coding for sequential NM-runs

6 messages 6 people Latest: Mar 15, 2011

coding for sequential NM-runs

From: Markus Joerger Date: March 15, 2011 technical
dear community, I wonder if someone can provide me a coding for starting (automatically) sequential NM7-runs from MS-DOS? thank you in advance and kind regards Markus -- Markus Joerger MD PhD Department of Medical Oncology Cantonal Hospital Rorschacherstr. 95 9007 St. Gallen Switzerland [email protected] [email protected] phone: +41-765591070 fax: +41-714946368

Re: coding for sequential NM-runs

From: Nick Holford Date: March 15, 2011 technical
Markus, Create a file called myruns.bat in a text editor Insert lines like this in file: call nmfe7 run1.ctl run1.lst call nmfe7 run2.ctl run2.lst .... Save the file myrun.bat (be sure it is not saved with a .txt extension!) in the same directory as the NM-TRAN control streams run1.ctl, run1.ctl, etc. Open a Windows command prompt (e.g. Start Programs Run then enter cmd in the dialog box) Change directory to the directory containing myruns.bat Execute the myruns.bat file by typing myruns.bat then press Enter Each of the runs will be executed by the nmfe7 command. Note that because nmfe7 is a DOS batch file you must use the 'call' command to get it to run and then return to the myruns.bat file for the next command. Nick
Quoted reply history
On 15/03/2011 10:50 a.m., markus joerger wrote: > dear community, > > I wonder if someone can provide me a coding for starting (automatically) sequential NM7-runs from MS-DOS? > > thank you in advance and kind regards > Markus > > -- > Markus Joerger MD PhD > Department of Medical Oncology > Cantonal Hospital > Rorschacherstr. 95 > 9007 St. Gallen > Switzerland > [email protected] <mailto:[email protected]> > [email protected] <mailto:[email protected]> > phone: +41-765591070 > fax: +41-714946368 -- Nick Holford, Professor Clinical Pharmacology Dept Pharmacology& Clinical Pharmacology University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53 email: [email protected] http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford

Re: coding for sequential NM-runs

From: Paolo Denti Date: March 15, 2011 technical
Markus, I don't know if this is what you need, but I was using this code (below) in a batch (.bat) file to run a model, then update the initial estimates, and then run the resulting model. This uses the Perl Speaks NONMEM scripts "execute" and "update_inits", but I guess you can modify the individual commands and run with nmfe. Beware that in this code I was passing the number of the run as first argument calling the script, and in the code it substitutes %1. But obviously you can hard-code the filenames of your model files. Paste the content into a file (e.g. script.bat) To call the script (on run123), type script.bat 123 CALL execute run%1.mod -nm_ver=7 -no-tail_output CALL update_inits run%1.mod run%1.lst -nm_ver=7 -output=run%1a.mod CALL execute run%1a.mod -nm_ver=7 -no-tail_output CALL update_inits run%1a.mod run%1a.lst -nm_ver=7 -output=run%1b.mod CALL execute run%1b.mod -nm_ver=7 -no-tail_output CALL update_inits run%1b.mod run%1b.lst -nm_ver=7 -output=run%1c.mod CALL execute run%1c.mod -nm_ver=7 -no-tail_output Also, if you don't want to update the initial estimates (but you just want to run lots of file) and you are using PsN, you can just type execute run1.mod run2.mod run3.mod run4.mod -thread=1 thread=1 will make sure that the runs are executed sequentially. Hope this helps. Ciao, Paolo
Quoted reply history
On 15/03/2011 10:50, markus joerger wrote: > dear community, > > I wonder if someone can provide me a coding for starting (automatically) sequential NM7-runs from MS-DOS? > > thank you in advance and kind regards > Markus > > -- > Markus Joerger MD PhD > Department of Medical Oncology > Cantonal Hospital > Rorschacherstr. 95 > 9007 St. Gallen > Switzerland > [email protected] <mailto:[email protected]> > [email protected] <mailto:[email protected]> > phone: +41-765591070 > fax: +41-714946368 -- ------------------------------------------------ Paolo Denti, PhD Post-Doctoral Fellow Division of Clinical Pharmacology Department of Medicine University of Cape Town K45 Old Main Building Groote Schuur Hospital Observatory, Cape Town 7925 South Africa phone: +27 21 404 7719 fax: +27 21 448 1989 email: [email protected] ------------------------------------------------ ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

