Merge branch 'develop' into feature/fixaux

DeniseWorthen · Aug 27, 2024 · f306585 · f306585
2 parents 9e51704 + 94a3cd7
commit f306585
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Showing 63 changed files with 2,593 additions and 2,778 deletions.
diff --git a/CDEPS-interface/CDEPS b/CDEPS-interface/CDEPS
diff --git a/CDEPS-interface/cdeps_files.cmake b/CDEPS-interface/cdeps_files.cmake
@@ -41,14 +41,11 @@ list(APPEND cdeps_dshr_files
 
 list(APPEND cdeps_datm_files
   CDEPS/datm/atm_comp_nuopc.F90
-  CDEPS/datm/datm_datamode_cfsr_mod.F90
   CDEPS/datm/datm_datamode_clmncep_mod.F90
   CDEPS/datm/datm_datamode_core2_mod.F90
   CDEPS/datm/datm_datamode_cplhist_mod.F90
   CDEPS/datm/datm_datamode_era5_mod.F90
   CDEPS/datm/datm_datamode_gefs_mod.F90
-  CDEPS/datm/datm_datamode_gfs_mod.F90
-  CDEPS/datm/datm_datamode_gfs_hafs_mod.F90
   CDEPS/datm/datm_datamode_jra_mod.F90
   CDEPS/datm/datm_datamode_simple_mod.F90
 )

diff --git a/FV3 b/FV3
diff --git a/build.sh b/build.sh
@@ -1,17 +1,10 @@
 #!/bin/bash
 set -eu
-uname_s=$(uname -s)
-if [[ ${uname_s} == Darwin ]]; then
-  UFS_MODEL_DIR=$(greadlink -f -n "${BASH_SOURCE[0]}")
-  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
-  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
-else
-  UFS_MODEL_DIR=$(readlink -f -n "${BASH_SOURCE[0]}")
-  UFS_MODEL_DIR=$(dirname "${UFS_MODEL_DIR}")
-  UFS_MODEL_DIR=$(cd "${UFS_MODEL_DIR}" && pwd -P)
-fi
-echo "UFS MODEL DIR: ${UFS_MODEL_DIR}"
+
+SCRIPT_REALPATH=$(realpath "${BASH_SOURCE[0]}")
+UFS_MODEL_DIR=$(dirname "${SCRIPT_REALPATH}")
 readonly UFS_MODEL_DIR
+echo "UFS MODEL DIR: ${UFS_MODEL_DIR}"
 
 export CC=${CC:-mpicc}
 export CXX=${CXX:-mpicxx}
@@ -26,4 +19,4 @@ for i in ${CMAKE_FLAGS}; do ARR_CMAKE_FLAGS+=("${i}") ; done
 cmake "${UFS_MODEL_DIR}" "${ARR_CMAKE_FLAGS[@]}"
 # Turn off OpenMP threading for parallel builds
 # to avoid exhausting the number of user processes
-OMP_NUM_THREADS=1 make -j "${BUILD_JOBS:-4}" "VERBOSE=${BUILD_VERBOSE:-}"
+OMP_NUM_THREADS=1 make -j "${BUILD_JOBS:-4}" "VERBOSE=${BUILD_VERBOSE:-}"
diff --git a/tests/ci/Jenkinsfile.combined b/tests/ci/Jenkinsfile.combined
@@ -312,14 +312,6 @@ def generateStage(nodeLabel) {
                       echo "Testing concluded...removing labels for $machine from $GIT_URL"
                       git remote -v | grep -w sshorigin > /dev/null 2>&1 && git remote remove sshorigin > /dev/null 2>&1
                       git remote add sshorigin $SSH_ORIGIN > /dev/null 2>&1
-
-                      if [[ -f $WORKSPACE/tests/logs/RT-run-$machine.log ]] ; then
-                         git add $WORKSPACE/tests/logs/RT-run-$machine.log
-                      fi
-                      git commit  --allow-empty -m "[AutoRT] $machine Job Failed!\n\n\n on-behalf-of @ufs-community <ecc.platform@noaa.gov>"
-
-                      git pull sshorigin $FORK_BRANCH
-                      git push sshorigin HEAD:$FORK_BRANCH
 
                       tar --create --gzip --verbose --dereference --file "${machine_name_logs}.tgz" ${WORKSPACE}/tests/logs/*.log
 

diff --git a/tests/compile.sh b/tests/compile.sh
@@ -12,14 +12,8 @@ function trim {
 
