Merge remote-tracking branch 'origin/develop' into feature/hpc-stack

* origin/develop:
  remove flags that were not present in Makefiles
  update jasper to 2.x.25. remove compiler flag in fv3nc2nemsio
  Update EMC_verif-global tag to verif_global_v1.13.4
  another use of _d where an _4 is needed
  Adjust how target is set for build_workflow_utils
  Add workflow_utils to build_all and link scripts
  copy/paste error from enkf_chgres_recenter.fd to enkf_chgres_recenter_nc.fd.  When going from nemsio to netcdf, the linking of ip, sp and w3nco changed from _d to _4.
  update .gitignore to exclude build and install directories as well as compiled files. bugfix in build_workflow_utils.sh hack. nceplibs-ncio now creates the module ncio and not fv3gfs_ncio.
  add cmake build capability for workflow utilities
  Update Fit2Obs tag to newm.1.3 for bugfix
  Update Fit2Obs tag to newm.1.3 for bugfix
  Update EMC_verif-global tag for Hera bug
  Pull in nwpara/gfsv16.0.6 updates for parse-storm-type.pl
  HOTFIX: Update EMC_verif-global tag for Hera bug
  Issue #1 and issue #238 - update Externals.cfg to match checkout.sh updates for v16.0.6
  move errchk definition from script to job for wave prdgen and gempak
  adding definition of errchk which was undefined in these scripts
  Issue #1 and issue #233 - update GLDAS tag to gldas_gfsv16_release.v1.13.0
  Issue #1 and issue #241 - update EMC_verif-global tag
  Issue #1 and issue #238 - remove ak_10m grid from config.wave and update checkout.sh tags for ufs-weather-model and EMC_gfs_wafs
  Issue #1 and issue #226 - update UPP tag to upp_gfsv16_release.v1.1.3 in Externals.cfg
  Issue #1 and issue #226 - update UPP tag to upp_gfsv16_release.v1.1.3
  Issue #1 and issue #226 - update exgfs_atmos_grib2_special_npoess.sh for dbn_alert
  issue #227 reducing output bufr files to 64 levels per NCO request
  issue #227 reducing output bufr files to 64 levels per NCO request
  Issue #1:  update ecflow to be consistent with NCO's gfs.v16.0.4 and            update checkout to bring in new UPP tag (see issue #226)
  Upaded ush script scale_dec.sh
  Updated scripts gfs_v16.0

Conflicts:
	Externals.cfg
	sorc/checkout.sh

Refs: #164

.gitignore

@@ -2,12 +2,14 @@
 #--------------------------
 __pycache__
 *.pyc
-*.o
+*.[aox]
 *.mod
 
-# Ignore exec folder
+# Ignore folders
 #-------------------
 exec/
+build*/
+install*/
 
 # Ignore fix directory symlinks
 #------------------------------

Externals.cfg

@@ -37,14 +37,14 @@ protocol = git
 required = True
 
 [EMC_verif-global]
-tag = verif_global_v1.13.1
+tag = verif_global_v1.13.4
 local_path = sorc/verif-global.fd
 repo_url = https://github.com/NOAA-EMC/EMC_verif-global.git
 protocol = git
 required = True
 
 [EMC_gfs_wafs]
-tag = gfs_wafs.v6.0.17
+tag = gfs_wafs.v6.0.18
 local_path = sorc/gfs_wafs.fd
 repo_url = https://github.com/NOAA-EMC/EMC_gfs_wafs.git
 protocol = git

ecflow/ecf/scripts/gdas/atmos/analysis/jgdas_atmos_analysis.ecf

@@ -3,7 +3,6 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_analysis_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-##BSUB -W 0:45   # 11/02/2020 temporarily change
 #BSUB -W 1:00
 #BSUB -n 1000
 #BSUB -R affinity[core(7)]

ecflow/ecf/scripts/gdas/atmos/gempak/jgdas_atmos_gempak.ecf

@@ -3,9 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_gempak_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-## JY temporarily increase wall clock as the submit time is long 
-##BSUB -W 0:15
-#BSUB -W 0:30
+#BSUB -W 0:15
 #BSUB -n 2
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=1]

ecflow/ecf/scripts/gdas/atmos/init/jgdas_atmos_gldas.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_gldas_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 2:00
+#BSUB -W 0:20
 #BSUB -n 112
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=28]

ecflow/ecf/scripts/gdas/atmos/obsproc/prep/jgdas_atmos_emcsfc_sfc_prep.ecf

@@ -3,7 +3,7 @@
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
 #BSUB -L /bin/sh
-#BSUB -W 0:10
+#BSUB -W 0:08
 #BSUB -n 1
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=1]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_anl.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f000.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f001.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f002.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f003.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f004.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f005.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f006.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f007.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f008.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/post/jgdas_atmos_post_f009.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_post_%FHR%_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:20
+#BSUB -W 0:12
 #BSUB -n 98
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=14]

ecflow/ecf/scripts/gdas/atmos/verf/jgdas_atmos_verfozn.ecf

@@ -3,7 +3,7 @@
 #BSUB -o %COM%/output/%ENVIR%/today/gdas_atmos_verfozn_%CYC%.o%J
 #BSUB -q %QUEUE%
 #BSUB -P %PROJ%
-#BSUB -W 0:10
+#BSUB -W 0:05
 #BSUB -n 1
 #BSUB -R affinity[core(1)]
 #BSUB -R span[ptile=1]

