From 257a7389cf5064bf0d77e2aa1205a59e344e1754 Mon Sep 17 00:00:00 2001
From: Sofiane Bendoukha <bendoukha@dkrz.de>
Date: Wed, 7 Oct 2020 13:45:33 +0200
Subject: [PATCH] Added first support for singularity.
---
start-jupyter | 19 ++++++++++++++++---
1 file changed, 16 insertions(+), 3 deletions(-)
diff --git a/start-jupyter b/start-jupyter
index 55e0587..37baed4 100755
--- a/start-jupyter
+++ b/start-jupyter
@@ -93,6 +93,11 @@ SJ_INCFILE=""
# where jupyter is running need a shared home file system.
readonly SJ_FRONTEND_HOST="mistralpp.dkrz.de"
+# Image
+#
+# start the jupyter notebook in a singularity container from a given
+# image name.
+SJ_IMAGE=""
function clean_up () {
trap - ERR EXIT
@@ -136,13 +141,14 @@ Available values for OPTION include:
-p partition run job on partition
-t time job runtime
-u username use username for login
+ -s image singularity image
EOF
}
function parse_options () {
local option
- while getopts 'A:c:di:n:p:t:u:' option; do
+ while getopts 'A:c:di:n:p:t:u:s:' option; do
case ${option} in
A) SJ_ACCTCODE="$OPTARG"
;;
@@ -160,6 +166,8 @@ function parse_options () {
;;
u) SJ_USERNAME="$OPTARG"
;;
+ s) SJ_IMAGE="$OPTARG"
+ ;;
?) usage
exit 1
;;
@@ -173,6 +181,7 @@ function parse_options () {
readonly SJ_PARTITION
readonly SJ_RUNTIME
readonly SJ_USERNAME
+ readonly SJ_IMAGE
}
function ssh_frontend () {
@@ -206,16 +215,19 @@ function which_jupyter() {
local which
which="$(source_incfile "which jupyter")"
ssh_frontend "/bin/bash -lc \"${which}\""
-}
+}
function assemble_commandline () {
local logfile="$1"
- local commandline="jupyter ${SJ_COMMAND} --no-browser 2>> ${logfile}"
+ local commandline="jupyter ${SJ_COMMAND} --no-browser 2>> ${logfile}"
# If we are not running a job, we have to perform our own scheduling
if [[ -z ${SJ_ACCTCODE} ]]; then
commandline="nohup ${commandline} > /dev/null & echo \$!"
fi
+ if [[ -n ${SJ_IMAGE} ]]; then
+ commandline="singularity exec ${SJ_IMAGE} ${commandline}"
+ fi
commandline="$(source_incfile "${commandline}")"
echo "${commandline}"
}
@@ -342,6 +354,7 @@ function main () {
trap clean_up INT QUIT TERM ERR EXIT
echo "Establishing ssh master connection."
+ set -x
# Set up control master for connection sharing
mkdir -p "${HOME}/.ssh"
ssh_socket_dir="$(mktemp -d "${HOME}/.ssh/socket.XXXXX")"
--
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