Merge pull request #3123 from ESMCI/jgfouca/branch-for-acme-split-201…

…9-05-28 Jgfouca/branch for acme split 2019 05 28 Change List: Add first stage of ocean/ice shelf coupling Bring COMPOSE semi-Lagrangian tracer transport code into HOMME and E3SM (required minor changes to build.py) Add checkpoint of timing data immediately after initialization bless_test_results: Be able to handle build-only tests Test suite: scripts_regression_tests Test baseline: Test namelist changes: Test status: BFB Fixes [CIME Github issue #] User interface changes?: Update gh-pages html (Y/N)?: Code review: @jedwards4b
ESMCI · Jun 3, 2019 · 5c43a15 · 5c43a15
2 parents 6493b34 + e218c9b
commit 5c43a15
Show file tree

Hide file tree

Showing 16 changed files with 1,395 additions and 165 deletions.
diff --git a/config/e3sm/config_grids.xml b/config/e3sm/config_grids.xml
@@ -1232,6 +1232,16 @@
       <mask>oQU120</mask>
     </model_grid>
 
+    <model_grid alias="T62_oEC60to30v3wLI_ais20" compset="MPASO.*_MALI">
+      <grid name="atm">T62</grid>
+      <grid name="lnd">T62</grid>
+      <grid name="ocnice">oEC60to30v3wLI</grid>
+      <grid name="rof">rx1</grid>
+      <grid name="glc">mpas.ais20km</grid>
+      <grid name="wav">null</grid>
+      <mask>oEC60to30v3wLI</mask>
+    </model_grid>
+
     <!-- The following grid is only used for ADWAV testing -->
     <model_grid alias="ww3a" compset="_WW3|DWAV">
       <grid name="wav">ww3a</grid>
@@ -2955,12 +2965,25 @@
     </gridmap>
 
     <gridmap glc_grid="mpas.ais20km" ocn_grid="oQU120">
+      <map name="GLC2ICE_FMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oQU120_aave.160331.nc</map>
+      <map name="GLC2ICE_SMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oQU120_nearestdtos.160331.nc</map>
       <map name="GLC2OCN_FMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oQU120_aave.160331.nc</map>
-      <map name="OCN2GLC_FMAPNAME">cpl/gridmaps/oQU120/map_oQU120_to_ais20km_aave.160331.nc</map>
       <map name="GLC2OCN_SMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oQU120_nearestdtos.160331.nc</map>
       <map name="GLC2OCN_LIQ_RMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oQU120_nearestdtos.160331.nc</map>
       <map name="GLC2OCN_ICE_RMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oQU120_nearestdtos.160331.nc</map>
-      <map name="OCN2GLC_SMAPNAME">cpl/gridmaps/oQU120/map_oQU120_to_ais20km_nearestdtos.160331.nc</map>
+      <map name="OCN2GLC_FMAPNAME">cpl/gridmaps/oQU120/map_oQU120_to_ais20km_aave.160331.nc</map>
+      <map name="OCN2GLC_SMAPNAME">cpl/gridmaps/oQU120/map_oQU120_to_ais20km_neareststod.160331.nc</map>
+    </gridmap>
+
+    <gridmap glc_grid="mpas.ais20km" ocn_grid="oEC60to30v3wLI">
+      <map name="GLC2ICE_FMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oEC60to30v3wLI_nomask_aave.190207.nc</map>
+      <map name="GLC2ICE_SMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oEC60to30v3wLI_nomask_nearestdtos.190207.nc</map>
+      <map name="GLC2OCN_FMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oEC60to30v3wLI_nomask_aave.190207.nc</map>
+      <map name="GLC2OCN_SMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oEC60to30v3wLI_nomask_nearestdtos.190207.nc</map>
+      <map name="GLC2OCN_LIQ_RMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oEC60to30v3wLI_nomask_nearestdtos.190207.nc</map>
+      <map name="GLC2OCN_ICE_RMAPNAME">cpl/gridmaps/mpas.ais20km/map_ais20km_to_oEC60to30v3wLI_nomask_nearestdtos.190207.nc</map>
+      <map name="OCN2GLC_FMAPNAME">cpl/gridmaps/oEC60to30v3wLI/map_oEC60to30v3wLI_nomask_to_ais20km_aave.190207.nc</map>
+      <map name="OCN2GLC_SMAPNAME">cpl/gridmaps/oEC60to30v3wLI/map_oEC60to30v3wLI_nomask_to_ais20km_neareststod.190207.nc</map>
     </gridmap>
 
