Split prepare_rundir.sh into three different stages for the whole experiment,...

Split prepare_rundir.sh into three different stages for the whole experiment, the start date and each member.

conf/jobs.yaml

@@ -68,15 +68,27 @@ JOBS:
     WALLCLOCK: 01:00
     PROCESSORS: 16
 
-  PREPARE_RUNDIR:
-    FILE: templates/prepare_rundir.sh
+  PREPARE_EXPERIMENT:
+    FILE: templates/prepare_experiment.sh
     DEPENDENCIES: BUILD_ICON
+    RUNNING: once
+    WALLCLOCK: 01:00
+
+  PREPARE_DATE:
+    FILE: templates/prepare_date.sh
+    DEPENDENCIES: PREPARE_EXPERIMENT
+    RUNNING: once
+    WALLCLOCK: 01:00
+
+  PREPARE_MEMBER:
+    FILE: templates/prepare_member.sh
+    DEPENDENCIES: PREPARE_DATE
     RUNNING: member
     WALLCLOCK: 01:00
 
   PREPARE_CHUNK:
     FILE: templates/prepare_chunk.sh
-    DEPENDENCIES: PREPARE_RUNDIR RUN_ICON-1
+    DEPENDENCIES: PREPARE_MEMBER RUN_ICON-1
     WALLCLOCK: 00:05
     RUNNING: chunk
 
@@ -94,7 +106,7 @@ JOBS:
     DEPENDENCIES: RUN_ICON BUILD_PYTHON_ENVIRONMENT COMPRESS-1
     RUNNING: chunk
     TYPE: python
-    EXECUTABLE: "%HPCROOTDIR%/venv/bin/python3"
+    EXECUTABLE: "%HPCROOTDIR%/%python_environment.folder_name%/bin/python3"
     PROCESSORS: 16
     MEMORY: 16384
 

templates/prepare_date.sh

+#!/bin/bash -l
+
+# Get some variables provided by autosubmit.
+WORKDIR=%HPCROOTDIR%
+STARTDATE=%SDATE%
+
+# Define date directory, create it and go there
+COMMON_DATE_FOLDER=${WORKDIR}/${STARTDATE}/inidata
+# Create member folder and go there
+mkdir -p ${COMMON_DATE_FOLDER}
+cd ${COMMON_DATE_FOLDER} || exit
+
+# some settings
+AN_MEMBER=$(printf "%03d" %initial_conditions.member%)
+INITIAL_CONDITIONS_PARENT_FOLDER=%initial_conditions.parent_folder%
+
+INITIAL_CONDITIONS_PATH=${INITIAL_CONDITIONS_PARENT_FOLDER}/${STARTDATE:0:6}/${STARTDATE:0:8}T00
+
+AN_SOURCE=$(find ${INITIAL_CONDITIONS_PATH} -name "igaf*00.m${AN_MEMBER}.grb" | sort | tail -n 1)
+FG_SOURCE=$(find ${INITIAL_CONDITIONS_PATH} -name "igfff00030000.m${AN_MEMBER}.grb" | sort | tail -n 1)
+
+if [ ! -f "${AN_SOURCE}" ]; then
+  echo "Analysis file for date ${STARTDATE} not found!"
+  exit 1
+fi
+
+if [ ! -f "${FG_SOURCE}" ]; then
+  echo "FG file for date ${STARTDATE} not found!"
+  exit 1
+fi
+
+AN_FILE=$(basename "${AN_SOURCE}")
+FG_FILE=$(basename "${FG_SOURCE}")
+
+# Save filenames to be used later by other scripts.
+echo "${AN_FILE}" > an_file.txt
+echo "${FG_FILE}" > fg_file.txt
+
+# Copy the first-guess and analysis files.
+cp "${FG_SOURCE}" "${FG_FILE}"
+cp "${AN_SOURCE}" "${AN_FILE}"

templates/prepare_rundir.sh → templates/prepare_experiment.sh

@@ -10,24 +10,18 @@ BGRID=%simulation.BGRID%
 RGRID=%simulation.RGRID%
 BEXTPAR=%simulation.BEXTPAR%
 