Re: coding for sequential NM-runs

From: Saik Urien Svp Date: March 15, 2011 technical
Markus Hope that this answers your question : Write a code like this (use of nmgo Wings command here) call nmgo d4d call nmgo d4d2 call nmgo dat4c call nmgo dat4d or with nmfe6 or 7 call nmfe d4d call nmfe d4d2 call nmfe dat4c call nmfe dat4d The d***are control streams Then save it in in a "myname.bat" file then run myname in the dos command windows : > myname Saïk ----- Original Message -----
Quoted reply history
From: markus joerger To: NONMEM Sent: Tuesday, March 15, 2011 9:50 AM Subject: [NMusers] coding for sequential NM-runs dear community, I wonder if someone can provide me a coding for starting (automatically) sequential NM7-runs from MS-DOS? thank you in advance and kind regards Markus -- Markus Joerger MD PhD Department of Medical Oncology Cantonal Hospital Rorschacherstr. 95 9007 St. Gallen Switzerland [email protected] [email protected] phone: +41-765591070 fax: +41-714946368

RE: coding for sequential NM-runs

From: Alan Xiao Date: March 15, 2011 technical
You could also add the full path for your input and output files for flexibility. Alan
Quoted reply history
From: [email protected] [mailto:[email protected]] On Behalf Of Nick Holford Sent: Tuesday, March 15, 2011 6:18 AM To: NONMEM Subject: Re: [NMusers] coding for sequential NM-runs Markus, Create a file called myruns.bat in a text editor Insert lines like this in file: call nmfe7 run1.ctl run1.lst call nmfe7 run2.ctl run2.lst .... Save the file myrun.bat (be sure it is not saved with a .txt extension!) in the same directory as the NM-TRAN control streams run1.ctl, run1.ctl, etc. Open a Windows command prompt (e.g. Start Programs Run then enter cmd in the dialog box) Change directory to the directory containing myruns.bat Execute the myruns.bat file by typing myruns.bat then press Enter Each of the runs will be executed by the nmfe7 command. Note that because nmfe7 is a DOS batch file you must use the 'call' command to get it to run and then return to the myruns.bat file for the next command. Nick On 15/03/2011 10:50 a.m., markus joerger wrote: dear community, I wonder if someone can provide me a coding for starting (automatically) sequential NM7-runs from MS-DOS? thank you in advance and kind regards Markus -- Markus Joerger MD PhD Department of Medical Oncology Cantonal Hospital Rorschacherstr. 95 9007 St. Gallen Switzerland [email protected] [email protected] phone: +41-765591070 fax: +41-714946368 -- Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & Clinical Pharmacology University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53 email: [email protected] http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford -------------------------------------------------------------------------- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

RE: coding for sequential NM-runs

From: William Bachman Date: March 15, 2011 technical
Or you could use PDx-Pop's graphical interface and it would run any runs you select either sequentially or in parallel on the number of cores you select to run on. _____
Quoted reply history
From: [email protected] [mailto:[email protected]] On Behalf Of Xiao, Alan Sent: Tuesday, March 15, 2011 9:11 AM To: Nick Holford; NONMEM Subject: RE: [NMusers] coding for sequential NM-runs You could also add the full path for your input and output files for flexibility. Alan _____ Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. From: [email protected] [mailto:[email protected]] On Behalf Of Nick Holford Sent: Tuesday, March 15, 2011 6:18 AM To: NONMEM Subject: Re: [NMusers] coding for sequential NM-runs Markus, Create a file called myruns.bat in a text editor Insert lines like this in file: call nmfe7 run1.ctl run1.lst call nmfe7 run2.ctl run2.lst .... Save the file myrun.bat (be sure it is not saved with a .txt extension!) in the same directory as the NM-TRAN control streams run1.ctl, run1.ctl, etc. Open a Windows command prompt (e.g. Start Programs Run then enter cmd in the dialog box) Change directory to the directory containing myruns.bat Execute the myruns.bat file by typing myruns.bat then press Enter Each of the runs will be executed by the nmfe7 command. Note that because nmfe7 is a DOS batch file you must use the 'call' command to get it to run and then return to the myruns.bat file for the next command. Nick On 15/03/2011 10:50 a.m., markus joerger wrote: dear community, I wonder if someone can provide me a coding for starting (automatically) sequential NM7-runs from MS-DOS? thank you in advance and kind regards Markus -- Markus Joerger MD PhD Department of Medical Oncology Cantonal Hospital Rorschacherstr. 95 9007 St. Gallen Switzerland [email protected] [email protected] phone: +41-765591070 fax: +41-714946368 -- Nick Holford, Professor Clinical Pharmacology Dept Pharmacology & Clinical Pharmacology University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53 email: [email protected] http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford