Bug fixes in machine files (#692)

## DESCRIPTION OF CHANGES: Cleaning up bugs in the machine files. The first bug prompted this PR, and the rest were found subsequently. The bugs (and their fixes) are as follows: 1) A space is missing after the `print_info_msg` and `print_err_msg_exit` function calls in the `file_location` functions. Inserting a space gets passed this bug, but subsequent issues were found as described below. **For machine files that call the `print_info_msg` function in `file_location` (`cheyenne.sh`, `hera.sh`, `jet.sh`, and `orion.sh`):** Fixing this bug leads to other failures because when the "*" stanza is encountered in the `file_location` function, the `EXTRN_MDL_SYSBASEDIR_ICS|LBCS` variable gets set to the message that `file_location` returns. Since that message contains spaces, it leads to other failures in downstream scripts (the ex-scripts). Simply removing the printing out of the message (thus causing `EXTRN_MDL_SYSBASEDIR_ICS|LBCS` to be set to a null string) fixes the failures, so this was the fix implemented. If desired, a message for an empty value for `EXTRN_MDL_SYSBASEDIR_ICS|LBCS` can be placed in another script (where those variables are used). **For machine files that use `print_err_msg_exit` in `file_location` (`stampede.sh` and `wcoss_dell_p3.sh`):** These should not exit if the file location is not available since the experiment can still complete successfully. So just removing the `print_err_msg_exit` call should work (and make the behavior of these machine files consistent with the set above). 2) In all the machine files, the variable `FV3GFS_FILE_FMT_ICS` should be changed to `FV3GFS_FILE_FMT_LBCS` in the definition of `EXTRN_MDL_SYSBASEDIR_LBCS`. This was fixed in all the files. 3) In `stampede.sh`, a variable named `SYSBASEDIR_ICS` is defined. This is a typo. Modify to `EXTRN_MDL_SYSBASEDIR_ICS`. ## TESTS CONDUCTED: Ran the WE2E test `grid_RRFS_CONUS_25km_ics_HRRR_lbcs_RAP_suite_GSD_SAR` on: * Hera -- successful * Jet -- successful except for UPP tasks * Cheyenne -- successful except for UPP tasks The UPP task failures are new and being experienced by other PRs as well (e.g. #689). The original issue with machine files seems resolved. ## CONTRIBUTORS (optional): @JeffBeck-NOAA encountered and reported the original error.
ufs-community · Mar 8, 2022 · 2d3fcf4 · 2d3fcf4
1 parent 78f8512
commit 2d3fcf4
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Showing 8 changed files with 46 additions and 77 deletions.
diff --git a/ush/machine/cheyenne.sh b/ush/machine/cheyenne.sh
@@ -9,16 +9,12 @@ function file_location() {
   external_model=${1}
   external_file_fmt=${2}
 
+  location=""
   case ${external_model} in
 
     "FV3GFS")
       location='/glade/p/ral/jntp/UFS_CAM/COMGFS/gfs.${yyyymmdd}/${hh}'
       ;;
-    "*")
-      print_info_msg"\
-        External model \'${external_model}\' does not have a default
-      location on Cheyenne. Please set a user-defined file location."
-      ;;
 
   esac
   echo ${location:-}
@@ -30,7 +26,7 @@ EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${FV3GFS_FILE_FMT_ICS})}
 EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
   ${EXTRN_MDL_NAME_LBCS} \
-  ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_LBCS})}
 
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
@@ -57,6 +53,7 @@ TOPO_DIR=${TOPO_DIR:-"/glade/p/ral/jntp/UFS_CAM/fix/fix_orog"}
 SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/glade/p/ral/jntp/UFS_CAM/fix/climo_fields_netcdf"}
 FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
 
+# Run commands for executables
 RUN_CMD_SERIAL="time"
 RUN_CMD_UTILS='mpirun -np $nprocs'
 RUN_CMD_FCST='mpirun -np ${PE_MEMBER01}'
@@ -71,6 +68,6 @@ NDAS_OBS_DIR="/glade/p/ral/jntp/UFS_SRW_app/develop/obs_data/ndas/proc"
 MET_BIN_EXEC="bin"
 
 # Test Data Locations
-TEST_PREGEN_BASEDIR=/glade/p/ral/jntp/UFS_CAM/FV3LAM_pregen
-TEST_COMINgfs=/glade/scratch/ketefian/NCO_dirs/COMGFS
-TEST_EXTRN_MDL_SOURCE_BASEDIR=/glade/p/ral/jntp/UFS_SRW_app/staged_extrn_mdl_files
+TEST_PREGEN_BASEDIR="/glade/p/ral/jntp/UFS_CAM/FV3LAM_pregen"
+TEST_COMINgfs="/glade/scratch/ketefian/NCO_dirs/COMGFS"
+TEST_EXTRN_MDL_SOURCE_BASEDIR="/glade/p/ral/jntp/UFS_SRW_app/staged_extrn_mdl_files"
diff --git a/ush/machine/hera.sh b/ush/machine/hera.sh
@@ -9,27 +9,24 @@ function file_location() {
   external_model=${1}
   external_file_fmt=${2}
 
+  location=""
   case ${external_model} in
 
     "FV3GFS")
       location='/scratch1/NCEPDEV/rstprod/com/gfs/prod/gfs.${yyyymmdd}/${hh}/atmos'
       ;;
-    *)
-      print_info_msg"\
-        External model \'${external_model}\' does not have a default
-      location on Hera. Will try to pull from HPSS"
-      ;;
 
   esac
   echo ${location:-}
+
 }
 
 EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${EXTRN_MDL_NAME_ICS} \
   ${FV3GFS_FILE_FMT_ICS})}
 EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
   ${EXTRN_MDL_NAME_LBCS} \
-  ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_LBCS})}
 
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
@@ -59,6 +56,7 @@ TOPO_DIR=${TOPO_DIR:-"/scratch1/NCEPDEV/global/glopara/fix/fix_orog"}
 SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/scratch1/NCEPDEV/global/glopara/fix/fix_sfc_climo"}
 FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/scratch2/BMC/det/FV3LAM_pregen"}
 
+# Run commands for executables
 RUN_CMD_SERIAL="time"
 RUN_CMD_UTILS="srun"
 RUN_CMD_FCST="srun"
@@ -73,8 +71,8 @@ NDAS_OBS_DIR="/scratch2/BMC/det/UFS_SRW_app/develop/obs_data/ndas/proc"
 MET_BIN_EXEC="bin"
 
 # Test Data Locations
-TEST_PREGEN_BASEDIR=/scratch2/BMC/det/FV3LAM_pregen
-TEST_COMINgfs=/scratch2/NCEPDEV/fv3-cam/noscrub/UFS_SRW_App/COMGFS
-TEST_EXTRN_MDL_SOURCE_BASEDIR=/scratch2/BMC/det/Gerard.Ketefian/UFS_CAM/staged_extrn_mdl_files
-TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS=/scratch2/BMC/det/UFS_SRW_app/dummy_FV3GFS_sys_dir
-TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS=/scratch2/BMC/det/UFS_SRW_app/dummy_FV3GFS_sys_dir
+TEST_PREGEN_BASEDIR="/scratch2/BMC/det/FV3LAM_pregen"
+TEST_COMINgfs="/scratch2/NCEPDEV/fv3-cam/noscrub/UFS_SRW_App/COMGFS"
+TEST_EXTRN_MDL_SOURCE_BASEDIR="/scratch2/BMC/det/Gerard.Ketefian/UFS_CAM/staged_extrn_mdl_files"
+TEST_ALT_EXTRN_MDL_SYSBASEDIR_ICS="/scratch2/BMC/det/UFS_SRW_app/dummy_FV3GFS_sys_dir"
+TEST_ALT_EXTRN_MDL_SYSBASEDIR_LBCS="/scratch2/BMC/det/UFS_SRW_app/dummy_FV3GFS_sys_dir"
diff --git a/ush/machine/jet.sh b/ush/machine/jet.sh
@@ -9,7 +9,9 @@ function file_location() {
   external_model=${1}
   external_file_fmt=${2}
 
+  location=""
   case ${external_model} in
+
     "FV3GFS")
       case $external_file_fmt in
         "nemsio")
@@ -29,22 +31,18 @@ function file_location() {
     "HRRR")
       location='/public/data/grids/hrrr/conus/wrfprs/grib2'
       ;;
-    "*")
-      print_info_msg"\
-        External model \'${external_model}\' does not have a default
-      location on Jet. Will try to pull from HPSS."
-      ;;
 
   esac
   echo ${location:-}
+
 }
 
 EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${EXTRN_MDL_NAME_ICS} \
   ${FV3GFS_FILE_FMT_ICS})}
 EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
   ${EXTRN_MDL_NAME_LBCS} \
-  ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_LBCS})}
 
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
@@ -74,12 +72,13 @@ TOPO_DIR=${TOPO_DIR:-"/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix/fix_orog"}
 SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix/fix_sfc_climo"}
 FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/mnt/lfs4/BMC/wrfruc/FV3-LAM/pregen"}
 
+# Run commands for executables
 RUN_CMD_SERIAL="time"
 RUN_CMD_UTILS="srun"
 RUN_CMD_FCST="srun"
 RUN_CMD_POST="srun"
 
 # Test Data Locations
-TEST_PREGEN_BASEDIR=/mnt/lfs4/BMC/wrfruc/FV3-LAM/pregen
-TEST_COMINgfs=/lfs1/HFIP/hwrf-data/hafs-input/COMGFS
-TEST_EXTRN_MDL_SOURCE_BASEDIR=/mnt/lfs1/BMC/gsd-fv3/Gerard.Ketefian/UFS_CAM/staged_extrn_mdl_files
+TEST_PREGEN_BASEDIR="/mnt/lfs4/BMC/wrfruc/FV3-LAM/pregen"
+TEST_COMINgfs="/lfs1/HFIP/hwrf-data/hafs-input/COMGFS"
+TEST_EXTRN_MDL_SOURCE_BASEDIR="/mnt/lfs1/BMC/gsd-fv3/Gerard.Ketefian/UFS_CAM/staged_extrn_mdl_files"
diff --git a/ush/machine/odin.sh b/ush/machine/odin.sh
@@ -9,6 +9,7 @@ function file_location() {
   external_model=${1}
   external_file_fmt=${2}
 
+  location=""
   case ${external_model} in
 
     "GSMGFS")
@@ -17,11 +18,7 @@ function file_location() {
     "FV3GFS")
       location='/scratch/ywang/test_runs/FV3_regional/gfs/${yyyymmdd}'
       ;;
-    "*")
-      print_info_msg"\
-        External model \'${external_model}\' does not have a default
-      location on Odin Please set a user-defined file location."
-      ;;
+
   esac
   echo ${location:-}
 
@@ -32,7 +29,7 @@ EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${FV3GFS_FILE_FMT_ICS})}
 EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
   ${EXTRN_MDL_NAME_LBCS} \
-  ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_LBCS})}
 
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
@@ -62,6 +59,7 @@ TOPO_DIR=${TOPO_DIR:-"/scratch/ywang/fix/theia_fix/fix_orog"}
 SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/scratch/ywang/fix/climo_fields_netcdf"}
 FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
 
+# Run commands for executables
 RUN_CMD_SERIAL="srun -n 1"
 RUN_CMD_UTILS='srun -n $nprocs'
 RUN_CMD_FCST='srun -n ${PE_MEMBER01}'

diff --git a/ush/machine/orion.sh b/ush/machine/orion.sh
@@ -10,25 +10,17 @@ function file_location() {
   external_model=${1}
   external_file_fmt=${2}
 
-  case ${external_model} in
-
-    "*")
-      print_info_msg"\
-        External model \'${external_model}\' does not have a default
-      location on Orion. Please set a user-defined file location."
-      ;;
-
-  esac
+  location=""
   echo ${location:-}
 
 }
 
 EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${EXTRN_MDL_NAME_ICS} \
-    ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_ICS})}
 EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
   ${EXTRN_MDL_NAME_LBCS} \
-  ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_LBCS})}
 
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
@@ -58,6 +50,7 @@ TOPO_DIR=${TOPO_DIR:-"/work/noaa/global/glopara/fix/fix_orog"}
 SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/work/noaa/global/glopara/fix/fix_sfc_climo"}
 FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
 
+# Run commands for executables
 RUN_CMD_SERIAL="time"
 RUN_CMD_UTILS="srun"
 RUN_CMD_FCST='srun -n ${PE_MEMBER01}'

diff --git a/ush/machine/singularity.sh b/ush/machine/singularity.sh
@@ -9,26 +9,17 @@ function file_location() {
   external_model=${1}
   external_file_fmt=${2}
 
-  case ${external_model} in
-
-    "*")
-      print_info_msg"\
-        External model \'${external_model}\' does not have a default
-      location. Please set a user-defined file location."
-      ;;
-
-  esac
+  location=""
   echo ${location:-}
 
 }
 
-
 EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${EXTRN_MDL_NAME_ICS} \
-    ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_ICS})}
 EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
   ${EXTRN_MDL_NAME_LBCS} \
-  ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_LBCS})}
 
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
@@ -58,6 +49,7 @@ TOPO_DIR=${TOPO_DIR:-"/contrib/global/glopara/fix/fix_orog"}
 SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/contrib/global/glopara/fix/fix_sfc_climo"}
 FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
 
