NONMEM Users Network Archive

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Re: [NMusers] Cleaning Up After NONMEM

From: Mark Tepeck <mark.tepeck_at_gmail.com>
Date: Sat, 9 Jun 2018 23:25:51 -0400

Hi Bill and Bob,

Bill - I tried the method psn clean=4 you provided. It worked very well.
The size of the sub-directories is now cut by more than 90%, even though I
still cannot completely get rid of all the sub-directories. The
sub-directory after psn contains only a few plain text files around several
kb. On the other hand, to do troubleshooting, I can simply re-run the
models without a psn clean augment. An lst file and an output table file
provide sufficient information to me most of the time. I really appreciate
your offering the psn solution.

Bob - Thank you for providing the batch script solution. I haven't tried
that due to my lack of knowledge of batch scripting at this point. Anyway,
it may be too much and unrealistic to add that feature to NONMEM in the
near future, but using a built-in NONMEM script to suppress sub-directories
seems really appealing in the long run.

Thank you all for your help.

Mark


On Fri, Jun 8, 2018 at 5:13 PM, Bauer, Robert <Robert.Bauer_at_iconplc.com>
wrote:

> Mark:
>
> You can create a batch file, such as nmfe74_cleanup.bat (or whatever name
> you wish), with contents such as
>
>
>
> call nmfe74.bat %*
>
> del *.set
>
>
>
> which will run the original nonmem script (and all arguments are passed
> with %*), and when done, go on to delete whichever files you wish.
>
>
>
>
>
>
>
> Robert J. Bauer, Ph.D.
>
> Senior Director
>
> Pharmacometrics R&D
>
> ICON Early Phase
>
> 820 W. Diamond Avenue
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>
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>
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>
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>
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>
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>
> www.iconplc.com
>
>
>
> *From:* owner-nmusers_at_globomaxnm.com [mailto:owner-nmusers_at_globomaxnm.com]
> *On Behalf Of *Bill Denney
> *Sent:* Friday, June 08, 2018 1:49 PM
> *To:* Mark Tepeck
> *Cc:* nmusers_at_globomaxnm.com
> *Subject:* RE: [NMusers] Cleaning Up After NONMEM
>
>
>
> Hi Mark,
>
>
>
> To totally avoid them, not that I know of (others may know an option that
> can help there). With PsN, you can use -clean=4, and I think it will
> remove everything. If you have a run with a problem, you may end up with
> no information to troubleshoot it, though.
>
>
>
> Thanks,
>
>
>
> Bill
>
>
>
> *From:* Mark Tepeck <mark.tepeck_at_gmail.com>
> *Sent:* Friday, June 8, 2018 4:36 PM
> *To:* Bill Denney <wdenney_at_humanpredictions.com>
> *Cc:* nmusers_at_globomaxnm.com
> *Subject:* Re: [NMusers] Cleaning Up After NONMEM
>
>
>
> Hi Bill,
>
>
>
> Thank you for the tip. Is there anyway to avoid those sub-directories?
> For example, let NONMEM clean it up automatically? let NONMEM run those
> temporary files in another cache space invisible to end-users. Those
> sub-directories increasingly eats a lot of my disk space.
>
>
>
> Mark
>
>
>
>
>
>
>
> On Fri, Jun 8, 2018 at 3:56 PM, Bill Denney <wdenney_at_humanpredictions.com>
> wrote:
>
> Hi Mark,
>
>
>
> The simplest answer that I know of is to use PsN (
> https://uupharmacometrics.github.io/PsN/). It runs NONMEM in a
> subdirectory and will only bring the most useful files back into the main
> directory.
>
>
>
> Thanks,
>
>
>
> Bill
>
>
>
> *From:* owner-nmusers_at_globomaxnm.com <owner-nmusers_at_globomaxnm.com> *On
> Behalf Of *Mark Tepeck
> *Sent:* Friday, June 8, 2018 3:43 PM
> *To:* nmusers_at_globomaxnm.com
> *Subject:* Re: [NMusers] FW: testing nmusers number 12001. Please ignore
>
>
>
> Hi All,
>
> Is there any native way for NONMEM to opt out of generating running
> file/folders. Right now, I use some tools to post clean the NONMEM run
> directory. However, it will be fantastic to have such a NONMEM built-in
> option to run "cleanly". Those temporary files and folders create heavy
> burdens on storing and sharing the results.
>
> Thank you,
>
> Mark
>
>
>
>
>
>
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Received on Sat Jun 09 2018 - 23:25:51 EDT

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