From 185fa65dcb5e84f3a67c27d0501d54adce19d2ea Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 4 May 2023 13:01:01 +0200
Subject: [PATCH] SCHWED-5907 Fixes for updated OST Singularity image
The following issues were observed:
- warning about non-writable directory which was set as IPYTHONDIR env var
Not very surprising, it's a directory that lives in container space...
- stale kernels
I didn't investigate that one properly. It had something to do with bending
around all Jupyter/IPython relevant directories to custom set directories
in the image. Reason for doing that is potential Python modules that reside
in user home of the host that get imported in the container. I removed the
bending around with the full knowledge that the described problem may occur.
- version updates
Some changes related to different Python versions between old base image
(Ubuntu 20.04) and the new one (Ubuntu 22.04).
---
singularity/Singularity | 35 ++++++-----------------------------
1 file changed, 6 insertions(+), 29 deletions(-)
diff --git a/singularity/Singularity b/singularity/Singularity
index 899e8e54e..1d1a0da33 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -5,18 +5,15 @@ From: registry.scicore.unibas.ch/schwede/openstructure:2.4.0-jammy
# POST
##############################################################################
-
# CHANGE DASH TO BASH
rm /bin/sh
ln -sf /bin/bash /bin/sh
-
# INSTALL SYSTEM DEPS
#####################
-apt-get update -y && apt-get install -y python3-pip
+apt-get update -y && apt-get install -y ipython3 jupyter python3-pip
+pip3 install ipywidgets==7.6.0
pip3 install nglview \
- ipython \
- jupyter \
six
# SET LOCALE
@@ -28,23 +25,9 @@ locale-gen en_US.UTF-8
# SETUP IPYTHON / JUPYTER
#########################
-# As the Singularity mounts $HOME by default Jupyter and Ipython config files
-# are moved to separate directories. Proper environmental variables are also
-# set
-export IPYTHONDIR="/usr/local/share/ipython"
-export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="/tmp/jupyter_runtime"
-
-mkdir -p /usr/local/share/ipython
mkdir -p $JUPYTER_PATH
-mkdir -p $JUPYTER_RUNTIME_DIR
-mkdir -p $JUPYTER_CONFIG_DIR
mkdir -p $JUPYTER_PATH/kernels/ost-kernel
-chmod a+rw -R /usr/local/share/ipython
-chmod a+rw -R $JUPYTER_PATH
-chmod a+rw -R $JUPYTER_CONFIG_DIR
-chmod a+rw -R $JUPYTER_RUNTIME_DIR
cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
{
"display_name": "OST",
@@ -54,7 +37,7 @@ cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
"-m", "ipykernel",
"-f", "{connection_file}",
"--InteractiveShellApp.exec_PYTHONSTARTUP=False",
- "--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.8/site-packages/ost/ost_startup.py']"
+ "--InteractiveShellApp.exec_files=/usr/local/lib64/python3.10/site-packages/ost/ost_startup.py"
],
"env": {
}
@@ -71,10 +54,7 @@ export TEMP="/tmp"
export TEMPDIR="/tmp"
export TMPDIR="/tmp"
export TMP="/tmp"
-export IPYTHONDIR="/usr/local/share/ipython"
-export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="$TMPDIR/jupyter_runtime"
%apprun ChemdictTool
##############################################################################
@@ -173,15 +153,15 @@ goes to CWD. Thus this sould work as expected out of the box.
%appenv IPython
##############################################################################
-# NOTEBOOK ENV
+# IPYTHON ENV
##############################################################################
export DNG_ROOT=$OST_ROOT
-export DNG_INITDIR=${DNG_ROOT}/lib64/python3.8/site-packages/ost
+export DNG_INITDIR=${DNG_ROOT}/lib64/python3.10/site-packages/ost
%apprun IPython
##############################################################################
-# OST IPYTON APP
+# OST IPYTHON APP
##############################################################################
ipython3 -i $DNG_INITDIR/ost_startup.py "$@"
@@ -235,9 +215,6 @@ load all necessary OST components just like in the OST shell. We also enabled
the nglview widget to interactively view molecular structures and trajectories.
For more details on how to use nglview see http://nglviewer.org/nglview/latest/.
-As the Singularity mounts $HOME by default Jupyter and Ipython config files
-are moved to separate directories. Proper environmental variables are also set.
-
To list of all available options:
singularity run --app Notebook <IMAGE> --help
--
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