clone when -dev
                        is passed.
  -scratchPath SCRATCHPATH
                        Path to a folder working at high speed(like SSDs) to
                        be used temporarily during processing.
 
Happy Scipioning!
[root@centos7 ~]#

venv

[root@centos7 ~]# pip3 install scipion-installer
[root@centos7 ~]# python3 -m scipioninstaller /apps/scipion -j 4

conda

(git clone https://github.com/yyuu/pyenv.git /apps/pyenv)
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
eval "$(pyenv init - --no-rehash)"
 
(pyenv install anaconda3-5.3.1)
(pyenv global anaconda3-5.3.1)
 
export PATH=$PYENV_ROOT/versions/anaconda3-5.3.1/bin/:$PATH
(conda update conda)
 
[root@centos7 ~]# which pip3
/apps/pyenv/versions/anaconda3-5.3.1/bin/pip3
 
[root@centos7 ~]# pip3 install scipion-installer
 
[root@centos7 ~]# python3 -m scipioninstaller -conda -j 4 /apps/scipion
Collecting package metadata (current_repodata.json): done
Solving environment: done
 
## Package Plan ##
 
  environment location: /apps/pyenv/versions/anaconda3-5.3.1/envs/scipion3
 
  added / updated specs:
    - python=3.8
 :
#
# To activate this environment, use
#
#     $ conda activate scipion3
#
# To deactivate an active environment, use
#
#     $ conda deactivate
 :
 :
[root@centos7 ~]#

めも:
cuda-11.2には未対応. 「nvcc --version」の出力値を使ってインストールを行っているのだが、
そのパース機能が 10.2 までは対応済み. それ以降はエラーを吐くので無理っぽい


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Last-modified: 2021-04-16 (金) 03:39:20 (67d)