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Merge branch 'jedwards4b-more_mira_port'
2 parents 367d47f + 1df3edd commit 1f9f0b3

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-85
lines changed

14 files changed

+108
-85
lines changed

‎cime_config/acme/machines/config_batch.xml‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -39,14 +39,15 @@
3939
<batch_directive></batch_directive>
4040
<jobid_pattern>(\d+)</jobid_pattern>
4141
<depend_string> --dependencies</depend_string>
42-
<walltime_format>%H:%M:%S</walltime_format>
42+
<walltime_format>%M</walltime_format>
4343
<submit_args>
44-
<arg flag="--cwd" name="$CASEROOT"/>
45-
<arg flag="-A" name="$PROJECT"/>
46-
<arg flag="-t" name="$JOB_WALLCLOCK_TIME"/>
44+
<arg flag="--cwd" name="CASEROOT"/>
45+
<arg flag="-A" name="PROJECT"/>
46+
<arg flag="-t" name="JOB_WALLCLOCK_TIME"/>
4747
<arg flag="-n" name="$TOTALPES/$PES_PER_NODE"/>
48-
<arg flag="-q" name="$JOB_QUEUE"/>
48+
<arg flag="-q" name="JOB_QUEUE"/>
4949
<arg flag="--mode script"/>
50+
<arg flag="--env" name='"CIMEROOT=$CIMEROOT"'/>
5051
</submit_args>
5152
</batch_system>
5253

‎cime_config/acme/machines/config_machines.xml‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -820,7 +820,6 @@
820820
<arg name="bg_threadlayout"> --envs BG_THREADLAYOUT=1</arg>
821821
<arg name="omp_stacksize"> --envs OMP_STACKSIZE=64M</arg>
822822
<arg name="thread_count"> --envs OMP_NUM_THREADS={{ thread_count }}</arg>
823-
<arg name="colon">:</arg>
824823
</arguments>
825824
</mpirun>
826825
<module_system type="soft">

‎cime_config/cesm/allactive/config_compsets.xml‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
TIME_ATM[%phys]_LND[%phys]_ICE[%phys]_OCN[%phys]_ROF[%phys]_GLC[%phys]_WAV[%phys][_ESP%phys][_BGC%phys]
1414
Where for the CAM specific compsets below the following is supported
1515
TIME = Time period (e.g. 2000, HIST, RCP8...)
16-
ATM = [CAM4, CAM5]
16+
ATM = [CAM40, CAM50, CAM60]
1717
LND = [CLM40, CLM45, CLM50, SLND]
1818
ICE = [CICE, DICE, SICE]
1919
OCN = [DOCN, ,AQUAP, SOCN]
@@ -42,17 +42,17 @@
4242

4343
<compset>
4444
<alias>B1850Ws</alias>
45-
<lname>1850_CAM55_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_SWAV_BGC%BDRD</lname>
45+
<lname>1850_CAM60_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_SWAV_BGC%BDRD</lname>
4646
</compset>
4747

4848
<compset>
4949
<alias>B1850</alias>
50-
<lname>1850_CAM55_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_WW3_BGC%BDRD</lname>
50+
<lname>1850_CAM60_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_WW3_BGC%BDRD</lname>
5151
</compset>
5252

5353
<compset>
54-
<alias>B1850CwWs</alias>
55-
<lname>1850_CAM55%WTSM_CLM50%BGC_CICE_POP2%ECO_MOSART_SGLC_SWAV</lname>
54+
<alias>B1850CwWs</alias>
55+
<lname>1850_CAM60%WTSM_CLM50%BGC_CICE_POP2%ECO_MOSART_SGLC_SWAV</lname>
5656
</compset>
5757

5858

@@ -144,7 +144,7 @@
144144
<lname>HIST_CAM50_CLM40%CN_CICE_POP2_RTM_SGLC_SWAV</lname>
145145
</compset>
146146

147-
<compset>
147+
<compset>
148148
<alias>BiHISTC5CN</alias>
149149
<lname>HIST_CAM50_CLM40%CN_WISO_CICE%WISO_POP2%ISO_RTM%WISO_SGLC_SWAV</lname>
150150
</compset>
@@ -261,7 +261,7 @@
261261

262262
<compset>
263263
<alias>ETEST</alias>
264-
<lname>2000_CAM55_CLM50_CICE_DOCN%SOM_MOSART_SGLC_SWAV_TEST</lname>
264+
<lname>2000_CAM60_CLM50_CICE_DOCN%SOM_MOSART_SGLC_SWAV_TEST</lname>
265265
</compset>
266266

267267
<compset>
@@ -281,17 +281,17 @@
281281

282282
<entry id="RUN_TYPE">
283283
<values>
284-
<value grid="a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%gland5UM_w%null" compset="1850_CAM55_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_SWAV_BGC%BDRD" >hybrid</value>
284+
<value grid="a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%gland5UM_w%null" compset="1850_CAM60_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_SWAV_BGC%BDRD" >hybrid</value>
285285
</values>
286286
</entry>
287287
<entry id="RUN_REFCASE">
288288
<values>
289-
<value grid="a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%gland5UM_w%null" compset="1850_CAM55_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_SWAV_BGC%BDRD">b.e15.B1850G.f09_g16.pi_control.25</value>
289+
<value grid="a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%gland5UM_w%null" compset="1850_CAM60_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_SWAV_BGC%BDRD">b.e15.B1850G.f09_g16.pi_control.25</value>
290290
</values>
291291
</entry>
292292
<entry id="RUN_REFDATE">
293293
<values>
294-
<value grid="a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%gland5UM_w%null" compset="1850_CAM55_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_SWAV_BGC%BDRD" >0041-01-01</value>
294+
<value grid="a%0.9x1.25_l%0.9x1.25_oi%gx1v6_r%r05_m%gx1v6_g%gland5UM_w%null" compset="1850_CAM60_CLM50%BGC_CICE_POP2%ECO_MOSART_CISM1%NOEVOLVE_SWAV_BGC%BDRD" >0041-01-01</value>
295295
</values>
296296
</entry>
297297
<!-- Reference cases from older cesm versions are no longer valid

‎cime_config/cesm/machines/config_batch.xml‎

Lines changed: 18 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -63,13 +63,14 @@
6363
<depend_string> --dependencies</depend_string>
6464
<walltime_format>%M</walltime_format>
6565
<submit_args>
66-
<arg flag="--cwd" name="$CASEROOT"/>
67-
<arg flag="-A" name="$PROJECT"/>
68-
<arg flag="-t" name="$JOB_WALLCLOCK_TIME"/>
66+
<arg flag="--cwd" name="CASEROOT"/>
67+
<arg flag="-A" name="PROJECT"/>
68+
<arg flag="-t" name="JOB_WALLCLOCK_TIME"/>
6969
<arg flag="-n" name="$TOTALPES/$PES_PER_NODE"/>
70-
<arg flag="-q" name="$JOB_QUEUE"/>
70+
<arg flag="-q" name="JOB_QUEUE"/>
7171
<arg flag="--mode script"/>
72-
</submit_args>
72+
<arg flag="--env" name='"CIMEROOT=$CIMEROOT"'/>
73+
</submit_args>
7374
</batch_system>
7475

7576
<batch_system type="lsf" version="9.1">
@@ -142,21 +143,21 @@
142143
</batch_system>
143144

144145
<!-- babbage is PBS -->
145-
<batch_system MACH="babbage" version="x.y">
146+
<batch_system MACH="babbage" type="pbs">
146147
<directives>
147148
<directive default="/bin/bash" > -S {{ shell }} </directive>
148149
</directives>
149150
</batch_system>
150151

151152
<!-- babbageKnc is PBS -->
152-
<batch_system MACH="babbageKnc" version="x.y">
153+
<batch_system MACH="babbageKnc" type="pbs">
153154
<directives>
154155
<directive default="/bin/bash" > -S {{ shell }} </directive>
155156
</directives>
156157
</batch_system>
157158

158159
<!-- brutus is PBS -->
159-
<batch_system type="pbs" MACH="brutus" version="x.y">
160+
<batch_system type="pbs" MACH="brutus" >
160161
<directives>
161162
<directive default="/bin/bash" > -S {{ shell }} </directive>
162163
</directives>
@@ -186,25 +187,25 @@
186187
</batch_system>
187188

188189
<!-- brutus is PBS -->
189-
<batch_system MACH="brutus" version="x.y">
190+
<batch_system MACH="brutus" type="pbs">
190191
<directives>
191192
<directive default="/bin/bash" > -S {{ shell }} </directive>
192193
</directives>
193194
</batch_system>
194195

195-
<!-- eos is PBS -->
196-
<batch_system MACH="eos" version="x.y">
196+
<!-- eos is PBS -->
197+
<batch_system MACH="eos" type="pbs">
197198
<jobid_pattern>^(\d+)</jobid_pattern>
198199
<directives>
199200
<directive>-A $PROJECT</directive>
200201
<directive>-l mppwidth={{ mppwidth }}</directive>
201202
<directive>-l nodes={{ num_nodes }}</directive>
202203
<directive default="/bin/bash" > -S {{ shell }} </directive>
203204
</directives>
204-
</batch_system>
205+
</batch_system>
205206

206207
<!-- erebus is PBS -->
207-
<batch_system MACH="erebus" version="x.y">
208+
<batch_system MACH="erebus" type="pbs">
208209
<directives>
209210
<directive default="/bin/bash" > -S {{ shell }} </directive>
210211
</directives>
@@ -232,14 +233,6 @@
232233
</walltimes>
233234
</batch_system>
234235

235-
<!-- goldbach is PBS -->
236-
<batch_system MACH="goldbach" version="x.y">
237-
<directives>
238-
<directive>-l nodes={{ num_nodes }}:ppn={{ tasks_per_node }}</directive>
239-
<directive default="/bin/bash" > -S {{ shell }} </directive>
240-
</directives>
241-
</batch_system>
242-
243236
<!-- hobart is PBS -->
244237
<batch_system type="pbs" MACH="hobart" version="x.y">
245238
<directives>
@@ -253,28 +246,14 @@
253246
</batch_system>
254247

255248
<!-- hera is SLURM -->
256-
<batch_system MACH="hera">
249+
<batch_system MACH="hera" type="slurm">
257250
<batch_directive>#MSUB</batch_directive>
258251
<directives>
259252
<directive>-A ees</directive>
260253
<directive>-l gres=lscratchd</directive>
261254
</directives>
262255
</batch_system>
263256

264-
<!-- hopper is PBS -->
265-
<batch_system MACH="hopper" version="x.y">
266-
<directives>
267-
<directive default="/bin/bash" > -S {{ shell }} </directive>
268-
</directives>
269-
</batch_system>
270-
271-
<!-- janus is PBS -->
272-
<batch_system MACH="janus" version="x.y">
273-
<directives>
274-
<directive default="/bin/bash" > -S {{ shell }} </directive>
275-
</directives>
276-
</batch_system>
277-
278257
<batch_system MACH="mira" type="cobalt">
279258
<queues>
280259
<queue waltimemin="0" walltimemax="360" jobmin="512" jobmax="4096" default="true">default</queue>
@@ -361,7 +340,7 @@
361340
</batch_system>
362341

363342
<!-- all pleiades machines are PBS -->
364-
<batch_system MACH="pleiades-wes" version="x.y">
343+
<batch_system MACH="pleiades-wes" version="x.y" type="pbs">
365344
<jobid_pattern>^(\S+)</jobid_pattern>
366345
<directives>
367346
<directive>-W group_list=$PROJECT </directive>
@@ -372,7 +351,7 @@
372351
</batch_system>
373352

374353
<!-- sierra is SLURM -->
375-
<batch_system MACH="sierra">
354+
<batch_system MACH="sierra" type="slurm">
376355
<batch_directive>#MSUB</batch_directive>
377356
<directives>
378357
<directive> </directive>
@@ -431,7 +410,7 @@
431410
</batch_system>
432411

433412
<!-- titan is PBS -->
434-
<batch_system MACH="titan" version="x.y">
413+
<batch_system MACH="titan" type="pbs">
435414
<directives>
436415
<directive default="/bin/bash" > -S {{ shell }} </directive>
437416
</directives>

‎cime_config/cesm/machines/config_machines.xml‎

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -789,18 +789,17 @@
789789
<PES_PER_NODE>8</PES_PER_NODE>
790790
<PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>
791791
<mpirun mpilib="default">
792-
<executable>/usr/bin/runjob</executable>
792+
<executable>/usr/bin/runjob</executable>
793793
<arguments>
794794
<arg name="label"> --label short</arg>
795795
<!-- Ranks per node!! -->
796-
<arg name="tasks_per_node"> -p {{ tasks_per_node }}</arg>
796+
<arg name="tasks_per_node"> --ranks-per-node $PES_PER_NODE</arg>
797797
<!-- Total MPI Tasks -->
798-
<arg name="num_tasks"> -n {{ num_tasks }}</arg>
799-
<arg name="locargs"> $LOCARGS</arg>
798+
<arg name="num_tasks"> --np $TOTALPES</arg>
799+
<arg name="locargs">--block $COBALT_PARTNAME --envs OMP_WAIT_POLICY=active --envs BG_SMP_FAST_WAKEUP=yes $LOCARGS</arg>
800800
<arg name="bg_threadlayout"> --envs BG_THREADLAYOUT=1</arg>
801801
<arg name="omp_stacksize"> --envs OMP_STACKSIZE=32M</arg>
802802
<arg name="thread_count"> --envs OMP_NUM_THREADS={{ thread_count }}</arg>
803-
<arg name="colon">:</arg>
804803
</arguments>
805804
</mpirun>
806805
<module_system type="soft">

‎scripts/Tools/code_checker‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@ from CIME.utils import run_cmd, run_cmd_no_fail, expect, get_python_libs_root
1111

1212
import argparse, sys, os, doctest
1313
from multiprocessing.dummy import Pool as ThreadPool
14+
from distutils.spawn import find_executable
1415

1516
###############################################################################
1617
def parse_command_line(args, description):
@@ -49,7 +50,10 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
4950
###############################################################################
5051
def run_pylint(on_file):
5152
###############################################################################
52-
cmd = "pylint --disable I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement %s" % on_file
53+
pylint = find_executable("pylint")
54+
expect(pylint is not None,"pylint not found")
55+
56+
cmd = "%s --disable I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement %s" % (pylint, on_file)
5357
stat = run_cmd(cmd)[0]
5458
if stat != 0:
5559
sys.stdout.write("File %s has pylint problems, please fix\n Use command: %s\n" % (on_file, cmd))

‎utils/python/CIME/SystemTests/system_tests_common.py‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -202,8 +202,12 @@ def _check_for_memleak(self, cpllog):
202202
originaldate = int(memlist[0][0])
203203
finalmem = float(memlist[-1][1])
204204
originalmem = float(memlist[0][1])
205-
memdiff = (finalmem - originalmem)/originalmem
206-
if memdiff < 0.1:
205+
memdiff = -1
206+
if originalmem > 0:
207+
memdiff = (finalmem - originalmem)/originalmem
208+
if memdiff < 0:
209+
append_status("COMMENT: insuffiencient data for memleak test",sfile="TestStatus")
210+
elif memdiff < 0.1:
207211
append_status("PASS %s memleak"%(self._case.get_value("CASEBASEID")),
208212
sfile="TestStatus")
209213
else:

‎utils/python/CIME/XML/env_batch.py‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -315,6 +315,12 @@ def get_submit_args(self, case, job):
315315
for arg in submit_arg_nodes:
316316
flag = arg.get("flag")
317317
name = arg.get("name")
318+
if self.batchtype == "cobalt" and job == "case.st_archive":
319+
if flag == "-n":
320+
name = 'task_count'
321+
if flag == "--mode":
322+
continue
323+
318324
if name is None:
319325
submitargs+=" %s"%flag
320326
else:
@@ -346,16 +352,18 @@ def submit_jobs(self, case, no_batch=False, job=None):
346352
startindex = alljobs.index(job)
347353

348354
for index, job in enumerate(alljobs):
355+
logger.debug( "Index %d job %s startindex %d"%(index, job, startindex))
349356
if index < startindex:
350357
continue
351-
logger.debug( "Index %d job %s"%(index, job))
352358
try:
353359
prereq = case.get_resolved_value(self.get_value('prereq', subgroup=job))
354360
prereq = eval(prereq)
355361
except:
356362
expect(False,"Unable to evaluate prereq expression '%s' for job '%s'"%(self.get_value('prereq',subgroup=job), job))
357363
if prereq:
358364
jobs.append((job,self.get_value('dependency', subgroup=job)))
365+
if self.batchtype == "cobalt":
366+
break
359367
depid = {}
360368
for job, dependency in jobs:
361369
if dependency is not None:
@@ -379,9 +387,13 @@ def submit_jobs(self, case, no_batch=False, job=None):
379387
if slen == 0:
380388
jobid = None
381389

390+
logger.warn("job is %s"%job)
382391
depid[job] = self.submit_single_job(case, job, jobid, no_batch=no_batch)
392+
if self.batchtype == "cobalt":
393+
break
383394

384395
def submit_single_job(self, case, job, depid=None, no_batch=False):
396+
logger.warn("Submit job %s"%job)
385397
caseroot = case.get_value("CASEROOT")
386398
batch_system = self.get_value("BATCH_SYSTEM", subgroup=None)
387399
if batch_system is None or batch_system == "none" or no_batch:

‎utils/python/CIME/XML/machines.py‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -337,7 +337,10 @@ def get_full_mpirun(self, check_members, case, job):
337337
executable, args = self.get_mpirun(mpi_attribs, check_members, case, job)
338338

339339
mpi_arg_string = " ".join(args.values())
340-
340+
batch_system = self.get_value("BATCH_SYSTEM")
341+
if batch_system == "cobalt":
342+
mpi_arg_string += " : "
343+
341344
return "%s %s %s" % (executable if executable is not None else "", mpi_arg_string, default_run_suffix)
342345

343346
def print_values(self):

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