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Commit f5f0830c authored by Athanasios Karmas's avatar Athanasios Karmas
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Changes to load tools transparently with the spack env modules and

parametrized even more the path that the JupyterLab kernel will be
created
parent ff3a36f7
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#!/bin/bash
#title :create_JupyterLab_kernel.sh
#description :Script to create a spackified JupyterLab kernel conf and place it to NFS where it can be loaded by all users.
#usage :./create_JupyterLab_kernel.sh $BUILD-ENV
#usage :./create_JupyterLab_kernel.sh $INSTALLATION_ROOT $ENV $LAB_KERNEL_PATH
#==============================================================================
INSTALLATION_ROOT=$1
SPACKIFIED_ENV=$2
CONF_PATH="/srv/jupyterlab_kernels/int/release20210930"
LAB_KERNEL_PATH=$3
# load spack and spack repos
cp -r /srv/$INSTALLATION_ROOT/spack/.spack ~
......@@ -14,26 +14,26 @@ source /srv/$INSTALLATION_ROOT/spack/share/spack/setup-env.sh
spack repo add /srv/$INSTALLATION_ROOT/ebrains-spack-builds
# prepare the env file
mkdir $CONF_PATH/bin
cat <<EOF > $CONF_PATH/bin/env.sh
mkdir $LAB_KERNEL_PATH/bin
cat <<EOF > $LAB_KERNEL_PATH/bin/env.sh
#!/usr/bin/env bash
set -euxo pipefail
EOF
# load here all tools
spack load --sh -r python@3.8.11 py-ipykernel py-pip py-numpy@1.21.0 py-scipy py-pandas py-seaborn py-matplotlib arbor nest@3.0 neuron py-pynn tvb-data tvb-library %gcc@10.3.0 >> $CONF_PATH/bin/env.sh
#spack env activate $SPACKIFIED_ENV --sh >> $CONF_PATH/bin/env.sh
spack load --sh -r python@3.8.11 py-ipykernel py-pip py-numpy@1.21.0 py-scipy py-pandas py-seaborn py-matplotlib arbor nest@3.0 neuron py-pynn tvb-data tvb-library %gcc@10.3.0 >> $LAB_KERNEL_PATH/bin/env.sh
#spack env activate $SPACKIFIED_ENV --sh >> $LAB_KERNEL_PATH/bin/env.sh
# end of env creation
cat <<EOF >>$CONF_PATH/bin/env.sh
cat <<EOF >>$LAB_KERNEL_PATH/bin/env.sh
python -m ipykernel_launcher -f \$@
EOF
chmod +x $CONF_PATH/bin/env.sh
chmod +x $LAB_KERNEL_PATH/bin/env.sh
# create the new kernel's configuration file
mkdir $CONF_PATH/spack_python_kernel_release_20210930
cat <<EOF >$CONF_PATH/spack_python_kernel_release_20210930/kernel.json
mkdir $LAB_KERNEL_PATH/spack_python_kernel_release_20210930
cat <<EOF >$LAB_KERNEL_PATH/spack_python_kernel_release_20210930/kernel.json
{
"argv": ["$CONF_PATH/bin/env.sh", "{connection_file}"],
"argv": ["$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}"],
"display_name": "EBRAINS_release_20210930",
"name": "spack_python_kernel_release_20210930",
"language": "python"
......
......@@ -8,13 +8,17 @@
echo "Setting up environment..."
cp -r /srv/test-build/spack/.spack ~
source /srv/test-build/spack/share/spack/setup-env.sh
INSTALLATION_ROOT="test-build"
SPACKIFIED_ENV="ebrains-spack-builds"
cd /srv/test-build/
cp -r /srv/$INSTALLATION_ROOT/spack/.spack ~
source /srv/$INSTALLATION_ROOT/spack/share/spack/setup-env.sh
cd /srv/$INSTALLATION_ROOT
spack repo add ebrains-spack-builds
spack env activate ebrains-spack-builds
spack env activate $SPACKIFIED_ENV
module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-broadwell/
source /srv/$INSTALLATION_ROOT/spack/var/spack/environments/$SPACKIFIED_ENV/loads
echo "Everything ready!"
#echo "Starting Python..."
#python
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