Merge branch 'v3.1-rc' of github.com:C2SM/processing-chain into docs-…

…v3.1

.gitignore

@@ -7,6 +7,6 @@ input_processing-chain.tgz
 input/
 output/
 work/
-src/*/
+ext/*/
 *.code-workspace
-.vscode/
+.vscode/

cases/cosmo-ghg-spinup-test/config.yaml

@@ -1,7 +1,9 @@
 # Configuration file for the 'cosmo-ghg-spinup-test' case with COSMO-GHG
 
-model: cosmo-ghg
+workflow: cosmo-ghg-spinup
 constraint: gpu
+run_on: gpu
+compute_queue: normal
 ntasks_per_node: 12
 restart_step: PT6H
 spinup: 3

cases/cosmo-ghg-spinup-test/cosmo_runjob.cfg

@@ -1,5 +1,5 @@
 #!/bin/bash -l
-#SBATCH --job-name="cosmo_{cfg.startdate_sim_yyyymmddhh}_{cfg.forecasttime}"
+#SBATCH --job-name=cosmo
 #SBATCH --account={cfg.compute_account}
 #SBATCH --time={walltime}
 #SBATCH --nodes={np_tot}
@@ -34,7 +34,7 @@ echo "============== StartTime: `date +%s` s"
 echo "============== StartTime: `date`"
 echo "====================================================="
 
-srun -u ./{execname} >> {logfile} 2>&1
+srun -u ./{cfg.cosmo_execname} >> {logfile} 2>&1
 pid=$?
 
 echo "====================================================="

cases/cosmo-ghg-spinup-test/int2lm_runjob.cfg

@@ -1,5 +1,5 @@
 #!/bin/bash -l
-#SBATCH --job-name=int2lm_{cfg.startdate_sim_yyyymmddhh}_{cfg.enddate_sim_yyyymmddhh}
+#SBATCH --job-name=int2lm
 #SBATCH --account={cfg.compute_account}
 #SBATCH --time={walltime}
 #SBATCH --nodes={nodes}

cases/cosmo-ghg-test/config.yaml

@@ -1,7 +1,9 @@
 # Configuration file for the 'cosmo-ghg-test' case with COSMO-GHG
 
-model: cosmo-ghg
+workflow: cosmo-ghg
 constraint: gpu
+run_on: gpu
+compute_queue: normal
 ntasks_per_node: 12
 restart_step: PT6H
 startdate: 2015-01-01T00:00:00Z

cases/cosmo-ghg-test/cosmo_runjob.cfg

@@ -1,5 +1,5 @@
 #!/bin/bash -l
-#SBATCH --job-name="cosmo_{cfg.startdate_sim_yyyymmddhh}_{cfg.forecasttime}"
+#SBATCH --job-name=cosmo
 #SBATCH --account={cfg.compute_account}
 #SBATCH --time={walltime}
 #SBATCH --nodes={np_tot}
@@ -34,7 +34,7 @@ echo "============== StartTime: `date +%s` s"
 echo "============== StartTime: `date`"
 echo "====================================================="
 
-srun -u ./{execname} >> {logfile} 2>&1
+srun -u ./{cfg.cosmo_execname} >> {logfile} 2>&1
 pid=$?
 
 echo "====================================================="

cases/cosmo-ghg-test/int2lm_runjob.cfg

@@ -1,5 +1,5 @@
 #!/bin/bash -l
-#SBATCH --job-name=int2lm_{cfg.startdate_sim_yyyymmddhh}_{cfg.enddate_sim_yyyymmddhh}
+#SBATCH --job-name=int2lm
 #SBATCH --account={cfg.compute_account}
 #SBATCH --time={walltime}
 #SBATCH --nodes={nodes}

cases/icon-art-global-test/config.yaml

@@ -1,6 +1,6 @@
 # Configuration file for the 'icon-art-global-test' case with ICON
 
-model: icon-art-global
+workflow: icon-art-global
 constraint: gpu
 run_on: cpu
 compute_queue: normal
@@ -28,6 +28,11 @@ species_global_nudging: False
 species2nudge: []
 nudging_step: 6
 
+walltime:
+    prepare_icon: '00:15:00'
+    prepare_art_global: '00:10:00'
+    icon: '00:05:00'
+
 era5:
     inicond: False
     global_nudging: False
@@ -67,7 +72,6 @@ icon:
     species_nudgingjob: icon_species_nudging.sh
     output_writing_step: 6
     compute_queue: normal
-    walltime: '00:10:00'
     np_tot: 4
     np_io: 1
     np_restart: 1

cases/icon-art-global-test/icon_runjob.cfg

@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="{cfg.casename}_{cfg.startdate_sim_yyyymmddhh}_{cfg.forecasttime}"
+#SBATCH --job-name=icon
 #SBATCH --account={cfg.compute_account}
-#SBATCH --time={cfg.icon_walltime}
+#SBATCH --time={cfg.walltime_icon}
 #SBATCH --nodes={cfg.icon_np_tot}
 #SBATCH --ntasks-per-node={cfg.ntasks_per_node}
 #SBATCH --partition={cfg.compute_queue}
 #SBATCH --constraint={cfg.constraint}
 #SBATCH --hint=nomultithread
-#SBATCH --output={logfile}
+#SBATCH --output={cfg.logfile}
 #SBATCH --open-mode=append
 #SBATCH --chdir={cfg.icon_work}
 
