Felix issue106 hpc modules for juwels

Setup for HPC systems JUWELS and HDFML

HPC_setup/create_runscripts_HPC.sh

+#!/bin/csh -x
+
+# __author__ = Felix Kleinert
+# __date__  = '2020-04-30'
+# This script creates run scripts for JUWELS or HDFML
+
+# When you call this script directly you can use
+#   $1 which has to be `juwels' or `hdfml'.
+#   $2 which is the path where the run scripts should be stored
+
+if [[ $1 != '' ]]; then
+  hpcsys=$1
+else
+  if [[ $HOSTNAME == *"juwels"* ]]; then
+    hpcsys="juwels"
+  elif [[ $HOSTNAME == *"hdfml"* ]]; then
+    hpcsys="hdfml"
+  else
+     echo  "Unknown hpc host \`$HOSTNAME\`. Pass 'juwels' or 'hdfml' as first argument."
+     exit
+  fi
+fi
+
+if [[ $2 != '' ]]; then
+  cur=$2
+else
+  cur=$PWD
+fi
+
+echo "############################################################"
+echo "#                                                          #"
+echo "#            user interaction required                     #"
+echo "#                                                          #"
+echo "############################################################"
+echo 
+
+echo "This script creates the HPC batch scripts to run mlt on compute nodes on JUWELS or hdfml."
+echo "You can modify the created run scripts afterwards if needed."
+
+echo
+echo
+echo "Creating run script for $hpcsys:"
+echo
+
+budget=''
+while [[ $budget == '' ]]
+do
+ echo
+ read -p "Enter project budget for --account flag: " budget 
+done
+
+email=`jutil user show -o json | grep email | cut -f2 -d':' | cut -f1 -d',' | cut -f2 -d'"'`
+echo
+read -p "Enter e-mail address for --mail-user (default: ${email}): " new_email
+
+if [[ -z "$new_email" ]]; then
+    new_email=$email
+fi
+
+# create HPC_logging dir
+hpclogging="HPC_logging/"
+mkdir -p ${cur}/${hpclogging}
+
+
+# ordering for looping:
+# "partition nGPUs timing"
+if [[ $hpcsys = "juwels" ]]; then
+  for i in "develgpus 2  02:00:00" "gpus 4 08:00:00"; do
+      set -- $i
+
+cat <<EOT > ${cur}/run_${hpcsys}_$1.bash
+#!/bin/bash -x
+#SBATCH --account=${budget}
+#SBATCH --nodes=1
+#SBATCH --output=${hpclogging}mlt-out.%j
+#SBATCH --error=${hpclogging}mlt-err.%j
+#SBATCH --time=$3 
+#SBATCH --partition=$1 
+#SBATCH --gres=gpu:$2
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=${email}
+
+source HPC_setup/mlt_modules_${hpcsys}.sh
+source venv_${hpcsys}/bin/activate
+
+timestamp=\`date +"%Y-%m-%d_%H%M-%S"\`
+
+export PYTHONPATH=\${PWD}/venv_${hpcsys}/lib/python3.6/site-packages:\${PYTHONPATH}
+
+srun python run.py --experiment_date=\$timestamp
+EOT
+
+  echo "Created runscript: run_${hpcsys}_$1.bash"
+
+  done
+
+elif [[ $hpcsys = "hdfml" ]]; then
+cat <<EOT > ${cur}/run_${hpcsys}_batch.bash
+#!/bin/bash -x
+#SBATCH --account=${budget}
+#SBATCH --nodes=1
+#SBATCH --output=${hpclogging}mlt-out.%j
+#SBATCH --error=${hpclogging}mlt-err.%j
+#SBATCH --time=08:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=${email}
+
+source HPC_setup/mlt_modules_${hpcsys}.sh
+source venv_${hpcsys}/bin/activate
+
+timestamp=\`date +"%Y-%m-%d_%H%M-%S"\`
+
+export PYTHONPATH=\${PWD}/venv_${hpcsys}/lib/python3.6/site-packages:\${PYTHONPATH}
+
+srun python run.py --experiment_date=\$timestamp
+EOT
+
+fi
+
+echo
+echo "You have to run the the following command on a login node to download data:"
+echo "          \`python run.py'"
+echo
+
+echo "Please execute the following command to check if the setup went well:"
+if [[ ${hpcsys} = 'juwels' ]]; then
+  echo "          \`sbatch run_juwels_develgpus.bash'"
+else
+  echo "          \`sbatch run_hdfml_batch.bash'"
+fi
+