From caf5687f3d25770903f94ae0a90b153402acf85b Mon Sep 17 00:00:00 2001
From: Felix Kleinert <f.kleinert@fz-juelich.de>
Date: Thu, 30 Apr 2020 14:25:41 +0200
Subject: [PATCH] test
---
HPC_setup/create_runscripts_HPC.sh | 131 ++++++++++++++++++
.../requirements_JUWELS_outcommented.txt | 2 +-
HPC_setup/setup_venv_hdfml.sh | 19 ++-
HPC_setup/setup_venv_juwels.sh | 5 +-
create_runscripts_HPC.sh | 34 ++++-
setupHPC_test.sh | 4 +-
6 files changed, 180 insertions(+), 15 deletions(-)
create mode 100755 HPC_setup/create_runscripts_HPC.sh
diff --git a/HPC_setup/create_runscripts_HPC.sh b/HPC_setup/create_runscripts_HPC.sh
new file mode 100755
index 00000000..829379a1
--- /dev/null
+++ b/HPC_setup/create_runscripts_HPC.sh
@@ -0,0 +1,131 @@
+#!/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
+
diff --git a/HPC_setup/requirements_JUWELS_outcommented.txt b/HPC_setup/requirements_JUWELS_outcommented.txt
index 821dd802..f2a6b7df 100644
--- a/HPC_setup/requirements_JUWELS_outcommented.txt
+++ b/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
diff --git a/HPC_setup/setup_venv_hdfml.sh b/HPC_setup/setup_venv_hdfml.sh
index f6b0d5d5..d18e41d5 100644
--- a/HPC_setup/setup_venv_hdfml.sh
+++ b/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
diff --git a/HPC_setup/setup_venv_juwels.sh b/HPC_setup/setup_venv_juwels.sh
index 98edd754..ca362a8b 100755
--- a/HPC_setup/setup_venv_juwels.sh
+++ b/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
diff --git a/create_runscripts_HPC.sh b/create_runscripts_HPC.sh
index b2df1a25..af657fd1 100755
--- a/create_runscripts_HPC.sh
+++ b/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 [[ $budget == '' ]]
@@ -27,15 +45,15 @@ if [[ -z "$new_email" ]]; then
fi
# create HPC_logging dir
-hpclogging="HPC_logging/"
+hpclogging="../HPC_logging/"
mkdir -p $hpclogging
# ordering for looping:
# "partition nGPUs timing"
-
-for i in "develgpus 2 02:00:00" "gpus 4 08:00:00"; do
- set -- $i
+if [[ $juwels == True ]]; then
+ for i in "develgpus 2 02:00:00" "gpus 4 08:00:00"; do
+ set -- $i
cat <<EOT > run_$1.bash
#!/bin/bash -x
@@ -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"\`
@@ -59,9 +77,11 @@ export PYTHONPATH=\${PWD}/venv/lib/python3.6/site-packages:\${PYTHONPATH}
srun python run.py --experiment_date=\$timestamp
EOT
-echo "Created runscript: run_$1.bash"
+ echo "Created runscript: run_$1.bash"
+
+ done
+fi
-done
echo
echo "You have to run the the following command on a login node to download data:"
echo " \`python run.py'"
diff --git a/setupHPC_test.sh b/setupHPC_test.sh
index c67e2430..fad7c605 100644
--- a/setupHPC_test.sh
+++ b/setupHPC_test.sh
@@ -16,4 +16,6 @@ else
fi
source HPC_setup/setup_venv_${hpcsys}.sh $basepath/$settingpath
-#source $settingpath/testcall_juwels.sh $basepath/$settingpath
+
+source HPC_setup/create_runscripts_HPC.sh $hpcsys $basepath
+
--
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