diff --git a/video_prediction_tools/env_setup/create_env.sh b/video_prediction_tools/env_setup/create_env.sh
index 31f2065e9c7475762f654bcb878fcd5de7421ba4..82be2158275b527893c10e2347c6e858b49808f6 100755
--- a/video_prediction_tools/env_setup/create_env.sh
+++ b/video_prediction_tools/env_setup/create_env.sh
@@ -11,6 +11,25 @@
# Note that the basic output directory for the workflow may be set may passing a path as second argument to this script.
# **************** Description ****************
#
+# **************** Auxiliary functions ****************
+check_argin() {
+# Handle input arguments and check if one is equal to -lcontainer
+# Can also be used to check for non-positional arguments (such as -exp_id=*, see commented lines)
+ for argin in "$@"; do
+ if [[ $argin == *"-base_dir="* ]]; then
+ base_dir=${argin#"-base_dir="}
+ fi
+ if [[ $argin == *"-lcontainer"* ]]; then
+ bool_container=1
+ fi
+ done
+ if [[ -z "${bool_container}" ]]; then
+ bool_container=0
+ fi
+}
+# **************** Auxiliary functions ****************
+
+# **************** Actual script ****************
# some first sanity checks
if [[ ${BASH_SOURCE[0]} == ${0} ]]; then
echo "ERROR: 'create_env.sh' must be sourced, i.e. execute by prompting 'source create_env.sh [virt_env_name]'"
@@ -24,6 +43,11 @@ if [[ ! -n "$1" ]]; then
return
fi
+if [[ "$#" -gt 1 ]]; then
+ check_argin ${@:2} # sets base_dir if provided, always sets l_container
+fi
+
+# set some variables
HOST_NAME=`hostname`
ENV_NAME=$1
ENV_SETUP_DIR=`pwd`
@@ -31,15 +55,22 @@ WORKING_DIR="$(dirname "$ENV_SETUP_DIR")"
EXE_DIR="$(basename "$ENV_SETUP_DIR")"
ENV_DIR=${WORKING_DIR}/${ENV_NAME}
-# list of (Batch) scripts used for the steps in the workflow
-# !!! Expects that a template named [script_name]_template.sh exists!!!
-if [[ "${HOST_NAME}" == jwlogin2[1-4]* ]]; then
+## perform sanity checks
+# correct bool_container if host is Juwels Booster and ensure running singularity
+if [[ "${bool_container}" == 0 ]] && [[ "${HOST_NAME}" == jwlogin2[1-4]* ]]; then
+ echo "******************************************** NOTE ********************************************"
+ echo " Running on Juwels Booster is only possible inside a container environment. "
+ echo "******************************************** NOTE ********************************************"
+ bool_container=1
+fi
+
+if [[ "${bool_container}" == 1 ]]; then
echo "******************************************** NOTE ********************************************"
echo " Make use of dedicated Horovod-related working branches only!!! "
echo "******************************************** NOTE ********************************************"
- # another sanity check for Juwels Booster -> ensure running singularity
+ # Check if singularity is running
if [[ -z "${SINGULARITY_NAME}" ]]; then
- echo "ERROR: create_env.sh must be executed in a running singularity on Juwels Booster."
+ echo "ERROR: create_env.sh must be executed in a running singularity on Juwels in conjuction with container-usage."
echo "Thus, execute 'singularity shell [my_docker_image]' first!"
return
fi
@@ -57,12 +88,34 @@ fi
if [[ -d ${ENV_DIR} ]]; then
echo "Virtual environment has already been set up under ${ENV_DIR}. The present virtual environment will be activated now."
echo "NOTE: If you wish to set up a new virtual environment, delete the existing one or provide a different name."
-
ENV_EXIST=1
else
ENV_EXIST=0
fi
+## check integratability of modules
+if [[ "${HOST_NAME}" == hdfml* || "${HOST_NAME}" == *jwlogin* ]]; then
+ if [[ "${bool_container}" > 0 ]]; then
+ # on Juwels Booster, we are in a container environment -> loading modules is not possible
+ echo "***** Note for container environment! *****"
+ echo "Already checked the required modules?"
+ echo "To do so, run 'source modules_train.sh' after exiting the singularity."
