Dear NONMEN Users:
>
>What are the most efficient ways to restart NONMEM if it is interrupted?
>NONMEM allows only one MSFO statement when several methods are used.
>
>Can supporting software packages such as PsN, xpose, wings of NONMEM, etc.
>help?
>
>Cheers,
>Bob
restart NONMEM
hi Bob,
Pirana has a function "Duplicate for MSF restart", which takes care of making the changes in the model required for an MSF-restart. With a few mouseclicks your model will be on his/her way again... Additionally, PsN's execute has the "-handle_msfo" argument which should take care of this automatically. However, the argument is labelled "experimental", and is not further detailed in the help... so you'll have to see for yourself if that works.
cheers,
Ron
Quoted reply history
On 8/14/12 1:28 PM, Hiker Hiker wrote:
> Dear NONMEN Users:
> What are the most efficient ways to restart NONMEM if it is
> interrupted? NONMEM allows only one MSFO statement when several
> methods are used.
> Can supporting software packages such as PsN, xpose, wings of
> NONMEM, etc. help?
> Cheers,
> Bob
>
> --
> -----------------------------------
> Ron Keizer, PharmD PhD
> Post-doctoral fellow
> Pharmacometrics Research Group
> Uppsala University
> -----------------------------------
> Pirana Software & Consulting BV
> Sweden / the Netherlands
> www.pirana-software.com
>
Hello Everyone,
It seems like the $MSFI is not useful if the NONMEM job crash due to, for
example, power outage. Are there any other way to resturt the program in this
case?
Thank you,
Pavel
Quoted reply history
----- Original Message -----
From: Ron Keizer
Date: Tuesday, August 14, 2012 10:33 am
Subject: Re: [NMusers] restart NONMEM
To: Hiker Hiker
Cc: "[email protected]"
> hi Bob,
> Pirana has a function "Duplicate for MSF restart", which takes
> care of
> making the changes in the model required for an MSF-restart.
> With a few
> mouseclicks your model will be on his/her way again...
> Additionally, PsN's execute has the "-handle_msfo" argument
> which should
> take care of this automatically. However, the argument is
> labelled
> "experimental", and is not further detailed in the help... so
> you'll
> have to see for yourself if that works.
> cheers,
> Ron
>
>
> On 8/14/12 1:28 PM, Hiker Hiker wrote:
> >
> > Dear NONMEN Users:
> > What are the most efficient ways to restart NONMEM if it is
> > interrupted? NONMEM allows only one MSFO statement when several
> > methods are used.
> > Can supporting software packages such as PsN, xpose, wings of
> > NONMEM, etc. help?
> > Cheers,
> > Bob
> >
> >
> > --
> > -----------------------------------
> > Ron Keizer, PharmD PhD
> > Post-doctoral fellow
> > Pharmacometrics Research Group
> > Uppsala University
> > -----------------------------------
> > Pirana Software & Consulting BV
> > Sweden / the Netherlands
> > www.pirana-software.com
> > -----------------------------------
>
Actually, it is useful, we did is many times (but then got a better UPS :) )
Leonid
Quoted reply history
On 8/14/2012 12:37 PM, [email protected] wrote:
> Hello Everyone,
> It seems like the $MSFI is not useful if the NONMEM job crash due to,
> for example, power outage. Are there any other way to resturt the
> program in this case?
> Thank you,
> Pavel
>
> ----- Original Message -----
> From: Ron Keizer
> Date: Tuesday, August 14, 2012 10:33 am
> Subject: Re: [NMusers] restart NONMEM
> To: Hiker Hiker
> Cc: "[email protected]"
>
> > hi Bob,
> > Pirana has a function "Duplicate for MSF restart", which takes
> > care of
> > making the changes in the model required for an MSF-restart.
> > With a few
> > mouseclicks your model will be on his/her way again...
> > Additionally, PsN's execute has the "-handle_msfo" argument
> > which should
> > take care of this automatically. However, the argument is
> > labelled
> > "experimental", and is not further detailed in the help... so
> > you'll
> > have to see for yourself if that works.
