RE: NONMEM memory vs. run time
Nick,
Interesting observations. I however wouldn't be surprised if the
additional 4-5 seconds would be due to I/O activities (swapfile,
executable building etc.) rather than calculations. How do these
differences scale with model runtime, i.e. for models than run hours
rather than minutes, does the big/small nonmem difference increase from
seconds to minutes?
Best regards,
Jeroen
J. Elassaiss-Schaap
Scientist PK/PD
Clinical Pharmacology and Kinetics
Schering-Plough
PO Box 20, 5340 BH Oss, Netherlands
Phone: + 31 412 66 9320
Fax: + 31 412 66 2506
e-mail: [EMAIL PROTECTED]
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Nick Holford
Sent: Monday, 08 September, 2008 17:12
To: nmusers
Subject: Re: [NMusers] NONMEM memory vs. run time
Leonid, Darin,
Here are some experimental results rather than theoretical predictions.
I ran a problem (ADVAN6) with two 'sizes' of NONMEM created with NMQUAL
using Wings for NONMEM. The 'std' size is the default NONMEM
configuration. The '570' size is close to the 'big' version provided
with NMQUAL. I ran the problems with an Intel core duo processor with 1
Gb RAM compiled with Intel Fortran version 10.1024. I used NONMEM VI 2.0
installed with NMQUAL-6.3.2 and Windows XP.
I tried each size of problem two times. Run times exclude NM-TRAN and
the compile/link step. You will see that the bigger NONMEM size took 5%
longer to complete. There were no page faults visible with the Task
Manager using either size.
std =Mem Usage 51.1 M byte VM Size 97.1 Mbyte Runtimes: 80.88
sec/ 81.82 sec
570=Mem Usage 199.8 M byte VM Size 1107.9 Mbyte Runtimes: 84.10
sec/ 87.22 sec
These results are similar to those I have observed before. The bigger
versions of NONMEM run more slowly. This is why I prefer to match the
NONMEM size to the problem size. For smaller problems (fewer parameter,
fewer obs/subject) I use the std size. For bigger problems WFN allows a
choice to increase either parameters, obs/subject or both.
Nick
Darin Perusich wrote:
> The increase in memory consumption doesn't impact runtime positively
> or negatively, unless of course your system doesn't have enough
> physical memory to accommodate the increase. NONMEM's memory footprint
> is directly related to the buffer values in the SIZES file, as you
> increase the values the memory footprint increases to accommodate.
>
> In the end processor speed is really the only thing that positively or
> negatively effects NONMEM runtime.
>
> Leonid Gibiansky wrote:
>> Dear All,
>> I noticed that the Nonmem installed with NMQUAL "big nm6" defaults
>> instead of the standard ones results in approximately 10-times
increase
>> in the memory required to run Nonmem (on my recent problem, from 12
MB
>> to 140 MB). I am wondering whether anybody checked how this
influences
>> the run time. Is it better (in terms of the run time) to use standard
>> sizes, or "big" is OK if you have enough RAM?
>> Thanks!
>> Leonid
>>
>
--
Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New
Zealand
[EMAIL PROTECTED] tel:+64(9)923-6730 fax:+64(9)373-7090
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