Re: Error files when using multicore runs and psn ==> Fatal Error: Record SIZES is not valid
Hi Pascal
According to the documentation PsN 3.4.8 and later supports $SIZES.
http://psn.sourceforge.net/pdfdocs/PsN_and_NONMEM7.pdf
We are running version 3.5.3 and that works fine.
Regards
Julia
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Quoted reply history
On Fri, Jul 13, 2012 at 3:42 AM, <[email protected]> wrote:
> Hi Nastya,
>
> You were right : it is my psn installation that refuses to see something
> else than $PROB as first line as I just checked by running it directly from
> nmfe72 ....
>
> You cannot stop the progress!
>
> Thanks again and Kind regards
>
> Pascal
>
>
>
> From: "Kassir Nastya" <[email protected]>
> To: <[email protected]>, "Bauer, Robert" <
> [email protected]>, <[email protected]>
> Date: 12/07/2012 17:25
> Subject: RE: [NMusers] Error files when using multicore runs and
> psn ==> Fatal Error: Record SIZES is not valid
> ------------------------------
>
>
>
> Hi Pascal,
>
> I have already used it with NONMEM 72 and it works, but not in psn.
>
> $SIZES LIM6=1000
> $PROBLEM XXXXXX
>
> Best regards,
>
> Nastya
>
>
> ________________________________
>
> From: [email protected]
> [mailto:[email protected]<[email protected]>
> ]
> Sent: Thu 7/12/2012 11:09
> To: Kassir Nastya; Bauer, Robert; [email protected]
> Subject: RE: [NMusers] Error files when using multicore runs and psn ==>
> Fatal Error: Record SIZES is not valid
>
>
> Hi Nastia,
>
> I tried your trick which would have broken the first table law rule "The
> first NM-TRAN control record must be a $PROBLEM record" and put $SIZES as
> very first record and got following error:
>
> >_read_problems: First non-comment line in modelfile run.mod is not a
> $PROB record. NONMEM syntax violation.
>
> So the first table law rule still resists or you may have a different
> NONMEM version. :-)
>
> I also checked the bug list
> ftp://nonmem.iconplc.com/Public/nonmem720/nm720_bug_list.pdf <
> ftp://nonmem.iconplc.com/Public/nonmem720/nm720_bug_list.pdf> , but
> nothing is mentioned.
>
> Anyway, thanks for the suggestion!
>
> Kind regards
>
> Pascal
>
>
>
>
> From: "Kassir Nastya" <[email protected]>
> To: <[email protected]>, "Bauer, Robert" <
> [email protected]>
> Date: 12/07/2012 16:13
> Subject: RE: [NMusers] Error files when using multicore runs and
> psn ==> Fatal Error: Record SIZES is not valid
>
> ________________________________
>
>
>
>
> Hi Pascal,
>
> $SIZES goes at the begginning of your control stream, before $PROB.
>
> I hope it helps.
>
> Best regards,
>
> Nastya
>
>
> Nastya Kassir, Pharm.D.
>
> Senior Scientist
>
> Pharsight Consulting Services(tm)
> A division of Certara(tm)
> Email: [email protected]
> <mailto:[email protected]<[email protected]><
> mailto:[email protected] <[email protected]>> >
>
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> Mobile: 1 (438) 862-0935
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>
>
>
> ________________________________
>
> From: [email protected] on behalf of
> [email protected]
> Sent: Thu 7/12/2012 09:21
> To: Bauer, Robert
> Cc: [email protected]; "[email protected]"@merck.de;
> "[email protected]"@merck.de;
> [email protected]
> Subject: RE: [NMusers] Error files when using multicore runs and psn ==>
> Fatal Error: Record SIZES is not valid
>
>
> Hi Robert,
>
> Thanks for your quick reply. Unfortunately, I could not make it work.
>
> I have 17,000 records. So just after $PROB. I inserted your suggestion:
> $SIZES LIM1 = 20000
> and I got the following error :
> > Fatal Error: Record SIZES is not valid
>
> So I tried also the default value for LIM1:
> $SIZES LIM1=10000
> and also the example given on page 166 of Help guide viii
> $SIZES LIM1=30000 MAXFCN=2000000 NO=500
> and always got the "Fatal Error: Record SIZES is not valid" message.
>
> I looked into Help guide viii (pp 166-167 and 463-464) but did not find
> any relevant information how to set $SIZES. What would be your suggestion?
>
> Thanks again for your help, because it's highly frustrating not being able
> to use the multi-cores when you have such long runs.
