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 = 2 and I got the following error : Fatal Error: Record SIZES is not valid So I tried also the default value for LIM1: $SIZES LIM1=1 and also the example given on page 166 of Help guide viii $SIZES LIM1=3 MAXFCN=200 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, RD 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 PROBLEM1 (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
RE: [NMusers] Question about interoccation variability
Dear Claire, If you have data only from oral doses and covariances between disposition parameters (CL; V), then you will not get any further improvement by introducing variability in F1. Best regards, Mats Mats Karlsson, PhD Professor of Pharmacometrics FIRST WORLD CONFERENCE ON PHARMACOMETRICS, 5-7 September 2012, Seoul ( http://www.go-wcop.org/ www.go-wcop.org) Dept of Pharmaceutical Biosciences Faculty of Pharmacy Uppsala University Box 591 75124 Uppsala Phone: +46 18 4714105 Fax + 46 18 4714003 From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Xu, Claire Sent: 12 July 2012 15:11 Cc: nmusers Subject: Re: [NMusers] Question about interoccation variability Hi Nick, Thanks for your helpful comment. I will test BOV + BSV on my absorption model parameters first. Sorry for my typo. I meant neither of the models improved the fit. Thanks again for your help. Best, Claire On Thu, Jul 12, 2012 at 8:07 AM, Nick Holford n.holf...@auckland.ac.nz wrote: Claire, See below: On 11/07/2012 9:45 p.m., Xu, Claire wrote: Hi Nick, Thank you a lot for clarifying how to incorporate BOV in the model. I tested BOV on F1 with the same option as well as variable BOVs on F1 from different occasions. But either of them improved the fitting. I am not sure what you mean here. Do you mean that NEITHER of them improved the fit? If that is the case then it would be compatible with your other observation that AUC is very similar across occasions which suggests that there is negligible BOV in CL or F. I find that a bit surprising but it is not impossible. Actually according to the results from non-compartmental analysis, AUC0-inf are very similar across different occasions, while a trend of difference in Cmax and Tmax was observed. Do you think that more complex absorption models would help? Because you are do see BOV in Cmax and Tmax then it seems you should try to focus on looking for BSV+BOV on your absorption model parameters (Ka, Tlag). Of course you can also work on the absorption model structure as well. Open to any comments. Thanks again for your great input. Best, Claire -- Nick Holford, Professor Clinical Pharmacology First World Conference on Pharmacometrics, 5-7 September 2012 Seoul, Korea http://www.go-wcop.org http://www.go-wcop.org/ Dept Pharmacology Clinical Pharmacology, Bldg 505 Room 202D University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand tel:+64(9)923-6730 tel:%2B64%289%29923-6730 fax:+64(9)373-7090 tel:%2B64%289%29373-7090 mobile:+64(21)46 23 53 tel:%2B64%2821%2946%2023%2053 email: n.holf...@auckland.ac.nz http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford -- Xu, Claire Ph.D Candidate Division of Clinical Pharmacology, Wishard Hospital Indiana University School of Medicine 1001 West 10th Street, Myers W7122 Indianapolis, IN 46202 T - 317/7558242
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 , 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 Phone: 1 (514) 789-2180 # 2157 Mobile: 1 (438) 862-0935 Fax: (514) 789-2192 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 = 2 and I got the following error : Fatal Error: Record SIZES is not valid So I tried also the default value for LIM1: $SIZES LIM1=1 and also the example given on page 166 of Help guide viii $SIZES LIM1=3 MAXFCN=200 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, RD 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/ From: owner-nmus...@globomaxnm.com [mailto: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
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 XX Best regards, Nastya From: pascal.gir...@merckgroup.com [mailto: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 mailto: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 = 2 and I got the following error : Fatal Error: Record SIZES is not valid So I tried also the default value for LIM1: $SIZES LIM1=1 and also the example given on page 166 of Help guide viii $SIZES LIM1=3 MAXFCN=200 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, RD ICON Development Solutions 7740 Milestone Parkway Suite 150 Hanover, MD 21076 Tel: (215) 616-6428 Mob: (925) 286-0769 Email:
Re: [NMusers] Error files when using multicore runs and psn == Fatal Error: Record SIZES is not valid
Pascal, That error looks like a PSN error rather than NONMEM. I can confirm that for NM7.2 the $SIZES record must be the first record of the control stream. You might try bypassing PSN if possible and I bet you will not get that error. Bill Bill Knebel, PharmD, PhD Principal Scientist II Metrum Research Group LLC 2 Tunxis Road, Suite 112 Tariffville, CT 06081 O: 860.735.7043 C: 860.930.1370 F: 860.760.6014 On Thursday, July 12, 2012 at 11:09 AM, pascal.gir...@merckgroup.com wrote: 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 , but nothing is mentioned. Anyway, thanks for the suggestion! Kind regards Pascal From:Kassir Nastya nastya.kas...@umontreal.ca (mailto:nastya.kas...@umontreal.ca) To:pascal.gir...@merckgroup.com (mailto:pascal.gir...@merckgroup.com), Bauer, Robert robert.ba...@iconplc.com (mailto: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) mailto: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/ From: owner-nmus...@globomaxnm.com (mailto:owner-nmus...@globomaxnm.com) on behalf of pascal.gir...@merckgroup.com (mailto:pascal.gir...