   </gridmaps>

diff --git a/config/e3sm/machines/config_machines.xml b/config/e3sm/machines/config_machines.xml
@@ -699,7 +699,7 @@
         <command name="load">sems-git</command>
         <command name="load">acme-binutils</command>
         <command name="load">sems-python/2.7.9</command>
-        <command name="load">sems-cmake/2.8.12</command>
+        <command name="load">sems-cmake/3.10.3</command>
       </modules>
       <modules compiler="gnu">
         <command name="load">sems-gcc/7.3.0</command>

diff --git a/scripts/lib/CIME/build.py b/scripts/lib/CIME/build.py
@@ -33,6 +33,12 @@ def xml_to_make_variable(case, varname):
     return "{}=\"{}\" ".format(varname, varvalue)
 
 
+###############################################################################
+def uses_kokkos(case):
+###############################################################################
+    cam_target = case.get_value("CAM_TARGET")
+    return cam_target in ("preqx_kokkos", "theta-l")
+
 ###############################################################################
 def _build_model(build_threaded, exeroot, incroot, complist,
                  lid, caseroot, cimeroot, compiler, buildlist, comp_interface):
@@ -228,12 +234,11 @@ def _build_libraries(case, exeroot, sharedpath, caseroot, cimeroot, libroot, lid
             os.makedirs(shared_item)
 
     mpilib = case.get_value("MPILIB")
-    cam_target = case.get_value("CAM_TARGET")
     libs = ["gptl", "mct", "pio", "csm_share"]
     if mpilib == "mpi-serial":
         libs.insert(0, mpilib)
 
-    if cam_target == "preqx_kokkos":
+    if uses_kokkos(case):
         libs.append("kokkos")
 
     logs = []
@@ -444,8 +449,6 @@ def _case_build_impl(caseroot, case, sharedlib_only, model_only, buildlist,
     if get_model() == "e3sm" and mach == "titan" and compiler == "pgiacc":
         case.set_value("CAM_TARGET", "preqx_acc")
 
-    cam_target = case.get_value("CAM_TARGET")
-
     # This is a timestamp for the build , not the same as the testid,
     # and this case may not be a test anyway. For a production
     # experiment there may be many builds of the same case.
@@ -495,8 +498,7 @@ def _case_build_impl(caseroot, case, sharedlib_only, model_only, buildlist,
 
     if not sharedlib_only:
         os.environ["INSTALL_SHAREDPATH"] = os.path.join(exeroot, sharedpath) # for MPAS makefile generators
-        # Set USE_KOKKOS to true if cam is preqx_kokkos
-        if cam_target == "preqx_kokkos":
+        if uses_kokkos(case):
             os.environ["USE_KOKKOS"] = "TRUE"
 
         logs.extend(_build_model(build_threaded, exeroot, incroot, complist,

diff --git a/scripts/lib/CIME/case/check_lockedfiles.py b/scripts/lib/CIME/case/check_lockedfiles.py
@@ -9,8 +9,9 @@
 from CIME.XML.env_case import EnvCase
 from CIME.XML.env_mach_pes import EnvMachPes
 from CIME.XML.env_batch import EnvBatch
-from CIME.utils import run_cmd_no_fail
 from CIME.locked_files import unlock_file, LOCKED_DIR
+from CIME.build import clean
+
 logger = logging.getLogger(__name__)
 
 import glob, six
@@ -39,7 +40,7 @@ def check_pelayouts_require_rebuild(self, models):
                 if old_tasks != new_tasks or old_threads != new_threads or old_inst != new_inst:
                     logging.warning("{} pe change requires clean build {} {}".format(comp, old_tasks, new_tasks))
                     cleanflag = comp.lower()
-                    run_cmd_no_fail("./case.build --clean {}".format(cleanflag))
+                    clean(self, cleanlist=[cleanflag])
 
         unlock_file("env_mach_pes.xml", self.get_value("CASEROOT"))
 

diff --git a/scripts/lib/CIME/hist_utils.py b/scripts/lib/CIME/hist_utils.py
@@ -3,7 +3,7 @@
 """
 from CIME.XML.standard_module_setup import *
 from CIME.test_status import TEST_NO_BASELINES_COMMENT, TEST_STATUS_FILENAME
-from CIME.utils import get_current_commit, get_timestamp, get_model, safe_copy, SharedArea
+from CIME.utils import get_current_commit, get_timestamp, get_model, safe_copy, SharedArea, parse_test_name
 
 import logging, os, re, filecmp
 logger = logging.getLogger(__name__)
@@ -572,7 +572,10 @@ def _generate_baseline_impl(case, baseline_dir=None, allow_baseline_overwrite=Fa
         safe_copy(newestcpllogfile, os.path.join(basegen_dir, "{}.log.gz".format(cplname)), preserve_meta=False)
 