@@ -388,22 +388,12 @@ EOF
 # ----------------------------------------------------------------------
 # run the model!
 # ----------------------------------------------------------------------
- srun ./icon.exe
-
-
-
-#  ! output_nml: specifies an output stream --------------------------------------
-# &output_nml
-#  filetype                    =                          4                                        ! output format: 2=GRIB2, 4=NETCDFv2
-#  dom                         =                         -1                                        ! write all domains
-#  output_bounds               =        0., 2678400., 3600.                                        ! start, end, increment
-#  steps_per_file              =                          1                                        ! number of steps per file
-#  mode                        =                          1                                        ! 1: forecast mode (relative t-axis), 2: climate mode (absolute t-axis)
-#  include_last                =                      .TRUE.
-#  output_filename             =                    'ICON-ART'
-#  filename_format             =   '{cfg.icon_output}/<output_filename>_latlon_<datetime2>'         ! file name base
-#  remap                       =                          1                                         ! 1: remap to lat-lon grid
-#  reg_lon_def                 =              -179.,2,179                                      
-#  reg_lat_def                 =               90.,-1,-90.                               
-#  ml_varlist                  =  'z_ifc','z_mc','pres','pres_sfc','qc','rh','rho','temp','u','v','w','group:ART_CHEMISTRY',
-# /
+handle_error(){{
+    # Check for invalid pointer error at the end of icon-art
+    if grep -q "free(): invalid pointer" {cfg.logfile} && grep -q "clean-up finished" {cfg.logfile}; then
+        exit 0
+    else
+        exit 1
+    fi
+}}
+srun ./{cfg.icon_execname} || handle_error

cases/icon-art-oem-test/config.yaml

@@ -1,6 +1,6 @@
 # Configuration file for the 'icon-art-oem-test' case with ICON
 
-model: icon-art-oem
+workflow: icon-art-oem
 constraint: gpu
 run_on: cpu
 compute_queue: normal
@@ -21,6 +21,13 @@ filename_format: <output_filename>_DOM<physdom>_<ddhhmmss>
 lateral_boundary_grid_order: lateral_boundary
 art_input_folder: ./input/icon-art-oem/ART
 
+walltime:
+    prepare_icon: '00:10:00'
+    icontools: '00:30:00'
+    prepare_art: '00:10:00'
+    prepare_art_oem: '00:10:00'
+    icon: '00:30:00'
+
 meteo:
     dir: ./input/meteo
     prefix: ifs_

cases/icon-art-oem-test/icon_runjob.cfg

@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="{cfg.casename}_{cfg.startdate_sim_yyyymmddhh}_{cfg.forecasttime}"
+#SBATCH --job-name=icon
 #SBATCH --account={cfg.compute_account}
-#SBATCH --time={cfg.icon_walltime}
+#SBATCH --time={cfg.walltime_icon}
 #SBATCH --nodes={cfg.icon_np_tot}
 #SBATCH --ntasks-per-node={cfg.ntasks_per_node}
 #SBATCH --partition={cfg.compute_queue}
 #SBATCH --constraint={cfg.constraint}
 #SBATCH --hint=nomultithread
-#SBATCH --output={logfile}
+#SBATCH --output={cfg.logfile}
 #SBATCH --open-mode=append
 #SBATCH --chdir={cfg.icon_work}
 
@@ -368,4 +368,12 @@ EOF
 # ----------------------------------------------------------------------
 # run the model!
 # ----------------------------------------------------------------------
- srun ./icon.exe
+handle_error(){{
+    # Check for invalid pointer error at the end of icon-art
+    if grep -q "free(): invalid pointer" {cfg.logfile} && grep -q "clean-up finished" {cfg.logfile}; then
+        exit 0
+    else
+        exit 1
+    fi
+}}
+srun ./{cfg.icon_execname} || handle_error

cases/icon-art-oem-test/icontools_remap_00_lbc_runjob.cfg

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="iconsub_{cfg.startdate_sim_yyyymmddhh}"
+#SBATCH --job-name=iconsub
 #SBATCH --account={cfg.compute_account}
 #SBATCH --chdir={cfg.icon_work}
 #SBATCH --partition={cfg.compute_queue}

