adapted run.sh script for bologna env

Run/run.sh

-#!/bin/bash
-#
-# @Author: Anne Philipp
-#
-# @Date: October, 4 2018
-#
-# @Description: 
-#    This script defines the available command-line parameters
-#    for running flex_extract and combines them for the execution  
-#    of the Python program. It also does some checks to 
-#    guarantee necessary parameters were set and consistent.
-#
-# @Licence:
-#    (C) Copyright 2014-2020.
-#
-#    SPDX-License-Identifier: CC-BY-4.0
-#
-#    This work is licensed under the Creative Commons Attribution 4.0
-#    International License. To view a copy of this license, visit
-#    http://creativecommons.org/licenses/by/4.0/ or send a letter to
-#    Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
-#
-# -----------------------------------------------------------------
-# AVAILABLE COMMANDLINE ARGUMENTS TO SET
-# 
-# THE USER HAS TO SPECIFY THESE PARAMETERS:
-
-QUEUE='ecgate'
-START_DATE=None
-END_DATE=None
-DATE_CHUNK=None
-JOB_CHUNK=3
-BASETIME=None
-STEP=None
-LEVELIST=None
-AREA=None
-INPUTDIR=None
-OUTPUTDIR=None
-PP_ID=None
-JOB_TEMPLATE='submitscript.template' 
-CONTROLFILE='CONTROL_EA5' 
-DEBUG=0
-REQUEST=2
-PUBLIC=0
-
-# -----------------------------------------------------------------
-#
-# AFTER THIS LINE THE USER DOES NOT HAVE TO CHANGE ANYTHING !!!
-#
-# -----------------------------------------------------------------
-
-# PATH TO SUBMISSION SCRIPT
-pyscript=../Source/Python/submit.py
-
-# INITIALIZE EMPTY PARAMETERLIST
-parameterlist=""
-
-# CHECK IF ON ECMWF SERVER; 
-if [[ $HOST == *"ecgb"* ]] || [[ $HOST == *"cca"* ]] || [[ $HOST == *"ccb"* ]]; then
-# LOAD PYTHON3 MODULE
-  module load python3
-fi 
-
-# CHECK FOR MORE PARAMETER 
-if [ -n "$START_DATE" ]; then
-  parameterlist+=" --start_date=$START_DATE"
-fi
-if [ -n "$END_DATE" ]; then
-  parameterlist+=" --end_date=$END_DATE"
-fi
-if [ -n "$DATE_CHUNK" ]; then
-  parameterlist+=" --date_chunk=$DATE_CHUNK"
-fi
-if [ -n "$JOB_CHUNK" ]; then
-  parameterlist+=" --job_chunk=$JOB_CHUNK"
-fi
-if [ -n "$BASETIME" ]; then
-  parameterlist+=" --basetime=$BASETIME"
-fi
-if [ -n "$STEP" ]; then
-  parameterlist+=" --step=$STEP"
-fi
-if [ -n "$LEVELIST" ]; then
-  parameterlist+=" --levelist=$LEVELIST"
-fi
-if [ -n "$AREA" ]; then
-  parameterlist+=" --area=$AREA"
-fi
-if [ -n "$INPUTDIR" ]; then
-  parameterlist+=" --inputdir=$INPUTDIR"
-fi
-if [ -n "$OUTPUTDIR" ]; then
-  parameterlist+=" --outputdir=$OUTPUTDIR"
-fi
-if [ -n "$PP_ID" ]; then
-  parameterlist+=" --ppid=$PP_ID"
-fi
-if [ -n "$JOB_TEMPLATE" ]; then
-  parameterlist+=" --job_template=$JOB_TEMPLATE"
-fi
-if [ -n "$QUEUE" ]; then
-  parameterlist+=" --queue=$QUEUE"
-fi
-if [ -n "$CONTROLFILE" ]; then
-  parameterlist+=" --controlfile=$CONTROLFILE"
-fi
-if [ -n "$DEBUG" ]; then
-  parameterlist+=" --debug=$DEBUG"
-fi
-if [ -n "$REQUEST" ]; then
-  parameterlist+=" --request=$REQUEST"
-fi
-if [ -n "$PUBLIC" ]; then
-  parameterlist+=" --public=$PUBLIC"
-fi
-
-# -----------------------------------------------------------------
-# CALL SCRIPT WITH DETERMINED COMMANDLINE ARGUMENTS
-
-$pyscript $parameterlist
-

