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parallel computation with PBS error

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Old   July 3, 2014, 09:51
Default parallel computation with PBS error
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Tansu
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Hello everyone,
i am new with SU2 and trying to do tutorials. But i can't do the parallel computation with PBS.
i got an error when i wanted to submit PBS file using qsub command.Interior of the PBS file is as follows:

Quote:
#!/bin/bash

# Specify time limit of your job. (HH:MM:SS)
#PBS -l walltime=02:00:00
# Specify the number of CPU cores/parallel processes you need
#PBS -l procs=4

# mail alert at the (e)nd of execution
#PBS -m e
#PBS -M mail@ae.metu.edu.tr
# Give your job a name so it can be found readily with qstat.
#PBS -N name

# standard error output merge to the standard output file.
#PBS -j oe
# Specify the file name for the standard output/error
#PBS -o output
#PBS -e error

# Enter your work directory under /cfd
cd working_directory

# Execute your parallel program
/opt/SU2/bin/parallel_computation.py -f inv_ONERAM6_JST.cfg -n 4
And the error is:

Quote:
Traceback (most recent call last):
File "/opt/SU2/bin/parallel_computation.py", line 26, in <module>
import SU2
File "/opt/SU2/bin/SU2/__init__.py", line 3, in <module>
from . import run
File "/opt/SU2/bin/SU2/run/__init__.py", line 3, in <module>
from interface import \
File "/opt/SU2/bin/SU2/run/interface.py", line 28, in <module>
from ..io import Config
File "/opt/SU2/bin/SU2/io/__init__.py", line 3, in <module>
from tools import *
File "/opt/SU2/bin/SU2/io/tools.py", line 30, in <module>
from SU2.util import ordered_bunch
File "/opt/SU2/bin/SU2/util/__init__.py", line 5, in <module>
from lhc_unif import lhc_unif
File "/opt/SU2/bin/SU2/util/lhc_unif.py", line 1, in <module>
import numpy as np
ImportError: No module named numpy

On the other hand when i run the python script on command line as follows:

/opt/SU2/bin/parallel_computation.py -f inv_ONERAM6_JST.cfg -n 4

it works and creates all of results correctly.

i added paths SU2_RUN and SU2_HOME to my .bashrc
i don't know how to apply the python script (parallel_computation.py) in PBS.
Any help will be greatly appreciated.

Thanks in advance
Tansu
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Old   July 3, 2014, 10:24
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Jianming Liu
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Quote:
Originally Posted by tsevine View Post
Hello everyone,
i am new with SU2 and trying to do tutorials. But i can't do the parallel computation with PBS.
i got an error when i wanted to submit PBS file using qsub command.Interior of the PBS file is as follows:



And the error is:




On the other hand when i run the python script on command line as follows:

/opt/SU2/bin/parallel_computation.py -f inv_ONERAM6_JST.cfg -n 4

it works and creates all of results correctly.

i added paths SU2_RUN and SU2_HOME to my .bashrc
i don't know how to apply the python script (parallel_computation.py) in PBS.
Any help will be greatly appreciated.

Thanks in advance
Tansu
You should install some soft to make python run in parallel computation. In my case, I don't use parallel_computation script to run. I use following script as the PBS task

#
############################################
#PBS -l nodes=1: ppn=8

#Request hours of walltime
#
#PBS -l walltime=360:00:00
#
#PBS -j oe
#PBS -o BXdW.log
#PBS -N BXdW
#
#
cd /home/vela/jamesliu/DW
echo " "
echo " "
echo "Job started at `date`"
/opt/sgi/mpt/mpt-2.07/bin/mpirun -np 8 SU2_PRT turb_DW1.cfg
/opt/sgi/mpt/mpt-2.07/bin/mpirun -np 8 SU2_CFD turb_DW1.cfg
/opt/sgi/mpt/mpt-2.07/bin/mpirun -np 8 SU2_SOL turb_DW1.cfg
echo " "
echo "Job Ended at `date`"
echo " "
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Old   July 3, 2014, 11:59
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Tansu
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thank you very much Liu

it seems it worked
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Old   July 3, 2014, 16:59
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Jianming Liu
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Quote:
Originally Posted by tsevine View Post
thank you very much Liu

it seems it worked
If you want to SU2_SOL to post-process the solution, you should make sure the name of Restart flow input file is same with the name of Output file restart flow. You can try several times, then you can understand.
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Old   July 4, 2014, 06:21
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Tansu
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Quote:
Originally Posted by liujmljm View Post
If you want to SU2_SOL to post-process the solution, you should make sure the name of Restart flow input file is same with the name of Output file restart flow. You can try several times, then you can understand.
Thank you again. it is working
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