Lumi container

Documentation/sphinx/hpcusage.rst

@@ -0,0 +1,14 @@
+Usage in HPC environment
+========================
+
+
+LUMI Container
+--------------
+Script for building and running a container on LUMI can be found in ``containerization/lumi_container.sh``. 
+
+Simply execute the bash script to build the container, afterwards the same script can be used for launching the container.
+
+Before building the container set the python version for the container export the environment variable ``PY_VERSION``, which defaults to ``PY_VERSION="3.12"``.
+
+For binding folders into the container, set the environment variable ``SINGULARITY_BIND`` before running the container. For example,  ``export SINGULARITY_BIND="/opt,/data:/mnt"``, this will bind /opt to /opt and /data to /mnt in the container.
+For more information on singularity usage, see https://docs.sylabs.io/guides/3.0/user-guide/index.html

Documentation/sphinx/index.rst

@@ -24,6 +24,7 @@ analysator documentation
    analysator
    analysator_exercises
    analysator_supported
+   hpcusage
 
 .. toctree::
    :maxdepth: 2 

containerization/lumi_container.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+#Make container.def
+#Usage:
+# Simply run this bash script to build the container, be sure to export PY_VERSION to set the python version desired, for example PY_VERSION=3.12
+# After building one can run the script again to launch the container, alternatively call the .sif file directly with singularity
+# For binding folders export SINGULARITY_BIND see for example below in # Running:
+
+if [[ "$PY_VERSION" ]]; then
+  PY_PACKAGE=$(echo "$PY_VERSION" | sed 's/\.//g' )
+else
+  PY_VERSION="3.12"
+  PY_PACKAGE="312"
+fi
+
+if [ ! -f ./container.sif ]; then 
+  cat << EOF > container.def
+Bootstrap: docker
+From: docker.io/opensuse/leap:15.6
+
+%post
+   # Continue to install software into the container normally.
+   # Building:
+       # module load LUMI systools
+       # singularity build container.sif container.def
+   # Running:
+       # For example launching python (one can also launch bash for example)
+       # singularity exec container.sif python
+       # to bind folders once can use --bind /opt,/data:/mnt
+       # this will bind /opt to /opt and /data to /mnt, alternatively one can use environment variables
+       # export SINGULARITY_BIND="/opt,/data:/mnt"
+
+        zypper -n --no-gpg-checks install python$PY_PACKAGE python$PY_PACKAGE-pip python$PY_PACKAGE-setuptools python$PY_PACKAGE-devel git
+
+        update-alternatives --install /usr/bin/python python /usr/bin/python$PY_VERSION 3
+        update-alternatives --install /usr/bin/python3 python3 /usr/bin/python$PY_VERSION 3
+        update-alternatives --install /usr/bin/pip pip /usr/bin/pip$PY_VERSION 3
+        update-alternatives --install /usr/bin/pip3 pip3 /usr/bin/pip$PY_VERSION 3
+
+        export PYTHONNOUSERSITE=1
+        pip install --extra-index-url https://version.helsinki.fi/api/v4/projects/5244/packages/pypi/simple vlsvrs
+        pip install --editable git+"https://github.com/fmihpc/analysator#egg=analysator"
+EOF
+
+  #Build the container
+  module load LUMI systools
+  singularity build container.sif container.def
+else
+  export PYTHONNOUSERSITE=1
+  if [[ ! $SINGULARITY_BIND ]]; then
+     echo "Friendly reminder: no folders binded to the container, please use SINGULARITY_BIND environment variable"
+  fi 
+  singularity exec container.sif bash
+fi
+
+
+