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 *"If we knew what it was we were doing, it would not be called research, would it?" Albert Einstein* * * <http://nz.linkedin.com/in/juliakorell> LinkedIn<http://nz.linkedin.com/in/juliakorell> [image: Skype] juliakorell On Fri, Jul 13, 2012 at 3:42 AM, <pascal.gir...@merckgroup.com> 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" <nastya.kas...@umontreal.ca> > To: <pascal.gir...@merckgroup.com>, "Bauer, Robert" < > robert.ba...@iconplc.com>, <nmusers@globomaxnm.com> > 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: pascal.gir...@merckgroup.com > [mailto:pascal.gir...@merckgroup.com<pascal.gir...@merckgroup.com> > ] > Sent: Thu 7/12/2012 11:09 > To: Kassir Nastya; Bauer, Robert; nmusers@globomaxnm.com > 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" <nastya.kas...@umontreal.ca> > To: <pascal.gir...@merckgroup.com>, "Bauer, Robert" < > robert.ba...@iconplc.com> > 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: nkas...@pharsight.com > <mailto:nkas...@pharsight.com<nkas...@pharsight.com>< > mailto:nkas...@pharsight.com <nkas...@pharsight.com>> > > > Phone: 1 (514) 789-2180 # 2157 > Mobile: 1 (438) 862-0935 > > Fax: (514) 789-2192 > > www.pharsight.com <http://www.pharsight.com/ <http://www.pharsight.com/> > > > > > ________________________________ > > From: owner-nmus...@globomaxnm.com on behalf of > pascal.gir...@merckgroup.com > Sent: Thu 7/12/2012 09:21 > To: Bauer, Robert > Cc: nmusers@globomaxnm.com; "olaf.lichtenber...@merckgroup.com"@merck.de; > "orestis.papasoulio...@merckgroup.com"@merck.de; > owner-nmus...@globomaxnm.com > 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 > pascal.gir...@merckgroup.com > 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" <robert.ba...@iconplc.com> > To: "pascal.gir...@merckgroup.com" <pascal.gir...@merckgroup.com>, > "nmusers@globomaxnm.com" <nmusers@globomaxnm.com> > Cc: "orestis.papasoulio...@merckgroup.com" < > orestis.papasoulio...@merckgroup.com>, "olaf.lichtenber...@merckgroup.com" > <olaf.lichtenber...@merckgroup.com> > Date: 11/07/2012 18:55 > Subject: RE: [NMusers] Error files when using multicore runs and > psn > Sent by: owner-nmus...@globomaxnm.com > > ________________________________ > > > > > 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: robert.ba...@iconplc.com > > Web: www.iconplc.com <http://www.iconplc.com/ <http://www.iconplc.com/> > > > > > > > ________________________________ > > From: owner-nmus...@globomaxnm.com > [mailto:owner-nmus...@globomaxnm.com<owner-nmus...@globomaxnm.com>< > mailto:owner-nmus...@globomaxnm.com <owner-nmus...@globomaxnm.com>> < > mailto:owner-nmus...@globomaxnm.com <owner-nmus...@globomaxnm.com> < > mailto:owner-nmus...@globomaxnm.com <owner-nmus...@globomaxnm.com>> > ] > On Behalf Of pascal.gir...@merckgroup.com > Sent: Wednesday, July 11, 2012 11:19 AM > To: nmusers@globomaxnm.com > Cc: orestis.papasoulio...@merckgroup.com; > olaf.lichtenber...@merckgroup.com > 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 > pascal.gir...@merckgroup.com > Head of Modeling & Simulation - Oncology > Global Exploratory Medicine > Merck Serono S.A. · Geneva > Tel: +41.22.414.3549 > Cell: +41.79.508.7898 > > This message and any attachment are confidential and may be privileged or > otherwise protected from disclosure. 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