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parallel ReconstructPar with mpi?

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Old   April 16, 2013, 02:56
Default parallel ReconstructPar with mpi?
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Pj.
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Luca
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Hi everybody.

I'm running a quite big case on a supercomputer. The case runs pretty fast, but now i'm stucked in a bottle-neck: reconstructPar.

I need to reconstruct about 900 timesteps with 3.7 milion cells. With serial computing this takes more times that the solution!

I found a this topic that should help in my situation. But i can't understand how to use it with MPIRUN and PBS.

Can someone help me please?

Thank you very much
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Old   April 16, 2013, 04:19
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Hello Luca,

If you are asking about how to run a script in batch mode, I think this would work

#PBS -N Jobname
#PBS -l walltime=02:00:00
#PBS -l nodes=1 : ppn=1
#PBS -o $PBS_JOBNAME.log

cd $PBS_O_WORKDIR
./scriptname

The "scriptname" should be the script you should use from that thread you posted. Make sure its in your working directory. BEfore you submit the job I recommend testing if the script runs in your home directory directly. If it runs there, it should do so in batch mode as well.
I have used the above for the .exe files I had created - So I guess this should work for a script/any executable file too.

Let me know.

Regards

Atm
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Old   April 16, 2013, 04:27
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Hi Luca,

do you really need to reconstruct the case? I don't know if you are aware that most of the decomposed cases can be postprocessed while still being decomposed. If the issue is that you cannot open it with paraview try: "paraFoam -builtin". Having 3.7 million cells is not such a huge case to impede paraview from loading it at once ;-)

Regarding the reconstructPar question, you can see it from a simpler point of view, it only runs in serial, but you can send any simulataneous number of processes to shorten the time. For example, if you send 2 processes the wait time will become more or less a half. You can easily do this with the -time instruction:

Code:
reconstructPar -time '0:450'
reconstructPar -time '451:900'
If you run each command as a separate process you will obtain your reconstructed case earlier.

Best,

Pablo
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Old   April 16, 2013, 04:27
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Hi Atm,

I'm sorry but that's not my problem. I already know how to run scripts in batch mode.

What i'm asking is how to reconstruct big cases with more than one CPU.

I found a script wrote by a user but i don't understand how to run it. Since that thread was 3 years old i started a new one. I'm not experienced enough to write a batch script to automatize it by my own.

Is there any solution? Is it possible that i can run a case with 1200 CPU and then i have to reconstruct it with only 1?

My situation right know is that i need 4h to run a case, and then i take 1 day to reconstruct it. Quite silly...
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Old   April 16, 2013, 04:31
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Thanks Pablo,

No: i didn't know i could run paraView on a decomposed case. How can i do it? I haven't seen nothing pointing in that direction neither on the User Guide, now typing paraFoam -help in the bash. Can you please explain me how to do it or just give me a link?

Thank you very much
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Old   April 16, 2013, 04:33
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paraFoam -builtin

;-)
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Old   April 16, 2013, 08:08
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As soon as i'll be back to work i'll check this.

Thank you very much
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