Merge branch 'ufs-community:develop' into wav_ds2s

.gitignore

@@ -73,3 +73,8 @@ tests/fv3_conf/compile_qsub.IN
 tests/fv3_conf/fv3_slurm.IN
 tests/fv3_conf/fv3_qsub.IN
 build*.log*
+rocoto_workflow*
+fail_compile_*
+fail_test_*
+tests/run_dir
+tests/logs/log_*

cmake/Intel.cmake

@@ -20,7 +20,8 @@ endif()
 
 if(DEBUG)
     add_definitions(-DDEBUG)
-    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
+    #set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -check nopointer -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
+    set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS_DEBUG} -O0 -check -check noarg_temp_created -warn -warn noerrors -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv -init=snan,arrays")
     set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -ftrapuv")
 else()
     if(FASTER)

doc/UsersGuide/requirements.txt

@@ -8,7 +8,7 @@ alabaster==0.7.16
     # via sphinx
 babel==2.14.0
     # via sphinx
-certifi==2024.2.2
+certifi==2024.7.4
     # via requests
 charset-normalizer==3.3.2
     # via requests

modulefiles/ufs_frontera.intel.lua

@@ -0,0 +1,33 @@
+help([[
+loads UFS Model prerequisites for Frontera/Intel
+]])
+
+prepend_path("MODULEPATH", "/work2/06146/tg854455/frontera/spack-stack/modulefiles")
+load("ecflow/5.8.4")
+
+prepend_path("MODULEPATH", "/work2/01118/tg803972/frontera/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core")
+
+stack_intel_ver=os.getenv("stack_intel_ver") or "19.1.1.217"
+load(pathJoin("stack-intel", stack_intel_ver))
+
+stack_impi_ver=os.getenv("stack_impi_ver") or "2020.4.304"
+load(pathJoin("stack-intel-mpi", stack_impi_ver))
+
+cmake_ver=os.getenv("cmake_ver") or "3.24.2"
+load(pathJoin("cmake", cmake_ver))
+--load("cmake/3.24.2")
+
+load("ufs_common")
+
+stack_python_ver=os.getenv("stack_python_ver") or "3.10.13"
+load(pathJoin("stack-python", stack_python_ver))
+
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
+setenv("CC", "mpiicc")
+setenv("CXX", "mpiicpc")
+setenv("FC", "mpiifort")
+setenv("CMAKE_Platform", "frontera.intel")
+
+whatis("Description: UFS build environment")

tests/bl_date.conf

@@ -1 +1 @@
-export BL_DATE=20240624
+export BL_DATE=20240730

tests/default_vars.sh

@@ -764,6 +764,7 @@ export LDIAG3D=.false.
 export QDIAG3D=.false.
 export PRINT_DIFF_PGR=.false.
 export MAX_OUTPUT_FIELDS=310
+export UPDATE_FULL_OMEGA=.false.
 
 # Stochastic physics
 export STOCHINI=.false.
@@ -1101,6 +1102,12 @@ export NY_GLB=320
 export NPZ=127
 export NPZP=128
 
+# Use updated omega calculations if 
+#   hydrostatic is set to false
+if [[ "${HYDROSTATIC}" == .false. ]]; then
+  export UPDATE_FULL_OMEGA=.true.
+fi
+
 # default resources
 export DOMAINS_STACK_SIZE=8000000
 export INPES=${INPES_cpl_dflt}

tests/detect_machine.sh

@@ -48,6 +48,9 @@ case $(hostname -f) in
 
   login[1-4].stampede2.tacc.utexas.edu) MACHINE_ID=stampede ;; ### stampede1-4
 
+  login[1-4].frontera.tacc.utexas.edu) MACHINE_ID=frontera ;; ### frontera1-4
+  c*.frontera.tacc.utexas.edu) MACHINE_ID=frontera ;; ### frontera compute 
+
   login0[1-2].expanse.sdsc.edu) MACHINE_ID=expanse ;; ### expanse1-2
 
