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v8p1r0 - python 3: error running on cluster
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TOPIC: v8p1r0 - python 3: error running on cluster

v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35125

  • MohdAlaa
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Hi,

I have compiled the new release v8p1r0 on my university cluster using the python 3 option. When I run a simulation it fails and gives me the following error:

In /home/ma211/TEC3D/ReDAPT/:
mpirun --prefix /usr/lib64/openmpi -np 36 /home/ma211/TEC3D/ReDAPT/out_telemac3d


Warning: Permanently added '[node25]:34832,[10.10.10.125]:34832' (ECDSA) to the list of known hosts.
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: /home/ma211/TEC3D/ReDAPT/out_telemac3d
Node: node22

while attempting to start process rank 0.
--------------------------------------------------------------------------
36 total processes failed to start
Traceback (most recent call last):
  File "/home/ma211/telemac/v8p1//scripts/python3/telemac3d.py", line 7, in <module>
    main('telemac3d')
  File "/home/ma211/telemac/v8p1/scripts/python3/runcode.py", line 272, in main
    run_study(cas_file, code_name, options)
  File "/home/ma211/telemac/v8p1/scripts/python3/execution/run_cas.py", line 157, in run_study
    run_local_cas(my_study, options)
  File "/home/ma211/telemac/v8p1/scripts/python3/execution/run_cas.py", line 65, in run_local_cas
    my_study.run(options)
  File "/home/ma211/telemac/v8p1/scripts/python3/execution/study.py", line 610, in run
    self.run_local()
  File "/home/ma211/telemac/v8p1/scripts/python3/execution/study.py", line 445, in run_local
    run_code(self.run_cmd, self.sortie_file)
  File "/home/ma211/telemac/v8p1/scripts/python3/execution/run.py", line 182, in run_code
    raise TelemacException('Fail to run\n'+exe)
utils.exceptions.TelemacException: Fail to run
mpirun --prefix /usr/lib64/openmpi -np 36 /home/ma211/TEC3D/ReDAPT/out_telemac3d

When I re-compile it using python 2.75 it works fine.

Any thoughts on what could be the problem?

I've noticed when I compile using python 3, when I run the simulation it shows the trunk version. When I use python 2.7 is shows v8p1r0

Thanks,

Mohammed
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35133

  • yugi
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Hi,

Could you post your configuration file ?

As for the version it is taking the one from your configuration file.
If you have not put any it will say trunk.
There are 10 types of people in the world: those who understand binary, and those who don't.
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35138

  • MohdAlaa
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Hi,

Here is my config file. It is the same one I used for both Python 2.7 and Python 3. The only difference is in pysource I update the root to the relevant Python version.

Thanks,
Mohammed


File Attachment:

File Name: systel.gfort_2020-01-02.cfg
File Size: 2 KB
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35139

  • MohdAlaa
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Couldn't upload the pysource.sh

Here is the text:

# This file is a template for a Linux environment file
# running "source pysource.template.sh" will position all
# the necessary environment variables for telemac
# To adapt to your installation replace word <word> by their local value
###
### TELEMAC settings
###
# Path to telemac root dir
export HOMETEL=/home/ma211/telemac/v8p1/
# Adding python scripts to PATH
export PATH=$HOMETEL/scripts/python27:.:$PATH
# Configuration file
export SYSTELCFG=$HOMETEL/configs/systel.gfort.cfg
# Name of the configuration to use
export USETELCFG=gfortranHPC
# Path to this file
export SOURCEFILE=$HOMETEL/configs/pysource.sh
### Python
# To force python to flush its output
export PYTHONUNBUFFERED='true'
### API
export PYTHONPATH=$HOMETEL/scripts/python27:$PYTHONPATH
export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$PYTHONPATH
###
### COMPILERS
###
# Here are a few examples for external libraries
#export SYSTEL=/data/projets/projets.002/systel.002

