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Lock env_mach.xml file #1039

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Jan 25, 2017
Merged

Lock env_mach.xml file #1039

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20f5614
Lock env_mach.xml file
jgfouca Jan 24, 2017
49b1e4a
Update ACME batch configs, do not lock env_batch.xml
jgfouca Jan 25, 2017
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53 changes: 29 additions & 24 deletions cime_config/acme/machines/config_batch.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,13 +39,13 @@
<batch_directive></batch_directive>
<jobid_pattern>(\d+)</jobid_pattern>
<depend_string> --dependencies</depend_string>
<walltime_format>%H:%M:%S</walltime_format>
<walltime_format>%H:%M:%s</walltime_format>
<submit_args>
<arg flag="--cwd" name="CASEROOT"/>
<arg flag="-A" name="PROJECT"/>
<arg flag="-t" name="JOB_WALLCLOCK_TIME"/>
<!-- space is required here so that variable is resolved correctly -->
<arg flag="-n" name=" $TOTALPES/$PES_PER_NODE"/>
<arg flag="-n" name=" $TOTALPES / $PES_PER_NODE"/>
<arg flag="-q" name="JOB_QUEUE"/>
<arg flag="--mode script"/>
</submit_args>
Expand All @@ -72,43 +72,43 @@
<batch_redirect>&lt;</batch_redirect>
<batch_directive>#BSUB</batch_directive>
<jobid_pattern>&lt;(\d+)&gt;</jobid_pattern>
<depend_string> -w "done(jobid)"</depend_string>
<depend_string> -w 'done(jobid)'</depend_string>
<walltime_format>%H:%M</walltime_format>
<submit_args>
<arg flag="-q" name="$JOB_QUEUE"/>
<arg flag="-W" name="$JOB_WALLCLOCK_TIME"/>
<arg flag="-P" name="$PROJECT"/>
</submit_args>
<directives>
<directive > -n {{ totaltasks }} </directive>
<directive > -R "span[ptile={{ ptile }}]"</directive>
<directive > -q {{ job_queue }} </directive>
<directive > -n {{ total_tasks }} </directive>
<directive > -R "span[ptile={{ tasks_per_node }}]"</directive>
<directive > -N </directive>
<directive default="poe" > -a {{ poe }} </directive>
<directive > -x {{ queue_exclusive }} </directive>
<directive default="acme.stdout" > -o {{ acme_stdout }}.%J </directive>
<directive default="acme.stderr" > -e {{ acme_stderr }}.%J </directive>
<directive default="acme.stdout" > -o {{ output_error_path }}.%J </directive>
<directive default="acme.stderr" > -e {{ output_error_path }}.%J </directive>
<directive > -J {{ job_id }} </directive>
<directive > -W {{ job_wallclock_time }} </directive>
<directive > -P {{ account }} </directive>
</directives>
</batch_system>

<batch_system type="pbs" >
<batch_query args="-u $USER" >qselect</batch_query>
<batch_query args="-f" >qstat</batch_query>
<batch_submit>qsub </batch_submit>
<batch_directive>#PBS</batch_directive>
<jobid_pattern>^(\d+)</jobid_pattern>
<jobid_pattern>^(\S+)$</jobid_pattern>
<depend_string> -W depend=afterok:jobid</depend_string>
<walltime_format>%H:%M:%S</walltime_format>
<submit_args>
<arg flag="-q" name="JOB_QUEUE"/>
<arg flag="-l walltime=" name="JOB_WALLCLOCK_TIME"/>
<arg flag="-A" name="PROJECT"/>
<arg flag="-q" name="$JOB_QUEUE"/>
<arg flag="-l walltime=" name="$JOB_WALLCLOCK_TIME"/>
<arg flag="-A" name="$PROJECT"/>
</submit_args>
<directives>
<directive> -V </directive>
<directive> -N {{ job_id }}</directive>
<directive default="n"> -r {{ rerunnable }} </directive>
<!-- <directive> -j oe {{ output_error_path }} </directive> -->
<directive> -j oe </directive>
<directive default="ae" > -m {{ mail_options }} </directive>
<directive default="/bin/bash" > -S {{ shell }} </directive>
<directive> -V </directive>
</directives>
</batch_system>