   discover3[1-5].prv.cube) MACHINE_ID=discover ;; ### discover31-35

tests/error-test.conf

@@ -0,0 +1,27 @@
+# This file is an alternative to rt.conf that tests whether the regression test system rt.sh can detect failure conditions.
+#
+# ./rt.sh [options] -l error-test.conf
+#
+# If the rt.sh detects errors correctly, the workflow shouldn't finish. Some jobs should be failed or not submitted, and some should succeed.
+# See details below.
+
+# This should succeed
+COMPILE | atm_dyn32 | intel | -DAPP=ATM -DCCPP_SUITES=FV3_GFS_v16,FV3_GFS_v16_flake,FV3_GFS_v17_p8,FV3_GFS_v17_p8_rrtmgp,FV3_GFS_v15_thompson_mynn_lam3km,FV3_WoFS_v0,FV3_GFS_v17_p8_mynn,FV3_GFS_v17_p8_ugwpv1 -D32BIT=ON | | fv3 |
+
+# This should succeed
+RUN | control_c48.v2.sfc                                |                                      | baseline |
+
+# These tests should always fail, and prevent the workflow from completing.
+RUN | fail_to_copy                                      |                                      | baseline |
+RUN | fail_to_run                                       |                                      | baseline |
+
+# Using 64-bit dynamics ensures results change, but the test runs. The workflow jobs should complete
+# for the COMPILE and RUN, but the results should change.
+COMPILE | atm_dyn64 | intel | -DAPP=ATM -DCCPP_SUITES=FV3_GFS_v16,FV3_GFS_v16_flake,FV3_GFS_v17_p8,FV3_GFS_v17_p8_rrtmgp,FV3_GFS_v15_thompson_mynn_lam3km,FV3_WoFS_v0,FV3_GFS_v17_p8_mynn,FV3_GFS_v17_p8_ugwpv1 | | fv3 |
+RUN | control_c48                                       |                                      | baseline |
+
+# This compile job should fail, and prevent the workflow from completing.
+COMPILE | fail_to_compile | intel | --invalid-argument -DAPP=ATM -DCCPP_SUITES=whatever |  | fv3 |
+
+# This test should not be submitted, because its compile job has failed.
+RUN | dependency_unmet                                  |                                      | baseline |

tests/fv3_conf/compile_slurm.IN_gaea

@@ -7,6 +7,7 @@
 #SBATCH --partition=eslogin_c5
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=8
+#SBATCH --mem-per-cpu=4G
 #SBATCH --time=180
 #SBATCH --job-name="@[JBNME]"
 

tests/fv3_conf/fv3_qsub.IN_acorn

@@ -30,6 +30,13 @@ export ESMF_RUNTIME_COMPLIANCECHECK=OFF:depth=4
 export ESMF_RUNTIME_PROFILE=ON
 export ESMF_RUNTIME_PROFILE_OUTPUT="SUMMARY"
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 mpiexec -n @[TASKS] -ppn @[TPN] -depth @[THRD] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_qsub.IN_derecho

@@ -35,6 +35,13 @@ export MPICH_COLL_OPT_OFF=1
 # Avoid job errors because of filesystem synchronization delays
 sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 mpiexec -n @[UFS_TASKS] -ppn @[PPN] --hostfile $PBS_NODEFILE ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_qsub.IN_wcoss2

@@ -30,6 +30,13 @@ export ESMF_RUNTIME_COMPLIANCECHECK=OFF:depth=4
 export ESMF_RUNTIME_PROFILE=ON
 export ESMF_RUNTIME_PROFILE_OUTPUT="SUMMARY"
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 mpiexec -n @[TASKS] -ppn @[TPN] -depth @[THRD] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_slurm.IN_expanse

@@ -26,6 +26,14 @@ echo "Model started: "`date`
 export OMP_STACK_SIZE=512M
 export OMP_NUM_THREADS=@[THRD]
 export I_MPI_PMI_LIBRARY=/cm/shared/apps/slurm/current/lib64/libpmi.so
+
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 srun -n @[TASKS] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_slurm.IN_gaea

@@ -32,6 +32,13 @@ export ESMF_RUNTIME_PROFILE_OUTPUT="SUMMARY"
 # Avoid job errors because of filesystem synchronization delays
 sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 srun --label -n @[TASKS] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_slurm.IN_hera

@@ -38,6 +38,13 @@ export PSM_SHAREDCONTEXTS=1
 # Avoid job errors because of filesystem synchronization delays
 sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 # shellcheck disable=SC2102
 srun --label -n @[TASKS] ./fv3.exe
 

tests/fv3_conf/fv3_slurm.IN_hercules

@@ -46,6 +46,13 @@ fi
 # Avoid job errors because of filesystem synchronization delays
 sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 srun --label -n @[TASKS] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_slurm.IN_jet

@@ -36,6 +36,13 @@ export ESMF_RUNTIME_PROFILE_OUTPUT="SUMMARY"
 # Avoid job errors because of filesystem synchronization delays
 sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 srun --label -n @[TASKS] --cpus-per-task=@[THRD] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_slurm.IN_noaacloud

@@ -39,6 +39,13 @@ export OMP_NUM_THREADS=1
 # Avoid job errors because of filesystem synchronization delays
 sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 srun --mpi=pmi2 --label -n @[TASKS] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_slurm.IN_orion

@@ -39,6 +39,13 @@ export ESMF_RUNTIME_PROFILE_OUTPUT="SUMMARY"
 # Avoid job errors because of filesystem synchronization delays
 sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 srun --label -n @[TASKS] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_slurm.IN_s4

@@ -35,6 +35,13 @@ export PSM_SHAREDCONTEXTS=1
 # Avoid job errors because of filesystem synchronization delays
 sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 srun --label -n @[TASKS] ./fv3.exe
 
 echo "Model ended:    " `date`

tests/fv3_conf/fv3_slurm.IN_stampede

@@ -29,6 +29,13 @@ export LD_BIND_NOW=1
 # Avoid job errors because of filesystem synchronization delays
 #sync && sleep 1
 
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
 #mpirun -prepend-rank -np $SBATCH_NP ./fv3.exe
 ibrun -n @[TASKS] ./fv3.exe