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errors occur in submitting job script qsub -v .case.run --resubmit

C

chenyh1991@126_com

New Member
I meet some same problems in submitting job script qsub  -v .case.run --resubmitwhen i execute ./case.submit ,I get the error as follows:Finished creating component namelistsChecking that inputdata is available as part of case submissionLoading input file list: 'Buildconf/rtm.input_data_list'Loading input file list: 'Buildconf/cam.input_data_list'Loading input file list: 'Buildconf/cice.input_data_list'Loading input file list: 'Buildconf/pop.input_data_list'Loading input file list: 'Buildconf/clm.input_data_list'Loading input file list: 'Buildconf/cpl.input_data_list'Check case OKsubmit_jobs case.runSubmit job case.runSubmitting job script qsub  -v .case.run --resubmitERROR: Command: 'qsub  -v .case.run --resubmit' failed with error 'usage: qsub [-a date_time] [-A account_string] [-b secs]      [-c [ none | { enabled | periodic | shutdown |      depth= | dir= | interval=}... ]      [-C directive_prefix] [-d path] [-D path]      [-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m n|{abe}]      [-M user_list] [-N jobname] [-o path] [-p priority] [-P proxy_user] [-q queue]       [-r y|n] [-S path] [-t number_to_submit] [-T type]  [-u user_list] [-w] path      [-W additional_attributes] [-v variable_list] [-V ] [-x] [-X] [-z] [script]' from dir 

when i don't use pbs batch system submit my case. It run properly. Here is the batch system set:      qstat    qsub    qdel    -v    #PBS    --dependency=afterok:jobid    --dependency=afterany:jobid    :          batch       BUT i see the command ：qsub -v ARGS_FOR_SCRIPTS=“--resubmit” .case.run  can  execute successfully on the InternetI don't know where is the error existdo you have any advice？Any information about how to solve the problem is appreciated
 
J

jedwards

CSEG and Liaisons
Staff member
Use the command preview_run to view the qsub command being submitted.  This should indicate what the error is.
 
C

chenyh1991@126_com

New Member
when i execute ./preview_run . I get no error
here is the outcomeCASE INFO:  nodes: 9  total tasks: 72  tasks per node: 8  thread count: 1 BATCH INFO:  FOR JOB: case.run    ENV:      Setting Environment NETCDF_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment NETCDF_C_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment NETCDF_FORTRAN_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment mpi_PATH=/public/CESM/LIBRARIES/mpich      Setting Environment LAPACK_LIBDIR=/public/CESM/LIBRARIES/lapack-3.8.0    SUBMIT CMD:      qsub  -v .case.run --resubmit   FOR JOB: case.st_archive    ENV:      Setting Environment NETCDF_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment NETCDF_C_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment NETCDF_FORTRAN_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment mpi_PATH=/public/CESM/LIBRARIES/mpich      Setting Environment LAPACK_LIBDIR=/public/CESM/LIBRARIES/lapack-3.8.0    SUBMIT CMD:      qsub --dependency=afterok:0 -v case.st_archive --resubmit MPIRUN:   mpirun  -np 72 -prepend-rank /public/CESM/run/projects/ctrl/bld/cesm.exe  >> cesm.log.$LID 2>&1 So i just execute ./case.submit. BUT it get error.  I really don't know where the error come from.  
 
C

chenyh1991@126_com

New Member
As your advice, I remove the  line -vExecute ./preview.run     the outcome with no error exit is CASE INFO:  nodes: 9  total tasks: 72  tasks per node: 8  thread count: 1 BATCH INFO:  FOR JOB: case.run    ENV:      Setting Environment NETCDF_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment NETCDF_C_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment NETCDF_FORTRAN_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment mpi_PATH=/public/CESM/LIBRARIES/mpich      Setting Environment LAPACK_LIBDIR=/public/CESM/LIBRARIES/lapack-3.8.0    SUBMIT CMD:      qsub  .case.run --resubmit   FOR JOB: case.st_archive    ENV:      Setting Environment NETCDF_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment NETCDF_C_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment NETCDF_FORTRAN_PATH=/public/CESM/LIBRARIES/netcdf      Setting Environment mpi_PATH=/public/CESM/LIBRARIES/mpich      Setting Environment LAPACK_LIBDIR=/public/CESM/LIBRARIES/lapack-3.8.0    SUBMIT CMD:      qsub --dependency=afterok:0 case.st_archive --resubmit MPIRUN:  mpirun  -np 72 -prepend-rank /public/CESM/run/projects/ctrl/bld/cesm.exe  >> cesm.log.$LID 2>&1 when execute ./case.submit, the outcome isChecking that inputdata is available as part of case submissionLoading input file list: 'Buildconf/rtm.input_data_list'Loading input file list: 'Buildconf/cam.input_data_list'Loading input file list: 'Buildconf/cice.input_data_list'Loading input file list: 'Buildconf/pop.input_data_list'Loading input file list: 'Buildconf/clm.input_data_list'Loading input file list: 'Buildconf/cpl.input_data_list'Check case OKsubmit_jobs case.runSubmit job case.runSubmitting job script qsub  .case.run --resubmitERROR: Command: 'qsub  .case.run --resubmit' failed with error 'usage: qsub [-a date_time] [-A account_string] [-b secs]      [-c [ none | { enabled | periodic | shutdown |      depth= | dir= | interval=}... ]      [-C directive_prefix] [-d path] [-D path]      [-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m n|{abe}]      [-M user_list] [-N jobname] [-o path] [-p priority] [-P proxy_user] [-q queue]       [-r y|n] [-S path] [-t number_to_submit] [-T type]  [-u user_list] [-w] path      [-W additional_attributes] [-v variable_list] [-V ] [-x] [-X] [-z] [script]' from dir '/public/CESM/cesm/cime/scripts/ctrl'
I think the –resubmit at the end of commad(qsub  .case.run --resubmit) is not proper. Because when I independently run the command qsub .case.run(I know it is not right for the cesm.exe), I get no error about qsub usage.  And also, When I run ./case.submit with no batch system, I can get the proper nc outcome data, it mean the cesm2.0.0 folder I download from internet is ok. So I am confusedThe batch system at this time is
      qstat    qsub    qdel    #PBS    --dependency=afterok:jobid    --dependency=afterany:jobid    :          batch      
 
J

jedwards

CSEG and Liaisons
Staff member
I am not able to reproduce this problem.  Please try updating to the latest cime code as follows:cd cimegit fetch origingit checkout maint-5.6then recreate your case and try again.
 
J

jedwards

CSEG and Liaisons
Staff member
You don't want to remove the resubmit, you need it.   But you should have an argument preceeding it:  qsub -q regular -l walltime=12:00:00 -v ARGS_FOR_SCRIPT='--resubmit' .case.run
 
C

chenyh1991@126_com

New Member
BUt no matter how i set the xml files in my run case ，the --resubmit command  aways exits. So I don’t know how to get the command like this qsub -q regular -l walltime=12:00:00 -v ARGS_FOR_SCRIPT='--resubmit' .case.run  could you give some other detail set steps to the formation of this command？That may be very helpful for me. thanks a lot 
 
J

jedwards

CSEG and Liaisons
Staff member
Try removing all modifications to config_batch.xml and adding a the minimal        queuenamefilling in the correct values for your system 
 
C

chenyh1991@126_com

New Member
dear professorswhen i execute ./case.submit, I get an error mention that  File "/opt/tsce4/torque6/share/n091/mom_priv/jobs/67.cloud1.SC", line 35    parser = argparse.ArgumentParser(description=description,         ^IndentationError: expected an indented block Can't find file /public/ceh/.vnc/cloud1:68.pidYou'll have to kill the Xvnc process manuallydo this information tell the error come from config_batch.xml？of just from local machine？thanksYuhang
 
J

jedwards

CSEG and Liaisons
Staff member
Did you edit the file cime/config/cesm/machines/template.case.run?  Try removing any local changes you've made to that file.
 
C

chenyh1991@126_com

New Member
i have do nothing with cime/config/cesm/machines/template.case.run.  i can't achieve the qsub . I submit the command. the system allocate the job number. then it failed
 
E

evanbung

evanbung
New Member
chenyh1991@126_com said:
^IndentationError: expected an indented block Can't find file /public/ceh/.vnc/cloud1:68
Click to expand...

Putting in an extra space or leaving one out where it is needed will surely generate an error message . Some common causes of this error include:

  • Forgetting to indent the statements within a compound statement
  • Forgetting to indent the statements of a user-defined function.

The error message IndentationError: expected an indented block would seem to indicate that you have an indentation error. It is probably caused by a mix of tabs and spaces. The indentation can be any consistent white space . It is recommended to use 4 spaces for indentation in Python, tabulation or a different number of spaces may work, but it is also known to cause trouble at times. Tabs are a bad idea because they may create different amount if spacing in different editors .
 
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