Merge remote-tracking branch 'origin/master' into jgfouca/cam/cmakify

* origin/master: (159 commits) Update CIME to ESMCI cime5.8.2-3 (PR #2938) Update namelist scripts to reflect changes in mpas-ocean Registry files Update mpas source. bless_test_results: Be able to handle build-only tests Fix machine file entry for C++ compiler on melvin. Add x2g_*_from_lnd lists for use in prep_glc LND routines Update config_machines.xml Fix optics allocation Cleanup formatting in compute_melt_fluxes() Remove no longer-used cime_model variable Fix unallocated cloud optics Fix unallocated band midpoints COMPOSE: Fix the scope of the share_kokkos_ut standalone unit tests. Update CIME to ESMCI cime5.8.2-2 (#2908) Minor cleanup to previous commit Add default to PIO_CLOBBER if mode unset Test with changing logic for ocn-glc coupling Fix formatting and whitespace Remove `mode_in` in calls to `cam_pio_createfile` Add subroutine call to get PIO format ...
E3SM-Project · May 24, 2019 · 9d608ad · 9d608ad
2 parents b14f3d3 + fe07217
commit 9d608ad
Show file tree

Hide file tree

Showing 212 changed files with 32,795 additions and 6,543 deletions.
diff --git a/cime/ChangeLog b/cime/ChangeLog
@@ -1,5 +1,283 @@
 ======================================================================
 
