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case submit problem.

joshua

Hyunggyu, Song
New Member
Deal all.

Hi there! I am the new of CESM!

After ./case.build, I got

Building case in directory /home/joshua/my_cesm_sandbox/cime/scripts/cesm2_test5
sharedlib_only is False
model_only is False
Setting resource.RLIMIT_STACK to -1 from (-1, -1)
Generating component namelists as part of build
Creating component namelists
Calling /home/joshua/my_cesm_sandbox/components/cam//cime_config/buildnml
...calling cam buildcpp to set build time options
CAM namelist copy: file1 /home/joshua/my_cesm_sandbox/cime/scripts/cesm2_test5/Buildconf/camconf/atm_in file2 /home/joshua/cime/cesm2_test5/run/atm_in
Calling /home/joshua/my_cesm_sandbox/components/clm//cime_config/buildnml
Calling /home/joshua/my_cesm_sandbox/components/cice//cime_config/buildnml
...calling cice buildcpp to set build time options
Calling /home/joshua/my_cesm_sandbox/components/pop//cime_config/buildnml
...calling pop buildcpp to set build time options
Log4perl: Seems like no initialization happened. Forgot to call init()?
Calling /home/joshua/my_cesm_sandbox/components/mosart//cime_config/buildnml
Running /home/joshua/my_cesm_sandbox/components/cism//cime_config/buildnml
Log4perl: Seems like no initialization happened. Forgot to call init()?
Calling /home/joshua/my_cesm_sandbox/components/ww3//cime_config/buildnml
Calling /home/joshua/my_cesm_sandbox/cime/src/components/stub_comps/sesp/cime_config/buildnml
Calling /home/joshua/my_cesm_sandbox/cime/src/drivers/mct/cime_config/buildnml
Finished creating component namelists
Building gptl with output to file /home/joshua/cime/cesm2_test5/bld/gptl.bldlog.210607-112655
Calling /home/joshua/my_cesm_sandbox/cime/src/build_scripts/buildlib.gptl
Building mct with output to file /home/joshua/cime/cesm2_test5/bld/mct.bldlog.210607-112655
Calling /home/joshua/my_cesm_sandbox/cime/src/build_scripts/buildlib.mct
Building pio with output to file /home/joshua/cime/cesm2_test5/bld/pio.bldlog.210607-112655
Calling /home/joshua/my_cesm_sandbox/cime/src/build_scripts/buildlib.pio
Building csm_share with output to file /home/joshua/cime/cesm2_test5/bld/csm_share.bldlog.210607-112655
Calling /home/joshua/my_cesm_sandbox/cime/src/build_scripts/buildlib.csm_share
- Building clm4_5/clm5_0 Library
Building lnd with output to /home/joshua/cime/cesm2_test5/bld/lnd.bldlog.210607-112655
clm built in 0.806640 seconds
Building atm with output to /home/joshua/cime/cesm2_test5/bld/atm.bldlog.210607-112655
Building ice with output to /home/joshua/cime/cesm2_test5/bld/ice.bldlog.210607-112655
Building ocn with output to /home/joshua/cime/cesm2_test5/bld/ocn.bldlog.210607-112655
Building rof with output to /home/joshua/cime/cesm2_test5/bld/rof.bldlog.210607-112655
Building glc with output to /home/joshua/cime/cesm2_test5/bld/glc.bldlog.210607-112655
Building wav with output to /home/joshua/cime/cesm2_test5/bld/wav.bldlog.210607-112655
Building esp with output to /home/joshua/cime/cesm2_test5/bld/esp.bldlog.210607-112655
cice built in 0.833375 seconds
mosart built in 0.883082 seconds
pop built in 0.884339 seconds
cam built in 0.917406 seconds
sesp built in 1.432697 seconds
ww built in 2.636572 seconds
cism built in 2.637302 seconds
Building cesm with output to /home/joshua/cime/cesm2_test5/bld/cesm.bldlog.210607-112655
Time spent not building: 2.866303 sec
Time spent building: 6.564330 sec
MODEL BUILD HAS FINISHED SUCCESSFULLY

It made me very happy since I started to see something fun...But It went wrong after I ./case.submit

Job id Name User Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
1140.a001 cesm2_test5.run joshua 0 Q all
1141.a001 cesm2_test5.st_* joshua 0 H all

It looks like halted...no job goes in my cluster after I did this...

Does anyone have some idea about this?

Really appreciate it!
 

katec

CSEG and Liaisons
Staff member
Hi there, so the copied qstat command you have there shows that your job (cesm2_test5.run) was submitted to the cluster queue and is waiting for its turn to run. The "Q" status means "queued" or waiting in line. Most large machines use a queuing system to organize when a job gets to use the machine resources, and it can take a long period of waiting before your job gets to go. The second job in your qstat command (cesm2_test5.st_*) is the short-term archiving script that waits until the first job is finished and then copies over your output to the archive location. The "H" status means "hold" or "wait for the other job to finish before starting."

If you think there is another problem, it would be helpful if you could look at your log or output files for errors and then let us know what they are.
 

joshua

Hyunggyu, Song
New Member
Hi there, so the copied qstat command you have there shows that your job (cesm2_test5.run) was submitted to the cluster queue and is waiting for its turn to run. The "Q" status means "queued" or waiting in line. Most large machines use a queuing system to organize when a job gets to use the machine resources, and it can take a long period of waiting before your job gets to go. The second job in your qstat command (cesm2_test5.st_*) is the short-term archiving script that waits until the first job is finished and then copies over your output to the archive location. The "H" status means "hold" or "wait for the other job to finish before starting."

If you think there is another problem, it would be helpful if you could look at your log or output files for errors and then let us know what they are.
Thanks for reply.

I looked at the 'CaseStatus' and it says,

2021-06-08 00:32:42: case.setup starting
---------------------------------------------------
2021-06-08 00:32:43: case.setup success
---------------------------------------------------
2021-06-08 00:32:57: case.build starting
---------------------------------------------------
2021-06-08 00:34:36: case.build success
---------------------------------------------------
2021-06-08 00:35:02: case.submit starting
---------------------------------------------------
2021-06-08 00:35:05: case.submit success case.run:1146.a001, case.st_archive:1147.a001
---------------------------------------------------

and still nothing happens on my cluster when I check the 'htop'..
 

katec

CSEG and Liaisons
Staff member
When you say "nothing happens" does that mean that the job sits with the "Q" status until you delete the job? How long do you wait for the job with the Q status? Can you go to your run directory and attach the CESM.log.* file?
 
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