-STARTDATE=%SDATE%
-
-MEMBER=%MEMBER%
-
-# Define rundir
-RUNDIR=${WORKDIR}/${STARTDATE}/${MEMBER}
 
 # Activate spack
 SPACK_ENV=${WORKDIR}/spack/share/spack/setup-env.sh
 source ${SPACK_ENV}
 
-# Load icon module
+# Load icon module needed to retrieve some data
 spack load icon-nwp@%ICON_VERSION%
 
-# Create member folder and go there
-mkdir -p ${RUNDIR}
-
-cd ${RUNDIR}
+# Create a folder for the common inidata and go there
+COMMON_INIDATA_FOLDER=${WORKDIR}/inidata
+mkdir -p "${COMMON_INIDATA_FOLDER}"
+cd "${COMMON_INIDATA_FOLDER}" || exit
 
 # Download or copy required input files
 function download_file() {
@@ -39,43 +33,17 @@ function download_file() {
   fi
 }
 
-# some settings
-AN_MEMBER=$(printf "%03d" %initial_conditions.member%)
-INITIAL_CONDITIONS_PARENT_FOLDER=%initial_conditions.parent_folder%
-
-INITIAL_CONDITIONS_PATH=${INITIAL_CONDITIONS_PARENT_FOLDER}/${STARTDATE:0:6}/${STARTDATE:0:8}T00
-
-AN_SOURCE=$(find ${INITIAL_CONDITIONS_PATH} -name "igaf*00.m${AN_MEMBER}.grb" | sort | tail -n 1)
-FG_SOURCE=$(find ${INITIAL_CONDITIONS_PATH} -name igfff00030000.m${AN_MEMBER}.grb | sort | tail -n 1)
-
-if [ ! -f "${AN_SOURCE}" ]; then
-  echo "Analysis file for date ${STARTDATE} not found!"
-  exit 1
-fi
-
-if [ ! -f "${FG_SOURCE}" ]; then
-  echo "FG file for date ${STARTDATE} not found!"
-  exit 1
-fi
-
-AN_FILE=$(basename ${AN_SOURCE})
-FG_FILE=$(basename ${FG_SOURCE})
-
-# Save filenames to be used later by other scripts.
-echo ${AN_FILE} >an_file.txt
-echo ${FG_FILE} >fg_file.txt
-
 # Download grid files and external parameters
 BASEURL=http://icon-downloads.mpimet.mpg.de/grids/public/edzw
 download_file $BASEURL/$BGRID
 download_file $BASEURL/$RGRID
 download_file $BASEURL/$BEXTPAR
 
-# Link first-guess and analysis files.
-ln -sf ${FG_SOURCE} ${FG_FILE}
-ln -sf ${AN_SOURCE} ${AN_FILE}
-
 # Link input for radiation
-ln -sf ${ICON_DATA_PATH}/rrtmg_lw.nc .
-ln -sf ${ICON_DATA_PATH}/ECHAM6_CldOptProps.nc .
-ln -sf ${ICON_BASE_PATH}/run/ana_varnames_map_file.txt .
+ln -sf "${ICON_DATA_PATH}/rrtmg_lw.nc" .
+ln -sf "${ICON_DATA_PATH}/ECHAM6_CldOptProps.nc" .
+ln -sf "${ICON_BASE_PATH}/run/ana_varnames_map_file.txt" .
+
+
+# Set all permissions to read only
+chmod 700
\ No newline at end of file

templates/prepare_member.sh

+#!/bin/bash -l
+
+# Get some variables provided by autosubmit.
+WORKDIR=%HPCROOTDIR%
+STARTDATE=%SDATE%
+MEMBER=%MEMBER%
+
+# Common folder with data needed for all simulations
+COMMON_INIDATA_FOLDER=${WORKDIR}/
+# Common folder for the same start date
+COMMON_DATE_FOLDER=${WORKDIR}/${STARTDATE}/inidata
+
+# Member folder
+MEMBER_DIR=${WORKDIR}/${STARTDATE}/${MEMBER}
+
+# Create member folder and go there
+mkdir -p ${MEMBER_DIR}
+
+cd ${MEMBER_DIR} || exit
+
+
+# Link all files from the common inidata folder and the common date folder
+ln -sf ${COMMON_INIDATA_FOLDER}/* .
+ln -sf ${COMMON_DATE_FOLDER}/* .