ecflow/ecf/scripts/gdas/enkf/post/jgdas_enkf_post_f003.ecf

@@ -0,0 +1,62 @@
+#BSUB -L /bin/sh
+#BSUB -J %E%gdas_enkf_post_f%FHOUT_EPOS%_%CYC%
+#BSUB -o %COM%/output/%ENVIR%/today/gdas_enkf_post_f%FHOUT_EPOS%_%CYC%.o%J
+#BSUB -q %QUEUE%
+#BSUB -P %PROJ%
+#BSUB -W 0:15
+#BSUB -n 80
+#BSUB -R affinity[core(7)]
+#BSUB -R span[ptile=4]
+#BSUB -cwd /tmp
+
+%include <head.h>
+%include <envir-p3.h>
+
+set -x
+
+export NODES=20
+export ntasks=80
+export ptile=4
+
+export NET=%NET:gfs%
+export RUN=%RUN%
+export CDUMP=%RUN%
+
+model=gfs
+%include <model_ver.h>
+
+############################################################
+# Load modules
+############################################################
+module load lsf/$lsf_ver
+module load impi/$impi_ver
+module load NetCDF-parallel/${netcdf_parallel_ver}
+module load HDF5-parallel/${hdf5_parallel_ver}
+
+module list
+
+#############################################################
+# WCOSS environment settings
+#############################################################
+export FHMIN_EPOS=%FHOUT_EPOS%
+export FHMAX_EPOS=%FHOUT_EPOS%
+export FHOUT_EPOS=%FHOUT_EPOS%
+export cyc=%CYC%
+export cycle=t%CYC%z
+export USE_CFP=YES
+
+############################################################
+# CALL executable job script here
+############################################################
+$HOMEgfs/jobs/JGDAS_ENKF_POST
+
+if [ $? -ne 0 ]; then
+   ecflow_client --msg="***JOB ${ECF_NAME} ERROR RUNNING J-SCRIPT ***"
+   ecflow_client --abort
+   exit
+fi
+
+%include <tail.h>
+%manual
+
+%end

ecflow/ecf/scripts/gdas/enkf/post/jgdas_enkf_post_f004.ecf

@@ -0,0 +1,62 @@
+#BSUB -L /bin/sh
+#BSUB -J %E%gdas_enkf_post_f%FHOUT_EPOS%_%CYC%
+#BSUB -o %COM%/output/%ENVIR%/today/gdas_enkf_post_f%FHOUT_EPOS%_%CYC%.o%J
+#BSUB -q %QUEUE%
+#BSUB -P %PROJ%
+#BSUB -W 0:15
+#BSUB -n 80
+#BSUB -R affinity[core(7)]
+#BSUB -R span[ptile=4]
+#BSUB -cwd /tmp
+
+%include <head.h>
+%include <envir-p3.h>
+
+set -x
+
+export NODES=20
+export ntasks=80
+export ptile=4
+
+export NET=%NET:gfs%
+export RUN=%RUN%
+export CDUMP=%RUN%
+
+model=gfs
+%include <model_ver.h>
+
+############################################################
+# Load modules
+############################################################
+module load lsf/$lsf_ver
+module load impi/$impi_ver
+module load NetCDF-parallel/${netcdf_parallel_ver}
+module load HDF5-parallel/${hdf5_parallel_ver}
+
+module list
+
+#############################################################
+# WCOSS environment settings
+#############################################################
+export FHMIN_EPOS=%FHOUT_EPOS%
+export FHMAX_EPOS=%FHOUT_EPOS%
+export FHOUT_EPOS=%FHOUT_EPOS%
+export cyc=%CYC%
+export cycle=t%CYC%z
+export USE_CFP=YES
+
+############################################################
+# CALL executable job script here
+############################################################
+$HOMEgfs/jobs/JGDAS_ENKF_POST
+
+if [ $? -ne 0 ]; then
+   ecflow_client --msg="***JOB ${ECF_NAME} ERROR RUNNING J-SCRIPT ***"
+   ecflow_client --abort
+   exit
+fi
+
+%include <tail.h>
+%manual
+
+%end

ecflow/ecf/scripts/gdas/enkf/post/jgdas_enkf_post_f005.ecf

@@ -0,0 +1,62 @@
+#BSUB -L /bin/sh
+#BSUB -J %E%gdas_enkf_post_f%FHOUT_EPOS%_%CYC%
+#BSUB -o %COM%/output/%ENVIR%/today/gdas_enkf_post_f%FHOUT_EPOS%_%CYC%.o%J
+#BSUB -q %QUEUE%
+#BSUB -P %PROJ%
+#BSUB -W 0:15
+#BSUB -n 80
+#BSUB -R affinity[core(7)]
+#BSUB -R span[ptile=4]
+#BSUB -cwd /tmp
+
+%include <head.h>
+%include <envir-p3.h>
+
+set -x
+
+export NODES=20
+export ntasks=80
+export ptile=4
+
+export NET=%NET:gfs%
+export RUN=%RUN%
+export CDUMP=%RUN%
+
+model=gfs
+%include <model_ver.h>
+
+############################################################
+# Load modules
+############################################################
+module load lsf/$lsf_ver
+module load impi/$impi_ver
+module load NetCDF-parallel/${netcdf_parallel_ver}
+module load HDF5-parallel/${hdf5_parallel_ver}
+
+module list
+
+#############################################################
+# WCOSS environment settings
+#############################################################
+export FHMIN_EPOS=%FHOUT_EPOS%
+export FHMAX_EPOS=%FHOUT_EPOS%
+export FHOUT_EPOS=%FHOUT_EPOS%
+export cyc=%CYC%
+export cycle=t%CYC%z
+export USE_CFP=YES
+
+############################################################
+# CALL executable job script here
+############################################################
+$HOMEgfs/jobs/JGDAS_ENKF_POST
+
+if [ $? -ne 0 ]; then
+   ecflow_client --msg="***JOB ${ECF_NAME} ERROR RUNNING J-SCRIPT ***"
+   ecflow_client --abort
+   exit
+fi
+
+%include <tail.h>
+%manual
+
+%end