Dear Amir,
Well, 'ph.x' did not crash, let us put it that way: I stopped because of
the time limit. The only chance I see is to either increase the time
limit, to do several restarts (but your job hardly made it anywhere and
you have 88 representations to be done - it would take a looooong time)
with the option '' or to go to a bigger machine/run on more cores.
About the redirection, I just thought about directing it to the same
file because the message coming from the MPI is at the beginning of the
file and only then comes the real output from the job. It depends on how
you run the job: Via a queueing system, directly from the command line
etc. If from the command line, then the splitting - on a Bash shell - is
done like
#> mpirun -np 4 <path-to-ph.x> -in LTA.Ph.in > LTA.Ph.out 2> LTA.Ph.err &
Greetings from Montrouge,
apsi
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935
On Fri, 15 Jan 2016, Mofrad, Amir Mehdi (MU-Student) wrote:
Thank you for your reply Ari. I'm sure that the calculation did not finish properly
because as you know it should dump a "dyn" file (which in this case should be
LTA.dyn). However, It has actually dumped LTA.dyn file but it is blank and nothing is in
there. I have not been able to do it on a larger computer so far. However, is there
anything that I can change in my for example SCF or Phono input file to be able to run
it? I really have to perform this type of calculation.
P.S. What should I do in order not to redirect stdout and stderr in the same
file? Did I really did that in my calculation?
Best regards,
Amir M. Mofrad
Graduate Research Assistant
Chemical Engineering Department
University of Missouri
________________________________________
From: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on behalf of Ari P
Seitsonen <ari.p.seitso...@iki.fi>
Sent: Friday, January 15, 2016 12:38 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] Phonon_Calculations_Error
Dear Amir,
To me it looks like if the calculation has finished normally - the
output ends with "JOB DONE.", a message
---<cut>---------------------------------------------------------
Maximum CPU time exceeded
max_seconds = 350000.00
elapsed seconds = 361758.49
---</cut>--------------------------------------------------------
means that the calculation did not manage to finish in time for your
calculation - no wonder, only four cores, 72 atoms and thus many phonon
modes to be calculated, a relatively high cut-off energy etc. Why the
output looks weird, with the "error message" at the beginning, is possibly
because you redirect the stdout and stderr into the same file? The "STOP
1" is the normal exit code of QE/pw.x when running out of CPU time.
In principle the calculation could be restarted, but indeed, like you
say, the calculation is probably slowed down because of insufficient
memory and thus swapping. Are you able to switch to a larger computer?
Greetings,
apsi
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935
On Fri, 15 Jan 2016, Mofrad, Amir Mehdi (MU-Student) wrote:
Dear all Quantum Espresso users and developers,
I have been willing to do a phonon calculation on a zeolite but I have not
been successful. It gives me the following error in output file:
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus
causing
the job to be terminated. The first process to do so was:
Process name: [[46226,1],0]
Exit code: 1
I think it has something to do with memory. I have attached both my input
and output files. Any help would be thoroughly appreciated.
Amir M. Mofrad
Graduate Research Assistant
Chemical Engineering Department
University of Missouri
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