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script for parallel simulation?
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TOPIC: script for parallel simulation?

script for parallel simulation? 10 years 9 months ago #12029

  • sumit
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Dear All,

I am trying to use the latest telemac version 6.3, for submitting the job on the cluster-computer I am using and adapting one of the script that came with the code.

My RunScript_queue is attached, the simulations are not getting picked up and my error file is also attached.

Finally I execute the following command of the linux-treminal

./RunScript_queue -n 12 telemac3d Wain.cas

Could someone kindly tell me what step am I missing?

Best regards,
Sumit.
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File Attachment:

File Name: hac3a435.txt
File Size: 7 KB


File Attachment:

File Name: h370ec1e.txt
File Size: 2 KB
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script for parallel simulation? 10 years 9 months ago #12080

  • yugi
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Hello,

You might wanna try using the Python environement.
Which allows to run script in queue by defining the script in the configuration file see systel-hydra.cfg for example.

Cheers,
Yugi
There are 10 types of people in the world: those who understand binary, and those who don't.
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script for parallel simulation? 10 years 9 months ago #12105

  • sumit
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Hi Yugi,

I am using runcode.py and attached here is my config file.

File Attachment:

File Name: h496f86c.txt
File Size: 2 KB


I keep on getting the following error


File Attachment:

File Name: h76c9ba0.txt
File Size: 0 KB


Even though I have sourced and put everything in the environment setting.

Any further ideas?

Thanks for all the help.

Cheers,
Sumiy
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script for parallel simulation? 10 years 9 months ago #12106

  • amyrhulbakar
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Hello,

I'm sorry if I'm wrong, but maybe you could replace #$ -S /bin/bash with #$ -S /bin/sh at line 17, as referred to the configuration of systel.cis-hydra.

Regards,
Amyrhul
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script for parallel simulation? 10 years 9 months ago #12107

  • sumit
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Hi Amyrhul,

That didn't help; moreover my shell is bash.

Still stuck :(

Cheers,
Sumit
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script for parallel simulation? 10 years 9 months ago #12113

  • yugi
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The hydra config file does not seems to be up to date for v6p3r2.
Are you using v6p3r2 or v6p3r1 ?


Here is an example of configuration i use on our cluster for v6p3r2:
[ivanoe.ifort12]
#
root:       /home/projets/systel/V6P3R2
version:    v6p3
language:   2
modules:    update system
#
options:    mpi hpc
par_cmdexec: srun -n 1 <config>/partel < PARTEL.PAR >> <partel.log>
mpi_cmdexec: mpiexec.hydra -np <ncsize> <exename>
#
hpc_stdin: #!/bin/bash
  #SBATCH --job-name=<jobname>
  #SBATCH --output=<jobname>-<time>.out
  #SBATCH --error=<jobname>-<time>.err
  #SBATCH --time=<walltime>
  #SBATCH --ntasks=<ncsize>
  #SBATCH --partition=<queue>
  ##SBATCH --exclude=cn[0000-0000,0000]
  ##SBATCH --exclusive
  srun hostname | sort > mpid.conf
  hosts=''
  for line in $(echo | cat mpid.conf)
  do
    hosts=$hosts:$line
  done
  hosts=${hosts:1:${#hosts}}
  rm -f mpitasks mpitasks.conf mpid.conf
  source $SOURCEFILE
  <py_runcode>
#
hpc_runcode: sbatch < <hpc_stdin>
#
cmd_obj:    mpif90  -c -convert big_endian -O3 -DHAVE_MPI -DHAVE_DELWAQ -DHAVE_MED -DHAVE_TECPLOT -DHAVE_DREDGESIM <mods> <incs> <f95name>
cmd_lib:    ar cru <libname> <objs>
cmd_exe:    mpif90  -O3 -o <exename> <objs> <libs>
#
mods_all:   -I <config>
#
libs_partel:      /home/projets/systel/opt/metis-5.1.0/arch/ivanoe/lib/libmetis.a
libs_all:         -L/home/projets/systel/opt/med-3.0.6/arch/ivanoe/lib -lmed
                  -L/home/projets/systel/opt/hdf5-1.8.8/arch/ivanoe/lib -lhdf5
                  -lz -lstdc++ -v
                   /home/projets/systel/LIBRARY/tecplot/tecplot_10/ivanoe_intel_openmpi_64_12/tecplot10.a

As you can see there are little differences.

It could be worth try to change those.
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