Merge remote-tracking branch 'upstream/develop' into conv_hr5update

NOAHMP-interface/CMakeLists.txt

@@ -13,6 +13,7 @@ list(APPEND _noahmp_cap_files noahmp/drivers/nuopc/lnd_comp_kind.F90
 
 # CCPP interface
 list(APPEND _noahmp_ccpp_files noahmp/drivers/ccpp/noahmpdrv.F90
+                               noahmp/drivers/ccpp/lnd_iau_mod.F90
                                noahmp/drivers/ccpp/sfc_diff.f
                                noahmp/drivers/ccpp/machine.F
                                noahmp/drivers/ccpp/noahmp_tables.f90

modulefiles/ufs_gaea.intel.lua

@@ -1,5 +1,5 @@
 help([[
-  This module loads libraries required for building and running UFS Weather Model 
+  This module loads libraries required for building and running UFS Weather Model
   on the NOAA RDHPC machine Gaea C5 using Intel-2023.1.0.
 ]])
 

modulefiles/ufs_gaea.intelllvm.lua

@@ -1,16 +1,16 @@
 help([[
-  This module loads libraries required for building and running UFS Weather Model 
+  This module loads libraries required for building and running UFS Weather Model
   on the NOAA RDHPC machine Gaea C5 using Intel-2023.1.0.
 ]])
 
 whatis([===[Loads libraries needed for building the UFS Weather Model on Gaea ]===])
 
-prepend_path("MODULEPATH", "/ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/upp-addon-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/fms-2024.01/install/modulefiles/Core")
 
-stack_intel_ver=os.getenv("stack_intel_ver") or "2023.1.0"
+stack_intel_ver=os.getenv("stack_intel_ver") or "2023.2.0"
 load(pathJoin("stack-intel", stack_intel_ver))
 
-stack_cray_mpich_ver=os.getenv("stack_cray_mpich_ver") or "8.1.25"
+stack_cray_mpich_ver=os.getenv("stack_cray_mpich_ver") or "8.1.28"
 load(pathJoin("stack-cray-mpich", stack_cray_mpich_ver))
 
 stack_python_ver=os.getenv("stack_python_ver") or "3.10.13"
@@ -27,8 +27,7 @@ load(pathJoin("nccmp", nccmp_ver))
 unload("darshan-runtime")
 unload("cray-libsci")
 
-unload("intel-classic/2023.1.0")
-load("intel-oneapi/2023.1.0")
+load("intel-classic/2023.2.0")
 
 setenv("I_MPI_CC", "icx")
 setenv("I_MPI_CXX", "icpx")

modulefiles/ufs_hera.intelllvm.lua

@@ -2,7 +2,7 @@ help([[
 loads UFS Model prerequisites for Hera/IntelLLVM
 ]])
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/upp-addon-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/fms-2024.01/install/modulefiles/Core")
 
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 load(pathJoin("stack-intel", stack_intel_ver))

modulefiles/ufs_hercules.intelllvm.lua

@@ -2,7 +2,7 @@ help([[
 loads UFS Model prerequisites for Hercules/IntelLLVM
 ]])
 
-prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.6.0/envs/upp-addon-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.6.0/envs/fms-2024.01/install/modulefiles/Core")
 
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.9.0"
 load(pathJoin("stack-intel", stack_intel_ver))

modulefiles/ufs_noaacloud.intel.lua

@@ -4,23 +4,27 @@ loads UFS Model prerequisites for NOAA Parallelworks/Intel
 
 prepend_path("MODULEPATH", "/contrib/spack-stack-rocky8/spack-stack-1.6.0/envs/fms-2024.01/install/modulefiles/Core")
 prepend_path("MODULEPATH", "/apps/modules/modulefiles")
-prepend_path("PATH", "/contrib/EPIC/bin")
-load("gnu")
-load("stack-intel")
-load("stack-intel-oneapi-mpi")
 
-stack_intel_ver=os.getenv("stack_intel_ver") or "2021.10.0"
+gnu_ver=os.getenv("gnu_ver") or ""
+load(pathJoin("gnu", gnu_ver))
+
+stack_intel_ver=os.getenv("stack_intel_ver") or ""
 load(pathJoin("stack-intel", stack_intel_ver))
 