 SECONDS=0
 
-uname_s=$(uname -s)
-if [[ ${uname_s} == Darwin ]]; then
-  greadlnk=$(greadlink -f -n "${BASH_SOURCE[0]}" )
-  MYDIR=$(cd "$(dirname "${greadlnk}" )" && pwd -P)
-else
-  readlnk=$(readlink -f -n "${BASH_SOURCE[0]}" )
-  MYDIR=$(cd "$(dirname "${readlnk}" )" && pwd -P)
-fi
+SCRIPT_REALPATH=$(realpath "${BASH_SOURCE[0]}")
+MYDIR=$(dirname "${SCRIPT_REALPATH}")
 readonly MYDIR
 
 # ----------------------------------------------------------------------

diff --git a/tests/default_vars.sh b/tests/default_vars.sh
@@ -559,6 +559,7 @@ export MODEL_INITIALIZATION=false
 export WARM_START=.false.
 export READ_INCREMENT=.false.
 export RES_LATLON_DYNAMICS="''"
+export INCREMENT_FILE_ON_NATIVE_GRID=.false.
 export NGGPS_IC=.true.
 export EXTERNAL_IC=.true.
 export MAKE_NH=.true.
@@ -1332,10 +1333,10 @@ export_datm_cdeps ()
   export INPUT_NML=input.mom6.nml.IN
   export DIAG_TABLE=diag_table_template
   export DATM_SRC=CFSR
-  export FILENAME_BASE=cfsr.
-  export MESH_ATM=${FILENAME_BASE//.}_mesh.nc
-  export atm_datamode=${DATM_SRC}
-  export stream_files=INPUT/${FILENAME_BASE}201110.nc
+  export FILEBASE_DATM=cfsr
+  export MESH_ATM=${FILEBASE_DATM}_mesh.nc
+  export atm_datamode=GEFS
+  export stream_files=INPUT/${FILEBASE_DATM}.201110.nc
   export EXPORT_ALL=.false.
   export STREAM_OFFSET=0
 

diff --git a/tests/error-test.conf b/tests/error-test.conf
@@ -11,6 +11,9 @@ COMPILE | atm_dyn32 | intel | -DAPP=ATM -DCCPP_SUITES=FV3_GFS_v16,FV3_GFS_v16_fl
 # This should succeed
 RUN | control_c48.v2.sfc                                |                                      | baseline |
 
+# This should fail due to wall clock timeout
+RUN | control_c48.v2.sfc_timeout                        |                                      | baseline |
+
 # These tests should always fail, and prevent the workflow from completing.
 RUN | fail_to_copy                                      |                                      | baseline |
 RUN | fail_to_run                                       |                                      | baseline |

diff --git a/tests/logs/OpnReqTests_control_p8_hera.log b/tests/logs/OpnReqTests_control_p8_hera.log
@@ -1,9 +1,9 @@
-Wed Aug 21 22:05:02 UTC 2024
+Mon Aug 26 19:59:54 UTC 2024
 Start Operation Requirement Test
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/control_p8_bit_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3986824/bit_base_bit_base
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_255239/bit_base_bit_base
 Checking test bit_base results ....
 Moving baseline bit_base files ....
  Moving sfcf000.nc .........OK
@@ -51,14 +51,14 @@ Moving baseline bit_base files ....
  Moving RESTART/20210323.060000.sfc_data.tile5.nc .........OK
  Moving RESTART/20210323.060000.sfc_data.tile6.nc .........OK
 
