Do NOT override this method, this method is the framework that controls the build phase. build_phase is the extension point that subclasses should use.
diff --git a/versions/master/html/CIME_api/CIME.XML.html b/versions/master/html/CIME_api/CIME.XML.html index 65ced41acbb..5b1304a2681 100644 --- a/versions/master/html/CIME_api/CIME.XML.html +++ b/versions/master/html/CIME_api/CIME.XML.html @@ -781,6 +781,14 @@Bases: EnvBase
copy_globs()copy_local_macros_to_dir()copyifnewer()deprecate_action()does_file_have_string()expect()file_contains_python_function()TestTestStatusTestTestStatus.setUp()TestTestStatus.test_current_is()TestTestStatus.test_get_latest_phase()TestTestStatus.test_psdump_corePhasesPass()TestTestStatus.test_psdump_oneCorePhaseFails()TestTestStatus.test_psdump_oneCorePhaseFailsAbsentFromXFails()Bases: object
TestStatusTestStatus.current_is()TestStatus.flush()TestStatus.get_comment()TestStatus.get_latest_phase()TestStatus.get_name()TestStatus.get_overall_test_status()TestStatus.get_status()copy_globs()copy_local_macros_to_dir()copyifnewer()deprecate_action()does_file_have_string()expect()file_contains_python_function()$ ./bless_test_results --help
-ERROR: xmllint not found in PATH, xmllint is required for cime. PATH=/opt/hostedtoolcache/Python/3.11.3/x64/bin:/opt/hostedtoolcache/Python/3.11.3/x64:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ERROR: xmllint not found in PATH, xmllint is required for cime. PATH=/opt/hostedtoolcache/Python/3.11.4/x64/bin:/opt/hostedtoolcache/Python/3.11.4/x64:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
$ ./case.build --help
usage: case.build [-h] [-d] [-v] [-s] [--ninja] [--separate-builds]
- [--dry-run]
+ [--skip-submit] [--dry-run]
[--sharedlib-only | -m | -b {cpl,atm,lnd,ice,ocn,rof,glc,wav,esp,iac,csmshare,mct,pio,gptl} [{cpl,atm,lnd,ice,ocn,rof,glc,wav,esp,iac,csmshare,mct,pio,gptl} ...]
| --skip-provenance-check | --clean-all | --clean
[{cpl,atm,lnd,ice,ocn,rof,glc,wav,esp,iac,csmshare,mct,pio,gptl} ...]
@@ -207,6 +207,7 @@
-s, --silent Print only warnings and error messages
--ninja Use ninja backed for CMake (instead of gmake). The ninja backend is better at scanning fortran dependencies but seems to be less reliable across different platforms and compilers.
--separate-builds Build each component one at a time, separately, with output going to separate logs
+ --skip-submit Sets the current test phase to RUN, skipping the SUBMIT phase. This may be useful if rebuilding the model while this test is in the batch queue. ONLY USE IF A TEST CASE, OTHERWISE IGNORED.
--dry-run Just print the cmake and ninja commands.
--sharedlib-only Only build shared libraries.
-m, --model-only Assume shared libraries are already built.
diff --git a/versions/master/html/Tools_user/compare_test_results.html b/versions/master/html/Tools_user/compare_test_results.html
index 84cc85213dc..fc40e9376b6 100644
--- a/versions/master/html/Tools_user/compare_test_results.html
+++ b/versions/master/html/Tools_user/compare_test_results.html
@@ -147,7 +147,7 @@
$ ./compare_test_results --help
-ERROR: xmllint not found in PATH, xmllint is required for cime. PATH=/opt/hostedtoolcache/Python/3.11.3/x64/bin:/opt/hostedtoolcache/Python/3.11.3/x64:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ERROR: xmllint not found in PATH, xmllint is required for cime. PATH=/opt/hostedtoolcache/Python/3.11.4/x64/bin:/opt/hostedtoolcache/Python/3.11.4/x64:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
diff --git a/versions/master/html/Tools_user/create_test.html b/versions/master/html/Tools_user/create_test.html
index da2dceec56c..685bffa89a5 100644
--- a/versions/master/html/Tools_user/create_test.html
+++ b/versions/master/html/Tools_user/create_test.html
@@ -154,7 +154,7 @@
[--clean] [-m MACHINE] [--mpilib MPILIB] [-c COMPARE]
[-g GENERATE] [--xml-machine XML_MACHINE]
[--xml-compiler XML_COMPILER] [--xml-category XML_CATEGORY]
- [--xml-testlist XML_TESTLIST] [--driver {mct,nuopc,moab}]
+ [--xml-testlist XML_TESTLIST] [--driver {mct,nuopc}]
[--compiler COMPILER] [-n] [-p PROJECT] [-t TEST_ID]
[-j PARALLEL_JOBS] [--proc-pool PROC_POOL]
[--walltime WALLTIME] [-q QUEUE] [-f TESTFILE] [-o]
@@ -223,8 +223,7 @@
The default is all if any --xml- argument is used.
--xml-testlist XML_TESTLIST
Use this testlist to lookup tests.The default is specified in config_files.xml
- --driver {mct,nuopc,moab}
- Override driver specified in tests and use this one.
+ --driver {mct,nuopc} Override driver specified in tests and use this one.
--compiler COMPILER Compiler for building cime. Default will be the name in the
Testname or the default defined for the machine.
-n, --namelists-only Only perform namelist actions for tests
diff --git a/versions/master/html/Tools_user/query_config.html b/versions/master/html/Tools_user/query_config.html
index d7145bd69ad..cdf906b629f 100644
--- a/versions/master/html/Tools_user/query_config.html
+++ b/versions/master/html/Tools_user/query_config.html
@@ -147,7 +147,7 @@
$ ./query_config --help
-ERROR: xmllint not found in PATH, xmllint is required for cime. PATH=/opt/hostedtoolcache/Python/3.11.3/x64/bin:/opt/hostedtoolcache/Python/3.11.3/x64:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ERROR: xmllint not found in PATH, xmllint is required for cime. PATH=/opt/hostedtoolcache/Python/3.11.4/x64/bin:/opt/hostedtoolcache/Python/3.11.4/x64:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/snap/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
diff --git a/versions/master/html/_modules/CIME/SystemTests/system_tests_common.html b/versions/master/html/_modules/CIME/SystemTests/system_tests_common.html
index 311a3f53dfc..09f80e66e0d 100644
--- a/versions/master/html/_modules/CIME/SystemTests/system_tests_common.html
+++ b/versions/master/html/_modules/CIME/SystemTests/system_tests_common.html
@@ -240,6 +240,7 @@ Source code for CIME.SystemTests.system_tests_common
ninja=False,
dry_run=False,
separate_builds=False,
+ skip_submit=False,
):
"""
Do NOT override this method, this method is the framework that
@@ -250,6 +251,9 @@ Source code for CIME.SystemTests.system_tests_common
self._ninja = ninja
self._dry_run = dry_run
self._user_separate_builds = separate_builds
+
+ was_run_pend = self._test_status.current_is(RUN_PHASE, TEST_PEND_STATUS)
+
for phase_name, phase_bool in [
(SHAREDLIB_BUILD_PHASE, not model_only),
(MODEL_BUILD_PHASE, not sharedlib_only),
@@ -288,6 +292,15 @@ Source code for CIME.SystemTests.system_tests_common
comments=("time={:d}".format(int(time_taken))),
)
+ # Building model while job is queued and awaiting run
+ if (
+ skip_submit
+ and was_run_pend
+ and self._test_status.current_is(SUBMIT_PHASE, TEST_PEND_STATUS)
+ ):
+ with self._test_status:
+ self._test_status.set_status(SUBMIT_PHASE, TEST_PASS_STATUS)
+
return success
[docs] def build_phase(self, sharedlib_only=False, model_only=False):
diff --git a/versions/master/html/_modules/CIME/Tools/standard_script_setup.html b/versions/master/html/_modules/CIME/Tools/standard_script_setup.html
index 17e11420e3a..d76beeb9a3c 100644
--- a/versions/master/html/_modules/CIME/Tools/standard_script_setup.html
+++ b/versions/master/html/_modules/CIME/Tools/standard_script_setup.html
@@ -127,7 +127,6 @@ Source code for CIME.Tools.standard_script_setup
import CIME.utils
-
CIME.utils.stop_buffering_output()
import logging, argparse
diff --git a/versions/master/html/_modules/CIME/XML/env_batch.html b/versions/master/html/_modules/CIME/XML/env_batch.html
index 2ca7e949dda..af072f38c91 100644
--- a/versions/master/html/_modules/CIME/XML/env_batch.html
+++ b/versions/master/html/_modules/CIME/XML/env_batch.html
@@ -693,7 +693,6 @@ Source code for CIME.XML.env_batch
flag, name = self._get_argument(case, arg)
except ValueError:
continue
-
if self._batchtype == "cobalt" and job == "case.st_archive":
if flag == "-n":
name = "task_count"
@@ -1050,7 +1049,20 @@ Source code for CIME.XML.env_batch
return
- submitargs = case.get_value("BATCH_COMMAND_FLAGS", subgroup=job)
+ submitargs = case.get_value("BATCH_COMMAND_FLAGS", subgroup=job, resolved=False)
+
+ project = case.get_value("PROJECT", subgroup=job)
+
+ if not project:
+ # If there is no project then we need to remove the project flag
+ if (
+ batch_system == "pbs" or batch_system == "cobalt"
+ ) and " -A " in submitargs:
+ submitargs = submitargs.replace("-A", "")
+ elif batch_system == "lsf" and " -P " in submitargs:
+ submitargs = submitargs.replace("-P", "")
+ elif batch_system == "slurm" and " --account " in submitargs:
+ submitargs = submitargs.replace("--account", "")
if dep_jobs is not None and len(dep_jobs) > 0:
logger.debug("dependencies: {}".format(dep_jobs))
diff --git a/versions/master/html/_modules/CIME/XML/env_build.html b/versions/master/html/_modules/CIME/XML/env_build.html
index 57a2a3556f3..9416c153199 100644
--- a/versions/master/html/_modules/CIME/XML/env_build.html
+++ b/versions/master/html/_modules/CIME/XML/env_build.html
@@ -104,7 +104,22 @@ Source code for CIME.XML.env_build
initialize an object interface to file env_build.xml in the case directory
"""
schema = os.path.join(utils.get_schema_path(), "env_entry_id.xsd")
- EnvBase.__init__(self, case_root, infile, schema=schema, read_only=read_only)
+ self._caseroot = case_root
+ EnvBase.__init__(self, case_root, infile, schema=schema, read_only=read_only)
+
+[docs] def set_value(self, vid, value, subgroup=None, ignore_type=False):
+ """
+ Set the value of an entry-id field to value
+ Returns the value or None if not found
+ subgroup is ignored in the general routine and applied in specific methods
+ """
+ # Do not allow any of these to be the same as CASEROOT
+ if vid in ("EXEROOT", "OBJDIR", "LIBROOT"):
+ utils.expect(value != self._caseroot, f"Cannot set {vid} to CASEROOT")
+
+ return super(EnvBuild, self).set_value(
+ vid, value, subgroup=subgroup, ignore_type=ignore_type
+ )
diff --git a/versions/master/html/_modules/CIME/XML/grids.html b/versions/master/html/_modules/CIME/XML/grids.html
index 1e62acc293c..71aaefe6d82 100644
--- a/versions/master/html/_modules/CIME/XML/grids.html
+++ b/versions/master/html/_modules/CIME/XML/grids.html
@@ -111,6 +111,10 @@ Source code for CIME.XML.grids
infile = files.get_value("GRIDS_SPEC_FILE")
logger.debug(" Grid specification file is {}".format(infile))
schema = files.get_schema("GRIDS_SPEC_FILE")
+ expect(
+ os.path.isfile(infile) and os.access(infile, os.R_OK),
+ f" grid file not found {infile}",
+ )
try:
GenericXML.__init__(self, infile, schema)
except:
diff --git a/versions/master/html/_modules/CIME/XML/machines.html b/versions/master/html/_modules/CIME/XML/machines.html
index 177d4dda17d..9db19b5cc7a 100644
--- a/versions/master/html/_modules/CIME/XML/machines.html
+++ b/versions/master/html/_modules/CIME/XML/machines.html
@@ -127,9 +127,12 @@ Source code for CIME.XML.machines
logger.debug("Verifying using schema {}".format(schema))
self.machines_dir = os.path.dirname(infile)
+ if os.path.exists(infile):
+ checked_files.append(infile)
+ else:
+ expect(False, f"file not found {infile}")
GenericXML.__init__(self, infile, schema)
- checked_files.append(infile)
# Append the contents of $HOME/.cime/config_machines.xml if it exists.
#
diff --git a/versions/master/html/_modules/CIME/build.html b/versions/master/html/_modules/CIME/build.html
index 0c69af45b5f..8ec5ca0c3ee 100644
--- a/versions/master/html/_modules/CIME/build.html
+++ b/versions/master/html/_modules/CIME/build.html
@@ -334,8 +334,8 @@ Source code for CIME.build
)
ocn_model = case.get_value("COMP_OCN")
- atm_model = case.get_value("COMP_ATM")
- if ocn_model == "mom" or atm_model == "fv3gfs":
+ atm_dycore = case.get_value("CAM_DYCORE")
+ if ocn_model == "mom" or (atm_dycore and atm_dycore == "fv3"):
cmake_args += " -DUSE_FMS=TRUE "
cmake_args += " -DINSTALL_SHAREDPATH={} ".format(
@@ -352,6 +352,7 @@ Source code for CIME.build
for var in _CMD_ARGS_FOR_BUILD:
cmake_args += xml_to_make_variable(case, var, cmake=True)
+ atm_model = case.get_value("COMP_ATM")
if atm_model == "scream":
cmake_args += xml_to_make_variable(case, "HOMME_TARGET", cmake=True)
@@ -847,8 +848,9 @@ Source code for CIME.build
libs.append("CDEPS")
ocn_model = case.get_value("COMP_OCN")
- atm_model = case.get_value("COMP_ATM")
- if ocn_model == "mom" or atm_model == "fv3gfs":
+
+ atm_dycore = case.get_value("CAM_DYCORE")
+ if ocn_model == "mom" or (atm_dycore and atm_dycore == "fv3"):
libs.append("FMS")
files = Files(comp_interface=comp_interface)
@@ -1202,6 +1204,7 @@ Source code for CIME.build
ninst_build = case.get_value("NINST_BUILD")
smp_value = case.get_value("SMP_VALUE")
clm_use_petsc = case.get_value("CLM_USE_PETSC")
+ mpaso_use_petsc = case.get_value("MPASO_USE_PETSC")
cism_use_trilinos = case.get_value("CISM_USE_TRILINOS")
mali_use_albany = case.get_value("MALI_USE_ALBANY")
mach = case.get_value("MACH")
