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Jgfouca/branch for acme split 2019 05 28 #3123

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merged 49 commits into from
Jun 3, 2019
Merged

Jgfouca/branch for acme split 2019 05 28 #3123

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9333156
Add ocean/ice shelf coupling to CIME
Feb 5, 2019
a206830
Updates to get the LISIO test to run.
jonbob Feb 6, 2019
f0ce5ec
Cleanup to get LISIO test to run (plus reduce output)
jonbob Feb 7, 2019
52a5556
Updates for T62_oEC60to30v3wLI_ais20 grid and GMPAS-MALI-DIB-IAF-ISMF…
jonbob Feb 7, 2019
3f4ba10
Fix value check in BL flux computation
matthewhoffman Feb 7, 2019
e2c0949
Add floating mask to ice-shelf melt calculation
matthewhoffman Feb 20, 2019
fe0341b
CIME: Fix grid for ocean state vars in melt calc
matthewhoffman Feb 26, 2019
86baffb
CIME: Calculate T0 before it's used
matthewhoffman Feb 26, 2019
7e170e9
Change interface temp. soln formulation to match MPAS-O
matthewhoffman Feb 26, 2019
8023125
Modify ocean freezing temperature salinity dependence
matthewhoffman Feb 26, 2019
b728995
Correct index to pressure variable
matthewhoffman Feb 27, 2019
0429c1f
Add x2o direction to tbot and dztbot
matthewhoffman Feb 27, 2019
978a6ee
Update comments in prep_glc_mod
matthewhoffman Feb 27, 2019
b451905
Change sign of freshwater flux to ice sheet
matthewhoffman Mar 12, 2019
4a70eaa
Remove unused variable for g2x_gx
matthewhoffman Mar 27, 2019
b39f9ad
Add loop over GLC ensembles for subshelf melt calculation
matthewhoffman Mar 27, 2019
a584b20
Include missing integer assignment
jonbob Mar 27, 2019
9693e08
Reconcile changes with cime_run_glc_setup_send
matthewhoffman Apr 9, 2019
605b6bf
Remove GLC coupling details from cime_run()
matthewhoffman Apr 15, 2019
c0c8103
Improve logic in cime_run_ocnglc_coupling
matthewhoffman Apr 17, 2019
33d4c1f
Improve logic in cime_run_glc_setup_send
matthewhoffman Apr 17, 2019
9525cc6
Remove duplicate call to prep_glc_calculate_subshelf_boundary_fluxes
matthewhoffman Apr 18, 2019
0f5c740
Only enable iceshelf fluxes in E3SM
matthewhoffman Apr 18, 2019
155bb07
Cleanup in prep_glc_mod.F90
matthewhoffman Apr 18, 2019
a5874be
Replace hard-coded field list with generated list
matthewhoffman Apr 19, 2019
aea6529
Make new OCN/GLC cpl fields only in E3SM
matthewhoffman Apr 19, 2019
e430ae9
Adjust CPL restart i/o routines to handle new changes
matthewhoffman Apr 24, 2019
84833ac
Enable optional checkpointing of timing data during initialization
Apr 25, 2019
158682e
Change optional checkpoint of initialization to mandatory
Apr 26, 2019
6d92d78
COMPOSE: add COMPOSE options to namelist_*.xml; use COMPOSE in E3SM t…
ambrad Apr 29, 2019
9243e33
Merge remote-tracking branch 'upstream/master' into ambrad/homme/comp…
ambrad May 6, 2019
4a2265d
Test with changing logic for ocn-glc coupling
jonbob May 6, 2019
aa7c809
Minor cleanup to previous commit
matthewhoffman May 8, 2019
7167787
Merge remote-tracking branch 'upstream/master' into ambrad/homme/comp…
ambrad May 9, 2019
acc5d81
Remove no longer-used cime_model variable
matthewhoffman May 14, 2019
9c0de8d
Cleanup formatting in compute_melt_fluxes()
matthewhoffman May 14, 2019
5a886de
Update config_machines.xml
wadeburgess May 15, 2019
5d9d12b
Add x2g_*_from_lnd lists for use in prep_glc LND routines
matthewhoffman May 16, 2019
67373b9
Merge branch 'matthewhoffman/coupler/iceshelf_ocean_coupling_Fyke2_cl…
jonbob May 21, 2019
324e665
Merge branch 'worleyph/cime/init_profiling' into master (PR #2882)
jgfouca May 21, 2019
1093d45
bless_test_results: Be able to handle build-only tests
jgfouca May 21, 2019
860af52
Update CIME to ESMCI cime5.8.2-3 (PR #2938)
jgfouca May 23, 2019
1438086
Merge esmci_remote_for_split/master
jgfouca May 28, 2019
7c0ea93
Remove duped line
jgfouca May 28, 2019
93e1b5a
Import some fixes
jgfouca May 28, 2019
51de77f
Minor refactor of kokkos stuff in build.py
jgfouca May 28, 2019
fb19ae5
Cleanup whitespace / indentation
billsacks May 31, 2019
c19271c
Move MAP xml variables into shared config_component.xml
billsacks May 31, 2019
e218c9b
Use idmap_ignore for optional mapping files
billsacks May 31, 2019
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27 changes: 25 additions & 2 deletions config/e3sm/config_grids.xml
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Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand Down
2 changes: 1 addition & 1 deletion config/e3sm/machines/config_machines.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
14 changes: 8 additions & 6 deletions scripts/lib/CIME/build.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down Expand Up @@ -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 = []
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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,
Expand Down
5 changes: 3 additions & 2 deletions scripts/lib/CIME/case/check_lockedfiles.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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"))

Expand Down
7 changes: 5 additions & 2 deletions scripts/lib/CIME/hist_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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__)
Expand Down Expand Up @@ -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)
Expand Down
108 changes: 108 additions & 0 deletions src/drivers/mct/cime_config/config_component.xml
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Expand Up @@ -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>
Expand All @@ -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>
Expand Down Expand Up @@ -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>
Expand Down
78 changes: 7 additions & 71 deletions src/drivers/mct/cime_config/config_component_e3sm.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand Down Expand Up @@ -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>
Expand Down
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