-  0: The total amount of wall time                        = 280.831970
-  0: The maximum resident set size (KB)                   = 1448916
+  0: The total amount of wall time                        = 282.094574
+  0: The maximum resident set size (KB)                   = 1459728
 
 Test bit_base PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/control_p8_dbg_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3986824/dbg_base_dbg_base
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_255239/dbg_base_dbg_base
 Checking test dbg_base results ....
 Moving baseline dbg_base files ....
  Moving sfcf000.nc .........OK
@@ -106,14 +106,14 @@ Moving baseline dbg_base files ....
  Moving RESTART/20210323.060000.sfc_data.tile5.nc .........OK
  Moving RESTART/20210323.060000.sfc_data.tile6.nc .........OK
 
-  0: The total amount of wall time                        = 992.336985
-  0: The maximum resident set size (KB)                   = 1437772
+  0: The total amount of wall time                        = 985.479617
+  0: The maximum resident set size (KB)                   = 1417884
 
 Test dbg_base PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/control_p8_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3986824/dcp_dcp
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_255239/dcp_dcp
 Checking test dcp results ....
  Comparing sfcf000.nc .....USING NCCMP......OK
  Comparing sfcf021.nc .....USING NCCMP......OK
@@ -160,14 +160,14 @@ Checking test dcp results ....
  Comparing RESTART/20210323.060000.sfc_data.tile5.nc .....USING NCCMP......OK
  Comparing RESTART/20210323.060000.sfc_data.tile6.nc .....USING NCCMP......OK
 
-  0: The total amount of wall time                        = 255.618968
-  0: The maximum resident set size (KB)                   = 1425456
+  0: The total amount of wall time                        = 248.873990
+  0: The maximum resident set size (KB)                   = 1437132
 
 Test dcp PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/control_p8_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3986824/mpi_mpi
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_255239/mpi_mpi
 Checking test mpi results ....
  Comparing sfcf000.nc .....USING NCCMP......OK
  Comparing sfcf021.nc .....USING NCCMP......OK
@@ -214,14 +214,14 @@ Checking test mpi results ....
  Comparing RESTART/20210323.060000.sfc_data.tile5.nc .....USING NCCMP......OK
  Comparing RESTART/20210323.060000.sfc_data.tile6.nc .....USING NCCMP......OK
 
-  0: The total amount of wall time                        = 250.392410
-  0: The maximum resident set size (KB)                   = 1437096
+  0: The total amount of wall time                        = 252.449329
+  0: The maximum resident set size (KB)                   = 1422488
 
 Test mpi PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/control_p8_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3986824/rst_rst
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_255239/rst_rst
 Checking test rst results ....
  Comparing sfcf000.nc .....USING NCCMP......OK
  Comparing sfcf021.nc .....USING NCCMP......OK
@@ -268,14 +268,14 @@ Checking test rst results ....
  Comparing RESTART/20210323.060000.sfc_data.tile5.nc .....USING NCCMP......OK
  Comparing RESTART/20210323.060000.sfc_data.tile6.nc .....USING NCCMP......OK
 
-  0: The total amount of wall time                        = 257.380091
-  0: The maximum resident set size (KB)                   = 1423788
+  0: The total amount of wall time                        = 252.763505
+  0: The maximum resident set size (KB)                   = 1423640
 
 Test rst PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/control_p8_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3986824/std_base_std_base
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_255239/std_base_std_base
 Checking test std_base results ....
 Moving baseline std_base files ....
  Moving sfcf000.nc .........OK
@@ -323,14 +323,14 @@ Moving baseline std_base files ....
  Moving RESTART/20210323.060000.sfc_data.tile5.nc .........OK
  Moving RESTART/20210323.060000.sfc_data.tile6.nc .........OK
 
-  0: The total amount of wall time                        = 267.250624
-  0: The maximum resident set size (KB)                   = 1421992
+  0: The total amount of wall time                        = 253.485325
+  0: The maximum resident set size (KB)                   = 1438440
 
