Merge branch 'scarlet_issue#031_booster' of...

Merge branch 'scarlet_issue#031_booster' of https://gitlab.version.fz-juelich.de/toar/ambs into scarlet_issue#031_booster

video_prediction_tools/env_setup/create_env.sh

@@ -41,6 +41,12 @@ ENV_DIR=${WORKING_DIR}/${ENV_NAME}
 # !!! Expects that a template named [script_name]_template.sh exists!!!
 if [[ "${HOST_NAME}" == jwlogin21* || "${HOST_NAME}" == jwlogin22* ]]; then
   workflow_scripts=(train_model_era5_booster)
+  # another sanity check for Juwels Booster -> ensure running singularity
+  if [[ -z "${SINGULARITY_NAME}" ]]; then
+    echo "ERROR: create_env.sh must be executed in a running singularity on Juwels Booster."
+    echo "Thus, execute 'singularity shell [my_docker_image]' first!"
+    return
+  fi
 else
   workflow_scripts=(data_extraction_era5 preprocess_data_era5_step1 preprocess_data_era5_step2 train_model_era5 visualize_postprocess_era5 preprocess_data_moving_mnist train_model_moving_mnist visualize_postprocess_moving_mnist)
 fi
@@ -74,15 +80,26 @@ elif [[ "${HOST_NAME}" == "zam347" ]]; then
   unset PYTHONPATH
 # Juwels Booster
 elif [[ "${HOST_NAME}" == jwlogin21* || "${HOST_NAME}" == jwlogin22* ]]; then
-  echo "***** Checking modules required during the workflow on Juwels Booster... *****"
-  source ${ENV_SETUP_DIR}/modules_train.sh
+  echo "***** Note for Juwels Booster! *****"
+  echo "Already checked the required modules?"
+  echo "To do so, run 'source modules_train.sh' after exiting the singularity."
+  echo "***** Note for Juwels Booster! *****"
 fi
 
 if [[ "$ENV_EXIST" == 0 ]]; then
   # Activate virtual environmen and install additional Python packages.
   echo "Configuring and activating virtual environment on ${HOST_NAME}"
 
-  python3 -m venv $ENV_DIR
+  if [[ "${HOST_NAME}" == jwlogin21* || "${HOST_NAME}" == jwlogin22* ]]; then
+    # Horovod is part of the requirements on Booster since no binary module is available
+    # Additionally, venv needs access to the system site-packages of the running singularity
+    # Otherwise, TensorFlow would be missing
+    file_req_packages=requirements_booster.txt
+    python3 -m venv --system-site-packages $ENV_DIR
+  else
+    file_req_packages=requirements.txt
+    python3 -m venv --system-site-packages $ENV_DIR
+  fi
   
   activate_virt_env=${ENV_DIR}/bin/activate
   echo ${activate_virt_env}
@@ -93,7 +110,7 @@ if [[ "$ENV_EXIST" == 0 ]]; then
   if [[ "${HOST_NAME}" == hdfml* || "${HOST_NAME}" == *juwels* ]]; then
     # check module availability for the first time on known HPC-systems
     echo "***** Start installing additional Python modules with pip... *****"
-    pip3 install --no-cache-dir --ignore-installed -r ${ENV_SETUP_DIR}/requirements.txt
+    pip3 install --no-cache-dir --ignore-installed -r ${ENV_SETUP_DIR}/${file_req_packages}
     #pip3 install --user netCDF4
     #pip3 install --user numpy
   elif [[ "${HOST_NAME}" == "zam347" ]]; then

video_prediction_tools/env_setup/requirements_booster.txt

+opencv-python-headless==4.2.0.34
+horovod==0.16.2
+scipy
+matplotlib==3.3.0
+scikit-image
+pandas
+hickle