NONMEM memory vs. run time

-----Original Message----- From: owner-nmusers 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 n.holford http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete.

-----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 http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete.

-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Elassaiss - Schaap, J. (Jeroen) Sent: Monday, September 08, 2008 2:27 PM To: Nick Holford Cc: nmusers Subject: RE: [NMusers] NONMEM memory vs. run time Nick, Now I spot it indeed. And I certainly will give it a go, as I have never seen this big/small difference - actually hoped you would have an answer ready. Swapfile time: depends on other applications running, memory demands and the actual memory access. During my PhD I have had to program against swap-file behaviour often enough, so I wouldn't be surprised by 5 seconds. On the other hand, that was several years ago .... Jeroen ________________________________ From: Nick Holford [mailto:[EMAIL PROTECTED] Sent: Monday, 08 September, 2008 20:14 To: Elassaiss - Schaap, J. (Jeroen) Cc: nmusers Subject: Re: [NMusers] NONMEM memory vs. run time Jeroen, The executable building was explicitly excluded (please read my previous email carefully). I cannot say how long it takes to create a swapfile but I would be surprised if it took 5 seconds. If you want to know if these results scale with model runtime and other variables such as available RAM then I suggest you try it on your datasets. I did this a long time ago and made it easy with WFN to build and switch between different sizes of NONMEM according to the problem. That way I dont need to waste time running test problems :-) Nick Elassaiss - Schaap, J. (Jeroen) wrote: 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] -----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 http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete.