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

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chenyh1991@...
errors occur in submitting job script qsub -v .case.run --resubmit

I meet some same problems in submitting job script qsub  -v .case.run --resubmit

when i execute ./case.submit ,I get the error as follows:

Finished creating component namelists

Checking that inputdata is available as part of case submission

Loading 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 OK

submit_jobs case.run

Submit job case.run

Submitting job script qsub  -v .case.run --resubmit

ERROR: 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=<int> | dir=<path> | interval=<minutes>}... ]

      [-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:

  <batch_system type="pbs" >

    <batch_query args="">qstat</batch_query>

    <batch_submit>qsub</batch_submit>

    <batch_cancel>qdel</batch_cancel>

    <batch_redirect>-v</batch_redirect>

    <batch_directive>#PBS</batch_directive>

    <depend_string> --dependency=afterok:jobid</depend_string>

    <depend_allow_string> --dependency=afterany:jobid</depend_allow_string>

    <depend_separator>:</depend_separator>

    <queues>

      <queue walltimemax="00:59:00" nodemin="1" nodemax="624" default="true">batch</queue>

    </queues>

 

  </batch_system>

BUT i see the command :qsub -v ARGS_FOR_SCRIPTS=“--resubmit” .case.run  can  execute successfully on the Internet

I don't know where is the error exist

do you have any advice?

Any information about how to solve the problem is appreciated

jedwards

Use the command preview_run to view the qsub command being submitted.  This should indicate what the error is.

CESM Software Engineer

chenyh1991@...

when i execute ./preview_run . I get no error
here is the outcome

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  -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.

 

 

jedwards

Try removing the line <batch_redirect>-v</batch_redirect>

 

CESM Software Engineer

chenyh1991@...

As your advice, I remove the  line <batch_redirect>-v</batch_redirect>

Execute ./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 is

Checking that inputdata is available as part of case submission

Loading 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 OK

submit_jobs case.run

Submit job case.run

Submitting job script qsub  .case.run --resubmit

ERROR: Command: 'qsub  .case.run --resubmit' failed with error 'usage: qsub [-a date_time] [-A account_string] [-b secs]

      [-c [ none | { enabled | periodic | shutdown |

      depth=<int> | dir=<path> | interval=<minutes>}... ]

      [-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 confused

The batch system at this time is
  <batch_system type="pbs" >

    <batch_query args="">qstat</batch_query>

    <batch_submit>qsub</batch_submit>

    <batch_cancel>qdel</batch_cancel>

    <batch_directive>#PBS</batch_directive>

    <depend_string> --dependency=afterok:jobid</depend_string>

    <depend_allow_string> --dependency=afterany:jobid</depend_allow_string>

    <depend_separator>:</depend_separator>

    <queues>

      <queue walltimemax="00:59:00" nodemin="1" nodemax="624" default="true">batch</queue>

    </queues>

 

  </batch_system>

jedwards

I am not able to reproduce this problem.  Please try updating to the latest cime code as follows:

cd cime

git fetch origin

git checkout maint-5.6

then recreate your case and try again.

CESM Software Engineer

chenyh1991@...

I don't know where the --resubmit come from. How to set the xml files in my runcase to remove it? 

jedwards

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

CESM Software Engineer

chenyh1991@...

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

 

jedwards

Try removing all modifications to config_batch.xml and adding a the minimal

 

 

<batch_system MACH="mymach" type="pbs">

<queues>

      <queue nodemax="xxxx" nodemin="x" walltimemax="hh:mm">queuename</queue>

</queues>

</batch_system>

filling in the correct values for your system 

CESM Software Engineer

chenyh1991@...

I get the right outcome!

extremely grateful 
chenyh1991@...

dear professors

when 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.pid

You'll have to kill the Xvnc process manually

do this information tell the error come from config_batch.xml?of just from local machine?

thanks

Yuhang

jedwards

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

CESM Software Engineer

chenyh1991@...

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

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