### MPI
#export MPIHOME=$SYSTEL/LIBRARY/mpi/ifort.10.1.008
#export PATH=$MPIHOME/bin:$PATH
#export LD_LIBRARY_PATH=$MPIHOME/lib:$LD_LIBRARY_PATH
###
### EXTERNAL LIBRARIES
###
### HDF5
#export HDF5HOME=$SYSTEL/LIBRARY/hdf5-1.8.14/arch/C9
#export LD_LIBRARY_PATH=$HDF5HOME/lib:$LD_LIBRARY_PATH
#export LD_RUN_PATH=$HDF5HOME/lib:$MEDHOME/lib:$LD_RUN_PATH
### MED
#export MEDHOME=$SYSTEL/LIBRARY/med-3.2.0/arch/C9
#export LD_LIBRARY_PATH=$MEDHOME/lib:$LD_LIBRARY_PATH
#export PATH=$MEDHOME/bin:$PATH
### MUMPS
#export MUMPSHOME=$SYSTEL/LIBRARY/mumps/gnu
#export SCALAPACKHOME=$SYSTEL/LIBRARY/scalapack/gnu
#export BLACSHOME=$SYSTEL/LIBRARY/blacs/gnu
### METIS
#export METISHOME=$SYSTEL/LIBRARY/metis-5.1.0/arch/C9
#export LD_LIBRARY_PATH=$METISHOME/lib:$LD_LIBRARY_PATH
export METISHOME=$HOMETEL/optionals/metis-5.1.0/build/Linux-x86_64/libmetis/
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35141

  • yugi
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This is weird indeed.
When in Python 3 does it work if you manually run the command (mpirun ...) in the temporary folder ?
There are 10 types of people in the world: those who understand binary, and those who don't.
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35142

  • MohdAlaa
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I'm not sure if I can run it manually. I need to submit a job script to the cluster (qsub) in order to run things on it.
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35173

  • yugi
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How exactly are you submitting your jobs ? (what command)
There are 10 types of people in the world: those who understand binary, and those who don't.
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35174

  • MohdAlaa
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I submit the following jobscript:
#$ -S /bin/bash
#$ -pe mpi 36
#$ -l intel=true
#$ -j y
#$ -o /home/ma211/TEC3D/
#$ -N telemac3D36
#$ -V
#$ -R y

###module load mpi
module add mpi

###module load anaconda
source activate mypython
source /home/ma211/telemac/v8p1/configs/pysource.sh

#echo Start: 'date'
echo "Start: " $(date)

cd /home/ma211/TEC3D/
#./telemac3d.py NScot.cas --ncsize=36
telemac3d.py -w /home/ma211/TEC3D/ReDAPT/ --split --ncsize 36 NScot.cas
telemac3d.py -w /home/ma211/TEC3D/ReDAPT/ --run --ncsize 36 NScot.cas
telemac3d.py -w /home/ma211/TEC3D/ReDAPT/ --merge --ncsize 36 NScot.cas

echo "End: " $(date)
#echo "End: " 'date'

source deactivate mypython
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35175

  • yugi
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OK could you try the following things:
- Check if you have some listings in your temporary folder (PE*.log)
- If not run with aaddin -s to the telemac command

If this gives you nothing replace your telemac commands by:
cd /home/ma211/TEC3D/ReDAPT/
mpirun mpirun --prefix /usr/lib64/openmpi -np 36 /home/ma211/TEC3D/ReDAPT/out_telemac3d
There are 10 types of people in the world: those who understand binary, and those who don't.
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v8p1r0 - python 3: error running on cluster 4 years 10 months ago #35176

  • MohdAlaa
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Ok, I will try that and let you know how it goes. But I suspect that there is something wrong happens during the compilation, because when I run it, it shows trunk version although I'm using the same config file which I used for Python2.7. For python2.7 it shows the correct version as mentioned previously.
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v8p1r0 - python 3: error running on cluster

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