@@ -1226,7 +1229,7 @@ Source code for CIME.build
# the future there may be others -- so USE_PETSC will be true if
# ANY of those are true.
- use_petsc = clm_use_petsc
+ use_petsc = bool(clm_use_petsc) or bool(mpaso_use_petsc)
case.set_value("USE_PETSC", use_petsc)
# Set the overall USE_TRILINOS variable to TRUE if any of the
diff --git a/versions/master/html/_modules/CIME/case/case_st_archive.html b/versions/master/html/_modules/CIME/case/case_st_archive.html
index d6145b37a95..8e9edd79080 100644
--- a/versions/master/html/_modules/CIME/case/case_st_archive.html
+++ b/versions/master/html/_modules/CIME/case/case_st_archive.html
@@ -450,8 +450,10 @@ Source code for CIME.case.case_st_archive
histfiles = set()
rest_hist_varname = archive.get_entry_value("rest_history_varname", archive_entry)
if rest_hist_varname != "unset":
- cmd = "ncdump -v {} {} ".format(
- rest_hist_varname, os.path.join(rundir, restfile)
+ ncdump = shutil.which("ncdump")
+ expect(ncdump, "ncdump not found in path")
+ cmd = "{} -v {} {} ".format(
+ ncdump, rest_hist_varname, os.path.join(rundir, restfile)
)
if testonly:
out = "{} =".format(rest_hist_varname)
diff --git a/versions/master/html/_modules/CIME/scripts/create_newcase.html b/versions/master/html/_modules/CIME/scripts/create_newcase.html
index 4a5f2949b7c..a2003d6b807 100644
--- a/versions/master/html/_modules/CIME/scripts/create_newcase.html
+++ b/versions/master/html/_modules/CIME/scripts/create_newcase.html
@@ -325,6 +325,8 @@ Source code for CIME.scripts.create_newcase
parser.add_argument(
"--driver",
+ # use get_cime_default_driver rather than config.driver_default as it considers
+ # environment, user config then config.driver_default
default=get_cime_default_driver(),
choices=drv_choices,
help=drv_help,
diff --git a/versions/master/html/_modules/CIME/scripts/create_test.html b/versions/master/html/_modules/CIME/scripts/create_test.html
index 2e8eeabcb23..fff75423828 100644
--- a/versions/master/html/_modules/CIME/scripts/create_test.html
+++ b/versions/master/html/_modules/CIME/scripts/create_test.html
@@ -305,7 +305,7 @@ Source code for CIME.scripts.create_test
parser.add_argument(
"--driver",
- choices=("mct", "nuopc", "moab"),
+ choices=model_config.driver_choices,
help="Override driver specified in tests and use this one.",
)
diff --git a/versions/master/html/_modules/CIME/scripts/query_config.html b/versions/master/html/_modules/CIME/scripts/query_config.html
index 74f2b1427a0..003dd466ac1 100644
--- a/versions/master/html/_modules/CIME/scripts/query_config.html
+++ b/versions/master/html/_modules/CIME/scripts/query_config.html
@@ -94,7 +94,7 @@ Source code for CIME.scripts.query_config
from CIME.Tools.standard_script_setup import *
import re
-from CIME.utils import expect
+from CIME.utils import expect, get_cime_default_driver, deprecate_action
from CIME.XML.files import Files
from CIME.XML.component import Component
from CIME.XML.compsets import Compsets
@@ -400,8 +400,16 @@ Source code for CIME.scripts.query_config
parser.add_argument(
"--comp_interface",
- choices=supported_comp_interfaces,
+ choices=supported_comp_interfaces, # same as config.driver_choices
default="mct",
+ action=deprecate_action(", use --driver argument"),
+ help="DEPRECATED: Use --driver argument",
+ )
+
+ parser.add_argument(
+ "--driver",
+ choices=config.driver_choices,
+ default=get_cime_default_driver(),
help="Coupler/Driver interface",
)
@@ -418,7 +426,7 @@ Source code for CIME.scripts.query_config
args.machines,
args.long,
args.xml,
- files[args.comp_interface],
+ files[args.driver],
)
diff --git a/versions/master/html/_modules/CIME/test_status.html b/versions/master/html/_modules/CIME/test_status.html
index 3e96d272eb5..26b994174ce 100644
--- a/versions/master/html/_modules/CIME/test_status.html
+++ b/versions/master/html/_modules/CIME/test_status.html
@@ -360,6 +360,17 @@ Source code for CIME.test_status
[docs] def get_comment(self, phase):
return self._phase_statuses[phase][1] if phase in self._phase_statuses else None
+[docs] def current_is(self, phase, status):
+ try:
+ latest = self.get_latest_phase()
+ except KeyError:
+ return False
+
+ return latest == phase and self.get_status(phase) == status
+
+
+
[docs] def phase_statuses_dump(
self, prefix="", skip_passes=False, skip_phase_list=None, xfails=None
):
diff --git a/versions/master/html/_modules/CIME/tests/test_unit_test_status.html b/versions/master/html/_modules/CIME/tests/test_unit_test_status.html
index 6ce95fc9bde..2438f4c4480 100644
--- a/versions/master/html/_modules/CIME/tests/test_unit_test_status.html
+++ b/versions/master/html/_modules/CIME/tests/test_unit_test_status.html
@@ -127,6 +127,20 @@ Source code for CIME.tests.test_unit_test_status
with self._ts:
self._ts.set_status(phase, status)
+[docs] def test_get_latest_phase(self):
+ assert self._ts.get_latest_phase() == test_status.RUN_PHASE
+
+[docs] def test_current_is(self):
+ assert self._ts.current_is(test_status.RUN_PHASE, test_status.TEST_PASS_STATUS)
+
+ assert not self._ts.current_is(
+ test_status.RUN_PHASE, test_status.TEST_PEND_STATUS
+ )
+
+ assert not self._ts.current_is(
+ test_status.SUBMIT_PHASE, test_status.TEST_PASS_STATUS
+ )
+
# ------------------------------------------------------------------------
# Tests of TestStatus.phase_statuses_dump
# ------------------------------------------------------------------------
diff --git a/versions/master/html/_modules/CIME/tests/test_unit_xml_machines.html b/versions/master/html/_modules/CIME/tests/test_unit_xml_machines.html
index 6c43c647964..b12b77edff8 100644
--- a/versions/master/html/_modules/CIME/tests/test_unit_xml_machines.html
+++ b/versions/master/html/_modules/CIME/tests/test_unit_xml_machines.html
@@ -226,8 +226,8 @@ Source code for CIME.tests.test_unit_xml_machines
[docs]class TestUnitXMLMachines(unittest.TestCase):
[docs] def setUp(self):
Machines._FILEMAP = {}
-
- self.machine = Machines()
+ # read_only=False for github testing
+ self.machine = Machines(machine="centos7-linux")
self.machine.read_fd(io.StringIO(MACHINE_TEST_XML))
diff --git a/versions/master/html/_modules/CIME/utils.html b/versions/master/html/_modules/CIME/utils.html
index 66e20b3af64..abb91ca042f 100644
--- a/versions/master/html/_modules/CIME/utils.html
+++ b/versions/master/html/_modules/CIME/utils.html
@@ -94,6 +94,7 @@ Source code for CIME.utils
import importlib.util
import errno, signal, warnings, filecmp
import stat as statlib
+from argparse import Action
from contextlib import contextmanager
from distutils import file_util
@@ -107,6 +108,14 @@ Source code for CIME.utils
GLOBAL = {}
+[docs]def deprecate_action(message):
+ class ActionStoreDeprecated(Action):
+ def __call__(self, parser, namespace, values, option_string=None):
+ raise DeprecationWarning(f"{option_string} is deprecated{message}")
+
+ return ActionStoreDeprecated
+
+
[docs]def import_from_file(name, file_path):
loader = importlib.machinery.SourceFileLoader(name, file_path)
diff --git a/versions/master/html/_modules/Tools/standard_script_setup.html b/versions/master/html/_modules/Tools/standard_script_setup.html
index 4816f2c80bc..f43f9125887 100644
--- a/versions/master/html/_modules/Tools/standard_script_setup.html
+++ b/versions/master/html/_modules/Tools/standard_script_setup.html
@@ -127,7 +127,6 @@ Source code for Tools.standard_script_setup
import CIME.utils
-
CIME.utils.stop_buffering_output()
import logging, argparse
diff --git a/versions/master/html/_sources/users_guide/create-a-case.rst.txt b/versions/master/html/_sources/users_guide/create-a-case.rst.txt
index 71b39b5cbd8..c9257da19a6 100644
--- a/versions/master/html/_sources/users_guide/create-a-case.rst.txt
+++ b/versions/master/html/_sources/users_guide/create-a-case.rst.txt
@@ -207,6 +207,17 @@ As an example, the directory could contain the following files: ::
> shell_commands (this would contain ./xmlchange commands)
> SourceMods/src.cam/dyncomp.F90
+It is important to note that the file containing the **xmlchange**
+commands must be named ``shell_commands`` in order for it to be recognised
+and run upon case creation.
+
+The structure of the component directories do not need to be the
+same as in the component source code. As an example, should the user
+want to modify the ``src/dynamics/eul/dyncomp.F90`` file within the
+CAM source code, the modified file should be put into the directory
+``SourceMods/src.cam`` directly. There is no need to mimic the source
+code structure, such as ``SourceMods/src.cam/dynamics/eul``.
+
When the user calls **create_newcase** with the ``--user-mods-dir`` pointing to the
full pathname of the directory containing these changes, then the ``CASEROOT`` will be
created with these changes applied.
diff --git a/versions/master/html/genindex.html b/versions/master/html/genindex.html
index e926854ffcc..15b591d8bc0 100644
--- a/versions/master/html/genindex.html
+++ b/versions/master/html/genindex.html
@@ -1170,8 +1170,6 @@ C
- module
-
-
-
CIME.tests.test_sys_create_newcase
@@ -1179,6 +1177,8 @@
C
- module
+
-
CIME.tests.test_sys_full_system
@@ -1933,6 +1933,8 @@
C
- createUserMod() (CIME.tests.test_unit_user_mod_support.TestUserModSupport method)
- cs_status() (in module CIME.cs_status)
+
+ - current_is() (CIME.test_status.TestStatus method)
- CustomAssertionsTestStatus (class in CIME.tests.custom_assertions_test_status)
@@ -1975,10 +1977,12 @@ D
- day() (CIME.date.date method)
- delete_old_test_data() (in module CIME.jenkins_generic_job)
+
+ - delete_variable() (CIME.namelist.Namelist method)
- - delete_variable() (CIME.namelist.Namelist method)
+
- deprecate_action() (in module CIME.utils)
- dict_to_namelist() (CIME.XML.namelist_definition.NamelistDefinition method)
@@ -2385,6 +2389,8 @@ G
- get_latest_cpl_log() (CIME.case.case.Case method)
- get_latest_hist_files() (CIME.XML.archive_base.ArchiveBase method)
+
+ - get_latest_phase() (CIME.test_status.TestStatus method)
- get_lids() (in module CIME.utils)
@@ -3747,6 +3753,8 @@ S
- (CIME.XML.env_base.EnvBase method)
- (CIME.XML.env_batch.EnvBatch method)
+
+ - (CIME.XML.env_build.EnvBuild method)
- (CIME.XML.env_mach_pes.EnvMachPes method)
@@ -4136,6 +4144,8 @@ T
- test_create_macros_copy_user() (CIME.tests.test_unit_case_setup.TestCaseSetup method)
- test_create_test_longname() (CIME.tests.test_sys_cime_case.TestCimeCase method)
+
+ - test_current_is() (CIME.tests.test_unit_test_status.TestTestStatus method)
- test_d_create_clone_new_user() (CIME.tests.test_sys_create_newcase.TestCreateNewcase method)
@@ -4234,6 +4244,8 @@ T
- test_get_grid_info_extra_gridmaps() (CIME.tests.test_unit_grids.TestGrids method)
- test_get_grid_info_extra_required_gridmaps() (CIME.tests.test_unit_grids.TestGrids method)
+
+ - test_get_latest_phase() (CIME.tests.test_unit_test_status.TestTestStatus method)
- test_get_mpirun() (CIME.tests.test_unit_xml_env_mach_specific.TestXMLEnvMachSpecific method)
@@ -4304,11 +4316,11 @@ T
- test_jenkins_generic_job_kill() (CIME.tests.test_sys_jenkins_generic_job.TestJenkinsGenericJob method)
- test_jenkins_generic_job_realistic_dash() (CIME.tests.test_sys_jenkins_generic_job.TestJenkinsGenericJob method)
-
- - test_k_append_config() (CIME.tests.test_sys_create_newcase.TestCreateNewcase method)
+ - test_k_append_config() (CIME.tests.test_sys_create_newcase.TestCreateNewcase method)
+
- test_ka_createnewcase_extra_machines_dir() (CIME.tests.test_sys_create_newcase.TestCreateNewcase method)
- test_keepexe() (CIME.tests.test_unit_user_mod_support.TestUserModSupport method)
diff --git a/versions/master/html/objects.inv b/versions/master/html/objects.inv
index 9b35fb4442c..dad181ab27f 100644
Binary files a/versions/master/html/objects.inv and b/versions/master/html/objects.inv differ
diff --git a/versions/master/html/searchindex.js b/versions/master/html/searchindex.js
index cb22a4d94dc..d3395137f6a 100644
--- a/versions/master/html/searchindex.js
+++ b/versions/master/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["CIME_api/CIME", "CIME_api/CIME.BuildTools", "CIME_api/CIME.Servers", "CIME_api/CIME.SystemTests", "CIME_api/CIME.SystemTests.test_utils", "CIME_api/CIME.Tools", "CIME_api/CIME.XML", "CIME_api/CIME.build_scripts", "CIME_api/CIME.case", "CIME_api/CIME.data", "CIME_api/CIME.data.config", "CIME_api/CIME.data.templates", "CIME_api/CIME.scripts", "CIME_api/CIME.tests", "CIME_api/modules", "Tools_api/Tools", "Tools_api/modules", "Tools_user/advanced-py-prof", "Tools_user/archive_metadata", "Tools_user/bld_diff", "Tools_user/bless_test_results", "Tools_user/case.build", "Tools_user/case.cmpgen_namelists", "Tools_user/case.qstatus", "Tools_user/case.setup", "Tools_user/case.submit", "Tools_user/case_diff", "Tools_user/check_case", "Tools_user/check_input_data", "Tools_user/check_lockedfiles", "Tools_user/cime_bisect", "Tools_user/code_checker", "Tools_user/compare_namelists", "Tools_user/compare_test_results", "Tools_user/component_compare_baseline", "Tools_user/component_compare_copy", "Tools_user/component_compare_test", "Tools_user/component_generate_baseline", "Tools_user/concat_daily_hist.csh", "Tools_user/create_clone", "Tools_user/create_newcase", "Tools_user/create_test", "Tools_user/cs.status", "Tools_user/e3sm_check_env", "Tools_user/generate_cylc_workflow.py", "Tools_user/getTiming", "Tools_user/get_case_env", "Tools_user/get_standard_makefile_args", "Tools_user/index", "Tools_user/jenkins_generic_job", "Tools_user/list_e3sm_tests", "Tools_user/mkDepends", "Tools_user/mkSrcfiles", "Tools_user/mvsource", "Tools_user/normalize_cases", "Tools_user/pelayout", "Tools_user/preview_namelists", "Tools_user/preview_run", "Tools_user/query_config", "Tools_user/query_testlists", "Tools_user/save_provenance", "Tools_user/simple-py-prof", "Tools_user/simple_compare", "Tools_user/testreporter.py", "Tools_user/wait_for_tests", "Tools_user/xmlchange", "Tools_user/xmlquery", "Tools_user/xmltestentry", "build_cpl/adding-components", 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"CIME.XML.generic_xml module": [[6, "module-CIME.XML.generic_xml"]], "CIME.XML.grids module": [[6, "module-CIME.XML.grids"]], "CIME.XML.headers module": [[6, "module-CIME.XML.headers"]], "CIME.XML.inputdata module": [[6, "module-CIME.XML.inputdata"]], "CIME.XML.machines module": [[6, "module-CIME.XML.machines"]], "CIME.XML.namelist_definition module": [[6, "module-CIME.XML.namelist_definition"]], "CIME.XML.pes module": [[6, "module-CIME.XML.pes"]], "CIME.XML.pio module": [[6, "module-CIME.XML.pio"]], "CIME.XML.standard_module_setup module": [[6, "module-CIME.XML.standard_module_setup"]], "CIME.XML.stream module": [[6, "module-CIME.XML.stream"]], "CIME.XML.test_reporter module": [[6, "module-CIME.XML.test_reporter"]], "CIME.XML.testlist module": [[6, "module-CIME.XML.testlist"]], "CIME.XML.tests module": [[6, "module-CIME.XML.tests"]], "CIME.XML.testspec module": [[6, "module-CIME.XML.testspec"]], "CIME.XML.workflow module": [[6, "module-CIME.XML.workflow"]], "CIME.build_scripts package": [[7, "cime-build-scripts-package"]], "CIME.case package": [[8, "cime-case-package"]], "CIME.case.case module": [[8, "module-CIME.case.case"]], "CIME.case.case_clone module": [[8, "module-CIME.case.case_clone"]], "CIME.case.case_cmpgen_namelists module": [[8, "module-CIME.case.case_cmpgen_namelists"]], "CIME.case.case_run module": [[8, "module-CIME.case.case_run"]], "CIME.case.case_setup module": [[8, "module-CIME.case.case_setup"]], "CIME.case.case_st_archive module": [[8, "module-CIME.case.case_st_archive"]], "CIME.case.case_submit module": [[8, "module-CIME.case.case_submit"]], "CIME.case.case_test module": [[8, "module-CIME.case.case_test"]], "CIME.case.check_input_data module": [[8, "module-CIME.case.check_input_data"]], "CIME.case.check_lockedfiles module": [[8, "module-CIME.case.check_lockedfiles"]], "CIME.case.preview_namelists module": [[8, "module-CIME.case.preview_namelists"]], "CIME.data package": [[9, "cime-data-package"]], "CIME.data.config package": [[10, "cime-data-config-package"]], "CIME.data.templates package": [[11, "cime-data-templates-package"]], "CIME.scripts package": [[12, "cime-scripts-package"]], "CIME.scripts.create_clone module": [[12, "module-CIME.scripts.create_clone"]], "CIME.scripts.create_newcase module": [[12, "module-CIME.scripts.create_newcase"]], "CIME.scripts.create_test module": [[12, "module-CIME.scripts.create_test"]], "CIME.scripts.query_config module": [[12, "module-CIME.scripts.query_config"]], "CIME.scripts.query_testlists module": [[12, "module-CIME.scripts.query_testlists"]], "CIME.tests package": [[13, "cime-tests-package"]], "CIME.tests.base module": [[13, "module-CIME.tests.base"]], "CIME.tests.case_fake module": [[13, "module-CIME.tests.case_fake"]], "CIME.tests.custom_assertions_test_status module": [[13, "module-CIME.tests.custom_assertions_test_status"]], "CIME.tests.scripts_regression_tests module": [[13, "module-CIME.tests.scripts_regression_tests"]], "CIME.tests.test_sys_bless_tests_results module": [[13, "module-CIME.tests.test_sys_bless_tests_results"]], "CIME.tests.test_sys_build_system module": [[13, "module-CIME.tests.test_sys_build_system"]], "CIME.tests.test_sys_cime_case module": [[13, "module-CIME.tests.test_sys_cime_case"]], "CIME.tests.test_sys_cime_performance module": [[13, "module-CIME.tests.test_sys_cime_performance"]], "CIME.tests.test_sys_create_newcase module": [[13, "module-CIME.tests.test_sys_create_newcase"]], "CIME.tests.test_sys_full_system module": [[13, "module-CIME.tests.test_sys_full_system"]], "CIME.tests.test_sys_grid_generation module": [[13, "module-CIME.tests.test_sys_grid_generation"]], "CIME.tests.test_sys_jenkins_generic_job