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:* [email protected] <[email protected]> *On
Behalf Of *Mark Tepeck
*Sent:* Friday, June 8, 2018 3:43 PM
*To:* [email protected]
*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
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
Quoted reply history
On Fri, Jun 8, 2018 at 3:56 PM, Bill Denney <[email protected]>
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:* [email protected] <[email protected]> *On
> Behalf Of *Mark Tepeck
> *Sent:* Friday, June 8, 2018 3:43 PM
> *To:* [email protected]
> *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
>
>
>
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
Suite 100
Gaithersburg, MD 20878
Office: (215) 616-6428
Mobile: (925) 286-0769
[email protected]<mailto:[email protected]>
http://www.iconplc.com/
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Bill Denney
Sent: Friday, June 08, 2018 1:49 PM
To: Mark Tepeck
Cc: [email protected]
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 <[email protected]<mailto:[email protected]>>
Sent: Friday, June 8, 2018 4:36 PM
To: Bill Denney
<[email protected]<mailto:[email protected]>>
Cc: [email protected]<mailto:[email protected]>
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
<[email protected]<mailto:[email protected]>> 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: [email protected]<mailto:[email protected]>
<[email protected]<mailto:[email protected]>> On Behalf
Of Mark Tepeck
Sent: Friday, June 8, 2018 3:43 PM
To: [email protected]<mailto:[email protected]>
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
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
Quoted reply history
On Fri, Jun 8, 2018 at 5:13 PM, Bauer, Robert <[email protected]>
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
> https://maps.google.com/?q=820+W.+Diamond+Avenue+%0D%0A+Suite+100+%0D%0A+Gaithersburg,+MD+20878+%0D%0A+Office:+(215&entry=gmail&source=g
>
> Suite 100
> https://maps.google.com/?q=820+W.+Diamond+Avenue+%0D%0A+Suite+100+%0D%0A+Gaithersburg,+MD+20878+%0D%0A+Office:+(215&entry=gmail&source=g
>
> Gaithersburg, MD 20878
> https://maps.google.com/?q=820+W.+Diamond+Avenue+%0D%0A+Suite+100+%0D%0A+Gaithersburg,+MD+20878+%0D%0A+Office:+(215&entry=gmail&source=g
>
> Office: (215
> https://maps.google.com/?q=820+W.+Diamond+Avenue+%0D%0A+Suite+100+%0D%0A+Gaithersburg,+MD+20878+%0D%0A+Office:+(215&entry=gmail&source=g)
> 616-6428
>
> Mobile: (925) 286-0769
>
> [email protected]
>
> www.iconplc.com
>
>
>
> *From:* [email protected] [mailto:[email protected]]
> *On Behalf Of *Bill Denney
> *Sent:* Friday, June 08, 2018 1:49 PM
> *To:* Mark Tepeck
> *Cc:* [email protected]
> *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 <[email protected]>
> *Sent:* Friday, June 8, 2018 4:36 PM
> *To:* Bill Denney <[email protected]>
> *Cc:* [email protected]
> *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 <[email protected]>
> 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:* [email protected] <[email protected]> *On
> Behalf Of *Mark Tepeck
> *Sent:* Friday, June 8, 2018 3:43 PM
> *To:* [email protected]
> *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
>
>
>
>
>
>
>