Hi Pascal,

$SIZES should be before $PROB. It should be the first uncommented line in the file.

Regards,
Katya
Ekaterina Gibiansky, Ph.D.
CEO&CSO, QuantPharm LLC
Web:     www.quantpharm.com
Email:   egibian...@quantpharm.com
Tel:     (301)-717-7032 
On 7/12/2012 9:21 AM, pascal.gir...@merckgroup.com wrote:
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

 


From: owner-nmus...@globomaxnm.com [mailto: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


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