Initial commit

README.md

+# Walktrought for installing scipion3 on bis.pasteur.fr machines
+
+Feel free to adapt for other setup if needed (maestro, gpulab, ....)
+
+```
+/c7/shared/bin/install-miniconda3-HOME.sh
+source $HOME/bin/enable-miniconda3-HOME.sh
+module add cuda/11.7.0_515.43.04 openmpi/3.1.6-devtoolset-9
+python3 -m pip install scipion-installer
+python3 -m scipioninstaller $HOME/scipion3 -j 4
+$HOME/scipion3/scipion3
+```
+Reference: https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources.html#installing-scipion-v3-0 (2022/06/24)
+
+
+Tru <tru@pasteur.fr>
+

install-miniconda3-HOME.sh

+#!/bin/sh
+PATH=/sbin:/usr/sbin:/usr/bin:/bin
+
+set -e
+set -u
+
+tbindir=$(mktemp -d)
+trap "rm -rf \"$tbindir\"" TERM INT EXIT
+
+export TMPDIR=`mktemp -d /dev/shm/${USER}-XXXXX`
+miniconda3=$HOME/miniconda3
+
+_install() {
+cd $tbindir && \
+curl -qsSLkO https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+&& bash Miniconda3-latest-Linux-x86_64.sh -b -p ${miniconda3} \
+&& rm Miniconda3-latest-Linux-x86_64.sh
+${miniconda3}/bin/conda update conda -y && ${miniconda3}/bin/conda update --all -y
+}
+
+_install
+_o=~/bin/enable-miniconda3-HOME.sh
+[ ! -d ~/bin ] && mkdir -p ~/bin 
+cat <<EOF > ${_o}
+PATH=${miniconda3}/bin:\$PATH
+export PATH
+# do not use ~/.local python
+PYTHONNOUSERSITE=1
+export PYTHONNOUSERSITE
+export CONDA_ROOT=${miniconda3}
+eval "\$(\${CONDA_ROOT}/bin/conda shell.bash hook)"
+EOF
+chmod 755 ${_o}
+
+echo "${_o} created, to activate this conda installation:"
+echo "source ${_o}"
+

transcript.log

+1) install miniconda3 (using x86_64 linux version here)
+```
+[tru@ld21-1022 ~]$ /c7/shared/bin/install-miniconda3-HOME.sh
+PREFIX=/c7/home/tru/miniconda3
+Unpacking payload ...
+Collecting package metadata (current_repodata.json): done
+Solving environment: done
+
+<...>
+Preparing transaction: done
+Verifying transaction: done
+Executing transaction: done
+/c7/home/tru/bin/enable-miniconda3-HOME.sh created, to activate this conda
+installation:
+source /c7/home/tru/bin/enable-miniconda3-HOME.sh
+```
+
+2) enable miniconda3 enable the required modules and install scipion-installer
+
+You have the choice for openmi and cuda variants... just use a recent enough gcc suite
+compiled openmpi version.
+
+```
+[tru@ld21-1022 ~]$ source $HOME/bin/enable-miniconda3-HOME.sh
+(base) [tru@ld21-1022 ~]$ module add cuda/11.7.0_515.43.04 openmpi/3.1.6-devtoolset-9
+
+(base) [tru@ld21-1022 ~]$ module li
+Currently Loaded Modulefiles:
+  1) slurm/current                2) scl/devtoolset-9             3) openmpi/3.1.6-devtoolset-9   4) cuda/11.7.0_515.43.04
+
+(base) [tru@ld21-1022 ~]$ conda env list
+# conda environments:
+#
+base                  *  /c7/home/tru/miniconda3
+
+(base) [tru@ld21-1022 ~]$ python3 -m pip install scipion-installer
+<skipped>
+```
+3) install scipion3 as stated in the doc
+```
+(base) [tru@ld21-1022 ~]$ python3 -m scipioninstaller $HOME/scipion3 -j 4
+conda detected. Favouring it. If you want a virtualenv installation cancel installation and pass -venv .
+Collecting package metadata (current_repodata.json): done
+Solving environment: done
+<skipped>
+  ********************************************
+  *                                          *
+  *  Xmipp has been successfully installed!  *
+  *                                          *
+  ********************************************
+
+
+/c7/home/tru/scipion3/software/em/xmippSrc-v3.22.04.0
+cd /c7/home/tru/scipion3/software/em/xmippSrc-v3.22.04.0
+find /c7/home/tru/scipion3/software/em/xmipp/bindings/python -maxdepth 1 -mindepth 1 ! -name __pycache__ -exec ln -srfn {} /c7/home/tru/scipion3/software/bindings \; && ln -srfn /c7/home/tru/scipion3/software/em/xmipp/lib/libXmippCore.so /c7/home/tru/scipion3/software/lib && touch bindings_linked && rm installation_finished 2> /dev/null
+cd /c7/home/tru/scipion3/software/em/
+Link 'xmippSrc-3.22.04.0 -> xmippSrc-v3.22.04.0'
+Created link: 'xmippSrc-3.22.04.0 -> xmippSrc-v3.22.04.0'
+Done (9 m 52 s)
+
+ ______________________________________________________________________________
+|                                                                              |
+| Installation successfully finished!! Happy EM processing!!                   |
+ ______________________________________________________________________________
+
+  You can launch Scipion using the launcher at: /c7/home/tru/scipion3/scipion3
+ ______________________________________________________________________________
+(base) [tru@ld21-1022 ~]$
+```
+4) enjoy
+```
+$HOME/scipion3/scipion3
+```