From f5f0830c4aef8cb63545b6845b95538ed9457138 Mon Sep 17 00:00:00 2001
From: Athanasios Karmas <karmas@athenarc.gr>
Date: Tue, 21 Sep 2021 09:23:54 +0000
Subject: [PATCH] Changes to load tools transparently with the spack env
modules and parametrized even more the path that the JupyterLab kernel will
be created
---
create_JupyterLab_kernel.sh | 22 +++++++++++-----------
load_sim_tools.sh | 16 ++++++++++------
2 files changed, 21 insertions(+), 17 deletions(-)
diff --git a/create_JupyterLab_kernel.sh b/create_JupyterLab_kernel.sh
index f4dd73aa..f553a147 100644
--- a/create_JupyterLab_kernel.sh
+++ b/create_JupyterLab_kernel.sh
@@ -1,12 +1,12 @@
#!/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"
diff --git a/load_sim_tools.sh b/load_sim_tools.sh
index e515b407..52765ec7 100644
--- a/load_sim_tools.sh
+++ b/load_sim_tools.sh
@@ -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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