>
> Kind regards
>
> Pascal Girard, PhD
> [email protected]
> Head of Modeling & Simulation - Oncology
> Global Exploratory Medicine
> Merck Serono S.A. · Geneva
> Tel: +41.22.414.3549
> Cell: +41.79.508.7898
>
>
>
>
> From: "Bauer, Robert" <[email protected]>
> To: "[email protected]" <[email protected]>,
> "[email protected]" <[email protected]>
> Cc: "[email protected]" <
> [email protected]>, "[email protected]"
> <[email protected]>
> Date: 11/07/2012 18:55
> Subject: RE: [NMusers] Error files when using multicore runs and
> psn
> Sent by: [email protected]
>
> ________________________________
>
>
>
>
> Pascal:
> I cannot help regarding having all console messages sent to the proper
> files in the PSN environment, but I can assist in avoiding your present
> NONMEM error. If you insert at the beginning of the control stream file
> $SIZES LIM1=??
> and insert a large enough value for ??, then file buffer 10 will not be
> used, and the error is avoided. The value should be at least as large as
> the number of data records (lines) in your data file (see section I.6 of
> ..\guides\nm720.pdf).
>
> Although nmfe72 in parallel mode has been tested successfully in our hands
> to use the file buffers for large data sets, it may not work in all grid
> environments. Setting the LIM values large enough avoids using buffer
> files, and utilizes only memory. The problem also runs faster when buffer
> files are not used.
>
>
> Robert J. Bauer, Ph.D.
>
> Vice President, Pharmacometrics, R&D
>
> ICON Development Solutions
>
> 7740 Milestone Parkway
>
> Suite 150
>
> Hanover, MD 21076
>
> Tel: (215) 616-6428
>
> Mob: (925) 286-0769
>
> Email: [email protected]
>
> Web: www.iconplc.com http://www.iconplc.com/ http://www.iconplc.com/
>
>
>
>
>
> ________________________________
>
> From: [email protected]
> [mailto:[email protected]<[email protected]><
> mailto:[email protected] <[email protected]>> <
> mailto:[email protected] <[email protected]> <
> mailto:[email protected] <[email protected]>> > ]
> On Behalf Of [email protected]
> Sent: Wednesday, July 11, 2012 11:19 AM
> To: [email protected]
> Cc: [email protected];
> [email protected]
> Subject: [NMusers] Error files when using multicore runs and psn
>
> Dear All,
>
> We are using psn version: 3.4.2 together with NONMEM 7.2.0 on a Linux Sun
> Grid Engine (SGE). When using multi-cores run on SGE, it happens sometimes
> that NONMEM returns a log file where the "MONITORING OF SEARCH" starts and
> nothing is reported.
>
> Looking into the psn directory, I found files which have the name of my
> script file + an extension made of letters and numbers that contains an
> error message that is not shown on the log file. For example my nm-tran
> script file is run003.mod and my log file run003.lst ends with:
>
> MONITORING OF SEARCH:
>
> Stop Time:
> Wed Jul 10 21:05:18 CEST 2012
>
> Then I recover a file named run003.mod.o9501 in run003/NM_run1 directory
> created by psn. Sometimes this file contains an explicit error message,
> sometimes more cabalistic information as:
> WARNINGS AND ERRORS (IF ANY) FOR PROBLEM 1
>
> (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
> CREATING MUMODEL ROUTINE...
> Recompiling certain components
>
> USING PARALLEL PROFILE mpi_12cores.pnm
> MPI TRANSFER TYPE SELECTED
> Exit status = 1
> IN MPI
> Starting MPI version of nonmem execution ...
> License Registered to: Merck KGaA
> Expiration Date: 14 SEP 2013
> Current Date: 11 JUL 2012
> Days until program expires : 428
>
>
> Iterative Two Stage (No Prior)
> MONITORING OF SEARCH:
>
> At line 240 of file (unit = 10, file = 'WK1_FILE10')
> Fortran runtime error: End of file
> Fatal error in MPI_Send: Other MPI error, error stack:
> MPI_Send(174).....................: MPI_Send(buf=0xde71a0, count=80030,
> MPI_INTEGER, dest=1, tag=1, MPI_COMM_WORLD) failed
> MPIDI_CH3I_Progress(150)..........:
> MPID_nem_mpich2_blocking_recv(948):
> MPID_nem_tcp_connpoll(1720).......:
> state_commrdy_handler(1556).......:
> MPID_nem_tcp_recv_handler(1446)...: socket closed
> rank 1 in job 1 deda1x0481_36189 caused collective abort of all ranks
> exit status of rank 1: return code 2
>
> Questions:
> 1) Is there a way to force psn and/or NONMEM to collect the error message
> in the log file when using multi-cores run ?
> 2) What about "cabalistic" error messages as the one above?
>
> Thank you for your help,
>
> Kind regards
>
> Pascal Girard, PhD
> [email protected]
> Head of Modeling & Simulation - Oncology
> Global Exploratory Medicine
> Merck Serono S.A. · Geneva
> Tel: +41.22.414.3549
> Cell: +41.79.508.7898
>
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