Expand All @@ -119,32 +119,37 @@
<jobid_pattern>(\d+)$</jobid_pattern>
<depend_string> -W depend=afterok:jobid</depend_string>
<walltime_format>%H:%M:%S</walltime_format>
<submit_args>
<arg flag="-l walltime=" name="$JOB_WALLCLOCK_TIME"/>
<arg flag="-A" name="$PROJECT"/>
</submit_args>
<directives>
<directive> -N {{ job_id }}</directive>
<directive> -l walltime={{ job_wallclock_time }}</directive>
<directive> -j oe </directive>
<directive> -A {{ project }} </directive>
<directive default="n"> -r {{ rerunnable }} </directive>
<directive default="ae" > -m {{ mail_options }} </directive>
<directive default="/bin/bash" > -S {{ shell }}</directive>
</directives>
</batch_system>

<batch_system type="slurm" >
<batch_query args="-o '%i' -h -u $USER">squeue </batch_query>
<batch_query>squeue</batch_query>
<batch_submit>sbatch</batch_submit>
<batch_directive>#SBATCH</batch_directive>
<jobid_pattern>(\d+)$</jobid_pattern>
<depend_string> --dependency=afterok:jobid</depend_string>
<walltime_format>%H:%M:%S</walltime_format>
<submit_args>
<arg flag="--time" name="$JOB_WALLCLOCK_TIME"/>
<arg flag="-p" name="$JOB_QUEUE"/>
<arg flag="--account" name="$PROJECT"/>
</submit_args>
<directives>
<directive> --job-name={{ job_id }}</directive>
<directive> --nodes={{ num_nodes }}</directive>
<directive> --ntasks-per-node={{ tasks_per_node }}</directive>
<directive> --output={{ output_error_path }} </directive>
<directive> --exclusive </directive>
<directive> --time={{ job_wallclock_time }}</directive>
<directive> --partition={{ job_queue }}</directive>
<directive> --account={{ project }}</directive>
</directives>
</batch_system>

Expand Down
7 changes: 3 additions & 4 deletions scripts/create_newcase
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
#!/usr/bin/env python

from Tools.standard_script_setup import *
from shutil import copyfile
from CIME.utils import expect, get_model
from CIME.case import Case
from CIME.check_lockedfiles import lock_file

logger = logging.getLogger(__name__)

Expand Down Expand Up @@ -191,9 +191,8 @@ def _main_func(description):
user_mods_dir = os.path.abspath(user_mods_dir)
case.apply_user_mods(user_mods_dir)

# Copy env_case.xml into LockedFiles
copyfile(os.path.join(caseroot,"env_case.xml"),
os.path.join(caseroot,"LockedFiles","env_case.xml"))
# Lock env_case.xml
lock_file("env_case.xml", caseroot)

###############################################################################

Expand Down
31 changes: 14 additions & 17 deletions utils/python/CIME/SystemTests/erp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
from CIME.case_setup import case_setup
import CIME.utils
from CIME.SystemTests.system_tests_common import SystemTestsCommon
from CIME.check_lockedfiles import *

logger = logging.getLogger(__name__)

Expand Down Expand Up @@ -40,15 +41,15 @@ def build_phase(self, sharedlib_only=False, model_only=False):
# env_build.xml in LockedFiles if they are not there. If there
# are already copies there then simply copy them back to
# have the starting env_mach_pes.xml and env_build.xml
machpes1 = os.path.join("LockedFiles","env_mach_pes.ERP1.xml")
envbuild1 = os.path.join("LockedFiles","env_build.ERP1.xml")
if ( os.path.isfile(machpes1) ):
shutil.copy(machpes1,"env_mach_pes.xml")
machpes1 = "env_mach_pes.ERP1.xml"
envbuild1 = "env_build.ERP1.xml"
if is_locked(machpes1):
restore(machpes1, newname="env_mach_pes.xml")
else:
shutil.copy("env_mach_pes.xml","env_mach_pes.ERP1.xml")
lock_file("env_mach_pes.xml", newname=machpes1)

if ( os.path.isfile(envbuild1) ):
shutil.copy(envbuild1,"env_build.xml")
if is_locked(envbuild1):
restore(envbuild1, newname="env_build.xml")

# Build two executables, one using the original tasks and threads (ERP1) and
# one using the modified tasks and threads (ERP2)
Expand Down Expand Up @@ -86,23 +87,19 @@ def build_phase(self, sharedlib_only=False, model_only=False):

# Make copies of the new env_mach_pes.xml and the new
# env_build.xml to be used in the run phase
shutil.copy("env_mach_pes.xml", os.path.join("LockedFiles","env_mach_pes.ERP%s.xml"%bld ))
shutil.copy("env_build.xml", os.path.join("LockedFiles","env_build.ERP%s.xml"%bld ))
#
#
lock_file("env_mach_pes.xml", newname="env_mach_pes.ERP%s.xml" % bld)
lock_file("env_build.xml", newname="env_build.ERP%s.xml" % bld)

def run_phase(self):
# run will have values 1,2
for run in range(1,3):

expect(os.path.isfile(os.path.join("LockedFiles","env_mach_pes.ERP%d.xml"%run)),
"ERROR: LockedFiles/env_mach_pes.ERP%d.xml does not exist, run case.build"%run )
expect(is_locked("env_mach_pes.ERP%d.xml" % run),
"ERROR: LockedFiles/env_mach_pes.ERP%d.xml does not exist, run case.build" % run )

# Use the second env_mach_pes.xml and env_build.xml files
shutil.copy(os.path.join("LockedFiles","env_mach_pes.ERP%d.xml"%run), "env_mach_pes.xml")
shutil.copy("env_mach_pes.xml", os.path.join("LockedFiles","env_mach_pes.xml"))
shutil.copy(os.path.join("LockedFiles","env_build.ERP%d.xml")%run, "env_build.xml")
shutil.copy("env_build.xml", os.path.join("LockedFiles","env_build.xml"))
restore("env_mach_pes.ERP%d.xml" % run, newname="env_mach_pes.xml")
restore("env_build.ERP%d.xml" % run, newname="env_build.xml")

# update the case to use the new values
self._case.read_xml()
Expand Down
29 changes: 13 additions & 16 deletions utils/python/CIME/SystemTests/ncr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
from CIME.case_setup import case_setup
import CIME.utils
from CIME.SystemTests.system_tests_common import SystemTestsCommon
from CIME.check_lockedfiles import *

logger = logging.getLogger(__name__)

Expand All @@ -25,16 +26,16 @@ def build_phase(self, sharedlib_only=False, model_only=False):
exeroot = self._case.get_value("EXEROOT")
cime_model = CIME.utils.get_model()

machpes1 = os.path.join("LockedFiles","env_mach_pes.NCR1.xml")
if ( os.path.isfile(machpes1) ):
shutil.copy(machpes1,"env_mach_pes.xml")
machpes1 = "env_mach_pes.NCR1.xml"
if is_locked(machpes1):
restore(machpes1, newname="env_mach_pes.xml")

# Build two exectuables for this test, the first is a default build, the
# second halves the number of tasks and runs two instances for each component
# Lay all of the components out concurrently
for bld in range(1,3):
logging.warn("Starting bld %s"%bld)
machpes = os.path.join("LockedFiles","env_mach_pes.NCR%s.xml"%bld)
machpes = "env_mach_pes.NCR%s.xml" % bld
ntasks_sum = 0
for comp in ['ATM','OCN','WAV','GLC','ICE','ROF','LND']:
self._case.set_value("NINST_%s"%comp,str(bld))
Expand All @@ -54,14 +55,12 @@ def build_phase(self, sharedlib_only=False, model_only=False):
self.build_indv(sharedlib_only, model_only)
shutil.move("%s/%s.exe"%(exeroot,cime_model),
"%s/%s.exe.NCR%s"%(exeroot,cime_model,bld))
shutil.copy("env_build.xml",os.path.join("LockedFiles","env_build.NCR%s.xml"%bld))
shutil.copy("env_mach_pes.xml", machpes)
lock_file("env_build.xml", newname="env_build.NCR%s.xml" % bld)
lock_file("env_mach_pes.xml", newname=machpes)

# Because mira/cetus interprets its run script differently than
# other systems we need to copy the original env_mach_pes.xml back
shutil.copy(machpes1,"env_mach_pes.xml")
shutil.copy("env_mach_pes.xml",
os.path.join("LockedFiles","env_mach_pes.xml"))
restore(machpes1, newname="env_mach_pes.xml")

def run_phase(self):
os.chdir(self._caseroot)
Expand All @@ -70,16 +69,15 @@ def run_phase(self):
cime_model = CIME.utils.get_model()

# Reset beginning test settings
expect(os.path.exists("LockedFiles/env_mach_pes.NCR1.xml"),
expect(is_locked("env_mach_pes.NCR1.xml"),
"ERROR: LockedFiles/env_mach_pes.NCR1.xml does not exist\n"
" this would been produced in the build - must run case.test_build")

shutil.copy("LockedFiles/env_mach_pes.NCR1.xml", "env_mach_pes.xml")
shutil.copy("env_mach_pes.xml", "LockedFiles/env_mach_pes.xml")
restore("env_mach_pes.NCR1.xml", newname="env_mach_pes.xml")
restore("env_build.NCR1.xml", newname="env_build.xml")
shutil.copy("%s/%s.exe.NCR1" % (exeroot, cime_model),
"%s/%s.exe" % (exeroot, cime_model))
shutil.copy("LockedFiles/env_build.NCR1.xml", "env_build.xml")
shutil.copy("env_build.xml", "LockedFiles/env_build.xml")


stop_n = self._case.get_value("STOP_N")
stop_option = self._case.get_value("STOP_OPTION")
Expand All @@ -104,8 +102,7 @@ def run_phase(self):
os.remove("%s/%s.exe" % (exeroot, cime_model))
shutil.copy("%s/%s.exe.NCR2" % (exeroot, cime_model),
"%s/%s.exe" % (exeroot, cime_model))
shutil.copy("LockedFiles/env_build.NCR2.xml", "env_build.xml")
shutil.copy("env_build.xml", "LockedFiles/env_build.xml")
restore("env_build.NCR2.xml", "env_build.xml")

logger.info("default: doing a %s %s with NINST2" % (stop_n, stop_option))
self.run_indv(suffix="multiinst")
Expand Down
20 changes: 8 additions & 12 deletions utils/python/CIME/SystemTests/seq.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
from CIME.XML.standard_module_setup import *
from CIME.SystemTests.system_tests_common import SystemTestsCommon
from CIME.case_setup import case_setup
from CIME.check_lockedfiles import *
import shutil

logger = logging.getLogger(__name__)
Expand Down Expand Up @@ -31,12 +32,11 @@ def build_phase(self, sharedlib_only=False, model_only=False):
shutil.move("%s/%s.exe"%(exeroot,cime_model),
"%s/%s.exe.SEQ1"%(exeroot,cime_model))
any_changes = False
machpes1 = os.path.join("LockedFiles","env_mach_pes.SEQ1.xml")
if ( os.path.isfile(machpes1) ):
shutil.copy(machpes1,"env_mach_pes.xml")
machpes1 = "env_mach_pes.SEQ1.xml"
if is_locked(machpes1):
restore(machpes1, newname="env_mach_pes.xml")
else:
logging.info("Copying env_mach_pes.xml to %s"%(machpes1))
shutil.copy("env_mach_pes.xml", machpes1)
lock_file("env_mach_pes.xml", newname=machpes1)

comp_classes = self._case.get_values("COMP_CLASSES")
for comp in comp_classes:
Expand All @@ -63,9 +63,7 @@ def build_phase(self, sharedlib_only=False, model_only=False):
self.build_indv(sharedlib_only=sharedlib_only, model_only=model_only)
shutil.move("%s/%s.exe"%(exeroot,cime_model),
"%s/%s.exe.SEQ2"%(exeroot,cime_model))
machpes2 = os.path.join("LockedFiles","env_mach_pes.SEQ2.xml")
logging.info("Copying env_mach_pes.xml to %s"%(machpes2))
shutil.copy("env_mach_pes.xml", machpes2)
lock_file("env_mach_pes.xml", newname="env_mach_pes.SEQ2.xml")

def run_phase(self):
# Move to config_tests.xml once that's ready.
Expand All @@ -87,12 +85,10 @@ def run_phase(self):

shutil.copy("%s/%s.exe.SEQ1"%(exeroot,cime_model),
"%s/%s.exe"%(exeroot,cime_model))
shutil.copy(os.path.join("LockedFiles", "env_mach_pes.SEQ1.xml"), "env_mach_pes.xml")
shutil.copy("env_mach_pes.xml", os.path.join("LockedFiles", "env_mach_pes.xml"))
restore("env_mach_pes.SEQ1.xml", newname="env_mach_pes.xml")
self.run_indv()

shutil.copy(os.path.join("LockedFiles", "env_mach_pes.SEQ2.xml"), "env_mach_pes.xml")
shutil.copy("env_mach_pes.xml", os.path.join("LockedFiles", "env_mach_pes.xml"))
restore("env_mach_pes.SEQ2.xml", newname="env_mach_pes.xml")

os.remove("%s/%s.exe"%(exeroot,cime_model))
shutil.copy("%s/%s.exe.SEQ1"%(exeroot,cime_model),
Expand Down
20 changes: 8 additions & 12 deletions utils/python/CIME/SystemTests/system_tests_common.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
from CIME.case_run import case_run
from CIME.case_st_archive import case_st_archive
from CIME.test_status import *
from CIME.check_lockedfiles import *
from CIME.hist_utils import *

import CIME.build as build
Expand All @@ -20,7 +21,7 @@ class SystemTestsCommon(object):

def __init__(self, case, expected=None):
"""
initialize a CIME system test object, if the file LockedFiles/env_run.orig.xml
initialize a CIME system test object, if the locked env_run.orig.xml
does not exist copy the current env_run.xml file. If it does exist restore values
changed in a previous run of the test.
"""
Expand All @@ -43,20 +44,14 @@ def _init_environment(self, caseroot):

def _init_locked_files(self, caseroot, expected):
"""
If the file LockedFiles/env_run.orig.xml does not exist, copy the current
If the locked env_run.orig.xml does not exist, copy the current
env_run.xml file. If it does exist, restore values changed in a previous
run of the test.
"""
if os.path.isfile(os.path.join(caseroot, "LockedFiles", "env_run.orig.xml")):
if is_locked("env_run.orig.xml"):
self.compare_env_run(expected=expected)
elif os.path.isfile(os.path.join(caseroot, "env_run.xml")):
lockedfiles = os.path.join(caseroot, "LockedFiles")
try:
os.stat(lockedfiles)
except:
os.mkdir(lockedfiles)
shutil.copy(os.path.join(caseroot,"env_run.xml"),
os.path.join(lockedfiles, "env_run.orig.xml"))
lock_file("env_run.xml", caseroot=caseroot, newname="env_run.orig.xml")

def _resetup_case(self, phase):
"""
Expand Down Expand Up @@ -307,12 +302,13 @@ def _check_for_memleak(self):
self._test_status.set_status(MEMLEAK_PHASE, TEST_FAIL_STATUS, comments=comment)

def compare_env_run(self, expected=None):
# JGF implement in check_lockedfiles?
f1obj = EnvRun(self._caseroot, "env_run.xml")
f2obj = EnvRun(self._caseroot, os.path.join("LockedFiles", "env_run.orig.xml"))
f2obj = EnvRun(self._caseroot, os.path.join(LOCKED_DIR, "env_run.orig.xml"))
diffs = f1obj.compare_xml(f2obj)
for key in diffs.keys():
if expected is not None and key in expected:
logging.warn(" Resetting %s for test"%key)
logging.warn(" Resetting %s for test" % key)
f1obj.set_value(key, f2obj.get_value(key, resolved=False))
else:
print "Found difference in %s: case: %s original value %s" %\
Expand Down
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