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RE: The system cannot execute the specified program

From: Jurgen Bulitta <jbulitta>
Date: Thu, 5 Nov 2009 11:31:47 -0500

Dear Nick,
Dear All,

Please find below the results of some benchmarking with a customized instal=
lation
(i.e. std installation with no. of observations and no. of compartments set=
 to the smallest
values for the respective dataset) vs. the big installation with additional=
ly no. of compartments
increased to 50 and no. of observations increased to 1001.
I did not test any intermediately sized installations, since the results we=
re reasonably
surprising, at least to me.

The bottom line is that, memory use did not seem to be the bottleneck, at l=
east not on this
test system. The benefit of the small installation was biggest for ADVAN1 a=
nd ADVAN3.
However, one will probably only notice this benefit during bootstrapping.

I would interpret these differences in the benefit of the customized instal=
lation vs. the big
installation that some parts of NONMEM are memory dependent whereas others =
(especially
solving of differential equations) are not. As long as NONMEM does not retu=
rn a memory
overflow error and runs the job, I would not worry much about the size of t=
he NONMEM
installation.

Best wishes
Juergen


Cases 1, 2, and 3:
Customized installation: Virtual memory size: 84 MB
BIG installation: Virtual memory size: 828 MB
(nothing else ran on the server other than this one NONMEM VI version 6.2 r=
un)

Case 1: Linear 1-Cmt model, ADVAN1, 15 observations, 50 subjects,
100 bootstrap resplicates with nmbs (in WFN):
Customized installation finished 100 replicates
BIG installation finished 61 replicates in the same time (run on a differen=
t, but identical computer)
--> 64% advantage for the customized installation

Case 2: Linear 2-Cmt model, ADVAN3, 15 observations, 50 subjects,
100 bootstrap resplicates with nmbs (in WFN):
Customized installation finished 100 replicates
BIG installation finished 76 replicates in the same time (run on a differen=
t, but identical computer)
--> 32% advantage for the customized installation

Case 3: Linear 3-Cmt model, ADVAN11, 15 observations, 50 subjects,
100 bootstrap resplicates with nmbs (in WFN):
Customized installation finished 100 replicates
BIG installation finished 89 replicates in the same time (run on a differen=
t, but identical computer)
--> 12% advantage for the customized installation

Case 4: Population PK model, 5 compartments, ADVAN6, run as a single job
Customized installation: 131 min, peak memory use: 75 MB, virtual memory si=
ze: 86 MB
BIG installation: 140 min, peak memory use: 225 MB, virtual memory size: 72=
4 MB
--> 7% advantage for the customized installation

Case 5: same as 4, but with overloading of my laptop by running too many pr=
ograms simultaneously
--> 7% advantage for the customized installation (i.e. exactly the same ben=
efit as in case 4)

Case 6: Population PK/PD model, ADVAN6, about 40 compartments, 15 observati=
ons, run as a single job
Customized installation: 330.77 min
BIG installation: 331.12 min
--> 0.11% advantage for the customized installation



From: owner-nmusers
 Behalf Of Nick Holford
Sent: Sunday, October 18, 2009 12:04 AM
To: nmusers
Subject: Re: [NMusers] The system cannot execute the specified program

Juergen,

I'd be interested to know of your experience of how much estimation time yo=
u save by making project specific installations. Given that you must take a=
dditional time to setup SIZES and recompile NONMEM for each project (say 10=
-15 minutes) how much time do you save per run compared with having regular=
 and big installations of NONMEM?

Nick

Jurgen Bulitta wrote:
Dear Tom,
Dear All,

For those of us who prefer project specific NONMEM installations to save es=
timation time,
it might be helpful, if ICON can provide some rough guidance on the main co=
ntributor
to the RAM needs of NONMEM 7.
I.e. is it primarily the number of observations, compartments, thetas, omeg=
as, or
another variable or some function of these variables?

The following might be very cumbersome: Would it be possible to include a s=
witch
during the installation which disables certain NONMEM 7 features to save RA=
M.
(I recognize that this might cause a lot of unpredictable software issues.)
Dual CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM chips=
 are
reasonably priced. Thus, on the 64-bit server side, this is probably a mino=
r issue.

Best wishes
Juergen




From: owner-nmusers
ilto:owner-nmusers
Sent: Friday, October 16, 2009 3:14 PM
To: nonmem
Cc: nmusers
Subject: RE: [NMusers] The system cannot execute the specified program

Pavel,

The message you describe is usually the result of not having enough memory =
available for the NONMEM 7 memory image. If you are using the "big" versio=
n of SIZES you may need about 1.6-2 GB of available memory for each job. F=
or the efficient use of NONMEM 7's new methods more variables are now stor=
ed in memory than was the case for NONMEM VI. The memory image is larger e=
ven if one is not using the new methods.
When using NONMEM 7 and the "reg" SIZES, I have been able to run 8 jobs sim=
ultaneously on a dual processor dual core machine, but only 3-4 jobs when u=
sing the "big" version of SIZES depending upon what else is running. I hav=
e 3 GB of memory and the task manager indicates a maximum of about 7.4 GB v=
ia paging.

Tom

Thomas M. Ludden Ph.D.
Vice-President, Pharmacometrics R&D
ICON Development Solutions
Tel: + 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410 480 0776
Email: thomas.ludden
Web: www.icondevsolutions.com<http://www.icondevsolutions.com>
[cid:image001.jpg

________________________________
From: owner-nmusers
ilto:owner-nmusers
:nonmem
Sent: Friday, October 16, 2009 2:02 PM
To: nonmem
Cc: nmusers
Subject: [NMusers] The system cannot execute the specified program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>

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--

Nick Holford, Professor Clinical Pharmacology

Dept Pharmacology & Clinical Pharmacology

University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealan=
d

n.holford
0 fax:+64(9)373-7090

mobile: +64 21 46 23 53

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image001.jpg
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Received on Thu Nov 05 2009 - 11:31:47 EST

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