 Test std_base PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/control_p8_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3986824/thr_thr
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_255239/thr_thr
 Checking test thr results ....
  Comparing sfcf000.nc .....USING NCCMP......OK
  Comparing sfcf021.nc .....USING NCCMP......OK
@@ -377,11 +377,11 @@ Checking test thr results ....
  Comparing RESTART/20210323.060000.sfc_data.tile5.nc .....USING NCCMP......OK
  Comparing RESTART/20210323.060000.sfc_data.tile6.nc .....USING NCCMP......OK
 
-  0: The total amount of wall time                        = 257.163548
-  0: The maximum resident set size (KB)                   = 1434436
+  0: The total amount of wall time                        = 247.766378
+  0: The maximum resident set size (KB)                   = 1411920
 
 Test thr PASS
 
 OPERATION REQUIREMENT TEST WAS SUCCESSFUL
-Wed Aug 21 23:13:54 UTC 2024
-Elapsed time: 01h:08m:53s. Have a nice day!
+Mon Aug 26 21:14:01 UTC 2024
+Elapsed time: 01h:14m:07s. Have a nice day!
diff --git a/tests/logs/OpnReqTests_cpld_control_nowave_noaero_p8_hera.log b/tests/logs/OpnReqTests_cpld_control_nowave_noaero_p8_hera.log
@@ -1,9 +1,9 @@
-Wed Aug 21 20:56:23 UTC 2024
+Mon Aug 26 18:51:21 UTC 2024
 Start Operation Requirement Test
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/cpld_control_c96_noaero_p8_dbg_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3387682/dbg_base_dbg_base
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_2593550/dbg_base_dbg_base
 Checking test dbg_base results ....
 Moving baseline dbg_base files ....
  Moving sfcf021.tile1.nc .........OK
@@ -66,14 +66,14 @@ Moving baseline dbg_base files ....
  Moving RESTART/iced.2021-03-23-21600.nc .........OK
  Moving RESTART/ufs.cpld.cpl.r.2021-03-23-21600.nc .........OK
 
-  0: The total amount of wall time                        = 1337.925051
-  0: The maximum resident set size (KB)                   = 1527960
+  0: The total amount of wall time                        = 1361.846982
+  0: The maximum resident set size (KB)                   = 1537900
 
 Test dbg_base PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/cpld_control_c96_noaero_p8_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3387682/rst_rst
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_2593550/rst_rst
 Checking test rst results ....
  Comparing sfcf021.tile1.nc .....USING NCCMP......OK
  Comparing sfcf021.tile2.nc .....USING NCCMP......OK
@@ -135,14 +135,14 @@ Checking test rst results ....
  Comparing RESTART/iced.2021-03-23-21600.nc .....USING NCCMP......OK
  Comparing RESTART/ufs.cpld.cpl.r.2021-03-23-21600.nc .....USING NCCMP......OK
 
-  0: The total amount of wall time                        = 429.025844
-  0: The maximum resident set size (KB)                   = 1528532
+  0: The total amount of wall time                        = 715.515398
+  0: The maximum resident set size (KB)                   = 1525500
 
 Test rst PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/cpld_control_c96_noaero_p8_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3387682/std_base_std_base
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_2593550/std_base_std_base
 Checking test std_base results ....
 Moving baseline std_base files ....
  Moving sfcf021.tile1.nc .........OK
@@ -205,11 +205,11 @@ Moving baseline std_base files ....
  Moving RESTART/iced.2021-03-23-21600.nc .........OK
  Moving RESTART/ufs.cpld.cpl.r.2021-03-23-21600.nc .........OK
 
-  0: The total amount of wall time                        = 441.109791
-  0: The maximum resident set size (KB)                   = 1516924
+  0: The total amount of wall time                        = 435.784809
+  0: The maximum resident set size (KB)                   = 1528568
 
