def check_case(case, caseroot):
check_lockedfiles(caseroot)
preview_namelists(case, dryrun=False)
expect(case.get_value("BUILD_COMPLETE"), "Build complete is "
"not True please rebuild the model by calling case.build")
logger.info("Check case OK")
def pre_run_check(case):
###############################################################################
# Pre run initialization code..
caseroot = case.get_value("CASEROOT")
din_loc_root = case.get_value("DIN_LOC_ROOT")
batchsubmit = case.get_value("BATCHSUBMIT")
mpilib = case.get_value("MPILIB")
rundir = case.get_value("RUNDIR")
build_complete = case.get_value("BUILD_COMPLETE")
# check for locked files.
check_lockedfiles(case.get_value("CASEROOT"))
logger.debug("check_lockedfiles OK")
# check that build is done
expect (build_complete,
"BUILD_COMPLETE is not true\nPlease rebuild the model interactively")
logger.debug("build complete is %s " %build_complete)
# load the module environment...
env_module = case.get_env("mach_specific")
env_module.load_env_for_case(compiler=case.get_value("COMPILER"),
debug=case.get_value("DEBUG"),
mpilib=case.get_value("MPILIB"))
# set environment variables
# This is a requirement for yellowstone only
if mpilib == "mpi-serial" and "MP_MPILIB" in os.environ:
del os.environ["MP_MPILIB"]
else:
os.environ["MPILIB"] = mpilib
if batchsubmit is None or len(batchsubmit) == 0:
os.environ["LBQUERY"] = "FALSE"
os.environ["BATCHQUERY"] = "undefined"
elif batchsubmit == 'UNSET':
os.environ["LBQUERY"] = "FALSE"
os.environ["BATCHQUERY"] = "undefined"
else:
os.environ["LBQUERY"] = "TRUE"
# create the timing directories, optionally cleaning them if needed.
if not os.path.isdir(rundir):
os.mkdir(rundir)
if os.path.isdir(os.path.join(rundir,"timing")):
shutil.rmtree(os.path.join(rundir,"timing"))
os.makedirs(os.path.join(rundir,"timing","checkpoints"))
# run preview namelists
preview_namelists(case)
# document process
append_status("Run started ",caseroot=caseroot,
sfile="CaseStatus")
logger.info( "-------------------------------------------------------------------------")
logger.info( " - To prestage required restarts, untar a restart.tar file into %s" %(rundir))
logger.info( " - Case input data directory (DIN_LOC_ROOT) is %s " %(din_loc_root))
logger.info( " - Checking for required input datasets in DIN_LOC_ROOT")
logger.info( "-------------------------------------------------------------------------")
def case_build(caseroot, case=None, sharedlib_only=False, model_only=False):
###############################################################################
t1 = time.time()
expect(not (sharedlib_only and model_only),
"Contradiction: both sharedlib_only and model_only")
logger.info("sharedlib_only is %s" % sharedlib_only)
logger.info("model_only is %s" % model_only)
expect(os.path.isdir(caseroot), "'%s' is not a valid directory" % caseroot)
os.chdir(caseroot)
expect(os.path.exists("case.run"),
"ERROR: must invoke case.setup script before calling build script ")
case = Case() if case is None else case
cimeroot = case.get_value("CIMEROOT")
comp_classes = case.get_value("COMP_CLASSES").split(',')
if not sharedlib_only:
check_all_input_data(case)
run_cmd("./Tools/check_lockedfiles --caseroot %s" % caseroot)
# Retrieve relevant case data
# This environment variable gets set for cesm Make and
# needs to be unset before building again.
if "MODEL" in os.environ.keys():
del os.environ["MODEL"]
build_threaded = case.get_value("BUILD_THREADED")
casetools = case.get_value("CASETOOLS")
exeroot = case.get_value("EXEROOT")
incroot = case.get_value("INCROOT")
libroot = case.get_value("LIBROOT")
sharedlibroot = case.get_value("SHAREDLIBROOT")
complist = []
for comp_class in comp_classes:
if comp_class == "DRV":
comp_class = "CPL"
ninst = 1
config_dir = None
else:
ninst = case.get_value("NINST_%s"%comp_class)
config_dir = os.path.dirname(case.get_value("CONFIG_%s_FILE"%comp_class))
comp = case.get_value("COMP_%s"%comp_class)
thrds = case.get_value("NTHRDS_%s"%comp_class)
complist.append((comp_class.lower(), comp, thrds, ninst, config_dir ))
os.environ["COMP_%s"%comp_class] = comp
machines_file = case.get_value("MACHINES_SPEC_FILE")
ocn_submodel = case.get_value("OCN_SUBMODEL")
profile_papi_enable = case.get_value("PROFILE_PAPI_ENABLE")
compiler = case.get_value("COMPILER")
comp_interface = case.get_value("COMP_INTERFACE")
mpilib = case.get_value("MPILIB")
use_esmf_lib = case.get_value("USE_ESMF_LIB")
debug = case.get_value("DEBUG")
ninst_build = case.get_value("NINST_BUILD")
smp_value = case.get_value("SMP_VALUE")
clm_use_petsc = case.get_value("CLM_USE_PETSC")
cism_use_trilinos = case.get_value("CISM_USE_TRILINOS")
mpasli_use_albany = case.get_value("MPASLI_USE_ALBANY")
clm_config_opts = case.get_value("CLM_CONFIG_OPTS")
cam_config_opts = case.get_value("CAM_CONFIG_OPTS")
pio_config_opts = case.get_value("PIO_CONFIG_OPTS")
ninst_value = case.get_value("NINST_VALUE")
mach = case.get_value("MACH")
os_ = case.get_value("OS")
# Load some params into env
os.environ["CIMEROOT"] = cimeroot
os.environ["CASETOOLS"] = casetools
os.environ["EXEROOT"] = exeroot
os.environ["INCROOT"] = incroot
os.environ["LIBROOT"] = libroot
os.environ["SHAREDLIBROOT"] = sharedlibroot
os.environ["CASEROOT"] = caseroot
os.environ["COMPILER"] = compiler
os.environ["COMP_INTERFACE"] = comp_interface
os.environ["NINST_VALUE"] = str(ninst_value)
os.environ["BUILD_THREADED"] = stringify_bool(build_threaded)
os.environ["MACH"] = mach
os.environ["USE_ESMF_LIB"] = stringify_bool(use_esmf_lib)
os.environ["MPILIB"] = mpilib
os.environ["DEBUG"] = stringify_bool(debug)
os.environ["OS"] = os_
os.environ["CLM_CONFIG_OPTS"] = clm_config_opts if clm_config_opts is not None else ""
os.environ["CAM_CONFIG_OPTS"] = cam_config_opts if cam_config_opts is not None else ""
os.environ["PIO_CONFIG_OPTS"] = pio_config_opts if pio_config_opts is not None else ""
os.environ["OCN_SUBMODEL"] = ocn_submodel if ocn_submodel is not None else ""
os.environ["PROFILE_PAPI_ENABLE"] = stringify_bool(profile_papi_enable) if profile_papi_enable is not None else ""
os.environ["CLM_USE_PETSC"] = stringify_bool(clm_use_petsc) if clm_use_petsc is not None else ""
os.environ["CISM_USE_TRILINOS"] = stringify_bool(cism_use_trilinos) if cism_use_trilinos is not None else ""
os.environ["MPASLI_USE_ALBANY"] = stringify_bool(mpasli_use_albany) if mpasli_use_albany is not None else ""
# This is a timestamp for the build , not the same as the testid,
# and this case may not be a test anyway. For a production
# experiment there may be many builds of the same case.
lid = run_cmd("date +%y%m%d-%H%M%S")
os.environ["LID"] = lid
# Set the overall USE_PETSC variable to TRUE if any of the
# XXX_USE_PETSC variables are TRUE.
# For now, there is just the one CLM_USE_PETSC variable, but in
# the future there may be others -- so USE_PETSC will be true if
# ANY of those are true.
use_petsc = clm_use_petsc
case.set_value("USE_PETSC", use_petsc)
os.environ["USE_PETSC"] = stringify_bool(use_petsc)
# Set the overall USE_TRILINOS variable to TRUE if any of the
# XXX_USE_TRILINOS variables are TRUE.
# For now, there is just the one CISM_USE_TRILINOS variable, but in
# the future there may be others -- so USE_TRILINOS will be true if
# ANY of those are true.
use_trilinos = False if cism_use_trilinos is None else cism_use_trilinos
case.set_value("USE_TRILINOS", use_trilinos)
os.environ["USE_TRILINOS"] = stringify_bool(use_trilinos)
# Set the overall USE_ALBANY variable to TRUE if any of the
# XXX_USE_ALBANY variables are TRUE.
# For now, there is just the one MPASLI_USE_ALBANY variable, but in
# the future there may be others -- so USE_ALBANY will be true if
# ANY of those are true.
use_albany = mpasli_use_albany
case.set_value("USE_ALBANY", use_albany)
os.environ["USE_ALBANY"] = stringify_bool(use_albany)
# Load modules
env_module = case._get_env("mach_specific")
env_module.load_env_for_case(compiler=case.get_value("COMPILER"),
debug=case.get_value("DEBUG"),
mpilib=case.get_value("MPILIB"))
# Need to flush case xml to disk before calling preview_namelists
case.flush()
if not sharedlib_only:
preview_namelists(case)
build_checks(case, build_threaded, comp_interface, use_esmf_lib, debug, compiler, mpilib,
sharedlibroot, complist, ninst_build, smp_value)
t2 = time.time()
logs = []
if not model_only:
logs = build_libraries(case, exeroot, caseroot, cimeroot, libroot, mpilib, lid,
machines_file)
if not sharedlib_only:
logs.extend(build_model(case, build_threaded, exeroot, clm_config_opts, incroot, complist,
lid, caseroot, cimeroot, use_esmf_lib, comp_interface))
if not sharedlib_only:
post_build(case, logs)
t3 = time.time()
logger.info("Time spent not building: %f sec" % (t2 - t1))
logger.info("Time spent building: %f sec" % (t3 - t2))
def case_build(caseroot, case=None, testmode=False, sharedlib_only=False, model_only=False):
###############################################################################
t1 = time.time()
expect(not (sharedlib_only and model_only),
"Contradiction: both sharedlib_only and model_only")
logger.info("sharedlib_only is %s" % sharedlib_only)
logger.info("model_only is %s" % model_only)
expect(os.path.isdir(caseroot), "'%s' is not a valid directory" % caseroot)
os.chdir(caseroot)
expect(os.path.exists("case.run"),
"ERROR: must invoke case.setup script before calling build script ")
case = Case() if case is None else case
testcase = case.get_value("TESTCASE")
cimeroot = case.get_value("CIMEROOT")
expect(not (testcase is not None and
os.path.exists("%s/scripts/Testing/Testcases/%s_build.csh" %
(cimeroot, testcase)) and not testmode),
"%s build must be invoked via case.testbuild script" % testcase)
if not sharedlib_only:
check_all_input_data(case)
run_cmd("./Tools/check_lockedfiles --caseroot %s" % caseroot)
# Retrieve relevant case data
build_threaded = case.get_value("BUILD_THREADED")
casetools = case.get_value("CASETOOLS")
exeroot = case.get_value("EXEROOT")
incroot = case.get_value("INCROOT")
libroot = case.get_value("LIBROOT")
sharedlibroot = case.get_value("SHAREDLIBROOT")
comp_atm = case.get_value("COMP_ATM")
comp_lnd = case.get_value("COMP_LND")
comp_ice = case.get_value("COMP_ICE")
comp_ocn = case.get_value("COMP_OCN")
comp_glc = case.get_value("COMP_GLC")
comp_wav = case.get_value("COMP_WAV")
comp_rof = case.get_value("COMP_ROF")
compiler = case.get_value("COMPILER")
comp_interface = case.get_value("COMP_INTERFACE")
mpilib = case.get_value("MPILIB")
use_esmf_lib = case.get_value("USE_ESMF_LIB")
debug = case.get_value("DEBUG")
ninst_build = case.get_value("NINST_BUILD")
smp_value = case.get_value("SMP_VALUE")
clm_use_petsc = case.get_value("CLM_USE_PETSC")
cism_use_trilinos = case.get_value("CISM_USE_TRILINOS")
mpasli_use_albany = case.get_value("MPASLI_USE_ALBANY")
clm_config_opts = case.get_value("CLM_CONFIG_OPTS")
cam_config_opts = case.get_value("CAM_CONFIG_OPTS")
pio_config_opts = case.get_value("PIO_CONFIG_OPTS")
ninst_value = case.get_value("NINST_VALUE")
mach = case.get_value("MACH")
os_ = case.get_value("OS")
comp_cpl = case.get_value("COMP_CPL")
machines_file = case.get_value("MACHINES_SPEC_FILE")
ocn_submodel = case.get_value("OCN_SUBMODEL")
profile_papi_enable = case.get_value("PROFILE_PAPI_ENABLE")
nthrds_cpl = int(case.get_value("NTHRDS_CPL"))
nthrds_atm = int(case.get_value("NTHRDS_ATM"))
nthrds_lnd = int(case.get_value("NTHRDS_LND"))
nthrds_ice = int(case.get_value("NTHRDS_ICE"))
nthrds_ocn = int(case.get_value("NTHRDS_OCN"))
nthrds_glc = int(case.get_value("NTHRDS_GLC"))
nthrds_wav = int(case.get_value("NTHRDS_WAV"))
nthrds_rof = int(case.get_value("NTHRDS_ROF"))
# Load some params into env
os.environ["CIMEROOT"] = cimeroot
os.environ["CASETOOLS"] = casetools
os.environ["EXEROOT"] = exeroot
os.environ["INCROOT"] = incroot
os.environ["LIBROOT"] = libroot
os.environ["SHAREDLIBROOT"] = sharedlibroot
os.environ["CASEROOT"] = caseroot
os.environ["COMPILER"] = compiler
os.environ["COMP_INTERFACE"] = comp_interface
os.environ["NINST_VALUE"] = ninst_value
os.environ["BUILD_THREADED"] = build_threaded
os.environ["MACH"] = mach
os.environ["USE_ESMF_LIB"] = use_esmf_lib
os.environ["MPILIB"] = mpilib
os.environ["DEBUG"] = debug
os.environ["OS"] = os_
os.environ["COMP_CPL"] = comp_cpl
os.environ["COMP_ATM"] = comp_atm
os.environ["COMP_LND"] = comp_lnd
os.environ["COMP_ICE"] = comp_ice
os.environ["COMP_OCN"] = comp_ocn
os.environ["COMP_GLC"] = comp_glc
os.environ["COMP_WAV"] = comp_wav
os.environ["COMP_ROF"] = comp_rof
os.environ["CLM_CONFIG_OPTS"] = clm_config_opts if clm_config_opts is not None else ""
os.environ["CAM_CONFIG_OPTS"] = cam_config_opts if cam_config_opts is not None else ""
os.environ["PIO_CONFIG_OPTS"] = pio_config_opts if pio_config_opts is not None else ""
os.environ["OCN_SUBMODEL"] = ocn_submodel if ocn_submodel is not None else ""
os.environ["PROFILE_PAPI_ENABLE"] = profile_papi_enable if profile_papi_enable is not None else ""
os.environ["CLM_USE_PETSC"] = clm_use_petsc if clm_use_petsc is not None else ""
os.environ["CISM_USE_TRILINOS"] = cism_use_trilinos if cism_use_trilinos is not None else ""
os.environ["MPASLI_USE_ALBANY"] = mpasli_use_albany if mpasli_use_albany is not None else ""
# This is a timestamp for the build , not the same as the testid,
# and this case may not be a test anyway. For a production
# experiment there may be many builds of the same case.
lid = run_cmd("date +%y%m%d-%H%M%S")
os.environ["LID"] = lid
# Set the overall USE_PETSC variable to TRUE if any of the
# XXX_USE_PETSC variables are TRUE.
# For now, there is just the one CLM_USE_PETSC variable, but in
# the future there may be others -- so USE_PETSC will be true if
# ANY of those are true.
use_petsc = "TRUE" if clm_use_petsc == "TRUE" else "FALSE"
case.set_value("USE_PETSC", use_petsc)
os.environ["USE_PETSC"] = use_petsc
# Set the overall USE_TRILINOS variable to TRUE if any of the
# XXX_USE_TRILINOS variables are TRUE.
# For now, there is just the one CISM_USE_TRILINOS variable, but in
# the future there may be others -- so USE_TRILINOS will be true if
# ANY of those are true.
use_trilinos = "TRUE" if cism_use_trilinos == "TRUE" else "FALSE"
case.set_value("USE_TRILINOS", use_trilinos)
os.environ["USE_TRILINOS"] = use_trilinos
# Set the overall USE_ALBANY variable to TRUE if any of the
# XXX_USE_ALBANY variables are TRUE.
# For now, there is just the one MPASLI_USE_ALBANY variable, but in
# the future there may be others -- so USE_ALBANY will be true if
# ANY of those are true.
use_albany = "TRUE" if mpasli_use_albany == "TRUE" else "FALSE"
case.set_value("USE_ALBANY", use_albany)
os.environ["USE_ALBANY"] = use_albany
# Load modules
env_module = EnvModule(mach, compiler, cimeroot, caseroot, mpilib, debug)
env_module.load_env_for_case()
# Need to flush case xml to disk before calling preview_namelists
case.flush()
if not sharedlib_only:
preview_namelists(case=case)
build_checks(case, build_threaded, comp_interface, use_esmf_lib, debug, compiler, mpilib,
sharedlibroot, nthrds_cpl, nthrds_atm, nthrds_lnd, nthrds_ice, nthrds_ocn,
nthrds_glc, nthrds_wav, nthrds_rof, ninst_build, smp_value)
t2 = time.time()
logs = []
if not model_only:
logs = build_libraries(exeroot, caseroot, cimeroot, libroot, mpilib, lid, machines_file)
if sharedlib_only and comp_lnd == "clm" and not "clm4_0" in clm_config_opts:
logging.info(" - Building clm4_5/clm5_0 Library ")
esmfdir = "esmf" if use_esmf_lib == "TRUE" else "noesmf"
sharedpath = os.environ["SHAREDPATH"]
bldroot = os.path.join(sharedpath, comp_interface, esmfdir)
objdir = os.path.join(bldroot, "lnd", "obj")
libdir = os.path.join(bldroot, "lib")
file_build = os.path.join(exeroot, "lnd.bldlog.%s" % lid)
config_lnd_dir = os.path.dirname(case.get_value("CONFIG_LND_FILE"))
results = []
for ndir in [bldroot, objdir, libdir]:
if(not os.path.isdir(ndir)):
os.makedirs(ndir)
_build_model_thread(config_lnd_dir, caseroot, bldroot, "clm", file_build,
exeroot, "lnd", "clm", objdir, incroot, results)
if not sharedlib_only:
logs.extend(build_model(case, build_threaded, exeroot, clm_config_opts, incroot,
comp_atm, comp_lnd, comp_ice, comp_ocn, comp_glc, comp_wav, comp_rof,
nthrds_atm, nthrds_lnd, nthrds_ice, nthrds_ocn, nthrds_glc, nthrds_wav, nthrds_rof,
lid, caseroot, cimeroot, use_esmf_lib, comp_interface))
if not sharedlib_only:
post_build(case, logs)
t3 = time.time()
logger.info("Time spent not building: %f sec" % (t2 - t1))
logger.info("Time spent building: %f sec" % (t3 - t2))
def _case_setup_impl(case, caseroot, casebaseid, clean=False, test_mode=False, reset=False):
###############################################################################
os.chdir(caseroot)
msg = "case.setup starting"
append_status(msg, caseroot=caseroot, sfile="CaseStatus")
cimeroot = os.environ["CIMEROOT"]
# Check that $DIN_LOC_ROOT exists - and abort if not a namelist compare tests
din_loc_root = case.get_value("DIN_LOC_ROOT")
testcase = case.get_value("TESTCASE")
expect(not (not os.path.isdir(din_loc_root) and testcase != "SBN"),
"inputdata root is not a directory: \"$din_loc_root\" ")
# Check that userdefine settings are specified before expanding variable
for vid, value in case:
expect(not (type(value) is str and "USERDEFINED_required_build" in value),
"Parameter '%s' must be defined" % vid)
# Create batch script
if reset or clean:
# Clean batch script
backup_dir = "PESetupHist/b.%s" % time.strftime("%y%m%d-%H%M%S")
if not os.path.isdir(backup_dir):
os.makedirs(backup_dir)
# back up relevant files
for fileglob in ["case.run", "env_build.xml", "env_mach_pes.xml", "Macros*"]:
for filename in glob.glob(fileglob):
shutil.copy(filename, backup_dir)
if os.path.exists("case.run"):
os.remove("case.run")
# only do the following if are NOT in testmode
if not test_mode:
# rebuild the models (even on restart)
case.set_value("BUILD_COMPLETE", False)
# backup and then clean test script
if os.path.exists("case.test"):
shutil.copy("case.test", backup_dir)
os.remove("case.test")
logger.info("Successfully cleaned test script case.test")
if os.path.exists("case.testdriver"):
shutil.copy("case.testdriver", backup_dir)
os.remove("case.testdriver")
logger.info("Successfully cleaned test script case.testdriver")
logger.info("Successfully cleaned batch script case.run")
logger.info("Successfully cleaned batch script case.run")
logger.info("Some files have been saved to %s" % backup_dir)
msg = "case.setup clean complete"
append_status(msg, caseroot=caseroot, sfile="CaseStatus")
if not clean:
drv_comp = Component()
models = drv_comp.get_valid_model_components()
models.remove("DRV")
mach, compiler, debug, mpilib = \
case.get_value("MACH"), case.get_value("COMPILER"), case.get_value("DEBUG"), case.get_value("MPILIB")
expect(mach is not None, "xml variable MACH is not set")
# Create Macros file only if it does not exist
if not os.path.exists("Macros"):
logger.debug("Creating Macros file for %s" % mach)
compilers = Compilers(compiler=compiler, machine=mach, os_=case.get_value("OS"), mpilib=mpilib)
compilers.write_macros_file()
else:
logger.debug("Macros script already created ...skipping")
# Set tasks to 1 if mpi-serial library
if mpilib == "mpi-serial":
for vid, value in case:
if vid.startswith("NTASKS_") and value != 1:
case.set_value(vid, 1)
# Check ninst.
# In CIME there can be multiple instances of each component model (an ensemble) NINST is the instance of that component.
# Save ninst in a dict to use later in apply_user_mods
ninst = dict()
for comp in models:
comp_model = case.get_value("COMP_%s" % comp)
ninst[comp_model] = case.get_value("NINST_%s" % comp)
ntasks = case.get_value("NTASKS_%s" % comp)
if ninst[comp_model] > ntasks:
if ntasks == 1:
case.set_value("NTASKS_%s" % comp, ninst[comp_model])
else:
expect(False, "NINST_%s value %d greater than NTASKS_%s %d" % (comp, ninst[comp_model], comp, ntasks))
expect(not (case.get_value("BUILD_THREADED") and compiler == "nag"),
"it is not possible to run with OpenMP if using the NAG Fortran compiler")
if os.path.exists("case.run"):
logger.info("Machine/Decomp/Pes configuration has already been done ...skipping")
else:
_check_pelayouts_require_rebuild(case, models)
if os.path.exists("LockedFiles/env_build.xml"):
os.remove("LockedFiles/env_build.xml")
case.flush()
check_lockedfiles()
tm = TaskMaker(case)
mtpn = case.get_value("MAX_TASKS_PER_NODE")
pespn = case.get_value("PES_PER_NODE")
# This is hardcoded because on yellowstone by default we
# run with 15 pes per node
# but pay for 16 pes per node. See github issue #518
if case.get_value("MACH") == "yellowstone":
pespn = 16
pestot = tm.totaltasks
if mtpn > pespn:
pestot = pestot * (mtpn // pespn)
case.set_value("COST_PES", tm.num_nodes*pespn)
else:
# reset cost_pes to totalpes
case.set_value("COST_PES", 0)
case.set_value("TOTALPES", pestot)
# Compute cost based on PE count
pval = 1
pcnt = 0
while pval < pestot:
pval *= 2
pcnt += 6 # (scaling like sqrt(6/10))
pcost = 3 - pcnt / 10 # (3 is 64 with 6)
# Compute cost based on DEBUG
dcost = 3 if debug else 0
# Compute cost based on run length
# For simplicity, we use a heuristic just based on STOP_OPTION (not considering
# STOP_N), and only deal with options longer than ndays
lcost = 0
if "nmonth" in case.get_value("STOP_OPTION"):
# N months costs 30x as much as N days; since cost is based on log-base-2, add 5
lcost = 5
elif "nyear" in case.get_value("STOP_OPTION"):
# N years costs 365x as much as N days; since cost is based on log-base-2, add 9
lcost = 9
estcost = pcost + dcost + lcost
for cost in ["CCSM_CCOST", "CCSM_GCOST", "CCSM_TCOST", "CCSM_CCOST"]:
estcost += case.get_value(cost)
case.set_value("CCSM_PCOST", pcost)
case.set_value("CCSM_ESTCOST", estcost)
# create batch file
logger.info("Creating batch script case.run")
# Use BatchFactory to get the appropriate instance of a BatchMaker,
# use it to create our batch scripts
env_batch = case.get_env("batch")
for job in env_batch.get_jobs():
input_batch_script = os.path.join(case.get_value("MACHDIR"), env_batch.get_value('template', subgroup=job))
if job == "case.test" and testcase is not None and not test_mode:
logger.info("Writing %s script" % job)
testscript = os.path.join(cimeroot, "scripts", "Testing", "Testcases", "%s_script" % testcase)
# Short term fix to be removed when csh tests are removed
if not os.path.exists(testscript):
env_batch.make_batch_script(input_batch_script, job, case)
elif job != "case.test":
logger.info("Writing %s script" % job)
env_batch.make_batch_script(input_batch_script, job, case)
# Make a copy of env_mach_pes.xml in order to be able
# to check that it does not change once case.setup is invoked
logger.info("Locking file env_mach_pes.xml")
case.flush()
shutil.copy("env_mach_pes.xml", "LockedFiles")
# Create user_nl files for the required number of instances
if not os.path.exists("user_nl_cpl"):
logger.info("Creating user_nl_xxx files for components and cpl")
# loop over models
for model in models:
comp = case.get_value("COMP_%s" % model)
logger.info("Building %s usernl files"%model)
_build_usernl_files(case, model, comp)
if comp == "cism":
run_cmd_no_fail("%s/../components/cism/cime_config/cism.template %s" % (cimeroot, caseroot))
_build_usernl_files(case, "drv", "cpl")
user_mods_path = case.get_value("USER_MODS_FULLPATH")
if user_mods_path is not None:
apply_user_mods(caseroot, user_mods_path=user_mods_path, ninst=ninst)
elif case.get_value("TEST"):
test_mods = parse_test_name(casebaseid)[6]
if test_mods is not None:
user_mods_path = os.path.join(case.get_value("TESTS_MODS_DIR"), test_mods)
apply_user_mods(caseroot, user_mods_path=user_mods_path, ninst=ninst)
# Run preview namelists for scripts
logger.info("preview_namelists")
preview_namelists(case)
logger.info("See ./CaseDoc for component namelists")
logger.info("If an old case build already exists, might want to run \'case.build --clean\' before building")
# Create test script if appropriate
# Short term fix to be removed when csh tests are removed
if os.path.exists("env_test.xml"):
if not os.path.exists("case.test"):
logger.info("Starting testcase.setup")
run_cmd_no_fail("./testcase.setup -caseroot %s" % caseroot)
logger.info("Finished testcase.setup")
msg = "case.setup complete"
append_status(msg, caseroot=caseroot, sfile="CaseStatus")
# Record env information
env_module = case.get_env("mach_specific")
env_module.make_env_mach_specific_file(compiler, debug, mpilib, "sh")
env_module.make_env_mach_specific_file(compiler, debug, mpilib, "csh")
with open("software_environment.txt", "w") as f:
f.write(env_module.list_modules())
run_cmd_no_fail("echo -e '\n' >> software_environment.txt && \
env >> software_environment.txt")
def _case_setup_impl(case, caseroot, casebaseid, clean=False, test_mode=False, reset=False):
###############################################################################
os.chdir(caseroot)
msg = "case.setup starting"
append_status(msg, caseroot=caseroot, sfile="CaseStatus")
cimeroot = get_cime_root(case)
# Check that $DIN_LOC_ROOT exists - and abort if not a namelist compare tests
din_loc_root = case.get_value("DIN_LOC_ROOT")
testcase = case.get_value("TESTCASE")
expect(not (not os.path.isdir(din_loc_root) and testcase != "SBN"),
"inputdata root is not a directory: \"$din_loc_root\" ")
# Check that userdefine settings are specified before expanding variable
for vid, value in case:
expect(not (type(value) is str and "USERDEFINED_required_build" in value),
"Parameter '%s' must be defined" % vid)
# Create batch script
if reset or clean:
# Clean batch script
backup_dir = "PESetupHist/b.%s" % time.strftime("%y%m%d-%H%M%S")
if not os.path.isdir(backup_dir):
os.makedirs(backup_dir)
# back up relevant files
for fileglob in ["case.run", "env_build.xml", "env_mach_pes.xml", "Macros*"]:
for filename in glob.glob(fileglob):
shutil.copy(filename, backup_dir)
if os.path.exists("case.run"):
os.remove("case.run")
# only do the following if are NOT in testmode
if not test_mode:
# rebuild the models (even on restart)
case.set_value("BUILD_COMPLETE", False)
# backup and then clean test script
if os.path.exists("case.test"):
shutil.copy("case.test", backup_dir)
os.remove("case.test")
logger.info("Successfully cleaned test script case.test")
if os.path.exists("case.testdriver"):
shutil.copy("case.testdriver", backup_dir)
os.remove("case.testdriver")
logger.info("Successfully cleaned test script case.testdriver")
logger.info("Successfully cleaned batch script case.run")
logger.info("Successfully cleaned batch script case.run")
logger.info("Some files have been saved to %s" % backup_dir)
msg = "case.setup clean complete"
append_status(msg, caseroot=caseroot, sfile="CaseStatus")
if not clean:
models = case.get_values("COMP_CLASSES")
mach, compiler, debug, mpilib = \
case.get_value("MACH"), case.get_value("COMPILER"), case.get_value("DEBUG"), case.get_value("MPILIB")
expect(mach is not None, "xml variable MACH is not set")
# Create Macros file only if it does not exist
if not os.path.exists("Macros"):
logger.debug("Creating Macros file for %s" % mach)
compilers = Compilers(compiler=compiler, machine=mach, os_=case.get_value("OS"), mpilib=mpilib)
compilers.write_macros_file()
else:
logger.debug("Macros script already created ...skipping")
# Set tasks to 1 if mpi-serial library
if mpilib == "mpi-serial":
for vid, value in case:
if vid.startswith("NTASKS_") and value != 1:
case.set_value(vid, 1)
# Check ninst.
# In CIME there can be multiple instances of each component model (an ensemble) NINST is the instance of that component.
# Save ninst in a dict to use later in apply_user_mods
ninst = dict()
for comp in models:
if comp == "DRV":
continue
comp_model = case.get_value("COMP_%s" % comp)
ninst[comp_model] = case.get_value("NINST_%s" % comp)
ntasks = case.get_value("NTASKS_%s" % comp)
if ninst[comp_model] > ntasks:
if ntasks == 1:
case.set_value("NTASKS_%s" % comp, ninst[comp_model])
else:
expect(False, "NINST_%s value %d greater than NTASKS_%s %d" % (comp, ninst[comp_model], comp, ntasks))
if os.path.exists("case.run"):
logger.info("Machine/Decomp/Pes configuration has already been done ...skipping")
else:
_check_pelayouts_require_rebuild(case, models)
if os.path.exists("LockedFiles/env_build.xml"):
os.remove("LockedFiles/env_build.xml")
case.flush()
check_lockedfiles()
env_mach_pes = case.get_env("mach_pes")
pestot = env_mach_pes.get_total_tasks(models)
logger.debug("at update TOTALPES = %s"%pestot)
case.set_value("TOTALPES", pestot)
thread_count = env_mach_pes.get_max_thread_count(models)
if thread_count > 1:
case.set_value("BUILD_THREADED", True)
expect(not (case.get_value("BUILD_THREADED") and compiler == "nag"),
"it is not possible to run with OpenMP if using the NAG Fortran compiler")
cost_pes = env_mach_pes.get_cost_pes(pestot, thread_count, machine=case.get_value("MACH"))
case.set_value("COST_PES", cost_pes)
# create batch file
logger.info("Creating batch script case.run")
# Use BatchFactory to get the appropriate instance of a BatchMaker,
# use it to create our batch scripts
env_batch = case.get_env("batch")
num_nodes = env_mach_pes.get_total_nodes(pestot, thread_count)
tasks_per_node = env_mach_pes.get_tasks_per_node(pestot, thread_count)
for job in env_batch.get_jobs():
input_batch_script = os.path.join(case.get_value("MACHDIR"), env_batch.get_value('template', subgroup=job))
if job == "case.test" and testcase is not None and not test_mode:
logger.info("Writing %s script" % job)
testscript = os.path.join(cimeroot, "scripts", "Testing", "Testcases", "%s_script" % testcase)
# Short term fix to be removed when csh tests are removed
if not os.path.exists(testscript):
env_batch.make_batch_script(input_batch_script, job, case, pestot, tasks_per_node, num_nodes, thread_count)
elif job != "case.test":
logger.info("Writing %s script from input template %s" % (job, input_batch_script))
env_batch.make_batch_script(input_batch_script, job, case, pestot, tasks_per_node, num_nodes, thread_count)
# Make a copy of env_mach_pes.xml in order to be able
# to check that it does not change once case.setup is invoked
logger.info("Locking file env_mach_pes.xml")
case.flush()
logger.debug("at copy TOTALPES = %s"%case.get_value("TOTALPES"))
shutil.copy("env_mach_pes.xml", "LockedFiles")
# Create user_nl files for the required number of instances
if not os.path.exists("user_nl_cpl"):
logger.info("Creating user_nl_xxx files for components and cpl")
# loop over models
for model in models:
comp = case.get_value("COMP_%s" % model)
logger.info("Building %s usernl files"%model)
_build_usernl_files(case, model, comp)
if comp == "cism":
run_cmd_no_fail("%s/../components/cism/cime_config/cism.template %s" % (cimeroot, caseroot))
_build_usernl_files(case, "drv", "cpl")
user_mods_path = case.get_value("USER_MODS_FULLPATH")
if user_mods_path is not None:
apply_user_mods(caseroot, user_mods_path=user_mods_path, ninst=ninst)
elif case.get_value("TEST"):
test_mods = parse_test_name(casebaseid)[6]
if test_mods is not None:
user_mods_path = os.path.join(case.get_value("TESTS_MODS_DIR"), test_mods)
apply_user_mods(caseroot, user_mods_path=user_mods_path, ninst=ninst)
# Run preview namelists for scripts
logger.info("preview_namelists")
preview_namelists(case)
logger.info("See ./CaseDoc for component namelists")
logger.info("If an old case build already exists, might want to run \'case.build --clean\' before building")
# Create test script if appropriate
# Short term fix to be removed when csh tests are removed
if os.path.exists("env_test.xml"):
if not os.path.exists("case.test"):
logger.info("Starting testcase.setup")
run_cmd_no_fail("./testcase.setup -caseroot %s" % caseroot)
logger.info("Finished testcase.setup")
msg = "case.setup complete"
append_status(msg, caseroot=caseroot, sfile="CaseStatus")
# Record env information
env_module = case.get_env("mach_specific")
env_module.make_env_mach_specific_file(compiler, debug, mpilib, "sh")
env_module.make_env_mach_specific_file(compiler, debug, mpilib, "csh")
with open("software_environment.txt", "w") as f:
f.write(env_module.list_modules())
run_cmd_no_fail("echo -e '\n' >> software_environment.txt && \
env >> software_environment.txt")
