test

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 > ${hpcsys}/run_${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 > ${hpcsys}/run_${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 [[ ${hpcsys} = 'juwels' ]]; then
+  echo "          \`sbatch run_${hpcsys}_develgpus.bash'"
+else
+  echo "          \`sbatch run_${hpcsys}_batch.bash'"
+fi
+

HPC_setup/requirements_JUWELS_outcommented.txt

@@ -27,7 +27,7 @@ matplotlib==3.2.0              # in SciPy-Stack
 # more-itertools==8.2.0          # in Python 
 # numpy==1.18.1                  # in SciPy-Stack
 # packaging==20.3                # in Python
-# pandas==1.0.1                  # in SciPy-Stack
+pandas==1.0.1                  # in SciPy-Stack / but older version
 # partd==1.1.0                   # in Jupyter
 # patsy==0.5.1                   # in Jupyter 
 # Pillow==7.0.0                  # in Python 

HPC_setup/setup_venv_hdfml.sh

@@ -3,19 +3,28 @@
 # __date__  = '2020-04-06'
 
 # This script creates a virtual env which contains all modules which are not available via slrum/easybuild (see mlt_modules_hdfml.sh)
+# enter setting dir if called externally
+
+# $1 has to be an abs path to HPC_setup. If not provided, $PWD is used
+
+if [[ $1 != '' ]]; then
+  cur=$1
+else
+  cur=$PWD
+fi
 
 # load existing modules
-source mlt_modules_hdfml.sh
+source ${cur}mlt_modules_hdfml.sh
 
 # create venv
-python3 -m venv ../venv_hdfml
+python3 -m venv ${cur}../venv_hdfml
 
-source ../venv_hdfml/bin/activate
+source ${cur}/../venv_hdfml/bin/activate
 
 # export path for side-packages 
-export PYTHONPATH=${PWD}/../venv_hdfml/lib/python3.6/site-packages:${PYTHONPATH}
+export PYTHONPATH=${cur}/../venv_hdfml/lib/python3.6/site-packages:${PYTHONPATH}
 
-pip install -r requirements_HDFML_outcommented.txt
+pip install -r ${cur}/requirements_HDFML_outcommented.txt
 pip install --ignore-installed matplotlib==3.2.0
 pip install --ignore-installed pandas==1.0.1
 

HPC_setup/setup_venv_juwels.sh

@@ -4,9 +4,10 @@
 
 # This script creates a virtual env which contains all modules which are not available via slrum/easybuild (see mlt_modules.sh)
 
+# $1 has to be an abs path to HPC_setup. If not provided, $PWD is used
+
 # enter setting dir if called externally
 if [[ $1 != '' ]]; then
-  old=$PWD
   cur=$1
 else
   cur=$PWD
@@ -25,6 +26,8 @@ export PYTHONPATH=${cur}/../venv_juwels/lib/python3.6/site-packages:${PYTHONPATH
 
 pip install -r ${cur}requirements_JUWELS_outcommented.txt
 pip install --ignore-installed matplotlib==3.2.0
+pip install --ignore-installed pandas==1.0.1
+
 
 # Comment: Maybe we have to export PYTHONPATH a second time ater activating the venv (after job allocation)
 # source venv/bin/activate

create_runscripts_HPC.sh

@@ -10,6 +10,24 @@ echo
 echo "This script creates the HPC batch scripts to run mlt on compute nodes (gpus and develgpus)."
 echo "You can modify the created run scripts afterwards if needed."
 
+while true; do
+    read -p "Do you wish to create run scripts for JUWELS? [yes/no]" yn
+    case $yn in
+        [Yy]* ) juwels=True; break;;
+        [Nn]* ) juwels=False;;
+        * ) echo "Please answer yes or no.";;
+   esac
+done
+
+while true; do
+    read -p "Do you wish to create run script for HDFML? [yes/no]" yn
+    case $yn in
+        [Yy]* ) hdfml=True; break;;
+        [Nn]* ) hdfml=False;;
+        * ) echo "Please answer yes or no.";;
+   esac
+done
+
 
 budget=''
 while [[ $budget == '' ]]
@@ -27,13 +45,13 @@ if [[ -z "$new_email" ]]; then
 fi
 
 # create HPC_logging dir
-hpclogging="HPC_logging/"
+hpclogging="../HPC_logging/"
 mkdir -p $hpclogging
 
 
 # ordering for looping:
 # "partition nGPUs timing"
-
+if [[ $juwels == True ]]; then
   for i in "develgpus 2  02:00:00" "gpus 4 08:00:00"; do
       set -- $i
 
@@ -49,7 +67,7 @@ cat <<EOT > run_$1.bash
 #SBATCH --mail-type=ALL
 #SBATCH --mail-user=${email}
 
-source mlt_modules.sh
+source mlt_modules_.sh
 source venv/bin/activate
 
 timestamp=\`date +"%Y-%m-%d_%H%M-%S"\`
@@ -62,6 +80,8 @@ EOT
   echo "Created runscript: run_$1.bash"
 
   done
+fi
+
 echo
 echo "You have to run the the following command on a login node to download data:"
 echo "          \`python run.py'"

setupHPC_test.sh

@@ -16,4 +16,6 @@ else
 fi
 
 source HPC_setup/setup_venv_${hpcsys}.sh $basepath/$settingpath
-#source $settingpath/testcall_juwels.sh $basepath/$settingpath
+
+source HPC_setup/create_runscripts_HPC.sh $hpcsys $basepath
+