Run/run.sh

+run_bologna.sh
\ No newline at end of file

Run/run_bologna.sh

+#!/bin/bash
+#
+# @Author: Anne Philipp
+#
+# @Date: October, 4 2018
+#
+# @Description: 
+#    This script defines the available command-line parameters
+#    for running flex_extract and combines them for the execution  
+#    of the Python program. It also does some checks to 
+#    guarantee necessary parameters were set and consistent.
+#
+# @Licence:
+#    (C) Copyright 2014-2020.
+#
+#    SPDX-License-Identifier: CC-BY-4.0
+#
+#    This work is licensed under the Creative Commons Attribution 4.0
+#    International License. To view a copy of this license, visit
+#    http://creativecommons.org/licenses/by/4.0/ or send a letter to
+#    Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
+#
+# -----------------------------------------------------------------
+# AVAILABLE COMMANDLINE ARGUMENTS TO SET
+# 
+# THE USER HAS TO SPECIFY THESE PARAMETERS:
+
+QUEUE='ecs'
+START_DATE=None
+END_DATE=None
+DATE_CHUNK=None
+JOB_CHUNK=3
+BASETIME=None
+STEP=None
+LEVELIST=None
+AREA=None
+INPUTDIR=None
+OUTPUTDIR=None
+PP_ID=None
+JOB_TEMPLATE='submitscript.template' 
+CONTROLFILE='CONTROL_EA5' 
+DEBUG=0
+REQUEST=2
+PUBLIC=0
+
+# -----------------------------------------------------------------
+#
+# AFTER THIS LINE THE USER DOES NOT HAVE TO CHANGE ANYTHING !!!
+#
+# -----------------------------------------------------------------
+
+# PATH TO SUBMISSION SCRIPT
+pyscript=../Source/Python/submit.py
+
+# INITIALIZE EMPTY PARAMETERLIST
+parameterlist=""
+
+# CHECK IF ON ECMWF SERVER; 
+if [[ $EC_CLUSTER == "ecs"* ]] || [[ $EC_CLUSTER == "aa"* ]] || [[ $EC_CLUSTER == "ab"* ]] || [[ $EC_CLUSTER == "ac"* ]] || [[ $EC_CLUSTER == "ad"* ]]; then
+# LOAD PYTHON3 AND ECACCESS MODULES
+  module load python3 ecaccess
+fi 
+
+# CHECK FOR MORE PARAMETER 
+if [ -n "$START_DATE" ]; then
+  parameterlist+=" --start_date=$START_DATE"
+fi
+if [ -n "$END_DATE" ]; then
+  parameterlist+=" --end_date=$END_DATE"
+fi
+if [ -n "$DATE_CHUNK" ]; then
+  parameterlist+=" --date_chunk=$DATE_CHUNK"
+fi
+if [ -n "$JOB_CHUNK" ]; then
+  parameterlist+=" --job_chunk=$JOB_CHUNK"
+fi
+if [ -n "$BASETIME" ]; then
+  parameterlist+=" --basetime=$BASETIME"
+fi
+if [ -n "$STEP" ]; then
+  parameterlist+=" --step=$STEP"
+fi
+if [ -n "$LEVELIST" ]; then
+  parameterlist+=" --levelist=$LEVELIST"
+fi
+if [ -n "$AREA" ]; then
+  parameterlist+=" --area=$AREA"
+fi
+if [ -n "$INPUTDIR" ]; then
+  parameterlist+=" --inputdir=$INPUTDIR"
+fi
+if [ -n "$OUTPUTDIR" ]; then
+  parameterlist+=" --outputdir=$OUTPUTDIR"
+fi
+if [ -n "$PP_ID" ]; then
+  parameterlist+=" --ppid=$PP_ID"
+fi
+if [ -n "$JOB_TEMPLATE" ]; then
+  parameterlist+=" --job_template=$JOB_TEMPLATE"
+fi
+if [ -n "$QUEUE" ]; then
+  parameterlist+=" --queue=$QUEUE"
+fi
+if [ -n "$CONTROLFILE" ]; then
+  parameterlist+=" --controlfile=$CONTROLFILE"
+fi
+if [ -n "$DEBUG" ]; then
+  parameterlist+=" --debug=$DEBUG"
+fi
+if [ -n "$REQUEST" ]; then
+  parameterlist+=" --request=$REQUEST"
+fi
+if [ -n "$PUBLIC" ]; then
+  parameterlist+=" --public=$PUBLIC"
+fi
+
+# -----------------------------------------------------------------
+# CALL SCRIPT WITH DETERMINED COMMANDLINE ARGUMENTS
+
+$pyscript $parameterlist
+

