README.md

@@ -6,4 +6,12 @@ tunnel set-up, and start the client application on your local system.
 
 As bash scripts they run natively on Linux, MacOS, and other Unix-like
 systems. After installing WSL (Windows Subsystem for Linux), they also run
-on Microsoft Windows 10.
\ No newline at end of file
+on Microsoft Windows 10.
+
+## start-jupyter
+
+The script is being modified to allow further features:
+
+* connecting to different DKRZ systems: mistral, vader, levante (?)
+* start jupyter notebooks in singularity containers 
+

start-jupyter

@@ -43,6 +43,8 @@
 #
 # In case of problems contact Mathis Rosenhauer <rosenhauer@dkrz.de>.
 #
+# 2020, Oct. 7, S. Bendoukha, added support for singularity containers.
+# 2021, Apr. 14, S. Bendoukha, added option to specify frontend.
 
 set -eufo pipefail
 
@@ -91,8 +93,18 @@ SJ_INCFILE=""
 #
 # Must be directly accessible from client. The frontend and the node
 # where jupyter is running need a shared home file system.
-readonly SJ_FRONTEND_HOST="mistralpp.dkrz.de"
+SJ_FRONTEND_HOST="mistralpp.dkrz.de"
 
+# Image
+#
+# start the jupyter notebook in a singularity container from a given 
+# image name.
+SJ_IMAGE=""
+
+# Slurm Options
+# additional slurm options that users 
+# can pass to the sbatch script
+SJ_SLURM_OPTIONS=""
 
 function clean_up () {
     trap - ERR EXIT
@@ -131,18 +143,22 @@ Available values for OPTION include:
   -A acctcode    start a job with acctcode
   -c command     invoke jupyter with command
   -d             check for presence of jupyter
+  -f system      mistral, vader
   -i file        source file prior to running jupyter
+  -o options     slurm options
   -n ntasks      request ntasks tasks for job
   -p partition   run job on partition
+  -s image       singularity image
   -t time        job runtime
   -u username    use username for login
+  
 
 EOF
 }
 
 function parse_options () {
     local option
-    while getopts 'A:c:di:n:p:t:u:' option; do
+    while getopts 'A:c:di:o:f:n:p:t:u:s:' option; do
         case ${option} in
             A) SJ_ACCTCODE="$OPTARG"
                ;;
@@ -150,12 +166,18 @@ function parse_options () {
                ;;
             d) SJ_DEBUG=1
                ;;
+            f) SJ_FRONTEND_HOST="$OPTARG"
+               ;;
             i) SJ_INCFILE="$OPTARG"
                ;;
+            o) SJ_SLURM_OPTIONS="$OPTARG"
+               ;;
             n) SJ_NTASKS="$OPTARG"
                ;;
             p) SJ_PARTITION="$OPTARG"
                ;;
+            s) SJ_IMAGE="$OPTARG"
+               ;;
             t) SJ_RUNTIME="$OPTARG"
                ;;
             u) SJ_USERNAME="$OPTARG"
@@ -173,6 +195,9 @@ function parse_options () {
     readonly SJ_PARTITION
     readonly SJ_RUNTIME
     readonly SJ_USERNAME
+    readonly SJ_IMAGE
+    readonly SJ_FRONTEND_HOST
+    readonly SJ_SLURM_OPTIONS
 }
 
 function ssh_frontend () {
@@ -196,7 +221,7 @@ function source_incfile() {
         fi
         commandline="source ${incfile}; ${commandline}"
     else
-        commandline="module load python3/unstable; ${commandline}"
+        commandline="module use /sw/spack-rhel6/spack/modules/linux-rhel6-haswell/; module load python3/unstable; ${commandline}"
     fi
     echo "${commandline}"
 }
@@ -206,16 +231,19 @@ 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 --nv ${SJ_IMAGE} ${commandline}"
+    fi 
     commandline="$(source_incfile "${commandline}")"
     echo "${commandline}"
 }
@@ -233,7 +261,8 @@ function submit_jupyter_job () {
 #SBATCH --account=${SJ_ACCTCODE}
 #SBATCH --output=/dev/null
 #SBATCH --parsable
-#SBATCH --dkrzepilog=0
+#SBATCH ${SJ_SLURM_OPTIONS}
+##SBATCH --dkrzepilog=0
 cd \${HOME}
 echo "NODE:\${SLURM_JOB_NODELIST}" > ${logfile}
 ${commandline}