@merckgroup.com) Sent: Thu 7/12/2012 09:21 To: Bauer, Robert Cc: nmusers@globomaxnm.com (mailto:nmusers@globomaxnm.com); olaf.lichtenber...@merckgroup.com (mailto:olaf.lichtenber...@merckgroup.com)@merck.de; orestis.papasoulio...@merckgroup.com (mailto:orestis.papasoulio...@merckgroup.com)@merck.de; owner-nmus...@globomaxnm.com (mailto: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 = 2 and I got the following error : Fatal Error: Record SIZES is not valid So I tried also the default value for LIM1: $SIZES LIM1=1 and also the example given on page 166 of Help guide viii $SIZES LIM1=3 MAXFCN=200 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 (mailto: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 (mailto:robert.ba...@iconplc.com) To:pascal.gir...@merckgroup.com (mailto:pascal.gir...@merckgroup.com) pascal.gir...@merckgroup.com (mailto:pascal.gir...@merckgroup.com), nmusers@globomaxnm.com (mailto:nmusers@globomaxnm.com) nmusers@globomaxnm.com (mailto:nmusers@globomaxnm.com) Cc:orestis.papasoulio...@merckgroup.com (mailto:orestis.papasoulio...@merckgroup.com) orestis.papasoulio...@merckgroup.com (mailto:orestis.papasoulio...@merckgroup.com), olaf.lichtenber...@merckgroup.com (mailto:olaf.lichtenber...@merckgroup.com) olaf.lichtenber...@merckgroup.com (mailto: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 (mailto:owner-nmus...@globomaxnm.com) Pascal: I cannot help regarding having all console
RE: [NMusers] Error files when using multicore runs and psn == Fatal Error: Record SIZES is not valid
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 XX Best regards, Nastya From: pascal.gir...@merckgroup.com [mailto: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 mailto: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 = 2 and I got the following error : Fatal Error: Record SIZES is not valid So I tried also the default value for LIM1: $SIZES LIM1=1 and also the example given on page 166 of Help guide viii $SIZES LIM1=3 MAXFCN=200 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
[NMusers] Mixture model
Colleagues I am analyzing data in which there are two distinct populations as a result of CYP2D6 deficiency. In one dataset, there are 18 subjects with rich data; one of these subjects is markedly different. In that the incidence of 2D6 deficiency is reported to be 10%, one would expect only 1-2 deficient subjects in this sample (consistent with the data here). I was planning to use a mixture model as part of the analysis. However, with only one subject in the deficient population, I am not sure if that is appropriate. Does anyone have any relevant experience or insight into this issue? Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com
Re: [NMusers] 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 *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 LinkedInhttp://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 XX Best regards, Nastya From: pascal.gir...@merckgroup.com [mailto:pascal.gir...@merckgroup.compascal.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.comnkas...@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 = 2 and I got the following error : Fatal Error: Record SIZES is not valid So I tried also the default value for LIM1: $SIZES LIM1=1 and also the example given on page 166 of Help guide viii $SIZES LIM1=3 MAXFCN=200 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:
RE: [NMusers] Mixture model
Dear Dennis - Some approaches for you to consider: 1. Brute Force Model: I hope there is some prior information about the CL for poor and extensive metabolizers. I am also assuming the difference between PM and EM is meaningful. In that case, simply assume that this subject is a PM and estimate a fixed effect for the same. The objective function and uncertainty around parameter estimates should support this model over no CYP2D6 model. 2. Kind-of-Bayesian Model: Assuming you have the prior information on CL, provide a prior for the prevalence and magnitude of difference in PMs with perhaps a low uncertainty. This approach formally recognizes prior information, but materially wouldn't be different from the BFM. Either case, in my opinion, you would want to do justice to the 11 subjects who you think are non-PMers with respect to point estimate and variance. The single PM subject is unlikely to add conclusive information especially when a key covariate (genotype) is missing. [cid:image001.png@01CD6061.1420F1D0] Joga Gobburu, PhD, FCP, MBA | Professor | School of Pharmacy | School of Medicine Executive Director |Center for Translational Medicine N407, 20 N Pine, Baltimore, MD-21201 Office: (410) 706-5907 | E-mail: jgobb...@rx.umaryland.edumailto:shai...@rx.umaryland.edu To receive latest Pharmacometrics news subscribe at http://www.pharmacy.umaryland.edu/ctm/ To unsubscribe, send email to ctm-unsubscr...@lists.umaryland.edumailto:ctm-unsubscr...@lists.umaryland.edu From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On Behalf Of Fisher Dennis Sent: Thursday, July 12, 2012 4:25 PM To: nmusers@globomaxnm.com Subject: [NMusers] Mixture model Colleagues I am analyzing data in which there are two distinct populations as a result of CYP2D6 deficiency. In one dataset, there are 18 subjects with rich data; one of these subjects is markedly different. In that the incidence of 2D6 deficiency is reported to be 10%, one would expect only 1-2 deficient subjects in this sample (consistent with the data here). I was planning to use a mixture model as part of the analysis. However, with only one subject in the deficient population, I am not sure if that is appropriate. Does anyone have any relevant experience or insight into this issue? Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.comhttp://www.PLessThan.com inline: image001.png