 Test std_base PASS
 
 OPERATION REQUIREMENT TEST WAS SUCCESSFUL
-Wed Aug 21 22:05:01 UTC 2024
-Elapsed time: 01h:08m:39s. Have a nice day!
+Mon Aug 26 19:59:54 UTC 2024
+Elapsed time: 01h:08m:34s. Have a nice day!
diff --git a/tests/logs/OpnReqTests_regional_control_hera.log b/tests/logs/OpnReqTests_regional_control_hera.log
@@ -1,9 +1,9 @@
-Wed Aug 21 18:19:56 UTC 2024
+Mon Aug 26 16:17:09 UTC 2024
 Start Operation Requirement Test
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/regional_control_bit_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_65311/bit_base_bit_base
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3681501/bit_base_bit_base
 Checking test bit_base results ....
 Moving baseline bit_base files ....
  Moving dynf000.nc .........OK
@@ -15,14 +15,14 @@ Moving baseline bit_base files ....
  Moving NATLEV.GrbF00 .........OK
  Moving NATLEV.GrbF06 .........OK
 
-  0: The total amount of wall time                        = 1391.521656
-  0: The maximum resident set size (KB)                   = 777236
+  0: The total amount of wall time                        = 1404.274425
+  0: The maximum resident set size (KB)                   = 769724
 
 Test bit_base PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/regional_control_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_65311/dcp_dcp
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3681501/dcp_dcp
 Checking test dcp results ....
  Comparing dynf000.nc .....USING NCCMP......OK
  Comparing dynf006.nc .....USING NCCMP......OK
@@ -33,14 +33,14 @@ Checking test dcp results ....
  Comparing NATLEV.GrbF00 .....USING CMP......OK
  Comparing NATLEV.GrbF06 .....USING CMP......OK
 
-  0: The total amount of wall time                        = 2169.925001
-  0: The maximum resident set size (KB)                   = 743380
+  0: The total amount of wall time                        = 2178.286214
+  0: The maximum resident set size (KB)                   = 751032
 
 Test dcp PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/regional_control_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_65311/std_base_std_base
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3681501/std_base_std_base
 Checking test std_base results ....
 Moving baseline std_base files ....
  Moving dynf000.nc .........OK
@@ -52,14 +52,14 @@ Moving baseline std_base files ....
  Moving NATLEV.GrbF00 .........OK
  Moving NATLEV.GrbF06 .........OK
 
-  0: The total amount of wall time                        = 2169.154728
-  0: The maximum resident set size (KB)                   = 733176
+  0: The total amount of wall time                        = 2198.737097
+  0: The maximum resident set size (KB)                   = 734276
 
 Test std_base PASS
 
 
 baseline dir = /scratch1/NCEPDEV/stmp4/role.epic/FV3_OPNREQ_TEST/OPNREQ_TEST/regional_control_std_base_gnu
-working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_65311/thr_thr
+working dir  = /scratch1/NCEPDEV/stmp2/role.epic/FV3_OPNREQ_TEST/opnReqTest_3681501/thr_thr
 Checking test thr results ....
  Comparing dynf000.nc .....USING NCCMP......OK
  Comparing dynf006.nc .....USING NCCMP......OK
@@ -70,11 +70,11 @@ Checking test thr results ....
  Comparing NATLEV.GrbF00 .....USING CMP......OK
  Comparing NATLEV.GrbF06 .....USING CMP......OK
 
-  0: The total amount of wall time                        = 2203.506465
-  0: The maximum resident set size (KB)                   = 733136
+  0: The total amount of wall time                        = 2321.006507
+  0: The maximum resident set size (KB)                   = 742260
 
 Test thr PASS
 
 OPERATION REQUIREMENT TEST WAS SUCCESSFUL
-Wed Aug 21 20:56:22 UTC 2024
-Elapsed time: 02h:36m:27s. Have a nice day!
+Mon Aug 26 18:51:20 UTC 2024
+Elapsed time: 02h:34m:14s. Have a nice day!