> > cheers,
> > Ron
> >
> >
> > On 8/14/12 1:28 PM, Hiker Hiker wrote:
> > >
> > > Dear NONMEN Users:
> > > What are the most efficient ways to restart NONMEM if it is
> > > interrupted? NONMEM allows only one MSFO statement when several
> > > methods are used.
> > > Can supporting software packages such as PsN, xpose, wings of
> > > NONMEM, etc. help?
> > > Cheers,
> > > Bob
> > >
> > >
> > > --
> > > -----------------------------------
> > > Ron Keizer, PharmD PhD
> > > Post-doctoral fellow
> > > Pharmacometrics Research Group
> > > Uppsala University
> > > -----------------------------------
> > > Pirana Software & Consulting BV
> > > Sweden / the Netherlands
> > > www.pirana-software.com
> > > -----------------------------------
> >
>
> No virus found in this message.
> Checked by AVG - www.avg.com http://www.avg.com
> Version: 2012.0.2197 / Virus Database: 2437/5200 - Release Date: 08/14/12
Bob,
First of all you need to restart your spell checker -- this is the NONMEM user group :-)
WFN can help restart if you include the MSFO option in the $EST record.
The nmctl command with the 'i' option will copy the intermediate output parameter estimates (using the INTER file) from the last iteration into the NM-TRAN control stream. You can then restart the run.
Nick
Quoted reply history
On 14/08/2012 11:28 p.m., Hiker Hiker wrote:
> Dear NONMEN Users:
> What are the most efficient ways to restart NONMEM if it is
> interrupted? NONMEM allows only one MSFO statement when several
> methods are used.
> Can supporting software packages such as PsN, xpose, wings of
> NONMEM, etc. help?
> Cheers,
> Bob
--
Nick Holford, Professor Clinical Pharmacology
First World Conference on Pharmacometrics, 5-7 September 2012
Seoul, Korea 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 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: [email protected]
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Hi Bob,
Have you tried to use the option -rerun in PsN?
Here's the details from their manual:
-rerun='integer'
Default 1. PsN can redo or resume a run using information in PsN run
directory(see documentation for -directory). It is called a rerun. During a
rerun PsN will consider to redo parts of the run. With the -rerun option you
can control which parts will be redone. With rerun set to 1 PsN will rerun any
model with a missing list file. Notice that every "retry" (see the
documentation for -retries and -min_retries) will be considered for a rerun.
This means you can change the value of the -retries and -min_retries
options if you like more or less retries. Setting -rerun to 0 means that PsN
will not check for missing or incomplete "retry" list files. This is useful if
you have one or more run model-files and you wish to have a PsN raw_results
file. You do a run with them as arguments and specify -rerun=0, PsN will not do
any NONMEM run, but produce useful output summary. You can also set -rerun to
2, and PsN will ignore any existing list files and rerun everything, creating
raw_results from the new listfiles.
Hope it helps.
Karina R. Vega-Villa, Ph.D.
Post-Doctoral Research Associate
Mailing Address:
The University of Oklahoma
College of Pharmacy
P.O. Box 26901
Oklahoma City, OK 73126-0901
Building Address:
The University of Oklahoma
College of Pharmacy
Department of Pharmaceutical Sciences, Rm. 323
1110 N. Stonewall Ave.
Oklahoma City, OK 73117
Phone: (405) 271-6593 x 43831
Fax: (405) 271-7505
email: [email protected]
Quoted reply history
________________________________________
From: [email protected] [[email protected]] On Behalf Of
Leonid Gibiansky [[email protected]]
Sent: Tuesday, August 14, 2012 12:37 PM
To: [email protected]
Cc: Ron Keizer; Hiker Hiker; [email protected]
Subject: Re: [NMusers] restart NONMEM
Actually, it is useful, we did is many times (but then got a better UPS :) )
Leonid
On 8/14/2012 12:37 PM, [email protected] wrote:
> Hello Everyone,
> It seems like the $MSFI is not useful if the NONMEM job crash due to,
> for example, power outage. Are there any other way to resturt the
> program in this case?
> Thank you,
> Pavel
>
> ----- Original Message -----
> From: Ron Keizer
> Date: Tuesday, August 14, 2012 10:33 am
> Subject: Re: [NMusers] restart NONMEM
> To: Hiker Hiker
> Cc: "[email protected]"
>
> > hi Bob,
> > Pirana has a function "Duplicate for MSF restart", which takes
> > care of
> > making the changes in the model required for an MSF-restart.
> > With a few
> > mouseclicks your model will be on his/her way again...
> > Additionally, PsN's execute has the "-handle_msfo" argument
> > which should
> > take care of this automatically. However, the argument is
> > labelled
> > "experimental", and is not further detailed in the help... so
> > you'll
> > have to see for yourself if that works.
> > cheers,
> > Ron
> >
> >
> > On 8/14/12 1:28 PM, Hiker Hiker wrote:
> > >
> > > Dear NONMEN Users:
> > > What are the most efficient ways to restart NONMEM if it is
> > > interrupted? NONMEM allows only one MSFO statement when several
> > > methods are used.
> > > Can supporting software packages such as PsN, xpose, wings of
> > > NONMEM, etc. help?
> > > Cheers,
> > > Bob
> > >
> > >
> > > --
> > > -----------------------------------
> > > Ron Keizer, PharmD PhD
> > > Post-doctoral fellow
> > > Pharmacometrics Research Group
> > > Uppsala University
> > > -----------------------------------
> > > Pirana Software & Consulting BV
> > > Sweden / the Netherlands
> > > www.pirana-software.com
> > > -----------------------------------
> >
>
> No virus found in this message.
> Checked by AVG - www.avg.com http://www.avg.com
> Version: 2012.0.2197 / Virus Database: 2437/5200 - Release Date: 08/14/12
>
Hi Nick,
WFN provides a great support.
NONMEM7.2 is complex. INTER file is empty sometimes. The restart commants may
need some additional options when several methods are used in the same *.CTL
file.
Cheers,
Bob
________________________________
Quoted reply history
From: Nick Holford <[email protected]>
To: nmusers <[email protected]>
Sent: Tuesday, August 14, 2012 3:19 PM
Subject: Re: [NMusers] restart NONMEM
Bob,
First of all you need to restart your spell checker -- this is the NONMEM user
group :-)
WFN can help restart if you include the MSFO option in the $EST record.
The nmctl command with the 'i' option will copy the intermediate output
parameter estimates (using the INTER file) from the last iteration into the
NM-TRAN control stream. You can then restart the run.
Nick
On 14/08/2012 11:28 p.m., Hiker Hiker wrote:
>
> Dear NONMEN Users:
> What are the most efficient ways to restart NONMEM if it is
> interrupted? NONMEM allows only one MSFO statement when several
> methods are used.
> Can supporting software packages such as PsN, xpose, wings of
> NONMEM, etc. help?
> Cheers,
> Bob
>
-- Nick Holford, Professor Clinical Pharmacology
First World Conference on Pharmacometrics, 5-7 September 2012
Seoul, Korea 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 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: [email protected]
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Bob,
The complexity of restarting NM7.2 when multiple $EST are used is really something that needs to be addressed within NONMEM.
Its not something I will be attempting with WFN.
Best wishes,
Nick
Quoted reply history
On 15/08/2012 11:46 p.m., Hiker Hiker wrote:
> Hi Nick,
> WFN provides a great support.
>
> NONMEM7.2 is complex. INTER file is empty sometimes. The restart commants may need some additional options when several methods are used in the same *.CTL file.
>
> Cheers,
> Bob
>
> *From:* Nick Holford <[email protected]>
> *To:* nmusers <[email protected]>
> *Sent:* Tuesday, August 14, 2012 3:19 PM
> *Subject:* Re: [NMusers] restart NONMEM
>
> Bob,
>
> First of all you need to restart your spell checker -- this is the NONMEM user group :-)
>
> WFN can help restart if you include the MSFO option in the $EST record.
>
> The nmctl command with the 'i' option will copy the intermediate output parameter estimates (using the INTER file) from the last iteration into the NM-TRAN control stream. You can then restart the run.
