Merge pull request #4 from natalie-perlin/update_gaea_c5

Bring in changes from release/public-v2.2.0 to allow running on Gaea C5
natalie-perlin · Dec 12, 2023 · 31975f6 · 31975f6
2 parents 3e6de2d + b66dc3c
commit 31975f6
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Showing 84 changed files with 88 additions and 83 deletions.
diff --git a/jobs/JREGIONAL_AQM_ICS b/jobs/JREGIONAL_AQM_ICS
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_AQM_LBCS b/jobs/JREGIONAL_AQM_LBCS
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_BIAS_CORRECTION_O3 b/jobs/JREGIONAL_BIAS_CORRECTION_O3
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_BIAS_CORRECTION_PM25 b/jobs/JREGIONAL_BIAS_CORRECTION_PM25
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_CHECK_POST_OUTPUT b/jobs/JREGIONAL_CHECK_POST_OUTPUT
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_FIRE_EMISSION b/jobs/JREGIONAL_FIRE_EMISSION
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_GET_EXTRN_MDL_FILES b/jobs/JREGIONAL_GET_EXTRN_MDL_FILES
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_MAKE_GRID b/jobs/JREGIONAL_MAKE_GRID
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_MAKE_ICS b/jobs/JREGIONAL_MAKE_ICS
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_MAKE_LBCS b/jobs/JREGIONAL_MAKE_LBCS
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_MAKE_OROG b/jobs/JREGIONAL_MAKE_OROG
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_MAKE_SFC_CLIMO b/jobs/JREGIONAL_MAKE_SFC_CLIMO
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_NEXUS_EMISSION b/jobs/JREGIONAL_NEXUS_EMISSION
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_NEXUS_GFS_SFC b/jobs/JREGIONAL_NEXUS_GFS_SFC
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_NEXUS_POST_SPLIT b/jobs/JREGIONAL_NEXUS_POST_SPLIT
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_PLOT_ALLVARS b/jobs/JREGIONAL_PLOT_ALLVARS
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_POINT_SOURCE b/jobs/JREGIONAL_POINT_SOURCE
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_POST_STAT_O3 b/jobs/JREGIONAL_POST_STAT_O3
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_POST_STAT_PM25 b/jobs/JREGIONAL_POST_STAT_PM25
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_PRE_POST_STAT b/jobs/JREGIONAL_PRE_POST_STAT
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_FCST b/jobs/JREGIONAL_RUN_FCST
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_MET_GENENSPROD_OR_ENSEMBLESTAT b/jobs/JREGIONAL_RUN_MET_GENENSPROD_OR_ENSEMBLESTAT
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_MET_GRIDSTAT_OR_POINTSTAT_VX b/jobs/JREGIONAL_RUN_MET_GRIDSTAT_OR_POINTSTAT_VX
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_MET_GRIDSTAT_OR_POINTSTAT_VX_ENSMEAN b/jobs/JREGIONAL_RUN_MET_GRIDSTAT_OR_POINTSTAT_VX_ENSMEAN
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_MET_GRIDSTAT_OR_POINTSTAT_VX_ENSPROB b/jobs/JREGIONAL_RUN_MET_GRIDSTAT_OR_POINTSTAT_VX_ENSPROB
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_MET_PB2NC_OBS b/jobs/JREGIONAL_RUN_MET_PB2NC_OBS
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_MET_PCPCOMBINE b/jobs/JREGIONAL_RUN_MET_PCPCOMBINE
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_POST b/jobs/JREGIONAL_RUN_POST
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/jobs/JREGIONAL_RUN_PRDGEN b/jobs/JREGIONAL_RUN_PRDGEN
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/modulefiles/build_gaea-c5_intel.lua b/modulefiles/build_gaea-c5_intel.lua
@@ -20,6 +20,9 @@ load(pathJoin("cmake", cmake_ver))
 
 load("srw_common")
 
+unload("darshan-runtime/3.4.0")
+unload("cray-pmi/6.1.10")
+
 setenv("CFLAGS","-diag-disable=10441")
 setenv("FFLAGS","-diag-disable=10441")
 

diff --git a/modulefiles/tasks/gaea-c5/python_srw.lua b/modulefiles/tasks/gaea-c5/python_srw.lua
@@ -1,3 +1,4 @@
 unload("miniconda3")
 load("conda")
 setenv("SRW_ENV", "srw_app")
+load("darshan-runtime/3.4.0")
diff --git a/scripts/exregional_aqm_ics.sh b/scripts/exregional_aqm_ics.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_aqm_lbcs.sh b/scripts/exregional_aqm_lbcs.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_bias_correction_o3.sh b/scripts/exregional_bias_correction_o3.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_bias_correction_pm25.sh b/scripts/exregional_bias_correction_pm25.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_check_post_output.sh b/scripts/exregional_check_post_output.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_fire_emission.sh b/scripts/exregional_fire_emission.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_get_extrn_mdl_files.sh b/scripts/exregional_get_extrn_mdl_files.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_make_grid.sh b/scripts/exregional_make_grid.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------
@@ -70,6 +70,7 @@ else
   print_info_msg "$VERBOSE" "
   All executables will be submitted with command \'${RUN_CMD_SERIAL}\'."
 fi
+
 #
 #-----------------------------------------------------------------------
 #

diff --git a/scripts/exregional_make_ics.sh b/scripts/exregional_make_ics.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_make_lbcs.sh b/scripts/exregional_make_lbcs.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_make_orog.sh b/scripts/exregional_make_orog.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_make_sfc_climo.sh b/scripts/exregional_make_sfc_climo.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_nexus_emission.sh b/scripts/exregional_nexus_emission.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_nexus_gfs_sfc.sh b/scripts/exregional_nexus_gfs_sfc.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_nexus_post_split.sh b/scripts/exregional_nexus_post_split.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_point_source.sh b/scripts/exregional_point_source.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_post_stat_o3.sh b/scripts/exregional_post_stat_o3.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_post_stat_pm25.sh b/scripts/exregional_post_stat_pm25.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_pre_post_stat.sh b/scripts/exregional_pre_post_stat.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_fcst.sh b/scripts/exregional_run_fcst.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_met_genensprod_or_ensemblestat.sh b/scripts/exregional_run_met_genensprod_or_ensemblestat.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_met_gridstat_or_pointstat_vx.sh b/scripts/exregional_run_met_gridstat_or_pointstat_vx.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_met_gridstat_or_pointstat_vx_ensmean.sh b/scripts/exregional_run_met_gridstat_or_pointstat_vx_ensmean.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_met_gridstat_or_pointstat_vx_ensprob.sh b/scripts/exregional_run_met_gridstat_or_pointstat_vx_ensprob.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_met_pb2nc_obs.sh b/scripts/exregional_run_met_pb2nc_obs.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_met_pcpcombine.sh b/scripts/exregional_run_met_pcpcombine.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_post.sh b/scripts/exregional_run_post.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_run_prdgen.sh b/scripts/exregional_run_prdgen.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 #
 #-----------------------------------------------------------------------
@@ -212,7 +212,7 @@ sed -n -e '1,500p' $DATAprdgen/prslevf${fhr}.txt >& $DATAprdgen/hi_pr_1.txt
 sed -n -e '501,$p' $DATAprdgen/prslevf${fhr}.txt >& $DATAprdgen/hi_pr_2.txt
 
 # Create script to execute production generation tasks in parallel using CFP
-echo "#!/bin/bash" > $DATAprdgen/poescript_${fhr}
+echo "#!/usr/bin/env bash" > $DATAprdgen/poescript_${fhr}
 echo "export DATA=${DATAprdgen}" >> $DATAprdgen/poescript_${fhr}
 echo "export COMOUT=${COMOUT}" >> $DATAprdgen/poescript_${fhr}
 

diff --git a/scripts/exregional_run_prdgen_subpiece.sh b/scripts/exregional_run_prdgen_subpiece.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 ################################################################################
 ####  UNIX Script Documentation Block
 #                      .                                             .

diff --git a/ush/wrappers/job_cards/qsub/get_ics.qsub b/ush/wrappers/job_cards/qsub/get_ics.qsub
@@ -1,4 +1,4 @@
-#! /bin/sh
+#!/usr/bin/env bash
 #PBS -A epic
 #PBS -l select=1:mpiprocs=1:ncpus=1:mem=2G
 #PBS -q main

diff --git a/ush/wrappers/job_cards/qsub/get_lbcs.qsub b/ush/wrappers/job_cards/qsub/get_lbcs.qsub
@@ -1,4 +1,4 @@
-#! /bin/sh
+#!/usr/bin/env bash
 #PBS -A epic
 #PBS -l select=1:mpiprocs=1:ncpus=1:mem=2G
 #PBS -q main

diff --git a/ush/wrappers/job_cards/qsub/make_grid.qsub b/ush/wrappers/job_cards/qsub/make_grid.qsub
@@ -1,4 +1,4 @@
-#! /bin/sh
+#!/usr/bin/env bash
 #PBS -A epic
 #PBS -l select=1:mpiprocs=24:ncpus=24
 #PBS -q main