[Pw_forum] Phonon_Calculations_Error

[Ari P Seitsonen]

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.Seitsonen at 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-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Ari P Seitsonen <Ari.P.Seitsonen at 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.Seitsonen at 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
>>
>>
>>
>