     testname = case.get_value("TESTCASE")
-    expect(num_gen > 0 or testname == "PFS", "Could not generate any hist files for case '{}', something is seriously wrong".format(os.path.join(rundir, testcase)))
+    testopts = parse_test_name(case.get_value("CASEBASEID"))[1]
+    testopts = [] if testopts is None else testopts
+    expect(num_gen > 0 or (testname == "PFS" or "B" in testopts),
+           "Could not generate any hist files for case '{}', something is seriously wrong".format(os.path.join(rundir, testcase)))
 
     if get_model() == "e3sm":
         bless_log = os.path.join(basegen_dir, BLESS_LOG_NAME)

diff --git a/src/drivers/mct/cime_config/config_component.xml b/src/drivers/mct/cime_config/config_component.xml
@@ -1626,6 +1626,42 @@
     <desc>glc2lnd state mapping file decomp type</desc>
   </entry>
 
+  <entry id="GLC2ICE_FMAPNAME">
+    <type>char</type>
+    <default_value>idmap_ignore</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>glc2ice flux mapping file - the default value idmap_ignore, if set, will be ignored by buildnml and
+    will generate a runtime error if in fact a file is required for the given compset</desc>
+  </entry>
+
+  <entry id="GLC2ICE_FMAPTYPE">
+    <type>char</type>
+    <valid_values>X,Y</valid_values>
+    <default_value>X</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>glc2ice flux mapping file decomp type</desc>
+  </entry>
+
+  <entry id="GLC2ICE_SMAPNAME">
+    <type>char</type>
+    <default_value>idmap_ignore</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>glc2ice state mapping file - the default value idmap_ignore, if set, will be ignored by buildnml and
+    will generate a runtime error if in fact a file is required for the given compset</desc>
+  </entry>
+
+  <entry id="GLC2ICE_SMAPTYPE">
+    <type>char</type>
+    <valid_values>X,Y</valid_values>
+    <default_value>X</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>glc2ice state mapping file decomp type</desc>
+  </entry>
+
   <entry id="GLC2ICE_RMAPNAME">
     <type>char</type>
     <default_value>idmap_ignore</default_value>
@@ -1644,6 +1680,42 @@
     <desc>glc2ice runoff mapping file decomp type</desc>
   </entry>
 
+  <entry id="GLC2OCN_FMAPNAME">
+    <type>char</type>
+    <default_value>idmap_ignore</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>glc2ocn flux mapping file - the default value idmap_ignore, if set, will be ignored by buildnml and
+    will generate a runtime error if in fact a file is required for the given compset</desc>
+  </entry>
+
+  <entry id="GLC2OCN_FMAPTYPE">
+    <type>char</type>
+    <valid_values>X,Y</valid_values>
+    <default_value>Y</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>glc2ocn flux mapping file decomp type</desc>
+  </entry>
+
+  <entry id="GLC2OCN_SMAPNAME">
+    <type>char</type>
+    <default_value>idmap_ignore</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>glc2ocn state mapping file - the default value idmap_ignore, if set, will be ignored by buildnml and
+    will generate a runtime error if in fact a file is required for the given compset</desc>
+  </entry>
+
+  <entry id="GLC2OCN_SMAPTYPE">
+    <type>char</type>
+    <valid_values>X,Y</valid_values>
+    <default_value>Y</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>glc2ocn state mapping file decomp type</desc>
+  </entry>
+
   <entry id="GLC2OCN_LIQ_RMAPNAME">
     <type>char</type>
     <default_value>idmap_ignore</default_value>
@@ -1680,6 +1752,42 @@
     <desc>glc2ocn runoff mapping file decomp type for ice runoff</desc>
   </entry>
 
+  <entry id="OCN2GLC_FMAPNAME">
+    <type>char</type>
+    <default_value>idmap_ignore</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>ocn2glc flux mapping file - the default value idmap_ignore, if set, will be ignored by buildnml and
+    will generate a runtime error if in fact a file is required for the given compset</desc>
+  </entry>
+
+  <entry id="OCN2GLC_FMAPTYPE">
+    <type>char</type>
+    <valid_values>X,Y</valid_values>
+    <default_value>Y</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>ocn2glc flux mapping file decomp type</desc>
+  </entry>
+
+  <entry id="OCN2GLC_SMAPNAME">
+    <type>char</type>
+    <default_value>idmap_ignore</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>ocn2glc state mapping file - the default value idmap_ignore, if set, will be ignored by buildnml and
+    will generate a runtime error if in fact a file is required for the given compset</desc>
+  </entry>
+
+  <entry id="OCN2GLC_SMAPTYPE">
+    <type>char</type>
+    <valid_values>X,Y</valid_values>
+    <default_value>Y</default_value>
+    <group>run_domain</group>
+    <file>env_run.xml</file>
+    <desc>ocn2glc state mapping file decomp type</desc>
+  </entry>
+
   <entry id="OCN2WAV_SMAPNAME">
     <type>char</type>
     <default_value>idmap</default_value>

diff --git a/src/drivers/mct/cime_config/config_component_e3sm.xml b/src/drivers/mct/cime_config/config_component_e3sm.xml
@@ -88,7 +88,11 @@
     <default_value>12</default_value>
     <group>run_flags</group>
     <file>env_run.xml</file>
-    <desc>timer detail FIXME - add documentation</desc>
+    <desc>Sets maximum number of run loop timing data checkpoints.
+    This sets values for tprof_option and tprof_n that determine
+    the timing output file frequency. If less than one, uses
+    defaults for tprof_option and tprof_n and also allows them
+    to be set in user_nl_cpl.</desc>
   </entry>
 
   <entry id="DOUT_S_SAVE_INTERIM_RESTART_FILES">
@@ -352,7 +356,7 @@
       <value compset="_DLND.*_CISM\d">1</value>
       <value compset="_DLND.*_MALI">1</value>
       <value compset="_SLND.*SOCN.*_MALI">1</value>
-      <value compset="_DATM.*_SLND.*MPASO.*_MALI">24</value>
+      <value compset="_DATM.*_SLND.*MPASO.*_MALI">$ATM_NCPL</value>
       <value compset="_CAM.*_CLM.*MPASO">48</value>
       <value compset="_CAM.*_CLM.*MPASO" grid="a%ne4np4">$ATM_NCPL</value>
       <value compset="_CAM.*_CLM.*MPASO" grid="a%ne11np4">12</value>
@@ -372,7 +376,7 @@
       <value compset="_DLND.*_CISM\d">1</value>
       <value compset="_DLND.*_MALI">1</value>
       <value compset="_SLND.*SOCN.*_MALI">1</value>
-      <value compset="_DATM.*_SLND.*MPASO.*_MALI">24</value>
+      <value compset="_DATM.*_SLND.*MPASO.*_MALI">$ATM_NCPL</value>
       <value compset="_CAM.*_CLM.*MPASO">$ATM_NCPL</value>
     </values>
     <group>run_coupling</group>
@@ -722,74 +726,6 @@
       compsets.</desc>
   </entry>
 
-  <entry id="OCN2GLC_FMAPNAME">
-    <type>char</type>
-    <default_value>idmap</default_value>
-    <group>run_domain</group>
-    <file>env_run.xml</file>
-    <desc>ocn2glc flux mapping file</desc>
-  </entry>
-
-  <entry id="OCN2GLC_FMAPTYPE">
-    <type>char</type>
-    <valid_values>X,Y</valid_values>
-    <default_value>Y</default_value>
-    <group>run_domain</group>
-    <file>env_run.xml</file>
-    <desc>ocn2glc flux mapping file decomp type</desc>
-  </entry>
-
-  <entry id="OCN2GLC_SMAPNAME">
-    <type>char</type>
-    <default_value>idmap</default_value>
-    <group>run_domain</group>
-    <file>env_run.xml</file>
-    <desc>ocn2glc state mapping file</desc>
-  </entry>
-
-  <entry id="OCN2GLC_SMAPTYPE">
-    <type>char</type>
-    <valid_values>X,Y</valid_values>
-    <default_value>Y</default_value>
-    <group>run_domain</group>
-    <file>env_run.xml</file>
-    <desc>ocn2glc state mapping file decomp type</desc>
-  </entry>
-
-  <entry id="GLC2OCN_FMAPNAME">
-    <type>char</type>
-    <default_value>idmap</default_value>
-    <group>run_domain</group>
-    <file>env_run.xml</file>
-    <desc>glc2ocn flux mapping file</desc>
-  </entry>
-
-  <entry id="GLC2OCN_FMAPTYPE">
-    <type>char</type>
-    <valid_values>X,Y</valid_values>
-    <default_value>Y</default_value>
-    <group>run_domain</group>
-    <file>env_run.xml</file>
-    <desc>glc2ocn flux mapping file decomp type</desc>
-  </entry>
-
-  <entry id="GLC2OCN_SMAPNAME">
-    <type>char</type>
-    <default_value>idmap</default_value>
-    <group>run_domain</group>
-    <file>env_run.xml</file>
-    <desc>glc2ocn state mapping file</desc>
-  </entry>
-
-  <entry id="GLC2OCN_SMAPTYPE">
-    <type>char</type>
-    <valid_values>X,Y</valid_values>
-    <default_value>Y</default_value>
-    <group>run_domain</group>
-    <file>env_run.xml</file>
-    <desc>glc2ocn state mapping file decomp type</desc>
-  </entry>
-
   <entry id="CCSM_GCOST">
     <type>integer</type>
     <valid_values></valid_values>