cases/icon-art-oem-test/icontools_remap_ic_chem_runjob.cfg

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="{cfg.casename}_{cfg.startdate_sim_yyyymmddhh}_{cfg.forecasttime}"
+#SBATCH --job-name=iconremap_ic_chem
 #SBATCH --account={cfg.compute_account}
 #SBATCH --chdir={cfg.icon_work}
 #SBATCH --partition={cfg.compute_queue}

cases/icon-art-oem-test/icontools_remap_ic_runjob.cfg

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="iconremap_{cfg.startdate_sim_yyyymmddhh}"
+#SBATCH --job-name=iconremap_ic
 #SBATCH --account={cfg.compute_account}
 #SBATCH --chdir={cfg.icon_work}
 #SBATCH --partition={cfg.compute_queue}

cases/icon-art-oem-test/icontools_remap_lbc_chem_runjob.cfg

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="{cfg.casename}_{cfg.startdate_sim_yyyymmddhh}_{cfg.forecasttime}"
+#SBATCH --job-name=iconremap_lbc
 #SBATCH --account={cfg.compute_account}
 #SBATCH --chdir={cfg.icon_work}
 #SBATCH --partition={cfg.compute_queue}

cases/icon-art-oem-test/icontools_remap_lbc_rest_runjob.cfg

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="iconremap_lbc_{cfg.startdate_sim_yyyymmddhh}"
+#SBATCH --job-name=iconremap_lbc
 #SBATCH --account={cfg.compute_account}
 #SBATCH --chdir={cfg.icon_work}
 #SBATCH --partition={cfg.compute_queue}

cases/icon-test/config.yaml

@@ -1,6 +1,6 @@
-# Configuration file for the 'icon-test' case with ICON
+# Configuration file for the 'icon-async-test' case with ICON
 
-model: icon
+workflow: icon
 constraint: gpu
 run_on: cpu
 compute_queue: normal
@@ -18,6 +18,11 @@ output_filename: NWP_LAM
 filename_format: <output_filename>_DOM<physdom>_<ddhhmmss>
 lateral_boundary_grid_order: lateral_boundary
 
+walltime:
+    prepare_icon: '00:10:00'
+    icontools: '00:30:00'
+    icon: '00:30:00'
+
 meteo:
     dir: ./input/meteo
     prefix: ifs_
@@ -44,7 +49,6 @@ icon:
     binary_file: ./ext/icon/bin/icon
     runjob_filename: icon_runjob.cfg
     compute_queue: normal
-    walltime: '00:10:00'
     np_tot: 8
     np_io: 1
     np_restart: 1

cases/icon-test/icon_runjob.cfg

@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="{cfg.casename}_{cfg.startdate_sim_yyyymmddhh}_{cfg.enddate_sim_yyyymmddhh}"
+#SBATCH --job-name=icon
 #SBATCH --account={cfg.compute_account}
-#SBATCH --time={cfg.icon_walltime}
+#SBATCH --time={cfg.walltime_icon}
 #SBATCH --nodes={cfg.icon_np_tot}
 #SBATCH --ntasks-per-node={cfg.ntasks_per_node}
 #SBATCH --partition={cfg.compute_queue}
 #SBATCH --constraint={cfg.constraint}
 #SBATCH --hint=nomultithread
-#SBATCH --output={logfile}
+#SBATCH --output={cfg.logfile}
 #SBATCH --open-mode=append
 #SBATCH --chdir={cfg.icon_work}
 
@@ -342,4 +342,4 @@ EOF
 # ----------------------------------------------------------------------
 # run the model!
 # ----------------------------------------------------------------------
- srun ./icon.exe
+srun ./{cfg.icon_execname} || handle_error

cases/icon-test/icontools_remap_00_lbc_runjob.cfg

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="iconsub_{cfg.startdate_sim_yyyymmddhh}"
+#SBATCH --job-name=iconsub
 #SBATCH --account={cfg.compute_account}
 #SBATCH --chdir={cfg.icon_work}
 #SBATCH --partition={cfg.compute_queue}

cases/icon-test/icontools_remap_ic_runjob.cfg

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="iconremap_{cfg.startdate_sim_yyyymmddhh}"
+#SBATCH --job-name=iconremap_ic
 #SBATCH --account={cfg.compute_account}
 #SBATCH --chdir={cfg.icon_work}
 #SBATCH --partition={cfg.compute_queue}

cases/icon-test/icontools_remap_lbc_rest_runjob.cfg

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-#SBATCH --job-name="iconremap_lbc_{cfg.startdate_sim_yyyymmddhh}"
+#SBATCH --job-name=iconremap_lbc
 #SBATCH --account={cfg.compute_account}
 #SBATCH --chdir={cfg.icon_work}
 #SBATCH --partition={cfg.compute_queue}