+ echo "***** Note for container environment! *****"
+ else
+ # load modules and check for their availability
+ echo "***** Checking modules required during the workflow... *****"
+ source ${ENV_SETUP_DIR}/modules_preprocess.sh purge
+ source ${ENV_SETUP_DIR}/modules_train.sh purge
+ source ${ENV_SETUP_DIR}/modules_postprocess.sh
+ fi
+else
+ echo "ERROR: AMBS-workflow is currently only supported on the Juelich HPC-systems HDF-ML, Juwels and Juwels Booster"
+ return
+ # unset PYTHONPATH on every other machine that is not a known HPC-system
+ # unset PYTHONPATH
+fi
+
+
# Create fresh virtual environment or just activate the existing one
if [[ "$ENV_EXIST" == 0 ]]; then
# Check modules first
@@ -84,6 +137,9 @@ if [[ "$ENV_EXIST" == 0 ]]; then
# unset PYTHONPATH on every other machine that is not a known HPC-system
unset PYTHONPATH
fi
+
+## set up virtual environment
+if [[ "$ENV_EXIST" == 0 ]]; then
# Activate virtual environment and install additional Python packages.
echo "Configuring and activating virtual environment on ${HOST_NAME}"
@@ -95,11 +151,11 @@ if [[ "$ENV_EXIST" == 0 ]]; then
source ${activate_virt_env}
# install some requirements and/or check for modules
- if [[ "${HOST_NAME}" == hdfml* || "${HOST_NAME}" == *juwels* ]]; then
+ if [[ "${HOST_NAME}" == hdfml* || "${HOST_NAME}" == *jwlogin* ]]; then
# Install packages depending on host
echo "***** Start installing additional Python modules with pip... *****"
req_file=${ENV_SETUP_DIR}/requirements.txt
- if [[ "${HOST_NAME}" == jwlogin2[1-4]* ]]; then req_file=${ENV_SETUP_DIR}/requirements_booster.txt; fi
+ if [[ "${bool_container}" > 0 ]]; then req_file=${ENV_SETUP_DIR}/requirements_container.txt; fi
pip3 install --no-cache-dir -r ${req_file}
else
@@ -120,9 +176,9 @@ if [[ "$ENV_EXIST" == 0 ]]; then
export PYTHONPATH=${WORKING_DIR}/model_modules:$PYTHONPATH >> ${activate_virt_env}
export PYTHONPATH=${WORKING_DIR}/postprocess:$PYTHONPATH >> ${activate_virt_env}
- if [[ "${HOST_NAME}" == hdfml* || "${HOST_NAME}" == *juwels* ]]; then
+ if [[ "${HOST_NAME}" == hdfml* || "${HOST_NAME}" == *jwlogin* ]]; then
export PYTHONPATH=${ENV_DIR}/lib/python3.6/site-packages:$PYTHONPATH >> ${activate_virt_env}
- if [[ "${HOST_NAME}" == jwlogin2[1-4]* ]]; then
+ if [[ "${bool_container}" > 0 ]]; then
export PYTONPATH=/usr/locali/lib/python3.6/dist-packages:$PYTHONPATH
fi
fi
@@ -137,21 +193,26 @@ if [[ "$ENV_EXIST" == 0 ]]; then
if [[ "${HOST_NAME}" == hdfml* || "${HOST_NAME}" == *juwels* ]]; then
echo "export PYTHONPATH=${ENV_DIR}/lib/python3.6/site-packages:\$PYTHONPATH" >> ${activate_virt_env}
- if [[ "${HOST_NAME}" == jwlogin2[1-4]* ]]; then
+ if [[ "${bool_container}" > 0 ]]; then
echo "export PYTONPATH=/usr/locali/lib/python3.6/dist-packages:\$PYTHONPATH" >> ${activate_virt_env}
fi
fi
info_str="Virtual environment ${ENV_DIR} has been set up successfully."
elif [[ "$ENV_EXIST" == 1 ]]; then
# loading modules of postprocessing and activating virtual env are suifficient
- source ${ENV_SETUP_DIR}/modules_postprocess.sh
+ if [[ "${bool_container}" == 0 ]]; then
+ source ${ENV_SETUP_DIR}/modules_postprocess.sh
+ fi
source ${ENV_DIR}/bin/activate
info_str="Virtual environment ${ENV_DIR} has been activated successfully."
fi
echo "Set up runscript template for user ${USER}..."
-shift # shift parsed arguments so that name of venv is not parsed to setup_runscript_template.sh
-source "${WORKING_DIR}"/utils/runscript_generator/setup_runscript_templates.sh
+if [[ -z "${base_dir}" ]]; then
+ source "${WORKING_DIR}"/utils/runscript_generator/setup_runscript_templates.sh
+else
+ source "${WORKING_DIR}"/utils/runscript_generator/setup_runscript_templates.sh ${base_dir}
+fi
echo "******************************************** NOTE ********************************************"
echo "${info_str}"