-stack_impi_ver=os.getenv("stack_impi_ver") or "2021.10.0"
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
-unload("gnu")
+stack_intel_oneapi_mpi_ver=os.getenv("stack_intel_oneapi_mpi_ver") or ""
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
+
+gnu_ver=os.getenv("gnu_ver") or ""
+unload(pathJoin("gnu", gnu_ver))
 
 cmake_ver=os.getenv("cmake_ver") or "3.23.1"
 load(pathJoin("cmake", cmake_ver))
 
 load("ufs_common")
 
+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")

modulefiles/ufs_orion.intelllvm.lua

@@ -2,7 +2,7 @@ help([[
 loads UFS Model prerequisites for OrionLLVM/Intel
 ]])
 
-prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/upp-addon-env/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/fms-2024.01/install/modulefiles/Core")
 
 stack_intel_ver=os.getenv("stack_intel_ver") or "2021.9.0"
 load(pathJoin("stack-intel", stack_intel_ver))

tests-dev/baseline_setup.yaml

@@ -54,15 +54,15 @@ jet:
   QUEUE: batch
   COMPILE_QUEUE: batch
   PARTITION: xjet
-  dprefix: /mnt/lfs4/HFIP/hfv3gfs/${USER}
-  DISKNM: /mnt/lfs4/HFIP/hfv3gfs/role.epic/RT
-  STMP: /mnt/lfs4/HFIP/hfv3gfs/${USER}/RT_BASELINE
-  PTMP: /mnt/lfs4/HFIP/hfv3gfs/${USER}/RT_RUNDIRS
+  dprefix: /lfs5/HFIP/hfv3gfs/${USER}
+  DISKNM: /lfs5/HFIP/hfv3gfs/role.epic/RT
+  STMP: /lfs5/HFIP/hfv3gfs/${USER}/RT_BASELINE
+  PTMP: /lfs5/HFIP/hfv3gfs/${USER}/RT_RUNDIRS
   RUNDIR_ROOT:
   SCHEDULER: slurm
-  INPUTDATA_ROOT: /mnt/lfs4/HFIP/hfv3gfs/role.epic/RT/NEMSfv3gfs/input-data-20240501
-  INPUTDATA_ROOT_WW3: /mnt/lfs4/HFIP/hfv3gfs/role.epic/RT/NEMSfv3gfs/input-data-20240501/WW3_input_data_20240214
-  INPUTDATA_ROOT_BMIC: /mnt/lfs4/HFIP/hfv3gfs/role.epic/RT/NEMSfv3gfs/BM_IC-20220207
+  INPUTDATA_ROOT: /lfs5/HFIP/hfv3gfs/role.epic/RT/NEMSfv3gfs/input-data-20240501
+  INPUTDATA_ROOT_WW3: /lfs5/HFIP/hfv3gfs/role.epic/RT/NEMSfv3gfs/input-data-20240501/WW3_input_data_20240214
+  INPUTDATA_ROOT_BMIC: /lfs5/HFIP/hfv3gfs/role.epic/RT/NEMSfv3gfs/BM_IC-20220207
 derecho:
   QUEUE: main
   COMPILE_QUEUE: main
@@ -82,8 +82,8 @@ noaacloud:
   PARTITION:
   dprefix: /lustre
   DISKNM: /contrib/ufs-weather-model/RT
-  STMP: /lustre/stmp4
-  PTMP: /lustre/stmp2
+  STMP: /lustre/stmp
+  PTMP: /lustre/stmp
   RUNDIR_ROOT:
   SCHEDULER: slurm
   INPUTDATA_ROOT: /contrib/ufs-weather-model/RT/NEMSfv3gfs/input-data-20240501

tests-dev/create_log.py

@@ -3,10 +3,27 @@
 import subprocess
 import yaml
 from datetime import datetime
+#import datetime
 from ufs_test_utils import get_testcase, write_logfile, delete_files, machine_check_off
 
+def get_timestamps(path):
+    """Obtain experiment starting and ending time marks through file timestamps
+
+    Args:
+        path (str): experiment log directory
+    Returns:
+        str: experiment starting and ending time strings
+    """
+    dir_list = os.listdir(path)
+    dt = []
+    for f in dir_list:
+        m_time = os.path.getmtime(path+f)
+        dt.append(datetime.fromtimestamp(m_time))
+    dtsort=sorted(dt)
+    return str(dtsort[0]),str(dtsort[-1])
+
 def finish_log():
-    """Collects regression test results and generates log file.
+    """Collect regression test results and generate log file.
     """
     UFS_TEST_YAML = str(os.getenv('UFS_TEST_YAML'))
     PATHRT     = os.getenv('PATHRT')
@@ -40,40 +57,46 @@ def finish_log():
                         COMPILE_ID  = apps
                         COMPILE_LOG = 'compile_'+COMPILE_ID+'.log'
                         COMPILE_LOG_TIME ='compile_'+COMPILE_ID+'_timestamp.txt'
-                        with open('./logs/log_'+MACHINE_ID+'/'+COMPILE_LOG) as f:
-                            if "[100%] Linking Fortran executable" in f.read():
-                                COMPILE_PASS += 1
-                                f.seek(0)
-                                for line in f:
-                                    if 'export RUNDIR_ROOT=' in line:
-                                        RUNDIR_ROOT=line.split("=")[1]
-                                        break
-                                compile_err = RUNDIR_ROOT.strip('\n')+'/compile_'+COMPILE_ID+'/err'
-                                with open(compile_err) as ferr:
-                                    contents = ferr.read()
-                                    count_warning = contents.count(": warning #")
-                                    count_remarks = contents.count(": remark #")
-                                    ferr.close()
-                                warning_log = ""
-                                if count_warning > 0:
-                                    warning_log = "("+str(count_warning)+" warnings"
-                                if count_remarks > 0:
-                                    warning_log+= ","+str(count_remarks)+" remarks)"
-                                flog = open('./logs/log_'+MACHINE_ID+'/'+COMPILE_LOG_TIME)
-                                timing_data = flog.read()
-                                first_line = timing_data.split('\n', 1)[0]
-                                etime = int(first_line.split(",")[4].strip()) - int(first_line.split(",")[1].strip())
-                                btime = int(first_line.split(",")[3].strip()) - int(first_line.split(",")[2].strip())
-                                etime_min, etime_sec = divmod(int(etime), 60)
-                                etime_min = f"{etime_min:02}"; etime_sec = f"{etime_sec:02}"
-                                btime_min, btime_sec = divmod(int(btime), 60)
-                                btime_min = f"{btime_min:02}"; btime_sec = f"{btime_sec:02}"
-                                time_log = " ["+etime_min+':'+etime_sec+', '+btime_min+':'+btime_sec+"]"
-                                flog.close()
-                                compile_log = "PASS -- COMPILE "+COMPILE_ID+time_log+warning_log+"\n"
-                            else:
-                                compile_log = "FAIL -- COMPILE "+COMPILE_ID+"\n"                        
-                            f.close()
+                        COMPILE_CHECK1 ='Compile '+COMPILE_ID+' Completed'
+                        COMPILE_CHECK2 ='[100%] Linking Fortran executable'
+                        try:
+                            with open('./logs/log_'+MACHINE_ID+'/'+COMPILE_LOG) as f:
+                                if COMPILE_CHECK1 in f.read() or COMPILE_CHECK2 in f.read():                        
+                                    COMPILE_PASS += 1
+                                    f.seek(0)
+                                    for line in f:
+                                        if 'export RUNDIR_ROOT=' in line:
+                                            RUNDIR_ROOT=line.split("=")[1]
+                                            break
+                                    compile_err = RUNDIR_ROOT.strip('\n')+'/compile_'+COMPILE_ID+'/err'
+                                    with open(compile_err) as ferr:
+                                        contents = ferr.read()
+                                        count_warning = contents.count(": warning #")
+                                        count_remarks = contents.count(": remark #")
+                                        ferr.close()
+                                    warning_log = ""
+                                    if count_warning > 0:
+                                        warning_log = "("+str(count_warning)+" warnings"
+                                    if count_remarks > 0:
+                                        warning_log+= ","+str(count_remarks)+" remarks)"
+                                    flog = open('./logs/log_'+MACHINE_ID+'/'+COMPILE_LOG_TIME)
+                                    timing_data = flog.read()
+                                    first_line = timing_data.split('\n', 1)[0]
+                                    etime = int(first_line.split(",")[4].strip()) - int(first_line.split(",")[1].strip())
+                                    btime = int(first_line.split(",")[3].strip()) - int(first_line.split(",")[2].strip())
+                                    etime_min, etime_sec = divmod(int(etime), 60)
+                                    etime_min = f"{etime_min:02}"; etime_sec = f"{etime_sec:02}"
+                                    btime_min, btime_sec = divmod(int(btime), 60)
+                                    btime_min = f"{btime_min:02}"; btime_sec = f"{btime_sec:02}"
+                                    time_log = " ["+etime_min+':'+etime_sec+', '+btime_min+':'+btime_sec+"]"
+                                    flog.close()
+                                    compile_log = "PASS -- COMPILE "+COMPILE_ID+time_log+warning_log+"\n"
+                                else:
+                                    compile_log = "FAIL -- COMPILE "+COMPILE_ID+"\n"                                        
+                                f.close()
+                        except FileNotFoundError:
+                            compile_log = "FAIL -- COMPILE "+COMPILE_ID+"\n"
+                            print('./logs/log_'+MACHINE_ID+'/'+COMPILE_LOG+': does not exist')
                         run_logs += compile_log
                     else:
                         PASS_TESTS = True
@@ -94,47 +117,49 @@ def finish_log():
                             PASS_CHECK = 'Test '+TEST_ID+' PASS'
                             MAXS_CHECK = 'The maximum resident set size (KB)'
                             pass_flag = False
-                            create_dep_flag = False
-                            if (CREATE_BASELINE == 'true' and not DEP_RUN == ""):
-                                create_dep_flag = True
-                            if not create_dep_flag:
+                            try:
                                 with open('./logs/log_'+MACHINE_ID+'/'+TEST_LOG) as f:
                                     if PASS_CHECK in f.read():
                                         pass_flag = True
-                                        f.close()
-                                if pass_flag:
-                                    f = open('./logs/log_'+MACHINE_ID+'/'+TEST_LOG_TIME)
-                                    timing_data = f.read()
-                                    first_line = timing_data.split('\n', 1)[0]
-                                    etime = str(int(first_line.split(",")[4].strip()) - int(first_line.split(",")[1].strip()))
-                                    rtime = str(int(first_line.split(",")[3].strip()) - int(first_line.split(",")[2].strip()))
-                                    etime_min, etime_sec = divmod(int(etime), 60)
-                                    etime_min = f"{etime_min:02}"; etime_sec = f"{etime_sec:02}"
-                                    rtime_min, rtime_sec = divmod(int(rtime), 60)
-                                    rtime_min = f"{rtime_min:02}"; rtime_sec = f"{rtime_sec:02}"
-                                    time_log = " ["+etime_min+':'+etime_sec+', '+rtime_min+':'+rtime_sec+"]"
-                                    f.close()
-                                with open('./logs/log_'+MACHINE_ID+'/'+TEST_LOG) as f:
-                                    if pass_flag :
+                                        f.close()                                    
+                            except FileNotFoundError:
+                                print('./logs/log_'+MACHINE_ID+'/'+TEST_LOG+': does not exist')
+                            if pass_flag:
+                                f = open('./logs/log_'+MACHINE_ID+'/'+TEST_LOG_TIME)
+                                timing_data = f.read()
+                                first_line = timing_data.split('\n', 1)[0]
+                                etime = str(int(first_line.split(",")[4].strip()) - int(first_line.split(",")[1].strip()))
+                                rtime = str(int(first_line.split(",")[3].strip()) - int(first_line.split(",")[2].strip()))
+                                etime_min, etime_sec = divmod(int(etime), 60)
+                                etime_min = f"{etime_min:02}"; etime_sec = f"{etime_sec:02}"
+                                rtime_min, rtime_sec = divmod(int(rtime), 60)
+                                rtime_min = f"{rtime_min:02}"; rtime_sec = f"{rtime_sec:02}"
+                                time_log = " ["+etime_min+':'+etime_sec+', '+rtime_min+':'+rtime_sec+"]"
+                                f.close()
+                                if pass_flag :
+                                    with open('./logs/log_'+MACHINE_ID+'/'+TEST_LOG) as f:
                                         rtlog_file = f.readlines()
                                         for line in rtlog_file:
                                             if MAXS_CHECK in line:
                                                 memsize= line.split('=')[1].strip()
                                         test_log = 'PASS -- TEST '+TEST_ID+time_log+' ('+memsize+' MB)\n'
                                         PASS_NR += 1
-                                    else:
-                                        test_log = 'FAIL -- TEST '+TEST_ID+'\n'
-                                        failed_list.append(TEST_NAME+' '+RT_COMPILER)
-                                        FAIL_NR += 1
-                                    run_logs += test_log
-                                f.close()
+                                        f.close()
+                                else:
+                                    test_log = 'FAIL -- TEST '+TEST_ID+'\n'
+                                    failed_list.append(TEST_NAME+' '+RT_COMPILER)
+                                    FAIL_NR += 1
+                                run_logs += test_log
                     run_logs += '\n'
     write_logfile(filename, "a", output=run_logs)
 
-    TEST_START_TIME = os.getenv('TEST_START_TIME')
-    TEST_END_TIME   = os.getenv('TEST_END_TIME')
-    start_time      = datetime.strptime(TEST_START_TIME, "%Y%m%d %H:%M:%S")
-    end_time        = datetime.strptime(TEST_END_TIME, "%Y%m%d %H:%M:%S")
+    TEST_START_TIME, TEST_END_TIME = get_timestamps('./logs/log_'+MACHINE_ID+'/')
+
+    clean_START_TIME= TEST_START_TIME.split('.')[0]
+    start_time      = datetime.strptime(clean_START_TIME, "%Y-%m-%d %H:%M:%S")
+    clean_END_TIME= TEST_END_TIME.split('.')[0]
+    end_time        = datetime.strptime(clean_END_TIME, "%Y-%m-%d %H:%M:%S")
+
     hours, remainder= divmod((end_time - start_time).total_seconds(), 3600)
     minutes, seconds= divmod(remainder, 60)
     hours = int(hours);    minutes=int(minutes);     seconds =int(seconds)

tests-dev/create_xml.py

@@ -32,6 +32,7 @@ def rocoto_create_entries(RTPWD,MACHINE_ID,INPUTDATA_ROOT,INPUTDATA_ROOT_WW3,INP
   <!ENTITY INPUTDATA_ROOT "{INPUTDATA_ROOT}">
   <!ENTITY INPUTDATA_ROOT_WW3 "{INPUTDATA_ROOT_WW3}">
   <!ENTITY INPUTDATA_ROOT_BMIC "{INPUTDATA_ROOT_BMIC}">
+  <!ENTITY INPUTDATA_LM4 "{INPUTDATA_ROOT}/LM4_input_data">
   <!ENTITY RUNDIR_ROOT    "{RUNDIR_ROOT}">
   <!ENTITY NEW_BASELINE   "{NEW_BASELINE}">
 ]>
@@ -195,6 +196,7 @@ def write_runtest_env():
 export INPUTDATA_ROOT={INPUTDATA_ROOT}
 export INPUTDATA_ROOT_WW3={INPUTDATA_ROOT_WW3}
 export INPUTDATA_ROOT_BMIC={INPUTDATA_ROOT_BMIC}
+export INPUTDATA_LM4={INPUTDATA_ROOT}/LM4_input_data
 export PATHRT={PATHRT}
 export PATHTR={PATHTR}
 export NEW_BASELINE={NEW_BASELINE}
@@ -216,8 +218,8 @@ def write_runtest_env():
 export RTVERBOSE=false
 """
     if ( MACHINE_ID == 'jet' ):
-         runtest_envs+="export PATH=/lfs4/HFIP/hfv3gfs/software/miniconda3/4.8.3/envs/ufs-weather-model/bin:/lfs4/HFIP/hfv3gfs/software/miniconda3/4.8.3/bin:$PATH"
-         runtest_envs+="export PYTHONPATH=/lfs4/HFIP/hfv3gfs/software/miniconda3/4.8.3/envs/ufs-weather-model/lib/python3.8/site-packages:/lfs4/HFIP/hfv3gfs/software/miniconda3/4.8.3/lib/python3.8/site-packages"
+        runtest_envs += f"export PATH=/lfs4/HFIP/hfv3gfs/software/miniconda3/4.8.3/envs/ufs-weather-model/bin:/lfs4/HFIP/hfv3gfs/software/miniconda3/4.8.3/bin:$PATH\n"
+        runtest_envs += f"export PYTHONPATH=/lfs4/HFIP/hfv3gfs/software/miniconda3/4.8.3/envs/ufs-weather-model/lib/python3.8/site-packages:/lfs4/HFIP/hfv3gfs/software/miniconda3/4.8.3/lib/python3.8/site-packages\n"
 
     with open(filename,"w+") as f:
         f.writelines(runtest_envs)