+Originator: Chris Fischer 
+Date: 4-23-2019
+Tag: cime5.8.2
+Answer Changes: None
+Tests: scripts_regression_tests
+Dependencies:
+
+Brief Summary:
+    - Update the ne0CONUSne30x8 mapping files.
+    - Allow specific tests to ignore field list differences.
+    - Add NLDAS grid for CTSM and MOSART.
+    - Merge branch for acme split 2019-04-15
+    - Fix unit test.
+    - Introduces a new stub IAC.
+    - Master merge to nuopc cmeps.
+
+User interface changes: 
+
+PR summary: git log --oneline --first-parent [previous_tag]..master
+57cf4a5 Merge pull request #3086 from ESMCI/fischer/ne_conus
+421cc98 Merge pull request #3084 from billsacks/cprnc_ignore_fieldlist_diffs
+a356310 Merge pull request #3063 from billsacks/nldas_grid_v2
+14babd5 Merge pull request #3079 from ESMCI/jgfouca/branch-for-acme-split-2019-04-15
+74730fe fix for unit test
+4e86cc0 Merge pull request #3055 from bishtgautam/bishtgautam/iac
+279d30a Merge pull request #3075 from jedwards4b/master-merge-to-nuopc-cmeps
+
+
+Modified files: git diff --name-status [previous_tag]
+M	config/cesm/config_files.xml
+M	config/cesm/config_grids.xml
+M	config/cesm/config_grids_common.xml
+M	config/cesm/config_grids_mct.xml
+M	config/cesm/machines/config_machines.xml
+M	config/e3sm/allactive/config_compsets.xml
+M	config/e3sm/allactive/config_pesall.xml
+M	config/e3sm/config_archive.xml
+M	config/e3sm/config_files.xml
+M	config/e3sm/config_grids.xml
+M	config/e3sm/machines/config_batch.xml
+M	config/e3sm/machines/config_compilers.xml
+M	config/e3sm/machines/config_machines.xml
+M	config/e3sm/machines/config_pio.xml
+M	config/e3sm/tests.py
+M	config/xml_schemas/entry_id_base_version3.xsd
+M	scripts/Tools/Makefile
+M	scripts/Tools/archive_metadata
+M	scripts/Tools/case.build
+M	scripts/Tools/xmlconvertors/config_pes_converter.py
+M	scripts/Tools/xmlconvertors/grid_xml_converter.py
+M	scripts/lib/CIME/Servers/wget.py
+M	scripts/lib/CIME/SystemTests/system_tests_common.py
+M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
+M	scripts/lib/CIME/XML/grids.py
+M	scripts/lib/CIME/case/case.py
+M	scripts/lib/CIME/case/case_submit.py
+M	scripts/lib/CIME/hist_utils.py
+M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
+M	src/components/data_comps/datm/nuopc/atm_comp_nuopc.F90
+M	src/components/data_comps/datm/nuopc/datm_comp_mod.F90
+M	src/components/data_comps/datm/nuopc/datm_shr_mod.F90
+M	src/components/data_comps/dice/nuopc/dice_comp_mod.F90
+M	src/components/data_comps/dice/nuopc/dice_shr_mod.F90
+M	src/components/data_comps/dice/nuopc/ice_comp_nuopc.F90
+M	src/components/data_comps/dlnd/nuopc/dlnd_comp_mod.F90
+M	src/components/data_comps/dlnd/nuopc/dlnd_shr_mod.F90
+M	src/components/data_comps/dlnd/nuopc/lnd_comp_nuopc.F90
+M	src/components/data_comps/docn/nuopc/docn_comp_mod.F90
+M	src/components/data_comps/docn/nuopc/docn_shr_mod.F90
+M	src/components/data_comps/docn/nuopc/ocn_comp_nuopc.F90
+M	src/components/data_comps/drof/nuopc/drof_comp_mod.F90
+M	src/components/data_comps/drof/nuopc/rof_comp_nuopc.F90
+M	src/components/data_comps/dshr_nuopc/dshr_nuopc_mod.F90
+M	src/components/data_comps/dwav/nuopc/dwav_comp_mod.F90
+M	src/components/data_comps/dwav/nuopc/dwav_shr_mod.F90
+M	src/components/data_comps/dwav/nuopc/wav_comp_nuopc.F90
+A	src/components/stub_comps/siac/cime_config/buildlib
+A	src/components/stub_comps/siac/cime_config/buildnml
+A	src/components/stub_comps/siac/cime_config/config_component.xml
+A	src/components/stub_comps/siac/mct/iac_comp_mct.F90
+M	src/components/xcpl_comps/xatm/nuopc/atm_comp_nuopc.F90
+M	src/components/xcpl_comps/xglc/nuopc/glc_comp_nuopc.F90
+M	src/components/xcpl_comps/xice/nuopc/ice_comp_nuopc.F90
+M	src/components/xcpl_comps/xlnd/nuopc/lnd_comp_nuopc.F90
+M	src/components/xcpl_comps/xocn/nuopc/ocn_comp_nuopc.F90
+M	src/components/xcpl_comps/xrof/nuopc/rof_comp_nuopc.F90
+M	src/components/xcpl_comps/xshare/nuopc/dead_nuopc_mod.F90
+M	src/components/xcpl_comps/xwav/nuopc/wav_comp_nuopc.F90
+M	src/drivers/mct/cime_config/buildexe
+M	src/drivers/mct/cime_config/config_component.xml
+M	src/drivers/mct/cime_config/config_component_e3sm.xml
+M	src/drivers/mct/cime_config/config_compsets.xml
+M	src/drivers/mct/cime_config/config_pes.xml
+M	src/drivers/mct/cime_config/namelist_definition_drv.xml
+M	src/drivers/mct/cime_config/namelist_definition_modelio.xml
+M	src/drivers/mct/main/cime_comp_mod.F90
+M	src/drivers/mct/main/component_mod.F90
+M	src/drivers/mct/main/component_type_mod.F90
+M	src/drivers/mct/main/prep_atm_mod.F90
+A	src/drivers/mct/main/prep_iac_mod.F90
+M	src/drivers/mct/main/prep_lnd_mod.F90
+M	src/drivers/mct/main/seq_frac_mct.F90
+M	src/drivers/mct/main/seq_hist_mod.F90
+M	src/drivers/mct/main/seq_rest_mod.F90
+M	src/drivers/mct/shr/seq_comm_mct.F90
+M	src/drivers/mct/shr/seq_flds_mod.F90
+M	src/drivers/mct/shr/seq_infodata_mod.F90
+M	src/drivers/mct/shr/seq_timemgr_mod.F90
+M	src/drivers/mct/unit_test/CMakeLists.txt
+M	src/drivers/nuopc/cime_config/buildnml
+M	src/drivers/nuopc/cime_config/config_component.xml
+M	src/drivers/nuopc/cime_config/config_component_cesm.xml
+M	src/drivers/nuopc/cime_config/nuopc_runseq_A
+M	src/drivers/nuopc/cime_config/nuopc_runseq_ADLND
+M	src/drivers/nuopc/cime_config/nuopc_runseq_ADWAV
+M	src/drivers/nuopc/cime_config/nuopc_runseq_B
+D	src/drivers/nuopc/cime_config/nuopc_runseq_C_G_D
+A	src/drivers/nuopc/cime_config/nuopc_runseq_C_G_D_swav
+A	src/drivers/nuopc/cime_config/nuopc_runseq_C_G_D_ww3
+A	src/drivers/nuopc/cime_config/nuopc_runseq_C_wav
+M	src/drivers/nuopc/cime_config/nuopc_runseq_F
+M	src/drivers/nuopc/cime_config/nuopc_runseq_I
+M	src/drivers/nuopc/cime_config/nuopc_runseq_I_mosart
+M	src/drivers/nuopc/cime_config/nuopc_runseq_NEMS
+A	src/drivers/nuopc/cime_config/nuopc_runseq_NEMS.cold
+A	src/drivers/nuopc/cime_config/nuopc_runseq_NEMS.warm
+M	src/drivers/nuopc/cime_config/nuopc_runseq_Q
+M	src/drivers/nuopc/cime_config/nuopc_runseq_X
+M	src/drivers/nuopc/cime_config/nuopc_runseq_default
+M	src/drivers/nuopc/cime_driver/esmApp.F90
+M	src/drivers/nuopc/cime_flds/esmFlds.F90
+M	src/drivers/nuopc/cime_flds/esmFldsExchange.F90
+M	src/drivers/nuopc/cime_flds/fd.yaml
+M	src/drivers/nuopc/cime_flds_shr/seq_drydep_mod.F90
+M	src/drivers/nuopc/cime_flds_shr/shr_carma_mod.F90
+M	src/drivers/nuopc/cime_flds_shr/shr_fire_emis_mod.F90
+M	src/drivers/nuopc/cime_flds_shr/shr_megan_mod.F90
+M	src/drivers/nuopc/cime_flds_shr/shr_ndep_mod.F90
+M	src/drivers/nuopc/mediator/med.F90
+D	src/drivers/nuopc/mediator/med_connectors_mod.F90
+M	src/drivers/nuopc/mediator/med_fraction_mod.F90
+D	src/drivers/nuopc/mediator/med_infodata_mod.F90
+M	src/drivers/nuopc/mediator/med_internalstate_mod.F90
+M	src/drivers/nuopc/mediator/med_io_mod.F90
+M	src/drivers/nuopc/mediator/med_map_mod.F90
+M	src/drivers/nuopc/mediator/med_merge_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_aofluxes_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_history_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_ocnalb_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_prep_atm_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_prep_glc_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_prep_ice_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_prep_lnd_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_prep_ocn_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_prep_rof_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_prep_wav_mod.F90
+M	src/drivers/nuopc/mediator/med_phases_restart_mod.F90
+M	src/drivers/nuopc/shr/med_constants_mod.F90
+D	src/drivers/nuopc/shr/shr_nuopc_grid_mod.F90
+M	src/drivers/nuopc/shr/shr_nuopc_methods_mod.F90
+M	src/drivers/nuopc/shr/shr_nuopc_utils_mod.F90
+M	src/share/streams/shr_strdata_mod.F90
+M	src/share/util/shr_pio_mod.F90
+
+======================================================================
+
+======================================================================
+
+Originator: Chris Fischer 
+Date: 04-08-2019
+Tag: cime5.8.1
+Answer Changes: None
+Tests: scripts_regression_tests, many create_newcase with mangled compset names 
+       hand test xmllint
+Dependencies:
+
+Brief Summary:
+    - Support optional components by filling in stub models for any missing component class
+    - Merge maint-5.6 branch.
+    - Fix issue with xmllint.
+    - Use installed pio libraries.
+    - Make FIELDLIST message more informative.
+    - ACME merge 2019-03-29
+    - cprnc: allow differences in field lists for time-constant fields.
+    - Merge maint-5.6 branch.
+    - Add ne0CONUSne30x8_ne0CONUSne30x8_mg17 grid alias.
+    - Merge in latest nuopc-cmeps development.
+    - The check for an rpointer.drv file did not consider multidriver mode.
+    - Fix ./case.build --clean.
+    - PET and ERP tests were not setting compile_threaded correctly.
+    - Implement 'share' field of test suites.
+
+User interface changes: 
+    - Stub components are now optional in compset long names. Also there is less order dependency.
+
+PR summary: git log --oneline --first-parent [previous_tag]..master
+444b2f4 Merge pull request #3068 from gold2718/optional_components
+c1a4c49 Merge branch 'maint-5.6'
+150c2b5 Merge pull request #3061 from jedwards4b/fix_cesm_config_files
+9b0be41 Merge pull request #3058 from jedwards4b/use_installed_libraries
+ae332d4 Merge pull request #3059 from billsacks/fieldlist_differ_message
+d94860f Merge pull request #3054 from ESMCI/jgfouca/branch-for-acme-split-2019-03-29
+95e117c Merge pull request #3051 from billsacks/cprnc_allow_timeconst_fielddiffs
+338c143 Merge pull request #3052 from ESMCI/maint-5.6
+c82a5ee Merge pull request #3048 from ESMCI/fischer/SE_grids
+1bb357c Merge pull request #3046 from jedwards4b/nuopc-cmeps
+94d6da8 Merge pull request #3045 from jedwards4b/multi_driver_continue
+9f5fb60 Merge pull request #3043 from ESMCI/jgfouca/fix_build_clean
+ff06fd0 Merge pull request #3042 from ESMCI/jedwards/pet_test_fix
+bafad7e Merge pull request #3040 from ESMCI/jgfouca/impl_share_field
+
+
+Modified files: git diff --name-status [previous_tag]
+M       config/cesm/config_files.xml
+M       config/cesm/config_grids.xml
+M       config/cesm/machines/config_compilers.xml
+M       config/cesm/machines/config_machines.xml
+M       config/cesm/machines/userdefined_laptop_template/config_compilers.xml
+M       config/e3sm/config_grids.xml
+M       config/e3sm/config_inputdata.xml
+M       config/e3sm/machines/Depends.cetus
+M       config/e3sm/machines/Depends.mira
+M       config/e3sm/machines/Depends.summit.ibm
+M       config/e3sm/machines/Depends.summitdev.ibm
+M       config/e3sm/machines/config_batch.xml
+M       config/e3sm/machines/config_compilers.xml
+M       config/e3sm/machines/config_machines.xml
+M       config/e3sm/machines/config_pio.xml
+M       config/e3sm/machines/userdefined_laptop_template/config_compilers.xml
+M       config/e3sm/tests.py
+M       config/xml_schemas/config_batch.xsd
+M       config/xml_schemas/config_compilers_v2.xsd
+M       config/xml_schemas/config_machines.xsd
+M       config/xml_schemas/env_mach_specific.xsd
+M       doc/source/users_guide/cime-config.rst
+M       doc/source/users_guide/unit_testing.rst
+M       scripts/Tools/Makefile
+M       scripts/create_test
+M       scripts/fortran_unit_testing/run_tests.py
+M       scripts/lib/CIME/BuildTools/configure.py
+M       scripts/lib/CIME/BuildTools/valuesetting.py
+M       scripts/lib/CIME/XML/entry_id.py
+M       scripts/lib/CIME/XML/generic_xml.py
+M       scripts/lib/CIME/build.py
+M       scripts/lib/CIME/case/case.py
+M       scripts/lib/CIME/case/case_submit.py
+M       scripts/lib/CIME/case/check_input_data.py
+M       scripts/lib/CIME/hist_utils.py
+M       scripts/lib/CIME/test_scheduler.py
+M       scripts/lib/get_tests.py
+M       scripts/tests/scripts_regression_tests.py
+M       src/build_scripts/buildlib.gptl
+M       src/build_scripts/buildlib.kokkos
+M       src/build_scripts/buildlib.pio
+M       src/components/data_comps/datm/cime_config/config_component.xml
+M       src/components/data_comps/datm/nuopc/datm_comp_mod.F90
+M       src/components/data_comps/desp/cime_config/config_component.xml
+M       src/drivers/mct/cime_config/namelist_definition_drv.xml
+M       src/drivers/mct/main/seq_flux_mct.F90
+M       src/drivers/mct/shr/seq_infodata_mod.F90
+M       src/share/util/shr_flux_mod.F90
+M       tools/cprnc/README
+M       tools/cprnc/compare_vars_mod.F90.in
+M       tools/cprnc/cprnc.F90
+M       tools/cprnc/filestruct.F90
+M       tools/cprnc/run_tests
+M       tools/cprnc/test_inputs/README
+A       tools/cprnc/test_inputs/multipleTimes_someTimeless_extra_and_missing.nc
+A       tools/cprnc/test_inputs/noTime_extra_and_missing.nc
+M       tools/mapping/gen_domain_files/README
+M       tools/mapping/gen_domain_files/src/gen_domain.F90
+M       tools/mapping/gen_mapping_files/runoff_to_ocn/src/Makefile
+
+======================================================================
+
+
+======================================================================
+
 Originator: Chris Fischer 
 Date: 03-12-2019
 Tag: cime5.8.0

diff --git a/cime/config/cesm/config_grids.xml b/cime/config/cesm/config_grids.xml
@@ -1026,6 +1026,13 @@
       <mask>tx0.25v1</mask>
     </model_grid>
 
+    <model_grid alias="C384_t025" not_compset="_POP" >
+      <grid name="atm">C384</grid>
+      <grid name="lnd">C384</grid>
+      <grid name="ocnice">tx0.25v1</grid>
+      <mask>tx0.25v1</mask>
+    </model_grid>
+
     <!-- The following grid is only used for ADWAV testing -->
     <model_grid alias="ww3a" compset="_WW3|DWAV">
       <grid name="wav">ww3a</grid>
@@ -1048,7 +1055,6 @@
 
     <!-- LND domains for single column or regional -->
 
-
     <domain name="01col">
       <nx>1</nx> <ny>1</ny>
       <file>domain.ocn.01col.ArcticOcean.20150824.nc</file>
@@ -1568,6 +1574,13 @@
       <support>Experimental for fv3 dycore</support>
     </domain>
 
+    <domain name="C384">
+      <!-- The following nx is incorrect -->
+      <nx>100000</nx> <ny>1</ny>
+      <desc>C384 is a fvcubed xx-deg grid:</desc>
+      <support>Experimental for fv3 dycore</support>
+    </domain>
+
   </domains>
 
   <!-- ======================================================== -->

diff --git a/cime/config/cesm/machines/config_batch.xml b/cime/config/cesm/machines/config_batch.xml
@@ -402,6 +402,7 @@
 
   <batch_system type="pbs" MACH="izumi" >
     <batch_submit>ssh izumi cd $CASEROOT ; qsub</batch_submit>
+    <jobid_pattern>(\d+.izumi.unified.ucar.edu)$</jobid_pattern>
     <directives>
       <directive>-l nodes={{ num_nodes }}:ppn={{ tasks_per_node }}</directive>
       <directive default="/bin/bash" > -S {{ shell }}  </directive>

diff --git a/cime/config/cesm/machines/config_compilers.xml b/cime/config/cesm/machines/config_compilers.xml
@@ -313,8 +313,16 @@ using a fortran linker.
   <MPIFC> mpif90 </MPIFC>
   <SCC> gcc </SCC>
   <SFC> nagfor </SFC>
+
+  <LDFLAGS>
+    <append> -lpthread </append>
+  </LDFLAGS>
+  <CONFIG_ARGS>
+    <append> FCLIBS="-Wl,--as-needed,--allow-shlib-undefined  -L$(COMPILER_PATH)/lib/NAG_Fortran -lf62rts" </append>
+  </CONFIG_ARGS>
 </compiler>
 
+
 <compiler COMPILER="pgi">
   <CFLAGS>
     <base> -gopt  -time </base>
@@ -894,19 +902,6 @@ using a fortran linker.
   <PFUNIT_PATH MPILIB="mpi-serial" compile_threaded="FALSE">/fs/cgd/csm/tools/pFUnit/pFUnit3.2.8_hobart_Intel15.0.2_noMPI_noOpenMP</PFUNIT_PATH>
 </compiler>
 
-<compiler MACH="hobart" COMPILER="nag">
-  <CPPDEFS>
-    <!-- needed for nag pio build.. -->
-    <append> -DNO_C_SIZEOF </append>
-  </CPPDEFS>
-  <LDFLAGS>
-    <append> -lpthread</append>
-  </LDFLAGS>
-  <SLIBS>
-    <append> -L/usr/local/nag/lib/NAG_Fortran </append>
-  </SLIBS>
-</compiler>
-
 <compiler MACH="hobart" COMPILER="pgi">
   <CFLAGS>
     <append DEBUG="FALSE"> -O0 </append>