>
> Nick
>
> On 14/08/2012 11:28 p.m., Hiker Hiker wrote:
> >
> > Dear NONMEN Users:
> > What are the most efficient ways to restart NONMEM if it is
> > interrupted? NONMEM allows only one MSFO statement when several
> > methods are used.
> > Can supporting software packages such as PsN, xpose, wings of
> > NONMEM, etc. help?
> > Cheers,
> > Bob
> >
>
> -- Nick Holford, Professor Clinical Pharmacology
>
> First World Conference on Pharmacometrics, 5-7 September 2012
> Seoul, Korea 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 fax:+64(9)373-7090 mobile:+64(21)46 23 53
> email: [email protected] <mailto:[email protected]>
> http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
--
Nick Holford, Professor Clinical Pharmacology
First World Conference on Pharmacometrics, 5-7 September 2012
Seoul, Korea 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 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: [email protected]
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Yes, restarting NONMEM using the MSF system for a multi $EST methods problem is
sufficiently complex, that it is best to leave it to the user to decide what
needs to be done (that is, modifying the control stream file for the
appropriate re-start action), rather than trying to make an intelligent
algorithm within NONMEM that won't get tripped up. For example, in the case
where a problem is interrupted with several $EST statements, the user needs to
modify the control stream file by inserting the $MSFI statement. While there,
it is possible for the user to change the series or order, or even the options
of the $EST statements as well. As for the MSF file, even if it stored which
$EST statement it was on when interruption occurred, this was in accordance
with the original control stream file, and not in accordance with the present
control stream file. It is best to simply have the user note during which step
it crashed, and manually comment out the $EST steps that were already executed.
Furthermore, it may be desirable for the user to modify the options of the
$EST record that is being repeated, for example, to change the number of NBURN
iterations in an SAEM step, etc.
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
Quoted reply history
-----Original Message-----
From: [email protected] [mailto:[email protected]] On
Behalf Of Nick Holford
Sent: Wednesday, August 15, 2012 3:20 PM
To: nmusers
Subject: Re: [NMusers] restart NONMEM
Bob,
The complexity of restarting NM7.2 when multiple $EST are used is really
something that needs to be addressed within NONMEM.
Its not something I will be attempting with WFN.
Best wishes,
Nick
On 15/08/2012 11:46 p.m., Hiker Hiker wrote:
> Hi Nick,
> WFN provides a great support.
> NONMEM7.2 is complex. INTER file is empty sometimes. The restart
> commants may need some additional options when several methods are
> used in the same *.CTL file.
> Cheers,
> Bob
>
> *From:* Nick Holford <[email protected]>
> *To:* nmusers <[email protected]>
> *Sent:* Tuesday, August 14, 2012 3:19 PM
> *Subject:* Re: [NMusers] restart NONMEM
>
> Bob,
>
> First of all you need to restart your spell checker -- this is the
> NONMEM user group :-)
>
> WFN can help restart if you include the MSFO option in the $EST record.
> The nmctl command with the 'i' option will copy the intermediate
> output parameter estimates (using the INTER file) from the last
> iteration into the NM-TRAN control stream. You can then restart the run.
>
> Nick
>
>
>
> On 14/08/2012 11:28 p.m., Hiker Hiker wrote:
> >
> > Dear NONMEN Users:
> > What are the most efficient ways to restart NONMEM if it is
> > interrupted? NONMEM allows only one MSFO statement when several
> > methods are used.
> > Can supporting software packages such as PsN, xpose, wings of
> > NONMEM, etc. help?
> > Cheers,
> > Bob
> >
>
> -- Nick Holford, Professor Clinical Pharmacology
>
> First World Conference on Pharmacometrics, 5-7 September 2012
> Seoul, Korea 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 fax:+64(9)373-7090 mobile:+64(21)46 23 53
> email: [email protected] <mailto:[email protected]>
> http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
>
>
>
>
--
Nick Holford, Professor Clinical Pharmacology
First World Conference on Pharmacometrics, 5-7 September 2012
Seoul, Korea 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 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email: [email protected]
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford