Merge pull request #1502 from ekluzek/nuopc_default

Make the NUOPC driver the default

Externals.cfg

@@ -8,22 +8,22 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_87
+tag = cismwrap_2_1_93
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_77
+tag = rtm1_0_78
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_43
+tag = mosart1_0_45
 required = True
 
 [mizuRoute]
@@ -37,33 +37,33 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.4
+tag = cime6.0.11
 required = True
 
 [cmeps]
-tag = cmeps0.13.23
+tag = cmeps0.13.40
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.19
+tag = cdeps0.12.32
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
 externals =  Externals_CDEPS.cfg
 required = True
 
 [cpl7]
-tag = cpl7.0.3
+tag = cpl7.0.5
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
 local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.2
+tag = share1.0.8
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share

Externals_CLM.cfg

@@ -2,14 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.48.0_api.17.0.0
-required = True
-
-[PTCLM]
-local_path = tools/site_and_regional/PTCLM
-protocol = git
-repo_url = https://github.com/ESCOMP/PTCLM
-tag = PTCLM2_20210810
+tag = sci.1.49.1_api.17.0.0
 required = True
 
 [externals_description]

README

@@ -2,12 +2,24 @@ $CTSMROOT/README                                          06/08/2018
 
 Community Terrestrial Systems Model (CTSM) science version 5.1  series -- source code, tools, 
 offline-build and test scripts. This gives you everything you need
-to run CTSM with CESM with datm8 to provide CRU NCEP or GSWP3 forcing data in 
+to run CTSM with CESM with the CMEPS driver and CDEPS data models to provide CRU NCEP or GSWP3 forcing data in 
 place of a modeled atmosphere.
 
+CMEPS is the Community Mediator for Earth Prediction Systems. And CDEPS is the
+Community Data Models for Earth Prediction System. They are both NUOPC based models
+used to drive the CESM (Community Earth System Model) of which CTSM is a component of.
+NUOPC is the National Unified Operational Prediction Capability a standard way of building
+coupled model systems. The NUOPC layer is based on the Earth System Modeling Framework (ESMF).
+
 For lists of current bugs (issues) and current development see the CTSM GitHub page:
 
-https://github.com/ESCOMP/ctsm
+https://github.com/ESCOMP/CTSM
+
+INFORMATION ON THE CMEPS DRIVER:
+
+https://escomp.github.io/CMEPS
+
+https://earthsystemmodeling.org/nuopc/
 
 IMPORTANT NOTE ON CESM CHECKOUT VERSUS A CTSM CHECKOUT:
 
@@ -28,32 +40,28 @@ General directory structure ($CTSMROOT):
 doc --------------- Documentation of CTSM.
 bld --------------- Template, configure and build-namelist scripts for clm.
 src --------------- CTSM Source code.
+lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model)
 test -------------- CTSM Testing scripts for CTSM offline tools.
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
 manage_externals -- Script to manage the external source directories
-python ------------ Some python modules mostly for use by run_sys_tests (but could be used elsewhere)
+python ------------ Some python modules mostly for use by run_sys_tests (but could be used elsewhere l
 
 Directory structure only for a CTSM checkout:
 
 components -------- Other active sub-components needed for CTSM to run (river routing and land-ice models)
+libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO
+share ------------- CESM shared code
 
 cime/scripts --------------- cesm/cime driver scripts
 
-cime/src/drivers/mct/main ----------- CESM top level driver source code.
-cime/src/drivers/mct/shr ------------ CESM top level driver shared code.
-cime/src/components/data_comps/datm - CESM Data model version 8 source code.
-cime/src/components/stub_comps/sice - CESM stub sea-ice model source code.
-cime/src/components/stub_comps/socn - CESM stub ocean model source code.
-cime/src/components/stub_comps/sglc - CESM stub glacier model source code.
-cime/src/externals ------------------ CESM external utility codes 
-                                      (Model Coupling Toolkit (MCT)
-                                      (Earth System Model Framework)
-                                      (timing -- code timing utility)
-                                      (pio -- Parallel Input/Output)
+components/cmeps -------------------- CESM top level driver (for NUOPC driver [which is the default]) source code.
+components/cdeps -------------------- CESM top level data model shared code (for NUOPC driver).
+cime/src/externals ------------------ CESM external utility codes  (genf90)
 components/cism --------------------- CESM Community land Ice Sheet Model.
 components/mosart ------------------- Model for Scale Adaptive River Transport
 components/rtm ---------------------- CESM River Transport Model.
+components/cpl7 --------------------- CESM top level driver for MCT driver (being deprecated)
 
 Top level documentation ($CTSMROOT):
 
@@ -92,7 +100,7 @@ run_sys_tests --------------- Python script to send the standard CTSM testing of
 
 parse_cime.cs.status -------- Script to parse test status files cs.status.* created by create_test
                               (can be used along with run_sys_tests)
-doc/Quickstart.GUIDE -------- Quick guide to using cpl7 scripts.
+doc/Quickstart.GUIDE -------- Quick guide to using NUOPC scripts.
 doc/IMPORTANT_NOTES --------- Some important notes about this version of 
                                                  clm, configuration modes and namelist items 
                                                  that are not validated or functional.
@@ -149,7 +157,7 @@ Source code directory structure:
 
 src/biogeochem ---- Biogeochemisty
 src/main ---------- Main control and high level code
-src/cpl ----------- Land model high level MCT and ESMF drivers
+src/cpl ----------- Land model high level caps for NUOPC driver (and MCT and LILAC)
 src/biogeophys ---- Biogeophysics (Hydrology)
 src/dyn_subgrid --- Dynamic land unit change
 src/init_interp --- Online interpolation
@@ -161,7 +169,7 @@ src/unit_test_shr - Unit test shared modules for unit testing
 src/unit_test_stubs Unit test stubs that replicate CTSM code simpler
 
 =============================================================================================
-    QUICKSTART: using the CPL7 scripts
+    QUICKSTART: using the NUOPC driver scripts
 =============================================================================================
 
          cd $CIMEROOT/scripts

README.CHECKLIST.new_case

@@ -21,7 +21,7 @@ General Checklist to always do:
  - Make sure the LND_TUNING_MODE is correct 
    (./xmlquery LND_TUNING_MODE)
  - For an "I compset" make sure you are running over the right forcing years 
-   (usually ./xmlquery -p DATM_CLMNCEP_YR)
+   (usually ./xmlquery -p DATM_YR)
  - First and align year for streams should be the start year of a historical simulation 
    (./xmlquery RUN_STARTDATE)
    (grep stream_year_first CaseDocs/lnd_in; grep model_year_align CaseDocs/lnd_in)

README.NUOPC_driver.md

@@ -0,0 +1,56 @@
+# $CTSMROOT/README.NUOPC_driver
+
+CTSM now by default uses the NUOPC based CMEPS driver!
+
+
+## What's new?
+
+MESH Files:
+Mesh files to describe grids are new in both the driver namelist and for example in any
+streams files.
+Full ESMF Library is used:
+The full ESMF Library is used and required to be built in order to run the model.
+Single Point cases:
+Single point cases can now set their location using PTS_LAT and PTS_LON.
+
+## What's removed?
+
+Domain files are no longer used. And mapping for regriding is created on the fly
+rather than using fixed mapping files in almost all cases. Runoff mapping files
+still need to be generated offline.
+
+## What files change?
+
+rpointer.drv becomes rpointer.cpl
+cpl.log.* files get's split into med.log.* and drv.log.*
+user_datm.streams.txt.* file changes goes into the user_nl_datm_streams files
+datm.streams.txt.* files are all in one file called datm.streams.xml
+
+## What XML variables change in your case?
+
+DATM_CLMNCEP_YR_* variables change to DATM_YR_*
+
+## New obscure options:
+
+ESMF_AWARE_THREADING --- ESMF is aware of threading (can have differing number of threads in components)
+CREATE_ESMF_PET_FILES -- Create output log files from ESMF for each Processor (PET)
+ESMF_VERBOSITY_LEVEL --- Verbosity level for ESMF logging
+ESMF_PROFILING_LEVEL --- Verbosity level for ESMF profiling
+
+nuopc.runseq is a text file that determines how the driver operates. You can change the operation
+by having an updated copy in your case directory.
+
+
+## What if I want to use the previous MCT driver?
+
+The MCT driver will be available for sometime going forward, but
+new development won't go into it, and it will eventually be removed.
+But, if you have to...
+Use the "--driver mct" command line option to create_newcase
+You can set COMP_INTERFACE in a case as well, but it won't create it with everything needed
+so we recommend setting up a case from scratch.
+
+
+For more notes see:
+
+https://docs.google.com/presentation/d/1yjiKSEV53JDAJbYxhpY2T9GTxlWFzQAn

bld/CLMBuildNamelist.pm

@@ -253,7 +253,7 @@ sub process_commandline {
                co2_type              => undef,
                co2_ppmv              => undef,
                clm_demand            => "null",
-               driver                => "mct",
+               driver                => "nuopc",
                help                  => 0,
                glc_nec               => "default",
                glc_use_antarctica    => 0,
@@ -1528,10 +1528,10 @@ sub process_namelist_inline_logic {
   setup_logic_soilstate($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_demand($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_surface_dataset($opts,  $nl_flags, $definition, $defaults, $nl);
+  setup_logic_dynamic_subgrid($opts,  $nl_flags, $definition, $defaults, $nl);
   if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) {
     setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   }
-  setup_logic_dynamic_subgrid($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_spinup($opts,  $nl_flags, $definition, $defaults, $nl);
   setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
   setup_logic_snowpack($opts,  $nl_flags, $definition, $defaults, $nl);
@@ -2319,6 +2319,7 @@ sub setup_logic_initial_conditions {
     my $fsurdat          = $nl->get_value('fsurdat');
     $fsurdat             =~ s!(.*)/!!;
     $settings{'fsurdat'} = $fsurdat;
+    $settings{'do_transient_pfts'} = $nl->get_value('do_transient_pfts');
     #
     # If not transient use sim_year, otherwise use date
     #
@@ -4080,6 +4081,13 @@ sub setup_logic_misc {
    #
    my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
+   if ( $opts->{'driver'} ne "nuopc" ) {
+      my $var = "force_send_to_atm";
+      my $val = $nl->get_value($var);
+      if ( defined($val) ) {
+         $log->fatal_error( "$var can only be set for the nuopc driver" );
+      }
+   }
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_run_ncdiopio_tests');
    add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_master_list_file');
 }
@@ -4121,6 +4129,9 @@ sub write_output_files {
   if ( &value_is_true($nl_flags->{'use_lch4'}) ) {
      push @groups, "ch4par_in";
   }
+  if ( $opts->{'driver'} eq "nuopc" ) {
+     push @groups, "ctsm_nuopc_cap";
+  }
   push @groups, "clm_humanindex_inparm";
   push @groups, "cnmresp_inparm";
   push @groups, "photosyns_inparm";
@@ -4355,8 +4366,9 @@ sub check_input_files {
 
                 if ($input_pathname_type eq 'abs') {
                     if ($inputdata_rootdir) {
-                        #MV $pathname =~ s:$inputdata_rootdir::;
-                        print OUTFILE "$var = $pathname\n";
+                        if ( $pathname !~ /^\s*$/ ) {   # If pathname isn't blank or null
+                           print OUTFILE "$var = $pathname\n";
+                        }
                     }
                     else {
                         if (-e $pathname) {  # use -e rather than -f since the absolute pathname
@@ -4377,7 +4389,9 @@ sub check_input_files {
                     if ($inputdata_rootdir) {
                         $pathname = "$rootdir/$pathname";
                         #MV $pathname =~ s:$inputdata_rootdir::;
-                        print OUTFILE "$var = $pathname\n";
+                        if ( $pathname !~ /^\s*$/ ) {   # If pathname isn't blank or null
+                           print OUTFILE "$var = $pathname\n";
+                        }
                     }
                     else {
                         if (-f "$rootdir/$pathname") {

bld/namelist_files/createMapEntry.pl

@@ -55,12 +55,13 @@
 
    foreach my $foo ( @list ) {
       next if ($foo =~ m/^\./);  #~# skip anything in the directory with a leading or stand alone 'dot'
+      $foo =~ s/$grid/RES/;   # Replace grid trying to match with RES (so underscores in the grid name don't mess up the matching)
       my @tokens = split(/_/, $foo); #~# split foo name by the underscore
       #~# write out lines for namelist_defaults_ctsm.xml nomask" files
       my $from_mask = $tokens[2];
       if ( $from_mask =~ /nomask/ ) {
-         if ( $tokens[5] eq "nomask" && $tokens[4] eq $grid ) {
-            print "<map frm_hgrid=\"$tokens[1]\"    frm_lmask=\"$from_mask\"  to_hgrid=\"$tokens[4]\"   to_lmask=\"$tokens[5]\" \n";
+         if ( $tokens[5] eq "nomask" && $tokens[4] eq "RES" ) {
+            print "<map frm_hgrid=\"$tokens[1]\"    frm_lmask=\"$from_mask\"  to_hgrid=\"$grid\"   to_lmask=\"$tokens[5]\" \n";
             print ">$partialPath/$foo</map>\n";
          }
       }