module": [[13, "module-CIME.tests.test_sys_jenkins_generic_job"]], "CIME.tests.test_sys_manage_and_query module": [[13, "module-CIME.tests.test_sys_manage_and_query"]], "CIME.tests.test_sys_query_config module": [[13, "module-CIME.tests.test_sys_query_config"]], "CIME.tests.test_sys_run_restart module": [[13, "module-CIME.tests.test_sys_run_restart"]], "CIME.tests.test_sys_save_timings module": [[13, "module-CIME.tests.test_sys_save_timings"]], "CIME.tests.test_sys_single_submit module": [[13, "module-CIME.tests.test_sys_single_submit"]], "CIME.tests.test_sys_test_scheduler module": [[13, "module-CIME.tests.test_sys_test_scheduler"]], "CIME.tests.test_sys_unittest module": [[13, "module-CIME.tests.test_sys_unittest"]], "CIME.tests.test_sys_user_concurrent_mods module": [[13, "module-CIME.tests.test_sys_user_concurrent_mods"]], "CIME.tests.test_sys_wait_for_tests module": [[13, "module-CIME.tests.test_sys_wait_for_tests"]], "CIME.tests.test_unit_aprun module": [[13, "module-CIME.tests.test_unit_aprun"]], "CIME.tests.test_unit_case module": [[13, "module-CIME.tests.test_unit_case"]], "CIME.tests.test_unit_case_fake module": [[13, "module-CIME.tests.test_unit_case_fake"]], "CIME.tests.test_unit_case_setup module": [[13, "module-CIME.tests.test_unit_case_setup"]], "CIME.tests.test_unit_compare_test_results module": [[13, "module-CIME.tests.test_unit_compare_test_results"]], "CIME.tests.test_unit_compare_two module": [[13, "module-CIME.tests.test_unit_compare_two"]], "CIME.tests.test_unit_config module": [[13, "module-CIME.tests.test_unit_config"]], "CIME.tests.test_unit_cs_status module": [[13, "module-CIME.tests.test_unit_cs_status"]], "CIME.tests.test_unit_custom_assertions_test_status module": [[13, "module-CIME.tests.test_unit_custom_assertions_test_status"]], "CIME.tests.test_unit_doctest module": [[13, "module-CIME.tests.test_unit_doctest"]], "CIME.tests.test_unit_expected_fails_file module": [[13, "module-CIME.tests.test_unit_expected_fails_file"]], "CIME.tests.test_unit_grids module": [[13, "module-CIME.tests.test_unit_grids"]], "CIME.tests.test_unit_hist_utils module": [[13, "module-CIME.tests.test_unit_hist_utils"]], "CIME.tests.test_unit_nmlgen module": [[13, "module-CIME.tests.test_unit_nmlgen"]], "CIME.tests.test_unit_paramgen module": [[13, "module-CIME.tests.test_unit_paramgen"]], "CIME.tests.test_unit_system_tests module": [[13, "module-CIME.tests.test_unit_system_tests"]], "CIME.tests.test_unit_test_status module": [[13, "module-CIME.tests.test_unit_test_status"]], "CIME.tests.test_unit_two_link_to_case2_output module": [[13, "module-CIME.tests.test_unit_two_link_to_case2_output"]], "CIME.tests.test_unit_user_mod_support module": [[13, "module-CIME.tests.test_unit_user_mod_support"]], "CIME.tests.test_unit_user_nl_utils module": [[13, "module-CIME.tests.test_unit_user_nl_utils"]], "CIME.tests.test_unit_utils module": [[13, "module-CIME.tests.test_unit_utils"]], "CIME.tests.test_unit_xml_archive_base module": [[13, "module-CIME.tests.test_unit_xml_archive_base"]], "CIME.tests.test_unit_xml_env_batch module": [[13, "module-CIME.tests.test_unit_xml_env_batch"]], "CIME.tests.test_unit_xml_env_mach_specific module": [[13, "module-CIME.tests.test_unit_xml_env_mach_specific"]], "CIME.tests.test_unit_xml_machines module": [[13, "module-CIME.tests.test_unit_xml_machines"]], "CIME.tests.test_unit_xml_namelist_definition module": [[13, "module-CIME.tests.test_unit_xml_namelist_definition"]], "CIME.tests.test_unit_xml_tests module": [[13, "module-CIME.tests.test_unit_xml_tests"]], "CIME.tests.utils module": [[13, "module-CIME.tests.utils"]], "CIME": [[14, "cime"]], "Tools package": [[15, "tools-package"]], "Tools.generate_cylc_workflow module": [[15, "module-Tools.generate_cylc_workflow"]], "Tools.standard_script_setup module": [[15, "module-Tools.standard_script_setup"]], "Tools.testreporter module": [[15, "module-Tools.testreporter"]], "Tools": [[16, "tools"]], "advanced-py-prof": [[17, "advanced-py-prof"]], "archive_metadata": [[18, "archive-metadata"]], "bld_diff": [[19, "bld-diff"]], "bless_test_results": [[20, "bless-test-results"]], "case.build": [[21, "case-build"]], "case.cmpgen_namelists": [[22, "case-cmpgen-namelists"]], "case.qstatus": [[23, "case-qstatus"]], "case.setup": [[24, "case-setup"]], "case.submit": [[25, "case-submit"]], "case_diff": [[26, "case-diff"]], "check_case": [[27, "check-case"]], "check_input_data": [[28, "check-input-data"]], "check_lockedfiles": [[29, "check-lockedfiles"]], "cime_bisect": [[30, "cime-bisect"]], "code_checker": [[31, "code-checker"]], "compare_namelists": [[32, "compare-namelists"]], "compare_test_results": [[33, "compare-test-results"]], "component_compare_baseline": [[34, "component-compare-baseline"]], "component_compare_copy": [[35, "component-compare-copy"]], "component_compare_test": [[36, "component-compare-test"]], "component_generate_baseline": [[37, "component-generate-baseline"]], "concat_daily_hist.csh": [[38, "concat-daily-hist-csh"]], "create_clone": [[39, "create-clone"]], "create_newcase": [[40, "create-newcase"]], "create_test": [[41, "create-test"]], "cs.status": [[42, "cs-status"]], "e3sm_check_env": [[43, "e3sm-check-env"]], "generate_cylc_workflow.py": [[44, "generate-cylc-workflow-py"]], "getTiming": [[45, "gettiming"]], "get_case_env": [[46, "get-case-env"]], "get_standard_makefile_args": [[47, "get-standard-makefile-args"]], "User Tools": [[48, "user-tools"]], "jenkins_generic_job": [[49, "jenkins-generic-job"]], "list_e3sm_tests": [[50, "list-e3sm-tests"]], "mkDepends": [[51, "mkdepends"]], "mkSrcfiles": [[52, "mksrcfiles"]], "mvsource": [[53, "mvsource"]], "normalize_cases": [[54, "normalize-cases"]], "pelayout": [[55, "pelayout"]], "preview_namelists": [[56, "preview-namelists"]], "preview_run": [[57, "preview-run"]], "query_config": [[58, "query-config"]], "query_testlists": [[59, "query-testlists"]], "save_provenance": [[60, "save-provenance"]], "simple-py-prof": [[61, "simple-py-prof"]], "simple_compare": [[62, "simple-compare"]], "testreporter.py": [[63, "testreporter-py"]], "wait_for_tests": [[64, "wait-for-tests"]], "xmlchange": [[65, "xmlchange"]], "xmlquery": [[66, "xmlquery"]], "xmltestentry": [[67, "xmltestentry"]], "Adding components": [[68, "adding-components"]], "Building a Coupled Model with CIME": [[69, "building-a-coupled-model-with-cime"]], "Indices and tables": [[69, "indices-and-tables"], [75, "indices-and-tables"], [87, "indices-and-tables"]], "Introduction": [[70, "introduction"], [88, "introduction"], [98, "introduction"]], "Glossary": [[72, "glossary"]], "General": [[72, "general"]], "Coupling": [[72, "coupling"]], "Files and Directories": [[72, "files-and-directories"]], "Development": [[72, "development"], [100, "development"]], "Testing": [[72, "testing"], [76, "testing"], [95, "testing"]], "Miscellaneous": [[72, "miscellaneous"]], "CIME documentation": [[73, "cime-documentation"]], "Table of contents": [[73, "table-of-contents"]], "Appendices": [[73, "appendices"]], "Python Module Indices and Search": [[73, "python-module-indices-and-search"]], "CESM-ECT (CESM Ensemble Consistency Test):": [[74, "cesm-ect-cesm-ensemble-consistency-test"]], "Creating or obtaining a summary file:": [[74, "creating-or-obtaining-a-summary-file"]], "Creating test runs:": [[74, "creating-test-runs"]], "Miscellaneous Tools": [[75, "miscellaneous-tools"]], "CIME Load Balancing Tool": [[76, "cime-load-balancing-tool"]], "Running simulations using load_balancing_submit.py": [[76, "running-simulations-using-load-balancing-submit-py"]], "Optimizing the layout using load_balacing_solve.py": [[76, "optimizing-the-layout-using-load-balacing-solve-py"]], "More about the algorithm": [[76, "more-about-the-algorithm"]], "Extending the Load Balancing Tool": [[76, "extending-the-load-balancing-tool"]], "Building a Case": [[77, "building-a-case"]], "Calling case.build": [[77, "calling-case-build"]], "Rebuilding the model": [[77, "rebuilding-the-model"]], "Input data": [[77, "input-data"], [93, "input-data"]], "Customizing your input variables": [[78, "customizing-your-input-variables"]], "Customizing driver input variables": [[78, "customizing-driver-input-variables"]], "Setting up a multi-year run": [[78, "setting-up-a-multi-year-run"]], "Setting up a branch or hybrid run": [[78, "setting-up-a-branch-or-hybrid-run"]], "Customizing data model input variable and stream files": [[78, "customizing-data-model-input-variable-and-stream-files"]], "Data Atmosphere (DATM)": [[78, "data-atmosphere-datm"]], "Data Ocean (DOCN)": [[78, "data-ocean-docn"]], "Data Sea-ice (DICE)": [[78, "data-sea-ice-dice"]], "Data Land (DLND)": [[78, "data-land-dlnd"]], "Data River (DROF)": [[78, "data-river-drof"]], "Customizing CESM active component-specific namelist settings": [[78, "customizing-cesm-active-component-specific-namelist-settings"]], "CAM": [[78, "cam"]], "CLM": [[78, "clm"]], "MOSART": [[78, "mosart"]], "CICE": [[78, "cice"]], "POP2": [[78, "pop2"]], "CISM": [[78, "cism"]], "CIME user config directory": [[79, "cime-user-config-directory"]], "CIME config and hooks": [[80, "cime-config-and-hooks"]], "How does CIME load customizations?": [[80, "how-does-cime-load-customizations"]], "CIME config": [[80, "cime-config"]], "CIME hooks": [[80, "cime-hooks"]], "Directory content": [[81, "directory-content"]], "CIME directory in a climate model": [[81, "id1"]], "CIME directory content": [[81, "id2"]], "Main Configuration File": [[82, "main-configuration-file"]], "Cloning a Case": [[83, "cloning-a-case"]], "Component sets": [[84, "component-sets"]], "Compset longname": [[84, "compset-longname"]], "Component specific settings in a compset": [[84, "component-specific-settings-in-a-compset"]], "Creating New Compsets": [[84, "creating-new-compsets"]], "Todo": [[84, "id2"], [98, "id1"]], "Creating a Case": [[85, "creating-a-case"]], "Calling create_newcase": [[85, "calling-create-newcase"]], "Results of calling create_newcase": [[85, "results-of-calling-create-newcase"]], "Locked files in your case directory": [[85, "locked-files-in-your-case-directory"]], "Adding a \u2013user-mods-dir argument to create_newcase": [[85, "adding-a-user-mods-dir-argument-to-create-newcase"]], "Model grids": [[86, "model-grids"]], "Grid longname": [[86, "grid-longname"]], "Adding grids": [[86, "adding-grids"]], "Case Control System Part 1: Basic Usage": [[87, "case-control-system-part-1-basic-usage"]], "Case Control System Part 2: Configuration, Porting, Testing and Use Cases": [[87, "case-control-system-part-2-configuration-porting-testing-and-use-cases"]], "Prerequisites": [[88, "prerequisites"]], "Key Terms and concepts": [[88, "key-terms-and-concepts"]], "CIME and your environment": [[88, "cime-and-your-environment"]], "Quick start": [[88, "quick-start"]], "Discovering available cases with query_config": [[88, "discovering-available-cases-with-query-config"]], "Defining the machine": [[89, "defining-the-machine"]], "config_machines.xml - machine specific file": [[89, "config-machines-xml-machine-specific-file"]], "Batch system definition": [[89, "batch-system-definition"]], "config_batch.xml - batch directives": [[89, "config-batch-xml-batch-directives"]], "Compiler settings": [[89, "compiler-settings"]], "config_compilers.xml - compiler paths and options DEPRECATED use cmake_macros": [[89, "config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros"]], "Multi-instance component functionality": [[90, "multi-instance-component-functionality"]], "Controlling processors and threads": [[91, "controlling-processors-and-threads"]], "pe-settings for a case": [[91, "pe-settings-for-a-case"]], "Setting the PE layout": [[91, "setting-the-pe-layout"]], "Entries in env_mach_pes.xml": [[91, "id3"]], "Case Resource Allocation": [[91, "case-resource-allocation"]], "Optimizing processor layout": [[91, "optimizing-processor-layout"]], "Porting and validating CIME on a new platform": [[92, "porting-and-validating-cime-on-a-new-platform"]], "Required libraries/packages": [[92, "required-libraries-packages"]], "An MPI example": [[92, "an-mpi-example"]], "CESM Linux and Mac Support": [[92, "cesm-linux-and-mac-support"]], "Steps for porting": [[92, "steps-for-porting"]], "Validating a CESM port with prognostic components": [[92, "validating-a-cesm-port-with-prognostic-components"]], "Performance tuning of a CESM port": [[92, "performance-tuning-of-a-cesm-port"]], "Running a Case": [[93, "running-a-case"]], "Calling case.submit": [[93, "calling-case-submit"]], "Result of running case.submit": [[93, "result-of-running-case-submit"]], "Monitoring case job statuses": [[93, "monitoring-case-job-statuses"]], "Troubleshooting a job that fails": [[93, "troubleshooting-a-job-that-fails"]], "Distributed Input Data Repositories": [[93, "distributed-input-data-repositories"]], "Starting, Stopping and Restarting a Run": [[93, "starting-stopping-and-restarting-a-run"]], "Run-type initialization": [[93, "run-type-initialization"]], "Starting from a reference case (REFCASE)": [[93, "starting-from-a-reference-case-refcase"]], "Controlling output data": [[93, "controlling-output-data"]], "Restarting a run": [[93, "restarting-a-run"]], "Backing up to a previous restart": [[93, "backing-up-to-a-previous-restart"]], "Archiving model output data": [[93, "archiving-model-output-data"]], "No archiving": [[93, "no-archiving"]], "Short-term archiving": [[93, "short-term-archiving"]], "Long-term archiving": [[93, "long-term-archiving"]], "Data Assimilation and other External Processing": [[93, "data-assimilation-and-other-external-processing"]], "Pre and Post run scripts": [[93, "pre-and-post-run-scripts"]], "Data Assimilation scripts": [[93, "data-assimilation-scripts"]], "Setting up a Case": [[94, "setting-up-a-case"]], "Calling case.setup": [[94, "calling-case-setup"]], "Testname syntax": [[95, "testname-syntax"]], "Query_testlists": [[95, "query-testlists"]], "Using create_test (E3SM)": [[95, "using-create-test-e3sm"]], "Managing baselines": [[95, "managing-baselines"]], "Adding tests": [[95, "adding-tests"]], "CIME Developer\u2019s guide": [[95, "cime-developer-s-guide"]], "Timers and timing": [[96, "timers-and-timing"]], "Model timing data": [[96, "model-timing-data"]], "Controlling timers": [[96, "controlling-timers"]], "Advice on setting your wallclock time": [[96, "advice-on-setting-your-wallclock-time"]], "Troubleshooting": [[97, "troubleshooting"]], "Troubleshooting case creation": [[97, "troubleshooting-case-creation"]], "Troubleshooting problems in cime scripts": [[97, "troubleshooting-problems-in-cime-scripts"]], "Troubleshooting job submission": [[97, "troubleshooting-job-submission"]], "Troubleshooting runtime problems": [[97, "troubleshooting-runtime-problems"]], "Fortran Unit Testing": [[98, "fortran-unit-testing"]], "What is a unit test?": [[98, "what-is-a-unit-test"]], "Overview of unit test support in CIME": [[98, "overview-of-unit-test-support-in-cime"]], "Running CIME\u2019s Fortran unit tests": [[98, "running-cime-s-fortran-unit-tests"]], "How to add unit testing support on your machine": [[98, "how-to-add-unit-testing-support-on-your-machine"]], "Building pFUnit": [[98, "building-pfunit"]], "Adding to the appropriate cmake file": [[98, "adding-to-the-appropriate-cmake-file"]], "How to write a new unit test": [[98, "how-to-write-a-new-unit-test"]], "General guidelines for writing unit tests": [[98, "general-guidelines-for-writing-unit-tests"]], "More details on writing pFUnit-based unit tests": [[98, "more-details-on-writing-pfunit-based-unit-tests"]], "Assertion methods": [[98, "assertion-methods"]], "Defining a test class in order to define setUp and tearDown methods": [[98, "defining-a-test-class-in-order-to-define-setup-and-teardown-methods"]], "More on test teardown": [[98, "more-on-test-teardown"]], "Finding more documentation and examples": [[98, "finding-more-documentation-and-examples"]], "More detailed examples in CIME": [[98, "more-detailed-examples-in-cime"]], "Other pFUnit documentation sources": [[98, "other-pfunit-documentation-sources"]], "Documentation of the unit test build system": [[98, "documentation-of-the-unit-test-build-system"]], "Workflows": [[99, 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"wait_for_tests_impl() (in module cime.wait_for_tests)": [[0, "CIME.wait_for_tests.wait_for_tests_impl"]], "wait_for_unlocked() (in module cime.utils)": [[0, "CIME.utils.wait_for_unlocked"]], "write() (cime.namelist.namelist method)": [[0, "CIME.namelist.Namelist.write"]], "write_modelio_file() (cime.nmlgen.namelistgenerator method)": [[0, "CIME.nmlgen.NamelistGenerator.write_modelio_file"]], "write_nuopc() (cime.namelist.namelist method)": [[0, "CIME.namelist.Namelist.write_nuopc"]], "write_nuopc_config_file() (cime.nmlgen.namelistgenerator method)": [[0, "CIME.nmlgen.NamelistGenerator.write_nuopc_config_file"]], "write_nuopc_modelio_file() (cime.nmlgen.namelistgenerator method)": [[0, "CIME.nmlgen.NamelistGenerator.write_nuopc_modelio_file"]], "write_output_file() (cime.nmlgen.namelistgenerator method)": [[0, "CIME.nmlgen.NamelistGenerator.write_output_file"]], "write_seq_maps() (cime.nmlgen.namelistgenerator method)": [[0, "CIME.nmlgen.NamelistGenerator.write_seq_maps"]], 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"CIME.Servers.ftp.FTP.fileexists"]], "fileexists() (cime.servers.generic_server.genericserver method)": [[2, "CIME.Servers.generic_server.GenericServer.fileexists"]], "fileexists() (cime.servers.gftp.gridftp method)": [[2, "CIME.Servers.gftp.GridFTP.fileexists"]], "fileexists() (cime.servers.svn.svn method)": [[2, "CIME.Servers.svn.SVN.fileexists"]], "fileexists() (cime.servers.wget.wget method)": [[2, "CIME.Servers.wget.WGET.fileexists"]], "ftp_login() (cime.servers.ftp.ftp class method)": [[2, "CIME.Servers.ftp.FTP.ftp_login"]], "getdirectory() (cime.servers.ftp.ftp method)": [[2, "CIME.Servers.ftp.FTP.getdirectory"]], "getdirectory() (cime.servers.gftp.gridftp method)": [[2, "CIME.Servers.gftp.GridFTP.getdirectory"]], "getdirectory() (cime.servers.svn.svn method)": [[2, "CIME.Servers.svn.SVN.getdirectory"]], "getdirectory() (cime.servers.wget.wget method)": [[2, "CIME.Servers.wget.WGET.getdirectory"]], "getfile() (cime.servers.ftp.ftp method)": [[2, "CIME.Servers.ftp.FTP.getfile"]], 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[[3, "module-CIME.SystemTests.ers2"]], "cime.systemtests.ert": [[3, "module-CIME.SystemTests.ert"]], "cime.systemtests.funit": [[3, "module-CIME.SystemTests.funit"]], "cime.systemtests.homme": [[3, "module-CIME.SystemTests.homme"]], "cime.systemtests.hommebaseclass": [[3, "module-CIME.SystemTests.hommebaseclass"]], "cime.systemtests.hommebfb": [[3, "module-CIME.SystemTests.hommebfb"]], "cime.systemtests.icp": [[3, "module-CIME.SystemTests.icp"]], "cime.systemtests.irt": [[3, "module-CIME.SystemTests.irt"]], "cime.systemtests.ldsta": [[3, "module-CIME.SystemTests.ldsta"]], "cime.systemtests.mcc": [[3, "module-CIME.SystemTests.mcc"]], "cime.systemtests.mvk": [[3, "module-CIME.SystemTests.mvk"]], "cime.systemtests.nck": [[3, "module-CIME.SystemTests.nck"]], "cime.systemtests.ncr": [[3, "module-CIME.SystemTests.ncr"]], "cime.systemtests.nodefail": [[3, "module-CIME.SystemTests.nodefail"]], "cime.systemtests.pea": [[3, "module-CIME.SystemTests.pea"]], "cime.systemtests.pem": [[3, "module-CIME.SystemTests.pem"]], "cime.systemtests.pet": [[3, "module-CIME.SystemTests.pet"]], "cime.systemtests.pfs": [[3, "module-CIME.SystemTests.pfs"]], "cime.systemtests.pgn": [[3, "module-CIME.SystemTests.pgn"]], "cime.systemtests.pre": [[3, "module-CIME.SystemTests.pre"]], "cime.systemtests.rep": [[3, "module-CIME.SystemTests.rep"]], "cime.systemtests.restart_tests": [[3, "module-CIME.SystemTests.restart_tests"]], "cime.systemtests.reuseinitfiles": [[3, "module-CIME.SystemTests.reuseinitfiles"]], "cime.systemtests.seq": [[3, "module-CIME.SystemTests.seq"]], "cime.systemtests.sms": [[3, "module-CIME.SystemTests.sms"]], "cime.systemtests.system_tests_common": [[3, "module-CIME.SystemTests.system_tests_common"]], "cime.systemtests.system_tests_compare_n": [[3, "module-CIME.SystemTests.system_tests_compare_n"]], "cime.systemtests.system_tests_compare_two": [[3, "module-CIME.SystemTests.system_tests_compare_two"]], "cime.systemtests.tsc": [[3, "module-CIME.SystemTests.tsc"]], "dae 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cime.systemtests.hommebfb)": [[3, "CIME.SystemTests.hommebfb.HOMMEBFB"]], "hommebase (class in cime.systemtests.hommebaseclass)": [[3, "CIME.SystemTests.hommebaseclass.HommeBase"]], "icp (class in cime.systemtests.icp)": [[3, "CIME.SystemTests.icp.ICP"]], "irt (class in cime.systemtests.irt)": [[3, "CIME.SystemTests.irt.IRT"]], "ldsta (class in cime.systemtests.ldsta)": [[3, "CIME.SystemTests.ldsta.LDSTA"]], "mcc (class in cime.systemtests.mcc)": [[3, "CIME.SystemTests.mcc.MCC"]], "mvk (class in cime.systemtests.mvk)": [[3, "CIME.SystemTests.mvk.MVK"]], "nck (class in cime.systemtests.nck)": [[3, "CIME.SystemTests.nck.NCK"]], "ncr (class in cime.systemtests.ncr)": [[3, "CIME.SystemTests.ncr.NCR"]], "nodefail (class in cime.systemtests.nodefail)": [[3, "CIME.SystemTests.nodefail.NODEFAIL"]], "pea (class in cime.systemtests.pea)": [[3, "CIME.SystemTests.pea.PEA"]], "pem (class in cime.systemtests.pem)": [[3, "CIME.SystemTests.pem.PEM"]], "pet (class in cime.systemtests.pet)": [[3, "CIME.SystemTests.pet.PET"]], "pfs (class in cime.systemtests.pfs)": [[3, "CIME.SystemTests.pfs.PFS"]], "pgn (class in cime.systemtests.pgn)": [[3, "CIME.SystemTests.pgn.PGN"]], "pre (class in cime.systemtests.pre)": [[3, "CIME.SystemTests.pre.PRE"]], "rep (class in cime.systemtests.rep)": [[3, "CIME.SystemTests.rep.REP"]], "reuseinitfiles (class in cime.systemtests.reuseinitfiles)": [[3, "CIME.SystemTests.reuseinitfiles.REUSEINITFILES"]], "restarttest (class in cime.systemtests.restart_tests)": [[3, "CIME.SystemTests.restart_tests.RestartTest"]], "seq (class in cime.systemtests.seq)": [[3, "CIME.SystemTests.seq.SEQ"]], "sms (class in cime.systemtests.sms)": [[3, "CIME.SystemTests.sms.SMS"]], "systemtestscommon (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.SystemTestsCommon"]], "systemtestscomparen (class in cime.systemtests.system_tests_compare_n)": [[3, "CIME.SystemTests.system_tests_compare_n.SystemTestsCompareN"]], "systemtestscomparetwo (class in cime.systemtests.system_tests_compare_two)": [[3, "CIME.SystemTests.system_tests_compare_two.SystemTestsCompareTwo"]], "testbuildfail (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTBUILDFAIL"]], "testbuildfailexc (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTBUILDFAILEXC"]], "testmemleakfail (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTMEMLEAKFAIL"]], "testmemleakpass (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTMEMLEAKPASS"]], "testrundiff (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNDIFF"]], "testrundiffresubmit (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNDIFFRESUBMIT"]], "testrunfail (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNFAIL"]], "testrunfailexc (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNFAILEXC"]], "testrunfailreset (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNFAILRESET"]], "testrunpass (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNPASS"]], "testrunslowpass (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNSLOWPASS"]], "testrunstarcfail (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNSTARCFAIL"]], "testrunuserxmlchange (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTRUNUSERXMLCHANGE"]], "testtestdiff (class in cime.systemtests.system_tests_common)": [[3, "CIME.SystemTests.system_tests_common.TESTTESTDIFF"]], "tsc (class in cime.systemtests.tsc)": 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"CIME.XML.env_mach_pes.EnvMachPes.get_tasks_per_node"]], "get_test_node() (cime.xml.tests.tests method)": [[6, "CIME.XML.tests.Tests.get_test_node"]], "get_test_parameter() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.get_test_parameter"]], "get_tests() (cime.xml.testlist.testlist method)": [[6, "CIME.XML.testlist.Testlist.get_tests"]], "get_total_nodes() (cime.xml.env_mach_pes.envmachpes method)": [[6, "CIME.XML.env_mach_pes.EnvMachPes.get_total_nodes"]], "get_total_tasks() (cime.xml.env_mach_pes.envmachpes method)": [[6, "CIME.XML.env_mach_pes.EnvMachPes.get_total_tasks"]], "get_type_info() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.get_type_info"]], "get_type_info() (cime.xml.env_archive.envarchive method)": [[6, "CIME.XML.env_archive.EnvArchive.get_type_info"]], "get_type_info() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.get_type_info"]], "get_type_info() (cime.xml.env_mach_specific.envmachspecific 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"CIME.XML.entry_id.EntryID.get_value_match"]], "get_value_match() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.get_value_match"]], "get_values() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.get_values"]], "get_values() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.get_values"]], "get_version() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.get_version"]], "get_workflow_jobs() (cime.xml.workflow.workflow method)": [[6, "CIME.XML.workflow.Workflow.get_workflow_jobs"]], "has() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.has"]], "has_batch_system() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.has_batch_system"]], "invalidate() (cime.xml.generic_xml.genericxml class method)": [[6, "CIME.XML.generic_xml.GenericXML.invalidate"]], "is_valid_mpilib() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.is_valid_MPIlib"]], "is_valid_compiler() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.is_valid_compiler"]], "is_valid_value() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.is_valid_value"]], "list_available_machines() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.list_available_machines"]], "list_modules() (cime.xml.env_mach_specific.envmachspecific method)": [[6, "CIME.XML.env_mach_specific.EnvMachSpecific.list_modules"]], "load_env() (cime.xml.env_mach_specific.envmachspecific method)": [[6, "CIME.XML.env_mach_specific.EnvMachSpecific.load_env"]], "lock() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.lock"]], "make_all_batch_files() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.make_all_batch_files"]], "make_batch_script() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.make_batch_script"]], "make_child() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.make_child"]], "make_child_comment() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.make_child_comment"]], "make_env_mach_specific_file() (cime.xml.env_mach_specific.envmachspecific method)": [[6, "CIME.XML.env_mach_specific.EnvMachSpecific.make_env_mach_specific_file"]], "modtime (cime.xml.generic_xml.genericxml.cacheentry attribute)": [[6, "CIME.XML.generic_xml.GenericXML.CacheEntry.modtime"]], "name() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.name"]], "overwrite_existing_entries() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.overwrite_existing_entries"]], "pop() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.pop"]], "populate() (cime.xml.env_mach_specific.envmachspecific method)": [[6, "CIME.XML.env_mach_specific.EnvMachSpecific.populate"]], "print_values() (cime.xml.component.component method)": [[6, "CIME.XML.component.Component.print_values"]], "print_values() (cime.xml.compsets.compsets method)": [[6, "CIME.XML.compsets.Compsets.print_values"]], "print_values() (cime.xml.grids.grids method)": [[6, "CIME.XML.grids.Grids.print_values"]], "print_values() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.print_values"]], "print_values() (cime.xml.tests.tests method)": [[6, "CIME.XML.tests.Tests.print_values"]], "probe_machine_name() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.probe_machine_name"]], "proxy (cime.xml.namelist_definition.caseinsensitivedict attribute)": [[6, "CIME.XML.namelist_definition.CaseInsensitiveDict.proxy"]], "push2testdb() (cime.xml.test_reporter.testreporter method)": [[6, "CIME.XML.test_reporter.TestReporter.push2testdb"]], "queue_meets_spec() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.queue_meets_spec"]], "read() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.read"]], "read_fd() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.read_fd"]], "remove_child() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.remove_child"]], "rename_group() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.rename_group"]], "return_values() (cime.xml.component.component method)": [[6, "CIME.XML.component.Component.return_values"]], "return_values() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.return_values"]], "root (cime.xml.generic_xml.genericxml.cacheentry attribute)": [[6, "CIME.XML.generic_xml.GenericXML.CacheEntry.root"]], "run_phase_get_clone_name() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.run_phase_get_clone_name"]], "save_all_env_info() (cime.xml.env_mach_specific.envmachspecific method)": [[6, "CIME.XML.env_mach_specific.EnvMachSpecific.save_all_env_info"]], "scan_child() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.scan_child"]], "scan_children() (cime.xml.env_base.envbase method)": [[6, "CIME.XML.env_base.EnvBase.scan_children"]], "scan_children() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.scan_children"]], "scan_optional_child() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.scan_optional_child"]], "select_best_queue() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.select_best_queue"]], "set() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set"]], "set_batch_system() (cime.xml.batch.batch method)": [[6, "CIME.XML.batch.Batch.set_batch_system"]], "set_batch_system() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.set_batch_system"]], "set_batch_system_type() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.set_batch_system_type"]], "set_components() (cime.xml.env_base.envbase method)": [[6, "CIME.XML.env_base.EnvBase.set_components"]], "set_default_value() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.set_default_value"]], "set_element_text() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set_element_text"]], "set_header() (cime.xml.testspec.testspec method)": [[6, "CIME.XML.testspec.TestSpec.set_header"]], "set_initial_values() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.set_initial_values"]], "set_job_defaults() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.set_job_defaults"]], "set_machine() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.set_machine"]], "set_name() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set_name"]], "set_node_values() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.set_node_values"]], "set_nodes() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.set_nodes"]], "set_test_parameter() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.set_test_parameter"]], "set_text() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set_text"]], "set_valid_values() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.set_valid_values"]], "set_value() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.set_value"]], "set_value() (cime.xml.env_base.envbase method)": [[6, "CIME.XML.env_base.EnvBase.set_value"]], "set_value() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.set_value"]], "set_value() (cime.xml.env_mach_pes.envmachpes method)": [[6, "CIME.XML.env_mach_pes.EnvMachPes.set_value"]], "set_value() (cime.xml.env_run.envrun method)": [[6, "CIME.XML.env_run.EnvRun.set_value"]], "set_value() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.set_value"]], "set_value() (cime.xml.env_workflow.envworkflow method)": [[6, "CIME.XML.env_workflow.EnvWorkflow.set_value"]], "set_value() (cime.xml.files.files method)": [[6, "CIME.XML.files.Files.set_value"]], "set_value() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set_value"]], "set_value() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.set_value"]], "set_value() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.set_value"]], "setup() (cime.xml.archive.archive method)": [[6, "CIME.XML.archive.Archive.setup"]], "setup_header() (cime.xml.test_reporter.testreporter method)": [[6, "CIME.XML.test_reporter.TestReporter.setup_header"]], "split_type_string() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.split_type_string"]], "submit_jobs() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.submit_jobs"]], "support_single_exe() (cime.xml.tests.tests method)": [[6, "CIME.XML.tests.Tests.support_single_exe"]], "text() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.text"]], "to_string() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.to_string"]], "tree (cime.xml.generic_xml.genericxml.cacheentry attribute)": [[6, "CIME.XML.generic_xml.GenericXML.CacheEntry.tree"]], "unlock() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.unlock"]], "update_test_status() (cime.xml.testspec.testspec method)": [[6, "CIME.XML.testspec.TestSpec.update_test_status"]], "validate() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.validate"]], "validate_timestamp() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.validate_timestamp"]], "validate_xml_file() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.validate_xml_file"]], "write() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.write"]], "cime.build_scripts": [[7, "module-CIME.build_scripts"]], "cime.case": [[8, "module-CIME.case"]], "cime.case.case": [[8, "module-CIME.case.case"]], "cime.case.case_clone": [[8, "module-CIME.case.case_clone"]], "cime.case.case_cmpgen_namelists": [[8, "module-CIME.case.case_cmpgen_namelists"]], "cime.case.case_run": [[8, "module-CIME.case.case_run"]], "cime.case.case_setup": [[8, "module-CIME.case.case_setup"]], "cime.case.case_st_archive": [[8, "module-CIME.case.case_st_archive"]], "cime.case.case_submit": [[8, "module-CIME.case.case_submit"]], "cime.case.case_test": [[8, "module-CIME.case.case_test"]], "cime.case.check_input_data": [[8, "module-CIME.case.check_input_data"]], "cime.case.check_lockedfiles": [[8, "module-CIME.case.check_lockedfiles"]], "cime.case.preview_namelists": [[8, "module-CIME.case.preview_namelists"]], "case (class in cime.case.case)": [[8, "CIME.case.case.Case"]], "apply_user_mods() (cime.case.case.case method)": [[8, "CIME.case.case.Case.apply_user_mods"]], "archive_last_restarts() (cime.case.case.case method)": [[8, "CIME.case.case.Case.archive_last_restarts"]], "archive_last_restarts() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.archive_last_restarts"]], "cancel_batch_jobs() (cime.case.case.case method)": [[8, "CIME.case.case.Case.cancel_batch_jobs"]], "case_cmpgen_namelists() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_cmpgen_namelists"]], "case_cmpgen_namelists() (in module cime.case.case_cmpgen_namelists)": [[8, "CIME.case.case_cmpgen_namelists.case_cmpgen_namelists"]], "case_run() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_run"]], "case_run() (in module cime.case.case_run)": [[8, "CIME.case.case_run.case_run"]], "case_setup() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_setup"]], "case_setup() (in module cime.case.case_setup)": [[8, "CIME.case.case_setup.case_setup"]], "case_st_archive() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_st_archive"]], "case_st_archive() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.case_st_archive"]], "case_test() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_test"]], "case_test() (in module cime.case.case_test)": [[8, "CIME.case.case_test.case_test"]], "check_da_settings() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_DA_settings"]], "check_da_settings() (in module cime.case.case_submit)": [[8, "CIME.case.case_submit.check_DA_settings"]], "check_all_input_data() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_all_input_data"]], "check_all_input_data() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.check_all_input_data"]], "check_case() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_case"]], "check_case() (in module cime.case.case_submit)": [[8, "CIME.case.case_submit.check_case"]], "check_if_comp_var() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_if_comp_var"]], "check_input_data() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_input_data"]], "check_input_data() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.check_input_data"]], "check_lockedfile() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_lockedfile"]], "check_lockedfile() (in module cime.case.check_lockedfiles)": [[8, "CIME.case.check_lockedfiles.check_lockedfile"]], "check_lockedfiles() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_lockedfiles"]], "check_lockedfiles() (in module cime.case.check_lockedfiles)": [[8, "CIME.case.check_lockedfiles.check_lockedfiles"]], "check_pelayouts_require_rebuild() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_pelayouts_require_rebuild"]], "check_pelayouts_require_rebuild() (in module cime.case.check_lockedfiles)": [[8, "CIME.case.check_lockedfiles.check_pelayouts_require_rebuild"]], "check_timestamps() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_timestamps"]], "clean_up_lookups() (cime.case.case.case method)": [[8, "CIME.case.case.Case.clean_up_lookups"]], "configure() (cime.case.case.case method)": [[8, "CIME.case.case.Case.configure"]], "copy() (cime.case.case.case method)": [[8, "CIME.case.case.Case.copy"]], "create() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create"]], "create_caseroot() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create_caseroot"]], "create_clone() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create_clone"]], "create_clone() (in module cime.case.case_clone)": [[8, "CIME.case.case_clone.create_clone"]], "create_dirs() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create_dirs"]], "create_dirs() (in module cime.case.preview_namelists)": [[8, "CIME.case.preview_namelists.create_dirs"]], "create_namelists() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create_namelists"]], "create_namelists() (in module cime.case.preview_namelists)": [[8, "CIME.case.preview_namelists.create_namelists"]], "fix_sys_argv_quotes() (cime.case.case.case method)": [[8, "CIME.case.case.Case.fix_sys_argv_quotes"]], "flush() (cime.case.case.case method)": [[8, "CIME.case.case.Case.flush"]], "get_batch_jobs() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_batch_jobs"]], "get_build_threaded() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_build_threaded"]], "get_case_root() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_case_root"]], "get_compset_components() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_compset_components"]], "get_compset_var_settings() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_compset_var_settings"]], "get_env() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_env"]], "get_first_job() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_first_job"]], "get_histfiles_for_restarts() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.get_histfiles_for_restarts"]], "get_job_id() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_job_id"]], "get_job_info() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_job_info"]], "get_latest_cpl_log() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_latest_cpl_log"]], "get_mpirun_cmd() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_mpirun_cmd"]], "get_primary_component() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_primary_component"]], "get_primary_job() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_primary_job"]], "get_record_fields() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_record_fields"]], "get_resolved_value() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_resolved_value"]], "get_type_info() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_type_info"]], "get_value() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_value"]], "get_values() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_values"]], "initialize_derived_attributes() (cime.case.case.case method)": [[8, "CIME.case.case.Case.initialize_derived_attributes"]], "is_save_timing_dir_project() (cime.case.case.case method)": [[8, "CIME.case.case.Case.is_save_timing_dir_project"]], "load_env() (cime.case.case.case method)": [[8, "CIME.case.case.Case.load_env"]], "md5() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.md5"]], "new_hash() (cime.case.case.case method)": [[8, "CIME.case.case.Case.new_hash"]], "preview_run() (cime.case.case.case method)": [[8, "CIME.case.case.Case.preview_run"]], "read_xml() (cime.case.case.case method)": [[8, "CIME.case.case.Case.read_xml"]], "record_cmd() (cime.case.case.case method)": [[8, "CIME.case.case.Case.record_cmd"]], "report_job_status() (cime.case.case.case method)": [[8, "CIME.case.case.Case.report_job_status"]], "restore_from_archive() (cime.case.case.case method)": [[8, "CIME.case.case.Case.restore_from_archive"]], "restore_from_archive() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.restore_from_archive"]], "set_comp_classes() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_comp_classes"]], "set_file() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_file"]], "set_initial_test_values() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_initial_test_values"]], "set_lookup_value() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_lookup_value"]], "set_model_version() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_model_version"]], "set_valid_values() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_valid_values"]], "set_value() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_value"]], "stage_refcase() (cime.case.case.case method)": [[8, "CIME.case.case.Case.stage_refcase"]], "stage_refcase() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.stage_refcase"]], "submit() (cime.case.case.case method)": [[8, "CIME.case.case.Case.submit"]], "submit() (in module cime.case.case_submit)": [[8, "CIME.case.case_submit.submit"]], "submit_jobs() (cime.case.case.case method)": [[8, "CIME.case.case.Case.submit_jobs"]], "test_env_archive() (cime.case.case.case method)": [[8, "CIME.case.case.Case.test_env_archive"]], "test_env_archive() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.test_env_archive"]], "test_st_archive() (cime.case.case.case method)": [[8, "CIME.case.case.Case.test_st_archive"]], "test_st_archive() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.test_st_archive"]], "update_env() (cime.case.case.case method)": [[8, "CIME.case.case.Case.update_env"]], "valid_compset() (cime.case.case.case method)": [[8, "CIME.case.case.Case.valid_compset"]], "verify_chksum() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.verify_chksum"]], "cime.data": [[9, "module-CIME.data"]], "cime.data.config": [[10, "module-CIME.data.config"]], "cime.data.templates": [[11, "module-CIME.data.templates"]], "argumentparser (class in cime.scripts.query_config)": [[12, "CIME.scripts.query_config.ArgumentParser"]], "cime.scripts": [[12, "module-CIME.scripts"]], "cime.scripts.create_clone": [[12, "module-CIME.scripts.create_clone"]], "cime.scripts.create_newcase": [[12, "module-CIME.scripts.create_newcase"]], "cime.scripts.create_test": [[12, "module-CIME.scripts.create_test"]], "cime.scripts.query_config": [[12, "module-CIME.scripts.query_config"]], "cime.scripts.query_testlists": [[12, "module-CIME.scripts.query_testlists"]], "machines (class in cime.scripts.query_config)": [[12, "CIME.scripts.query_config.Machines"]], "count_test_data() (in module cime.scripts.query_testlists)": [[12, "CIME.scripts.query_testlists.count_test_data"]], "create_test() (in module cime.scripts.create_test)": [[12, "CIME.scripts.create_test.create_test"]], "error() (cime.scripts.query_config.argumentparser method)": [[12, "CIME.scripts.query_config.ArgumentParser.error"]], "get_components() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.get_components"]], "get_compsets() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.get_compsets"]], "get_default_setting() (in module cime.scripts.create_test)": [[12, "CIME.scripts.create_test.get_default_setting"]], "list_test_data() (in module cime.scripts.query_testlists)": [[12, "CIME.scripts.query_testlists.list_test_data"]], "parse_command_line() (in module cime.scripts.create_clone)": [[12, "CIME.scripts.create_clone.parse_command_line"]], "parse_command_line() (in module cime.scripts.create_newcase)": [[12, "CIME.scripts.create_newcase.parse_command_line"]], "parse_command_line() (in module cime.scripts.create_test)": [[12, "CIME.scripts.create_test.parse_command_line"]], "parse_command_line() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.parse_command_line"]], "parse_command_line() (in module cime.scripts.query_testlists)": [[12, "CIME.scripts.query_testlists.parse_command_line"]], "print_compset() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.print_compset"]], "print_test_data() (in module cime.scripts.query_testlists)": [[12, "CIME.scripts.query_testlists.print_test_data"]], "print_values() (cime.scripts.query_config.machines method)": [[12, "CIME.scripts.query_config.Machines.print_values"]], "query_all_components() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.query_all_components"]], "query_component() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.query_component"]], "query_compsets() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.query_compsets"]], "query_grids() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.query_grids"]], "query_machines() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.query_machines"]], "single_submit_impl() (in module cime.scripts.create_test)": [[12, "CIME.scripts.create_test.single_submit_impl"]], "basetestcase (class in cime.tests.base)": [[13, "CIME.tests.base.BaseTestCase"]], "cime.tests": [[13, "module-CIME.tests"]], "cime.tests.base": [[13, "module-CIME.tests.base"]], "cime.tests.case_fake": [[13, "module-CIME.tests.case_fake"]], "cime.tests.custom_assertions_test_status": [[13, "module-CIME.tests.custom_assertions_test_status"]], "cime.tests.scripts_regression_tests": [[13, "module-CIME.tests.scripts_regression_tests"]], "cime.tests.test_sys_bless_tests_results": [[13, "module-CIME.tests.test_sys_bless_tests_results"]], "cime.tests.test_sys_build_system": [[13, "module-CIME.tests.test_sys_build_system"]], "cime.tests.test_sys_cime_case": [[13, "module-CIME.tests.test_sys_cime_case"]], "cime.tests.test_sys_cime_performance": [[13, "module-CIME.tests.test_sys_cime_performance"]], "cime.tests.test_sys_create_newcase": [[13, "module-CIME.tests.test_sys_create_newcase"]], "cime.tests.test_sys_full_system": [[13, "module-CIME.tests.test_sys_full_system"]], "cime.tests.test_sys_grid_generation": [[13, "module-CIME.tests.test_sys_grid_generation"]], "cime.tests.test_sys_jenkins_generic_job": [[13, "module-CIME.tests.test_sys_jenkins_generic_job"]], "cime.tests.test_sys_manage_and_query": [[13, "module-CIME.tests.test_sys_manage_and_query"]], "cime.tests.test_sys_query_config": [[13, "module-CIME.tests.test_sys_query_config"]], "cime.tests.test_sys_run_restart": [[13, "module-CIME.tests.test_sys_run_restart"]], "cime.tests.test_sys_save_timings": [[13, "module-CIME.tests.test_sys_save_timings"]], "cime.tests.test_sys_single_submit": [[13, "module-CIME.tests.test_sys_single_submit"]], "cime.tests.test_sys_test_scheduler": [[13, "module-CIME.tests.test_sys_test_scheduler"]], "cime.tests.test_sys_unittest": [[13, "module-CIME.tests.test_sys_unittest"]], "cime.tests.test_sys_user_concurrent_mods": [[13, "module-CIME.tests.test_sys_user_concurrent_mods"]], "cime.tests.test_sys_wait_for_tests": [[13, "module-CIME.tests.test_sys_wait_for_tests"]], "cime.tests.test_unit_aprun": [[13, "module-CIME.tests.test_unit_aprun"]], "cime.tests.test_unit_case": [[13, "module-CIME.tests.test_unit_case"]], "cime.tests.test_unit_case_fake": [[13, "module-CIME.tests.test_unit_case_fake"]], "cime.tests.test_unit_case_setup": [[13, "module-CIME.tests.test_unit_case_setup"]], "cime.tests.test_unit_compare_test_results": [[13, "module-CIME.tests.test_unit_compare_test_results"]], "cime.tests.test_unit_compare_two": [[13, "module-CIME.tests.test_unit_compare_two"]], "cime.tests.test_unit_config": [[13, "module-CIME.tests.test_unit_config"]], "cime.tests.test_unit_cs_status": [[13, "module-CIME.tests.test_unit_cs_status"]], "cime.tests.test_unit_custom_assertions_test_status": [[13, "module-CIME.tests.test_unit_custom_assertions_test_status"]], "cime.tests.test_unit_doctest": [[13, "module-CIME.tests.test_unit_doctest"]], "cime.tests.test_unit_expected_fails_file": [[13, "module-CIME.tests.test_unit_expected_fails_file"]], "cime.tests.test_unit_grids": [[13, "module-CIME.tests.test_unit_grids"]], "cime.tests.test_unit_hist_utils": [[13, "module-CIME.tests.test_unit_hist_utils"]], "cime.tests.test_unit_nmlgen": [[13, "module-CIME.tests.test_unit_nmlgen"]], "cime.tests.test_unit_paramgen": [[13, "module-CIME.tests.test_unit_paramgen"]], "cime.tests.test_unit_system_tests": [[13, "module-CIME.tests.test_unit_system_tests"]], "cime.tests.test_unit_test_status": [[13, "module-CIME.tests.test_unit_test_status"]], "cime.tests.test_unit_two_link_to_case2_output": [[13, "module-CIME.tests.test_unit_two_link_to_case2_output"]], "cime.tests.test_unit_user_mod_support": [[13, "module-CIME.tests.test_unit_user_mod_support"]], "cime.tests.test_unit_user_nl_utils": [[13, "module-CIME.tests.test_unit_user_nl_utils"]], "cime.tests.test_unit_utils": [[13, "module-CIME.tests.test_unit_utils"]], "cime.tests.test_unit_xml_archive_base": [[13, "module-CIME.tests.test_unit_xml_archive_base"]], "cime.tests.test_unit_xml_env_batch": [[13, "module-CIME.tests.test_unit_xml_env_batch"]], "cime.tests.test_unit_xml_env_mach_specific": [[13, "module-CIME.tests.test_unit_xml_env_mach_specific"]], "cime.tests.test_unit_xml_machines": [[13, "module-CIME.tests.test_unit_xml_machines"]], "cime.tests.test_unit_xml_namelist_definition": [[13, "module-CIME.tests.test_unit_xml_namelist_definition"]], "cime.tests.test_unit_xml_tests": [[13, "module-CIME.tests.test_unit_xml_tests"]], "cime.tests.utils": [[13, "module-CIME.tests.utils"]], "cmaketester (class in cime.tests.utils)": [[13, "CIME.tests.utils.CMakeTester"]], "call (class in cime.tests.test_unit_compare_two)": [[13, "CIME.tests.test_unit_compare_two.Call"]], "casefake (class in cime.tests.case_fake)": [[13, "CIME.tests.case_fake.CaseFake"]], "customassertionsteststatus (class in cime.tests.custom_assertions_test_status)": [[13, "CIME.tests.custom_assertions_test_status.CustomAssertionsTestStatus"]], "dummycase (class in cime.tests.test_unit_paramgen)": [[13, "CIME.tests.test_unit_paramgen.DummyCase"]], "fast_only (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.FAST_ONLY"]], "global_timeout (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.GLOBAL_TIMEOUT"]], "machine (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.MACHINE"]], "makefiletester (class in cime.tests.utils)": [[13, "CIME.tests.utils.MakefileTester"]], "mockmachines (class in cime.tests.utils)": [[13, "CIME.tests.utils.MockMachines"]], "mocktime (class in cime.tests.test_unit_utils)": [[13, "CIME.tests.test_unit_utils.MockTime"]], "mocker (class in cime.tests.utils)": [[13, "CIME.tests.utils.Mocker"]], "no_batch (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.NO_BATCH"]], "no_cmake (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.NO_CMAKE"]], "no_fortran_run (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.NO_FORTRAN_RUN"]], "no_teardown (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.NO_TEARDOWN"]], "script_dir (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.SCRIPT_DIR"]], "systemtestscomparetwofake (class in cime.tests.test_unit_compare_two)": [[13, "CIME.tests.test_unit_compare_two.SystemTestsCompareTwoFake"]], "systemtestscomparetwofake (class in cime.tests.test_unit_two_link_to_case2_output)": [[13, "CIME.tests.test_unit_two_link_to_case2_output.SystemTestsCompareTwoFake"]], "test_compiler (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.TEST_COMPILER"]], "test_mpilib (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.TEST_MPILIB"]], "test_root (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.TEST_ROOT"]], "tools_dir (cime.tests.base.basetestcase attribute)": [[13, "CIME.tests.base.BaseTestCase.TOOLS_DIR"]], "temporarydirectory (class in cime.tests.utils)": [[13, 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"config_test": 103, "mct": 105, "namelist_definition_": 105, "esp": 107, "desp": 107, "sesp": 107, "slnd": 109, "xlnd": 109, "sglc": 110, "xglc": 110, "socn": 111, "xocn": 111, "runoff": 112, "srof": 112, "xrof": 112, "sice": 113, "xice": 113, "wave": 114, "dwav": 114, "swav": 114, "xwav": 114}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 57}, "alltitles": {"CIME package": [[0, "cime-package"]], "Subpackages": [[0, "subpackages"], [3, "subpackages"], [9, "subpackages"]], "Submodules": [[0, "submodules"], [1, "submodules"], [2, "submodules"], [3, "submodules"], [4, "submodules"], [5, "submodules"], [6, "submodules"], [8, "submodules"], [12, "submodules"], [13, "submodules"], [15, "submodules"]], "CIME.aprun module": [[0, "module-CIME.aprun"]], "CIME.bless_test_results module": [[0, "module-CIME.bless_test_results"]], "CIME.build module": [[0, "module-CIME.build"]], "CIME.buildlib module": [[0, "module-CIME.buildlib"]], "CIME.buildnml module": [[0, "module-CIME.buildnml"]], "CIME.code_checker module": [[0, "module-CIME.code_checker"]], "CIME.compare_namelists module": [[0, "module-CIME.compare_namelists"]], "CIME.compare_test_results module": [[0, "module-CIME.compare_test_results"]], "CIME.config module": [[0, "module-CIME.config"]], "CIME.cs_status module": [[0, "module-CIME.cs_status"]], "CIME.cs_status_creator module": [[0, "module-CIME.cs_status_creator"]], "CIME.date module": [[0, "module-CIME.date"]], "CIME.expected_fails module": [[0, "module-CIME.expected_fails"]], "CIME.get_tests module": [[0, "module-CIME.get_tests"]], "CIME.get_timing module": [[0, "module-CIME.get_timing"]], "CIME.hist_utils module": [[0, "module-CIME.hist_utils"]], "CIME.jenkins_generic_job module": [[0, "module-CIME.jenkins_generic_job"]], "CIME.locked_files module": [[0, "module-CIME.locked_files"]], "CIME.namelist module": [[0, "module-CIME.namelist"]], "CIME.nmlgen module": [[0, "module-CIME.nmlgen"]], "CIME.provenance module": [[0, "module-CIME.provenance"]], "CIME.simple_compare module": [[0, "module-CIME.simple_compare"]], "CIME.test_scheduler module": [[0, "module-CIME.test_scheduler"]], "CIME.test_status module": [[0, "module-CIME.test_status"]], "CIME.test_utils module": [[0, "module-CIME.test_utils"]], "CIME.user_mod_support module": [[0, "module-CIME.user_mod_support"]], "CIME.utils module": [[0, "module-CIME.utils"]], "CIME.wait_for_tests module": [[0, "module-CIME.wait_for_tests"]], "Module contents": [[0, "module-CIME"], [1, "module-CIME.BuildTools"], [2, "module-CIME.Servers"], [3, "module-CIME.SystemTests"], [4, "module-CIME.SystemTests.test_utils"], [5, "module-CIME.Tools"], [6, "module-CIME.XML"], [7, "module-CIME.build_scripts"], [8, "module-CIME.case"], [9, "module-CIME.data"], [10, "module-CIME.data.config"], [11, "module-CIME.data.templates"], [12, "module-CIME.scripts"], [13, "module-CIME.tests"], [15, "module-Tools"]], "CIME.BuildTools package": [[1, "cime-buildtools-package"]], "CIME.BuildTools.configure module": [[1, "module-CIME.BuildTools.configure"]], "CIME.Servers package": [[2, "cime-servers-package"]], "CIME.Servers.ftp module": [[2, "module-CIME.Servers.ftp"]], "CIME.Servers.generic_server module": [[2, "module-CIME.Servers.generic_server"]], "CIME.Servers.gftp module": [[2, "module-CIME.Servers.gftp"]], "CIME.Servers.svn module": [[2, "module-CIME.Servers.svn"]], "CIME.Servers.wget module": [[2, "module-CIME.Servers.wget"]], "CIME.SystemTests package": [[3, "cime-systemtests-package"]], "CIME.SystemTests.dae module": [[3, "module-CIME.SystemTests.dae"]], "CIME.SystemTests.eri module": [[3, "module-CIME.SystemTests.eri"]], "CIME.SystemTests.erio module": [[3, "module-CIME.SystemTests.erio"]], "CIME.SystemTests.erp module": [[3, "module-CIME.SystemTests.erp"]], "CIME.SystemTests.err module": [[3, "module-CIME.SystemTests.err"]], "CIME.SystemTests.erri module": [[3, "module-CIME.SystemTests.erri"]], "CIME.SystemTests.ers module": [[3, "module-CIME.SystemTests.ers"]], "CIME.SystemTests.ers2 module": [[3, "module-CIME.SystemTests.ers2"]], "CIME.SystemTests.ert module": [[3, "module-CIME.SystemTests.ert"]], "CIME.SystemTests.funit module": [[3, "module-CIME.SystemTests.funit"]], "CIME.SystemTests.homme module": [[3, "module-CIME.SystemTests.homme"]], "CIME.SystemTests.hommebaseclass module": [[3, "module-CIME.SystemTests.hommebaseclass"]], "CIME.SystemTests.hommebfb module": [[3, "module-CIME.SystemTests.hommebfb"]], "CIME.SystemTests.icp module": [[3, "module-CIME.SystemTests.icp"]], "CIME.SystemTests.irt module": [[3, "module-CIME.SystemTests.irt"]], "CIME.SystemTests.ldsta module": [[3, "module-CIME.SystemTests.ldsta"]], "CIME.SystemTests.mcc module": [[3, "module-CIME.SystemTests.mcc"]], "CIME.SystemTests.mvk module": [[3, "module-CIME.SystemTests.mvk"]], "CIME.SystemTests.nck module": [[3, "module-CIME.SystemTests.nck"]], "CIME.SystemTests.ncr module": [[3, "module-CIME.SystemTests.ncr"]], "CIME.SystemTests.nodefail module": [[3, "module-CIME.SystemTests.nodefail"]], "CIME.SystemTests.pea module": [[3, "module-CIME.SystemTests.pea"]], "CIME.SystemTests.pem module": [[3, "module-CIME.SystemTests.pem"]], "CIME.SystemTests.pet module": [[3, "module-CIME.SystemTests.pet"]], "CIME.SystemTests.pfs module": [[3, "module-CIME.SystemTests.pfs"]], "CIME.SystemTests.pgn module": [[3, "module-CIME.SystemTests.pgn"]], "CIME.SystemTests.pre module": [[3, "module-CIME.SystemTests.pre"]], "CIME.SystemTests.rep module": [[3, "module-CIME.SystemTests.rep"]], "CIME.SystemTests.restart_tests module": [[3, "module-CIME.SystemTests.restart_tests"]], "CIME.SystemTests.reuseinitfiles module": [[3, "module-CIME.SystemTests.reuseinitfiles"]], "CIME.SystemTests.seq module": [[3, "module-CIME.SystemTests.seq"]], "CIME.SystemTests.sms module": [[3, "module-CIME.SystemTests.sms"]], "CIME.SystemTests.system_tests_common module": [[3, "module-CIME.SystemTests.system_tests_common"]], "CIME.SystemTests.system_tests_compare_n module": [[3, "module-CIME.SystemTests.system_tests_compare_n"]], "CIME.SystemTests.system_tests_compare_two module": [[3, "module-CIME.SystemTests.system_tests_compare_two"]], "CIME.SystemTests.tsc module": [[3, "module-CIME.SystemTests.tsc"]], "CIME.SystemTests.test_utils package": [[4, "cime-systemtests-test-utils-package"]], "CIME.SystemTests.test_utils.user_nl_utils module": [[4, "module-CIME.SystemTests.test_utils.user_nl_utils"]], "CIME.Tools package": [[5, "cime-tools-package"]], "CIME.Tools.generate_cylc_workflow module": [[5, "module-CIME.Tools.generate_cylc_workflow"]], "CIME.Tools.standard_script_setup module": [[5, "module-CIME.Tools.standard_script_setup"]], "CIME.Tools.testreporter module": [[5, "module-CIME.Tools.testreporter"]], "CIME.XML package": [[6, "cime-xml-package"]], "CIME.XML.archive module": [[6, "module-CIME.XML.archive"]], "CIME.XML.archive_base module": [[6, "module-CIME.XML.archive_base"]], "CIME.XML.batch module": [[6, "module-CIME.XML.batch"]], "CIME.XML.component module": [[6, "module-CIME.XML.component"]], "CIME.XML.compsets module": [[6, "module-CIME.XML.compsets"]], "CIME.XML.entry_id module": [[6, "module-CIME.XML.entry_id"]], "CIME.XML.env_archive module": [[6, "module-CIME.XML.env_archive"]], "CIME.XML.env_base module": [[6, "module-CIME.XML.env_base"]], "CIME.XML.env_batch module": [[6, "module-CIME.XML.env_batch"]], "CIME.XML.env_build module": [[6, "module-CIME.XML.env_build"]], "CIME.XML.env_case module": [[6, "module-CIME.XML.env_case"]], "CIME.XML.env_mach_pes module": [[6, "module-CIME.XML.env_mach_pes"]], "CIME.XML.env_mach_specific module": [[6, "module-CIME.XML.env_mach_specific"]], "CIME.XML.env_run module": [[6, "module-CIME.XML.env_run"]], "CIME.XML.env_test module": [[6, "module-CIME.XML.env_test"]], "CIME.XML.env_workflow module": [[6, "module-CIME.XML.env_workflow"]], "CIME.XML.expected_fails_file module": [[6, "module-CIME.XML.expected_fails_file"]], "CIME.XML.files module": [[6, "module-CIME.XML.files"]], "CIME.XML.generic_xml module": [[6, "module-CIME.XML.generic_xml"]], "CIME.XML.grids module": [[6, "module-CIME.XML.grids"]], "CIME.XML.headers module": [[6, "module-CIME.XML.headers"]], "CIME.XML.inputdata module": [[6, "module-CIME.XML.inputdata"]], "CIME.XML.machines module": [[6, "module-CIME.XML.machines"]], "CIME.XML.namelist_definition module": [[6, "module-CIME.XML.namelist_definition"]], "CIME.XML.pes module": [[6, "module-CIME.XML.pes"]], "CIME.XML.pio module": [[6, "module-CIME.XML.pio"]], "CIME.XML.standard_module_setup module": [[6, "module-CIME.XML.standard_module_setup"]], "CIME.XML.stream module": [[6, "module-CIME.XML.stream"]], "CIME.XML.test_reporter module": [[6, "module-CIME.XML.test_reporter"]], "CIME.XML.testlist module": [[6, "module-CIME.XML.testlist"]], "CIME.XML.tests module": [[6, "module-CIME.XML.tests"]], "CIME.XML.testspec module": [[6, "module-CIME.XML.testspec"]], "CIME.XML.workflow module": [[6, "module-CIME.XML.workflow"]], "CIME.build_scripts package": [[7, "cime-build-scripts-package"]], "CIME.case package": [[8, "cime-case-package"]], "CIME.case.case module": [[8, "module-CIME.case.case"]], "CIME.case.case_clone module": [[8, "module-CIME.case.case_clone"]], "CIME.case.case_cmpgen_namelists module": [[8, "module-CIME.case.case_cmpgen_namelists"]], "CIME.case.case_run module": [[8, "module-CIME.case.case_run"]], "CIME.case.case_setup module": [[8, "module-CIME.case.case_setup"]], "CIME.case.case_st_archive module": [[8, "module-CIME.case.case_st_archive"]], "CIME.case.case_submit module": [[8, "module-CIME.case.case_submit"]], "CIME.case.case_test module": [[8, "module-CIME.case.case_test"]], "CIME.case.check_input_data module": [[8, "module-CIME.case.check_input_data"]], "CIME.case.check_lockedfiles module": [[8, "module-CIME.case.check_lockedfiles"]], "CIME.case.preview_namelists module": [[8, "module-CIME.case.preview_namelists"]], "CIME.data package": [[9, "cime-data-package"]], "CIME.data.config package": [[10, "cime-data-config-package"]], "CIME.data.templates package": [[11, "cime-data-templates-package"]], "CIME.scripts package": [[12, "cime-scripts-package"]], "CIME.scripts.create_clone module": [[12, "module-CIME.scripts.create_clone"]], "CIME.scripts.create_newcase module": [[12, "module-CIME.scripts.create_newcase"]], "CIME.scripts.create_test module": [[12, "module-CIME.scripts.create_test"]], "CIME.scripts.query_config module": [[12, "module-CIME.scripts.query_config"]], "CIME.scripts.query_testlists module": [[12, "module-CIME.scripts.query_testlists"]], "CIME.tests package": [[13, "cime-tests-package"]], "CIME.tests.base module": [[13, "module-CIME.tests.base"]], "CIME.tests.case_fake module": [[13, "module-CIME.tests.case_fake"]], "CIME.tests.custom_assertions_test_status module": [[13, "module-CIME.tests.custom_assertions_test_status"]], "CIME.tests.scripts_regression_tests module": [[13, "module-CIME.tests.scripts_regression_tests"]], "CIME.tests.test_sys_bless_tests_results module": [[13, "module-CIME.tests.test_sys_bless_tests_results"]], "CIME.tests.test_sys_build_system module": [[13, "module-CIME.tests.test_sys_build_system"]], "CIME.tests.test_sys_cime_case module": [[13, "module-CIME.tests.test_sys_cime_case"]], "CIME.tests.test_sys_cime_performance module": [[13, "module-CIME.tests.test_sys_cime_performance"]], "CIME.tests.test_sys_create_newcase module": [[13, "module-CIME.tests.test_sys_create_newcase"]], "CIME.tests.test_sys_full_system module": [[13, "module-CIME.tests.test_sys_full_system"]], "CIME.tests.test_sys_grid_generation module": [[13, "module-CIME.tests.test_sys_grid_generation"]], "CIME.tests.test_sys_jenkins_generic_job module": [[13, "module-CIME.tests.test_sys_jenkins_generic_job"]], "CIME.tests.test_sys_manage_and_query module": [[13, "module-CIME.tests.test_sys_manage_and_query"]], "CIME.tests.test_sys_query_config module": [[13, "module-CIME.tests.test_sys_query_config"]], "CIME.tests.test_sys_run_restart module": [[13, "module-CIME.tests.test_sys_run_restart"]], "CIME.tests.test_sys_save_timings module": [[13, "module-CIME.tests.test_sys_save_timings"]], "CIME.tests.test_sys_single_submit module": [[13, "module-CIME.tests.test_sys_single_submit"]], "CIME.tests.test_sys_test_scheduler module": [[13, "module-CIME.tests.test_sys_test_scheduler"]], "CIME.tests.test_sys_unittest module": [[13, "module-CIME.tests.test_sys_unittest"]], "CIME.tests.test_sys_user_concurrent_mods module": [[13, "module-CIME.tests.test_sys_user_concurrent_mods"]], "CIME.tests.test_sys_wait_for_tests module": [[13, "module-CIME.tests.test_sys_wait_for_tests"]], "CIME.tests.test_unit_aprun module": [[13, "module-CIME.tests.test_unit_aprun"]], "CIME.tests.test_unit_case module": [[13, "module-CIME.tests.test_unit_case"]], "CIME.tests.test_unit_case_fake module": [[13, "module-CIME.tests.test_unit_case_fake"]], "CIME.tests.test_unit_case_setup module": [[13, "module-CIME.tests.test_unit_case_setup"]], "CIME.tests.test_unit_compare_test_results module": [[13, "module-CIME.tests.test_unit_compare_test_results"]], "CIME.tests.test_unit_compare_two module": [[13, "module-CIME.tests.test_unit_compare_two"]], "CIME.tests.test_unit_config module": [[13, "module-CIME.tests.test_unit_config"]], "CIME.tests.test_unit_cs_status module": [[13, "module-CIME.tests.test_unit_cs_status"]], "CIME.tests.test_unit_custom_assertions_test_status module": [[13, "module-CIME.tests.test_unit_custom_assertions_test_status"]], "CIME.tests.test_unit_doctest module": [[13, "module-CIME.tests.test_unit_doctest"]], "CIME.tests.test_unit_expected_fails_file module": [[13, "module-CIME.tests.test_unit_expected_fails_file"]], "CIME.tests.test_unit_grids module": [[13, "module-CIME.tests.test_unit_grids"]], "CIME.tests.test_unit_hist_utils module": [[13, "module-CIME.tests.test_unit_hist_utils"]], "CIME.tests.test_unit_nmlgen module": [[13, "module-CIME.tests.test_unit_nmlgen"]], "CIME.tests.test_unit_paramgen module": [[13, "module-CIME.tests.test_unit_paramgen"]], "CIME.tests.test_unit_system_tests module": [[13, "module-CIME.tests.test_unit_system_tests"]], "CIME.tests.test_unit_test_status module": [[13, "module-CIME.tests.test_unit_test_status"]], "CIME.tests.test_unit_two_link_to_case2_output module": [[13, "module-CIME.tests.test_unit_two_link_to_case2_output"]], "CIME.tests.test_unit_user_mod_support module": [[13, "module-CIME.tests.test_unit_user_mod_support"]], "CIME.tests.test_unit_user_nl_utils module": [[13, "module-CIME.tests.test_unit_user_nl_utils"]], "CIME.tests.test_unit_utils module": [[13, "module-CIME.tests.test_unit_utils"]], "CIME.tests.test_unit_xml_archive_base module": [[13, "module-CIME.tests.test_unit_xml_archive_base"]], "CIME.tests.test_unit_xml_env_batch module": [[13, "module-CIME.tests.test_unit_xml_env_batch"]], "CIME.tests.test_unit_xml_env_mach_specific module": [[13, "module-CIME.tests.test_unit_xml_env_mach_specific"]], "CIME.tests.test_unit_xml_machines module": [[13, "module-CIME.tests.test_unit_xml_machines"]], "CIME.tests.test_unit_xml_namelist_definition module": [[13, "module-CIME.tests.test_unit_xml_namelist_definition"]], "CIME.tests.test_unit_xml_tests module": [[13, "module-CIME.tests.test_unit_xml_tests"]], "CIME.tests.utils module": [[13, "module-CIME.tests.utils"]], "CIME": [[14, "cime"]], "Tools package": [[15, "tools-package"]], "Tools.generate_cylc_workflow module": [[15, "module-Tools.generate_cylc_workflow"]], "Tools.standard_script_setup module": [[15, "module-Tools.standard_script_setup"]], "Tools.testreporter module": [[15, "module-Tools.testreporter"]], "Tools": [[16, "tools"]], "advanced-py-prof": [[17, "advanced-py-prof"]], "archive_metadata": [[18, "archive-metadata"]], "bld_diff": [[19, "bld-diff"]], "bless_test_results": [[20, "bless-test-results"]], "case.build": [[21, "case-build"]], "case.cmpgen_namelists": [[22, "case-cmpgen-namelists"]], "case.qstatus": [[23, "case-qstatus"]], "case.setup": [[24, "case-setup"]], "case.submit": [[25, "case-submit"]], "case_diff": [[26, "case-diff"]], "check_case": [[27, "check-case"]], "check_input_data": [[28, "check-input-data"]], "check_lockedfiles": [[29, "check-lockedfiles"]], "cime_bisect": [[30, "cime-bisect"]], "code_checker": [[31, "code-checker"]], "compare_namelists": [[32, "compare-namelists"]], "compare_test_results": [[33, "compare-test-results"]], "component_compare_baseline": [[34, "component-compare-baseline"]], "component_compare_copy": [[35, "component-compare-copy"]], "component_compare_test": [[36, "component-compare-test"]], "component_generate_baseline": [[37, "component-generate-baseline"]], "concat_daily_hist.csh": [[38, "concat-daily-hist-csh"]], "create_clone": [[39, "create-clone"]], "create_newcase": [[40, "create-newcase"]], "create_test": [[41, "create-test"]], "cs.status": [[42, "cs-status"]], "e3sm_check_env": [[43, "e3sm-check-env"]], "generate_cylc_workflow.py": [[44, "generate-cylc-workflow-py"]], "getTiming": [[45, "gettiming"]], "get_case_env": [[46, "get-case-env"]], "get_standard_makefile_args": [[47, "get-standard-makefile-args"]], "User Tools": [[48, "user-tools"]], "jenkins_generic_job": [[49, "jenkins-generic-job"]], "list_e3sm_tests": [[50, "list-e3sm-tests"]], "mkDepends": [[51, "mkdepends"]], "mkSrcfiles": [[52, "mksrcfiles"]], "mvsource": [[53, "mvsource"]], "normalize_cases": [[54, "normalize-cases"]], "pelayout": [[55, "pelayout"]], "preview_namelists": [[56, "preview-namelists"]], "preview_run": [[57, "preview-run"]], "query_config": [[58, "query-config"]], "query_testlists": [[59, "query-testlists"]], "save_provenance": [[60, "save-provenance"]], "simple-py-prof": [[61, "simple-py-prof"]], "simple_compare": [[62, "simple-compare"]], "testreporter.py": [[63, "testreporter-py"]], "wait_for_tests": [[64, "wait-for-tests"]], "xmlchange": [[65, "xmlchange"]], "xmlquery": [[66, "xmlquery"]], "xmltestentry": [[67, "xmltestentry"]], "Adding components": [[68, "adding-components"]], "Building a Coupled Model with CIME": [[69, "building-a-coupled-model-with-cime"]], "Indices and tables": [[69, "indices-and-tables"], [75, "indices-and-tables"], [87, "indices-and-tables"]], "Introduction": [[70, "introduction"], [88, "introduction"], [98, "introduction"]], "Glossary": [[72, "glossary"]], "General": [[72, "general"]], "Coupling": [[72, "coupling"]], "Files and Directories": [[72, "files-and-directories"]], "Development": [[72, "development"], [100, "development"]], "Testing": [[72, "testing"], [76, "testing"], [95, "testing"]], "Miscellaneous": [[72, "miscellaneous"]], "CIME documentation": [[73, "cime-documentation"]], "Table of contents": [[73, "table-of-contents"]], "Appendices": [[73, "appendices"]], "Python Module Indices and Search": [[73, "python-module-indices-and-search"]], "CESM-ECT (CESM Ensemble Consistency Test):": [[74, "cesm-ect-cesm-ensemble-consistency-test"]], "Creating or obtaining a summary file:": [[74, "creating-or-obtaining-a-summary-file"]], "Creating test runs:": [[74, "creating-test-runs"]], "Miscellaneous Tools": [[75, "miscellaneous-tools"]], "CIME Load Balancing Tool": [[76, "cime-load-balancing-tool"]], "Running simulations using load_balancing_submit.py": [[76, "running-simulations-using-load-balancing-submit-py"]], "Optimizing the layout using load_balacing_solve.py": [[76, "optimizing-the-layout-using-load-balacing-solve-py"]], "More about the algorithm": [[76, "more-about-the-algorithm"]], "Extending the Load Balancing Tool": [[76, "extending-the-load-balancing-tool"]], "Building a Case": [[77, "building-a-case"]], "Calling case.build": [[77, "calling-case-build"]], "Rebuilding the model": [[77, "rebuilding-the-model"]], "Input data": [[77, "input-data"], [93, "input-data"]], "Customizing your input variables": [[78, "customizing-your-input-variables"]], "Customizing driver input variables": [[78, "customizing-driver-input-variables"]], "Setting up a multi-year run": [[78, "setting-up-a-multi-year-run"]], "Setting up a branch or hybrid run": [[78, "setting-up-a-branch-or-hybrid-run"]], "Customizing data model input variable and stream files": [[78, "customizing-data-model-input-variable-and-stream-files"]], "Data Atmosphere (DATM)": [[78, "data-atmosphere-datm"]], "Data Ocean (DOCN)": [[78, "data-ocean-docn"]], "Data Sea-ice (DICE)": [[78, "data-sea-ice-dice"]], "Data Land (DLND)": [[78, "data-land-dlnd"]], "Data River (DROF)": [[78, "data-river-drof"]], "Customizing CESM active component-specific namelist settings": [[78, "customizing-cesm-active-component-specific-namelist-settings"]], "CAM": [[78, "cam"]], "CLM": [[78, "clm"]], "MOSART": [[78, "mosart"]], "CICE": [[78, "cice"]], "POP2": [[78, "pop2"]], "CISM": [[78, "cism"]], "CIME user config directory": [[79, "cime-user-config-directory"]], "CIME config and hooks": [[80, "cime-config-and-hooks"]], "How does CIME load customizations?": [[80, "how-does-cime-load-customizations"]], "CIME config": [[80, "cime-config"]], "CIME hooks": [[80, "cime-hooks"]], "Directory content": [[81, "directory-content"]], "CIME directory in a climate model": [[81, "id1"]], "CIME directory content": [[81, "id2"]], "Main Configuration File": [[82, "main-configuration-file"]], "Cloning a Case": [[83, "cloning-a-case"]], "Component sets": [[84, "component-sets"]], "Compset longname": [[84, "compset-longname"]], "Component specific settings in a compset": [[84, "component-specific-settings-in-a-compset"]], "Creating New Compsets": [[84, "creating-new-compsets"]], "Todo": [[84, "id2"], [98, "id1"]], "Creating a Case": [[85, "creating-a-case"]], "Calling create_newcase": [[85, "calling-create-newcase"]], "Results of calling create_newcase": [[85, "results-of-calling-create-newcase"]], "Locked files in your case directory": [[85, "locked-files-in-your-case-directory"]], "Adding a \u2013user-mods-dir argument to create_newcase": [[85, "adding-a-user-mods-dir-argument-to-create-newcase"]], "Model grids": [[86, "model-grids"]], "Grid longname": [[86, "grid-longname"]], "Adding grids": [[86, "adding-grids"]], "Case Control System Part 1: Basic Usage": [[87, "case-control-system-part-1-basic-usage"]], "Case Control System Part 2: Configuration, Porting, Testing and Use Cases": [[87, "case-control-system-part-2-configuration-porting-testing-and-use-cases"]], "Prerequisites": [[88, "prerequisites"]], "Key Terms and concepts": [[88, "key-terms-and-concepts"]], "CIME and your environment": [[88, "cime-and-your-environment"]], "Quick start": [[88, "quick-start"]], "Discovering available cases with query_config": [[88, "discovering-available-cases-with-query-config"]], "Defining the machine": [[89, "defining-the-machine"]], "config_machines.xml - machine specific file": [[89, "config-machines-xml-machine-specific-file"]], "Batch system definition": [[89, "batch-system-definition"]], "config_batch.xml - batch directives": [[89, "config-batch-xml-batch-directives"]], "Compiler settings": [[89, "compiler-settings"]], "config_compilers.xml - compiler paths and options DEPRECATED use cmake_macros": [[89, "config-compilers-xml-compiler-paths-and-options-deprecated-use-cmake-macros"]], "Multi-instance component functionality": [[90, "multi-instance-component-functionality"]], "Controlling processors and threads": [[91, "controlling-processors-and-threads"]], "pe-settings for a case": [[91, "pe-settings-for-a-case"]], "Setting the PE layout": [[91, "setting-the-pe-layout"]], "Entries in env_mach_pes.xml": [[91, "id3"]], "Case Resource Allocation": [[91, "case-resource-allocation"]], "Optimizing processor layout": [[91, "optimizing-processor-layout"]], "Porting and validating CIME on a new platform": [[92, "porting-and-validating-cime-on-a-new-platform"]], "Required libraries/packages": [[92, "required-libraries-packages"]], "An MPI example": [[92, "an-mpi-example"]], "CESM Linux and Mac Support": [[92, "cesm-linux-and-mac-support"]], "Steps for porting": [[92, "steps-for-porting"]], "Validating a CESM port with prognostic components": [[92, "validating-a-cesm-port-with-prognostic-components"]], "Performance tuning of a CESM port": [[92, "performance-tuning-of-a-cesm-port"]], "Running a Case": [[93, "running-a-case"]], "Calling case.submit": [[93, "calling-case-submit"]], "Result of running case.submit": [[93, "result-of-running-case-submit"]], "Monitoring case job statuses": [[93, "monitoring-case-job-statuses"]], "Troubleshooting a job that fails": [[93, "troubleshooting-a-job-that-fails"]], "Distributed Input Data Repositories": [[93, "distributed-input-data-repositories"]], "Starting, Stopping and Restarting a Run": [[93, "starting-stopping-and-restarting-a-run"]], "Run-type initialization": [[93, "run-type-initialization"]], "Starting from a reference case (REFCASE)": [[93, "starting-from-a-reference-case-refcase"]], "Controlling output data": [[93, "controlling-output-data"]], "Restarting a run": [[93, "restarting-a-run"]], "Backing up to a previous restart": [[93, "backing-up-to-a-previous-restart"]], "Archiving model output data": [[93, "archiving-model-output-data"]], "No archiving": [[93, "no-archiving"]], "Short-term archiving": [[93, "short-term-archiving"]], "Long-term archiving": [[93, "long-term-archiving"]], "Data Assimilation and other External Processing": [[93, "data-assimilation-and-other-external-processing"]], "Pre and Post run scripts": [[93, "pre-and-post-run-scripts"]], "Data Assimilation scripts": [[93, "data-assimilation-scripts"]], "Setting up a Case": [[94, "setting-up-a-case"]], "Calling case.setup": [[94, "calling-case-setup"]], "Testname syntax": [[95, "testname-syntax"]], "Query_testlists": [[95, "query-testlists"]], "Using create_test (E3SM)": [[95, "using-create-test-e3sm"]], "Managing baselines": [[95, "managing-baselines"]], "Adding tests": [[95, "adding-tests"]], "CIME Developer\u2019s guide": [[95, "cime-developer-s-guide"]], "Timers and timing": [[96, "timers-and-timing"]], "Model timing data": [[96, "model-timing-data"]], "Controlling timers": [[96, "controlling-timers"]], "Advice on setting your wallclock time": [[96, "advice-on-setting-your-wallclock-time"]], "Troubleshooting": [[97, "troubleshooting"]], "Troubleshooting case creation": [[97, "troubleshooting-case-creation"]], "Troubleshooting problems in cime scripts": [[97, "troubleshooting-problems-in-cime-scripts"]], "Troubleshooting job submission": [[97, "troubleshooting-job-submission"]], "Troubleshooting runtime problems": [[97, "troubleshooting-runtime-problems"]], "Fortran Unit Testing": [[98, "fortran-unit-testing"]], "What is a unit test?": [[98, "what-is-a-unit-test"]], "Overview of unit test support in CIME": [[98, "overview-of-unit-test-support-in-cime"]], "Running CIME\u2019s Fortran unit tests": [[98, "running-cime-s-fortran-unit-tests"]], "How to add unit testing support on your machine": [[98, "how-to-add-unit-testing-support-on-your-machine"]], "Building pFUnit": [[98, "building-pfunit"]], "Adding to the appropriate cmake file": [[98, "adding-to-the-appropriate-cmake-file"]], "How to write a new unit test": [[98, "how-to-write-a-new-unit-test"]], "General guidelines for writing unit tests": [[98, "general-guidelines-for-writing-unit-tests"]], "More details on writing pFUnit-based unit tests": [[98, "more-details-on-writing-pfunit-based-unit-tests"]], "Assertion methods": [[98, "assertion-methods"]], "Defining a test class in order to define setUp and tearDown methods": [[98, "defining-a-test-class-in-order-to-define-setup-and-teardown-methods"]], "More on test teardown": [[98, "more-on-test-teardown"]], "Finding more documentation and examples": [[98, "finding-more-documentation-and-examples"]], "More detailed examples in CIME": [[98, "more-detailed-examples-in-cime"]], "Other pFUnit documentation sources": [[98, "other-pfunit-documentation-sources"]], "Documentation of the unit test build system": [[98, "documentation-of-the-unit-test-build-system"]], "Workflows": [[99, "workflows"]], "What is CIME?": [[100, "what-is-cime"]], "Overview": [[100, "overview"]], "CIME Atmosphere Data and Stub XML Files": [[101, "cime-atmosphere-data-and-stub-xml-files"]], "CIMEROOT/src/components/data_comps/datm/cime_config": [[101, "cimeroot-src-components-data-comps-datm-cime-config"]], "CIMEROOT/src/components/stub_comps/satm/cime_config": [[101, "cimeroot-src-components-stub-comps-satm-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xatm/cime_config": [[101, "cimeroot-src-components-xcpl-comps-xatm-cime-config"]], "CESM Coupled Model XML Files": [[102, "cesm-coupled-model-xml-files"]], "CIMEROOT/config/cesm": [[102, "cimeroot-config-cesm"]], "Common XML Files": [[103, "common-xml-files"]], "CIMEROOT/config/config_headers.xml": [[103, "cimeroot-config-config-headers-xml"]], "CIMEROOT/config/config_tests.xml": [[103, "cimeroot-config-config-tests-xml"]], "Data, Stub and Driver Component XML Files": [[104, "data-stub-and-driver-component-xml-files"]], "Driver XML Files": [[105, "driver-xml-files"]], "CIMEROOT/src/drivers/mct/cime_config": [[105, "cimeroot-src-drivers-mct-cime-config"]], "CIMEROOT/src/drivers/mct/cime_config/namelist_definition_*.xml": [[105, "cimeroot-src-drivers-mct-cime-config-namelist-definition-xml"]], "E3SM Coupled Model XML Files": [[106, "e3sm-coupled-model-xml-files"]], "CIMEROOT/config/e3sm": [[106, "cimeroot-config-e3sm"]], "CIME ESP Data and Stub XML Files": [[107, "cime-esp-data-and-stub-xml-files"]], "CIMEROOT/src/components/data_comps/desp/cime_config": [[107, "cimeroot-src-components-data-comps-desp-cime-config"]], "CIMEROOT/src/components/stub_comps/sesp/cime_config": [[107, "cimeroot-src-components-stub-comps-sesp-cime-config"]], "XML Files": [[108, "xml-files"]], "CIME Land Data and Stub XML Files": [[109, "cime-land-data-and-stub-xml-files"]], "CIMEROOT/src/components/data_comps/dlnd/cime_config": [[109, "cimeroot-src-components-data-comps-dlnd-cime-config"]], "CIMEROOT/src/components/stub_comps/slnd/cime_config": [[109, "cimeroot-src-components-stub-comps-slnd-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xlnd/cime_config": [[109, "cimeroot-src-components-xcpl-comps-xlnd-cime-config"]], "CIME Land Ice Data and Stub XML Files": [[110, "cime-land-ice-data-and-stub-xml-files"]], "CIMEROOT/src/components/stub_comps/sglc/cime_config": [[110, "cimeroot-src-components-stub-comps-sglc-cime-config"]], "CIMEROOT/src/components/xcpl_comps/xglc/cime_config": [[110, "cimeroot-src-components-xcpl-comps-xglc-cime-config"]], "CIME Ocean Data and Stub XML Files": [[111, 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"CIME.XML.env_mach_specific.EnvMachSpecific.make_env_mach_specific_file"]], "modtime (cime.xml.generic_xml.genericxml.cacheentry attribute)": [[6, "CIME.XML.generic_xml.GenericXML.CacheEntry.modtime"]], "name() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.name"]], "overwrite_existing_entries() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.overwrite_existing_entries"]], "pop() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.pop"]], "populate() (cime.xml.env_mach_specific.envmachspecific method)": [[6, "CIME.XML.env_mach_specific.EnvMachSpecific.populate"]], "print_values() (cime.xml.component.component method)": [[6, "CIME.XML.component.Component.print_values"]], "print_values() (cime.xml.compsets.compsets method)": [[6, "CIME.XML.compsets.Compsets.print_values"]], "print_values() (cime.xml.grids.grids method)": [[6, "CIME.XML.grids.Grids.print_values"]], "print_values() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.print_values"]], "print_values() (cime.xml.tests.tests method)": [[6, "CIME.XML.tests.Tests.print_values"]], "probe_machine_name() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.probe_machine_name"]], "proxy (cime.xml.namelist_definition.caseinsensitivedict attribute)": [[6, "CIME.XML.namelist_definition.CaseInsensitiveDict.proxy"]], "push2testdb() (cime.xml.test_reporter.testreporter method)": [[6, "CIME.XML.test_reporter.TestReporter.push2testdb"]], "queue_meets_spec() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.queue_meets_spec"]], "read() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.read"]], "read_fd() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.read_fd"]], "remove_child() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.remove_child"]], "rename_group() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.rename_group"]], "return_values() (cime.xml.component.component method)": [[6, "CIME.XML.component.Component.return_values"]], "return_values() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.return_values"]], "root (cime.xml.generic_xml.genericxml.cacheentry attribute)": [[6, "CIME.XML.generic_xml.GenericXML.CacheEntry.root"]], "run_phase_get_clone_name() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.run_phase_get_clone_name"]], "save_all_env_info() (cime.xml.env_mach_specific.envmachspecific method)": [[6, "CIME.XML.env_mach_specific.EnvMachSpecific.save_all_env_info"]], "scan_child() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.scan_child"]], "scan_children() (cime.xml.env_base.envbase method)": [[6, "CIME.XML.env_base.EnvBase.scan_children"]], "scan_children() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.scan_children"]], "scan_optional_child() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.scan_optional_child"]], "select_best_queue() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.select_best_queue"]], "set() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set"]], "set_batch_system() (cime.xml.batch.batch method)": [[6, "CIME.XML.batch.Batch.set_batch_system"]], "set_batch_system() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.set_batch_system"]], "set_batch_system_type() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.set_batch_system_type"]], "set_components() (cime.xml.env_base.envbase method)": [[6, "CIME.XML.env_base.EnvBase.set_components"]], "set_default_value() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.set_default_value"]], "set_element_text() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set_element_text"]], "set_header() (cime.xml.testspec.testspec method)": [[6, "CIME.XML.testspec.TestSpec.set_header"]], "set_initial_values() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.set_initial_values"]], "set_job_defaults() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.set_job_defaults"]], "set_machine() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.set_machine"]], "set_name() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set_name"]], "set_node_values() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.set_node_values"]], "set_nodes() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.set_nodes"]], "set_test_parameter() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.set_test_parameter"]], "set_text() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set_text"]], "set_valid_values() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.set_valid_values"]], "set_value() (cime.xml.entry_id.entryid method)": [[6, "CIME.XML.entry_id.EntryID.set_value"]], "set_value() (cime.xml.env_base.envbase method)": [[6, "CIME.XML.env_base.EnvBase.set_value"]], "set_value() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.set_value"]], "set_value() (cime.xml.env_build.envbuild method)": [[6, "CIME.XML.env_build.EnvBuild.set_value"]], "set_value() (cime.xml.env_mach_pes.envmachpes method)": [[6, "CIME.XML.env_mach_pes.EnvMachPes.set_value"]], "set_value() (cime.xml.env_run.envrun method)": [[6, "CIME.XML.env_run.EnvRun.set_value"]], "set_value() (cime.xml.env_test.envtest method)": [[6, "CIME.XML.env_test.EnvTest.set_value"]], "set_value() (cime.xml.env_workflow.envworkflow method)": [[6, "CIME.XML.env_workflow.EnvWorkflow.set_value"]], "set_value() (cime.xml.files.files method)": [[6, "CIME.XML.files.Files.set_value"]], "set_value() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.set_value"]], "set_value() (cime.xml.machines.machines method)": [[6, "CIME.XML.machines.Machines.set_value"]], "set_value() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.set_value"]], "setup() (cime.xml.archive.archive method)": [[6, "CIME.XML.archive.Archive.setup"]], "setup_header() (cime.xml.test_reporter.testreporter method)": [[6, "CIME.XML.test_reporter.TestReporter.setup_header"]], "split_type_string() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.split_type_string"]], "submit_jobs() (cime.xml.env_batch.envbatch method)": [[6, "CIME.XML.env_batch.EnvBatch.submit_jobs"]], "support_single_exe() (cime.xml.tests.tests method)": [[6, "CIME.XML.tests.Tests.support_single_exe"]], "text() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.text"]], "to_string() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.to_string"]], "tree (cime.xml.generic_xml.genericxml.cacheentry attribute)": [[6, "CIME.XML.generic_xml.GenericXML.CacheEntry.tree"]], "unlock() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.unlock"]], "update_test_status() (cime.xml.testspec.testspec method)": [[6, "CIME.XML.testspec.TestSpec.update_test_status"]], "validate() (cime.xml.namelist_definition.namelistdefinition method)": [[6, "CIME.XML.namelist_definition.NamelistDefinition.validate"]], "validate_timestamp() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.validate_timestamp"]], "validate_xml_file() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.validate_xml_file"]], "write() (cime.xml.generic_xml.genericxml method)": [[6, "CIME.XML.generic_xml.GenericXML.write"]], "cime.build_scripts": [[7, "module-CIME.build_scripts"]], "cime.case": [[8, "module-CIME.case"]], "cime.case.case": [[8, "module-CIME.case.case"]], "cime.case.case_clone": [[8, "module-CIME.case.case_clone"]], "cime.case.case_cmpgen_namelists": [[8, "module-CIME.case.case_cmpgen_namelists"]], "cime.case.case_run": [[8, "module-CIME.case.case_run"]], "cime.case.case_setup": [[8, "module-CIME.case.case_setup"]], "cime.case.case_st_archive": [[8, "module-CIME.case.case_st_archive"]], "cime.case.case_submit": [[8, "module-CIME.case.case_submit"]], "cime.case.case_test": [[8, "module-CIME.case.case_test"]], "cime.case.check_input_data": [[8, "module-CIME.case.check_input_data"]], "cime.case.check_lockedfiles": [[8, "module-CIME.case.check_lockedfiles"]], "cime.case.preview_namelists": [[8, "module-CIME.case.preview_namelists"]], "case (class in cime.case.case)": [[8, "CIME.case.case.Case"]], "apply_user_mods() (cime.case.case.case method)": [[8, "CIME.case.case.Case.apply_user_mods"]], "archive_last_restarts() (cime.case.case.case method)": [[8, "CIME.case.case.Case.archive_last_restarts"]], "archive_last_restarts() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.archive_last_restarts"]], "cancel_batch_jobs() (cime.case.case.case method)": [[8, "CIME.case.case.Case.cancel_batch_jobs"]], "case_cmpgen_namelists() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_cmpgen_namelists"]], "case_cmpgen_namelists() (in module cime.case.case_cmpgen_namelists)": [[8, "CIME.case.case_cmpgen_namelists.case_cmpgen_namelists"]], "case_run() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_run"]], "case_run() (in module cime.case.case_run)": [[8, "CIME.case.case_run.case_run"]], "case_setup() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_setup"]], "case_setup() (in module cime.case.case_setup)": [[8, "CIME.case.case_setup.case_setup"]], "case_st_archive() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_st_archive"]], "case_st_archive() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.case_st_archive"]], "case_test() (cime.case.case.case method)": [[8, "CIME.case.case.Case.case_test"]], "case_test() (in module cime.case.case_test)": [[8, "CIME.case.case_test.case_test"]], "check_da_settings() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_DA_settings"]], "check_da_settings() (in module cime.case.case_submit)": [[8, "CIME.case.case_submit.check_DA_settings"]], "check_all_input_data() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_all_input_data"]], "check_all_input_data() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.check_all_input_data"]], "check_case() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_case"]], "check_case() (in module cime.case.case_submit)": [[8, "CIME.case.case_submit.check_case"]], "check_if_comp_var() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_if_comp_var"]], "check_input_data() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_input_data"]], "check_input_data() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.check_input_data"]], "check_lockedfile() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_lockedfile"]], "check_lockedfile() (in module cime.case.check_lockedfiles)": [[8, "CIME.case.check_lockedfiles.check_lockedfile"]], "check_lockedfiles() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_lockedfiles"]], "check_lockedfiles() (in module cime.case.check_lockedfiles)": [[8, "CIME.case.check_lockedfiles.check_lockedfiles"]], "check_pelayouts_require_rebuild() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_pelayouts_require_rebuild"]], "check_pelayouts_require_rebuild() (in module cime.case.check_lockedfiles)": [[8, "CIME.case.check_lockedfiles.check_pelayouts_require_rebuild"]], "check_timestamps() (cime.case.case.case method)": [[8, "CIME.case.case.Case.check_timestamps"]], "clean_up_lookups() (cime.case.case.case method)": [[8, "CIME.case.case.Case.clean_up_lookups"]], "configure() (cime.case.case.case method)": [[8, "CIME.case.case.Case.configure"]], "copy() (cime.case.case.case method)": [[8, "CIME.case.case.Case.copy"]], "create() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create"]], "create_caseroot() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create_caseroot"]], "create_clone() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create_clone"]], "create_clone() (in module cime.case.case_clone)": [[8, "CIME.case.case_clone.create_clone"]], "create_dirs() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create_dirs"]], "create_dirs() (in module cime.case.preview_namelists)": [[8, "CIME.case.preview_namelists.create_dirs"]], "create_namelists() (cime.case.case.case method)": [[8, "CIME.case.case.Case.create_namelists"]], "create_namelists() (in module cime.case.preview_namelists)": [[8, "CIME.case.preview_namelists.create_namelists"]], "fix_sys_argv_quotes() (cime.case.case.case method)": [[8, "CIME.case.case.Case.fix_sys_argv_quotes"]], "flush() (cime.case.case.case method)": [[8, "CIME.case.case.Case.flush"]], "get_batch_jobs() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_batch_jobs"]], "get_build_threaded() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_build_threaded"]], "get_case_root() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_case_root"]], "get_compset_components() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_compset_components"]], "get_compset_var_settings() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_compset_var_settings"]], "get_env() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_env"]], "get_first_job() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_first_job"]], "get_histfiles_for_restarts() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.get_histfiles_for_restarts"]], "get_job_id() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_job_id"]], "get_job_info() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_job_info"]], "get_latest_cpl_log() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_latest_cpl_log"]], "get_mpirun_cmd() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_mpirun_cmd"]], "get_primary_component() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_primary_component"]], "get_primary_job() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_primary_job"]], "get_record_fields() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_record_fields"]], "get_resolved_value() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_resolved_value"]], "get_type_info() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_type_info"]], "get_value() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_value"]], "get_values() (cime.case.case.case method)": [[8, "CIME.case.case.Case.get_values"]], "initialize_derived_attributes() (cime.case.case.case method)": [[8, "CIME.case.case.Case.initialize_derived_attributes"]], "is_save_timing_dir_project() (cime.case.case.case method)": [[8, "CIME.case.case.Case.is_save_timing_dir_project"]], "load_env() (cime.case.case.case method)": [[8, "CIME.case.case.Case.load_env"]], "md5() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.md5"]], "new_hash() (cime.case.case.case method)": [[8, "CIME.case.case.Case.new_hash"]], "preview_run() (cime.case.case.case method)": [[8, "CIME.case.case.Case.preview_run"]], "read_xml() (cime.case.case.case method)": [[8, "CIME.case.case.Case.read_xml"]], "record_cmd() (cime.case.case.case method)": [[8, "CIME.case.case.Case.record_cmd"]], "report_job_status() (cime.case.case.case method)": [[8, "CIME.case.case.Case.report_job_status"]], "restore_from_archive() (cime.case.case.case method)": [[8, "CIME.case.case.Case.restore_from_archive"]], "restore_from_archive() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.restore_from_archive"]], "set_comp_classes() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_comp_classes"]], "set_file() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_file"]], "set_initial_test_values() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_initial_test_values"]], "set_lookup_value() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_lookup_value"]], "set_model_version() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_model_version"]], "set_valid_values() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_valid_values"]], "set_value() (cime.case.case.case method)": [[8, "CIME.case.case.Case.set_value"]], "stage_refcase() (cime.case.case.case method)": [[8, "CIME.case.case.Case.stage_refcase"]], "stage_refcase() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.stage_refcase"]], "submit() (cime.case.case.case method)": [[8, "CIME.case.case.Case.submit"]], "submit() (in module cime.case.case_submit)": [[8, "CIME.case.case_submit.submit"]], "submit_jobs() (cime.case.case.case method)": [[8, "CIME.case.case.Case.submit_jobs"]], "test_env_archive() (cime.case.case.case method)": [[8, "CIME.case.case.Case.test_env_archive"]], "test_env_archive() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.test_env_archive"]], "test_st_archive() (cime.case.case.case method)": [[8, "CIME.case.case.Case.test_st_archive"]], "test_st_archive() (in module cime.case.case_st_archive)": [[8, "CIME.case.case_st_archive.test_st_archive"]], "update_env() (cime.case.case.case method)": [[8, "CIME.case.case.Case.update_env"]], "valid_compset() (cime.case.case.case method)": [[8, "CIME.case.case.Case.valid_compset"]], "verify_chksum() (in module cime.case.check_input_data)": [[8, "CIME.case.check_input_data.verify_chksum"]], "cime.data": [[9, "module-CIME.data"]], "cime.data.config": [[10, "module-CIME.data.config"]], "cime.data.templates": [[11, "module-CIME.data.templates"]], "argumentparser (class in cime.scripts.query_config)": [[12, "CIME.scripts.query_config.ArgumentParser"]], "cime.scripts": [[12, "module-CIME.scripts"]], "cime.scripts.create_clone": [[12, "module-CIME.scripts.create_clone"]], "cime.scripts.create_newcase": [[12, "module-CIME.scripts.create_newcase"]], "cime.scripts.create_test": [[12, "module-CIME.scripts.create_test"]], "cime.scripts.query_config": [[12, "module-CIME.scripts.query_config"]], "cime.scripts.query_testlists": [[12, "module-CIME.scripts.query_testlists"]], "machines (class in cime.scripts.query_config)": [[12, "CIME.scripts.query_config.Machines"]], "count_test_data() (in module cime.scripts.query_testlists)": [[12, "CIME.scripts.query_testlists.count_test_data"]], "create_test() (in module cime.scripts.create_test)": [[12, "CIME.scripts.create_test.create_test"]], "error() (cime.scripts.query_config.argumentparser method)": [[12, "CIME.scripts.query_config.ArgumentParser.error"]], "get_components() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.get_components"]], "get_compsets() (in module cime.scripts.query_config)": [[12, "CIME.scripts.query_config.get_compsets"]], "get_default_setting() (in module cime.scripts.create_test)": [[12, "CIME.scripts.create_test.get_default_setting"]], "list_test_data() (in module cime.scripts.query_testlists)": [[12, "CIME.scripts.query_testlists.list_test_data"]], "parse_command_line() (in module cime.scripts.create_clone)": [[12, "CIME.scripts.create_clone.parse_command_line"]], "parse_command_line() (in module 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[[13, "CIME.tests.test_unit_user_nl_utils.TestUserNLCopier.write_user_nl_file"]], "tools": [[15, "module-Tools"]], "tools.generate_cylc_workflow": [[15, "module-Tools.generate_cylc_workflow"]], "tools.standard_script_setup": [[15, "module-Tools.standard_script_setup"]], "tools.testreporter": [[15, "module-Tools.testreporter"]], "check_minimum_python_version() (in module tools.standard_script_setup)": [[15, "Tools.standard_script_setup.check_minimum_python_version"]], "cylc_batch_job_template() (in module tools.generate_cylc_workflow)": [[15, "Tools.generate_cylc_workflow.cylc_batch_job_template"]], "cylc_get_case_path_string() (in module tools.generate_cylc_workflow)": [[15, "Tools.generate_cylc_workflow.cylc_get_case_path_string"]], "cylc_get_ensemble_first_and_last() (in module tools.generate_cylc_workflow)": [[15, "Tools.generate_cylc_workflow.cylc_get_ensemble_first_and_last"]], "cylc_script_job_template() (in module tools.generate_cylc_workflow)": [[15, "Tools.generate_cylc_workflow.cylc_script_job_template"]], "get_testreporter_xml() (in module tools.testreporter)": [[15, "Tools.testreporter.get_testreporter_xml"]], "parse_command_line() (in module tools.generate_cylc_workflow)": [[15, "Tools.generate_cylc_workflow.parse_command_line"]], "parse_command_line() (in module tools.testreporter)": [[15, "Tools.testreporter.parse_command_line"]], "cime root (cimeroot)": [[72, "term-CIME-root-CIMEROOT"]], "esp": [[72, "term-ESP"]], "model coupling toolkit or mct": [[72, "term-Model-Coupling-Toolkit-or-MCT"]], "xml files": [[72, "term-XML-files"]], "active or prognostic component": [[72, "term-active-or-prognostic-component"]], "archive directory (dout_s_root)": [[72, "term-archive-directory-DOUT_S_ROOT"]], "baseline": [[72, "term-baseline"]], "baseline failure": [[72, "term-baseline-failure"]], "blessing": [[72, "term-blessing"]], "build directory (exeroot)": [[72, "term-build-directory-EXEROOT"]], "case (case)": [[72, "term-case-CASE"]], "case root (caseroot)": [[72, "term-case-root-CASEROOT"]], "component": [[72, "term-component"]], "component set (compset)": [[72, "term-component-set-COMPSET"]], "coupler": [[72, "term-coupler"]], "data component": [[72, "term-data-component"]], "driver": [[72, "term-driver"]], "forcing": [[72, "term-forcing"]], "grid (grid)": [[72, "term-grid-GRID"]], "history files": [[72, "term-history-files"]], "initial files": [[72, "term-initial-files"]], "input data stream (din_loc_root)": [[72, "term-input-data-stream-DIN_LOC_ROOT"]], "mapping": [[72, "term-mapping"]], "mask": [[72, "term-mask"]], "namelist files": [[72, "term-namelist-files"]], "regression test": [[72, "term-regression-test"]], "resolution": [[72, "term-resolution"]], "restart files": [[72, "term-restart-files"]], "rpointer files": [[72, "term-rpointer-files"]], "run directory (rundir)": [[72, "term-run-directory-RUNDIR"]], "sandbox (srcroot)": [[72, "term-sandbox-SRCROOT"]], "source modifications (caseroot/sourcemods)": [[72, "term-source-modifications-CASEROOT-SourceMods"]], "stub component": [[72, "term-stub-component"]], "tag": [[72, "term-tag"]], "unit testing": [[72, "term-unit-testing"]], "user namelist files (caseroot/user_nl_*)": [[72, "term-user-namelist-files-CASEROOT-user_nl_"]]}})
\ No newline at end of file
diff --git a/versions/master/html/users_guide/create-a-case.html b/versions/master/html/users_guide/create-a-case.html
index e25b4588ee2..2ddaa49c69f 100644
--- a/versions/master/html/users_guide/create-a-case.html
+++ b/versions/master/html/users_guide/create-a-case.html
@@ -352,6 +352,15 @@
2.4. Adding a –user-mods-dir argument
> SourceMods/src.cam/dyncomp.F90
+
It is important to note that the file containing the xmlchange
+commands must be named shell_commands in order for it to be recognised
+and run upon case creation.
+The structure of the component directories do not need to be the
+same as in the component source code. As an example, should the user
+want to modify the src/dynamics/eul/dyncomp.F90 file within the
+CAM source code, the modified file should be put into the directory
+SourceMods/src.cam directly. There is no need to mimic the source
+code structure, such as SourceMods/src.cam/dynamics/eul.
When the user calls create_newcase with the --user-mods-dir pointing to the
full pathname of the directory containing these changes, then the CASEROOT will be
created with these changes applied.