Run/run_reading.sh

+#!/bin/bash
+#
+# @Author: Anne Philipp
+#
+# @Date: October, 4 2018
+#
+# @Description: 
+#    This script defines the available command-line parameters
+#    for running flex_extract and combines them for the execution  
+#    of the Python program. It also does some checks to 
+#    guarantee necessary parameters were set and consistent.
+#
+# @Licence:
+#    (C) Copyright 2014-2020.
+#
+#    SPDX-License-Identifier: CC-BY-4.0
+#
+#    This work is licensed under the Creative Commons Attribution 4.0
+#    International License. To view a copy of this license, visit
+#    http://creativecommons.org/licenses/by/4.0/ or send a letter to
+#    Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
+#
+# -----------------------------------------------------------------
+# AVAILABLE COMMANDLINE ARGUMENTS TO SET
+# 
+# THE USER HAS TO SPECIFY THESE PARAMETERS:
+
+QUEUE='ecgate'
+START_DATE=None
+END_DATE=None
+DATE_CHUNK=None
+JOB_CHUNK=3
+BASETIME=None
+STEP=None
+LEVELIST=None
+AREA=None
+INPUTDIR=None
+OUTPUTDIR=None
+PP_ID=None
+JOB_TEMPLATE='submitscript.template' 
+CONTROLFILE='CONTROL_EA5' 
+DEBUG=0
+REQUEST=2
+PUBLIC=0
+
+# -----------------------------------------------------------------
+#
+# AFTER THIS LINE THE USER DOES NOT HAVE TO CHANGE ANYTHING !!!
+#
+# -----------------------------------------------------------------
+
+# PATH TO SUBMISSION SCRIPT
+pyscript=../Source/Python/submit.py
+
+# INITIALIZE EMPTY PARAMETERLIST
+parameterlist=""
+
+# CHECK IF ON ECMWF SERVER; 
+if [[ $HOST == *"ecgb"* ]] || [[ $HOST == *"cca"* ]] || [[ $HOST == *"ccb"* ]]; then
+# LOAD PYTHON3 MODULE
+  module load python3
+fi 
+
+# CHECK FOR MORE PARAMETER 
+if [ -n "$START_DATE" ]; then
+  parameterlist+=" --start_date=$START_DATE"
+fi
+if [ -n "$END_DATE" ]; then
+  parameterlist+=" --end_date=$END_DATE"
+fi
+if [ -n "$DATE_CHUNK" ]; then
+  parameterlist+=" --date_chunk=$DATE_CHUNK"
+fi
+if [ -n "$JOB_CHUNK" ]; then
+  parameterlist+=" --job_chunk=$JOB_CHUNK"
+fi
+if [ -n "$BASETIME" ]; then
+  parameterlist+=" --basetime=$BASETIME"
+fi
+if [ -n "$STEP" ]; then
+  parameterlist+=" --step=$STEP"
+fi
+if [ -n "$LEVELIST" ]; then
+  parameterlist+=" --levelist=$LEVELIST"
+fi
+if [ -n "$AREA" ]; then
+  parameterlist+=" --area=$AREA"
+fi
+if [ -n "$INPUTDIR" ]; then
+  parameterlist+=" --inputdir=$INPUTDIR"
+fi
+if [ -n "$OUTPUTDIR" ]; then
+  parameterlist+=" --outputdir=$OUTPUTDIR"
+fi
+if [ -n "$PP_ID" ]; then
+  parameterlist+=" --ppid=$PP_ID"
+fi
+if [ -n "$JOB_TEMPLATE" ]; then
+  parameterlist+=" --job_template=$JOB_TEMPLATE"
+fi
+if [ -n "$QUEUE" ]; then
+  parameterlist+=" --queue=$QUEUE"
+fi
+if [ -n "$CONTROLFILE" ]; then
+  parameterlist+=" --controlfile=$CONTROLFILE"
+fi
+if [ -n "$DEBUG" ]; then
+  parameterlist+=" --debug=$DEBUG"
+fi
+if [ -n "$REQUEST" ]; then
+  parameterlist+=" --request=$REQUEST"
+fi
+if [ -n "$PUBLIC" ]; then
+  parameterlist+=" --public=$PUBLIC"
+fi
+
+# -----------------------------------------------------------------
+# CALL SCRIPT WITH DETERMINED COMMANDLINE ARGUMENTS
+
+$pyscript $parameterlist
+