+# Run commands for executables
 RUN_CMD_SERIAL="time"
 RUN_CMD_UTILS='mpirun -np $nprocs --oversubscribe'
 RUN_CMD_FCST='mpirun -n ${PE_MEMBER01} --oversubscribe'

diff --git a/ush/machine/stampede.sh b/ush/machine/stampede.sh
@@ -9,30 +9,26 @@ function file_location() {
   external_model=${1}
   external_file_fmt=${2}
 
+  location=""
   case ${external_model} in
 
     "GSMGFS")
       ;& # Fall through. All files in same place
     "FV3GFS")
       location='/scratch/00315/tg455890/GDAS/20190530/2019053000_mem001'
       ;;
-    "*")
-      print_err_msg_exit"\
-        External model \'${external_model}\' does not have a default
-      location on Jet Please set a user-defined file location."
-      ;;
 
   esac
   echo ${location:-}
-}
 
+}
 
-SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
+EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${EXTRN_MDL_NAME_ICS} \
   ${FV3GFS_FILE_FMT_ICS})}
 EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
   ${EXTRN_MDL_NAME_LBCS} \
-  ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_LBCS})}
 
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
@@ -62,6 +58,7 @@ TOPO_DIR=${TOPO_DIR:-"/work/00315/tg455890/stampede2/regional_fv3/fix_orog"}
 SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/work/00315/tg455890/stampede2/regional_fv3/climo_fields_netcdf"}
 FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/needs/to/be/specified"}
 
+# Run commands for executables
 RUN_CMD_SERIAL="time"
 RUN_CMD_UTILS='ibrun -np $nprocs'
 RUN_CMD_FCST='ibrun -np $nprocs'

diff --git a/ush/machine/wcoss_dell_p3.sh b/ush/machine/wcoss_dell_p3.sh
@@ -9,6 +9,7 @@ function file_location() {
   external_model=${1}
   external_file_fmt=${2}
 
+  location=""
   case ${external_model} in
 
     "FV3GFS")
@@ -23,11 +24,6 @@ function file_location() {
     "NAM")
       location='/gpfs/dell1/nco/ops/com/nam/prod'
       ;;
-    "*")
-      print_err_msg_exit"\
-        External model \'${external_model}\' does not have a default
-      location on Jet Please set a user-defined file location."
-      ;;
 
   esac
   echo ${location:-}
@@ -39,7 +35,7 @@ EXTRN_MDL_SYSBASEDIR_ICS=${EXTRN_MDL_SYSBASEDIR_ICS:-$(file_location \
   ${FV3GFS_FILE_FMT_ICS})}
 EXTRN_MDL_SYSBASEDIR_LBCS=${EXTRN_MDL_SYSBASEDIR_LBCS:-$(file_location \
   ${EXTRN_MDL_NAME_LBCS} \
-  ${FV3GFS_FILE_FMT_ICS})}
+  ${FV3GFS_FILE_FMT_LBCS})}
 
 # System scripts to source to initialize various commands within workflow
 # scripts (e.g. "module").
@@ -66,7 +62,7 @@ TOPO_DIR=${TOPO_DIR:-"/gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fi
 SFC_CLIMO_INPUT_DIR=${SFC_CLIMO_INPUT_DIR:-"/gpfs/dell2/emc/modeling/noscrub/emc.glopara/git/fv3gfs/fix/fix_sfc_climo"}
 FIXLAM_NCO_BASEDIR=${FIXLAM_NCO_BASEDIR:-"/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/FV3LAM_pregen"}
 
-# Commands to run
+# Run commands for executables
 RUN_CMD_SERIAL="mpirun"
 RUN_CMD_UTILS="mpirun"
 RUN_CMD_FCST='mpirun -l -np ${PE_MEMBER01}'
@@ -80,8 +76,7 @@ MRMS_OBS_DIR="/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/obs_data/mrms/proc"
 NDAS_OBS_DIR="/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/obs_data/ndas/proc"
 MET_BIN_EXEC="exec"
 
-
 # Test Data Locations
-TEST_PREGEN_BASEDIR=/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/FV3LAM_pregen
-TEST_COMINgfs=/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/COMGFS
-TEST_EXTRN_MDL_SOURCE_BASEDIR=/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/extrn_mdl_files
+TEST_PREGEN_BASEDIR="/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/FV3LAM_pregen"
+TEST_COMINgfs="/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/COMGFS"
+TEST_EXTRN_MDL_SOURCE_BASEDIR="/gpfs/dell2/emc/modeling/noscrub/UFS_SRW_App/extrn_mdl_files"