From: "Rombout, Dr. Ferdinand"
Subject: [NMusers] NONMEM runtimes Date: Mon, 29 Apr 2002 14:36:14 +0200 We investigated the runtimes of a standardized run on several computer systems and operating systems. We found that the runtime was linearly related to the declared SPECint2000 (not to others like Mhz or SpecFP) of the processor and almost independent of operating system and compiler if the most agressive optimization was used. We tested Silicon Graphics under Irix as operating system, and Intel/AMD with W2K, XP and Linux. Intel/AMD processors tested ranged from a PII at 400 Mhz to a PIV at 2 Ghz and Sgi was a 250Mhz R10K. We however had an important but unsolved problem under Linux above a Processor speed of around 1Ghz we saw no further improvement in runtime although we changed the processor type AMD vs Intel, Linux distribution, compiler brand, DDR versus Rambus, and NONMEM buffersize. So we saw a 42% decrease in runtime when switching a 1Ghz PIII to a 2 Ghz PIV which is close to the increase in SPECINT of 46%. Under Linux our runtime stayed about the same. Any suggestions as for an explanation? Regards, Ferdie Rombout ******* From: "Joern Loetsch" Subject: Re: [NMusers] NONMEM runtimes Date: Mon, 29 Apr 2002 Any chance to get the results ? :-)) Is Intel or AMD better? Is Windows or Unix better ? Regards Jorn ______________________________________________________ Jorn Lotsch, MD pharmazentrum frankfurt, Dept. of Clinical Pharmacology Johann Wolfgang Goethe-University Hospital Theodor-Stern-Kai 7 D-60590 Frankfurt am Main GERMANY Tel.:+49-69-6301-4589 Fax.:+49-69-6301-7636 ******* From: Nick Holford [mailto:firstname.lastname@example.org] Subject: Re: [NMusers] NONMEM runtimes Date: Monday, 29. April 2002 Ferdie, It seems you have good evidence that the bottleneck is not CPU or RAM so it would seem likely that it is the disk I/O. There are a variety of parameters in NSIZES that control buffers for the data that might be changed to enhance performance. There were some suggestions made for SGI Iris systems (see NONMEM repository) that may help. Nick -- Nick Holford, Divn Pharmacology & Clinical Pharmacology University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand email:email@example.com tel:+64(9)373-7599x6730 fax:373-7556 http://www.phm.auckland.ac.nz/Staff/NHolford/nholford.htm ******* From: "Rombout, Dr. Ferdinand" Subject: Re: [NMusers] NONMEM runtimes Date: Mon, 29 Apr 2002 14:36:14 +0200 I know about the i/o, since I was the person who did all this with SGI. We have tried the buffers so we would have mainly disk i/o and less in memory since we first thought it was the Rambus. Since the problem also occurred at DDRam, we changed the buffers to the optimal so it would not involve any (almost) disk i/o. This did not solve the problem on Linux. On Windows the runtimes decreases 2 minutes from 14 to 12 minutes when the buffers were set optimal. Ferdie ******* From: Dirk.Zeumer@bc.boehringer-ingelheim.com Subject: Re: [NMusers] NONMEM runtimes Date: Mon, 29 Apr 2002 15:17:46 +0200 Dear all, I don't think that disk I/O is the main problem here. As far as I understand the hardware used for the (final) tests with Linux and Windows was (nearly?) the same - so it seems like a compiler problem - especially by mentioning "most agressive optimization". All newer Windows compilers are able to optimize the executable for newer CPUs (as PIV or Athlon XP) which use the "Streaming SIMD Extension 2 (SSE2)". These optimization results in a significant decrease in the runtime (especially compared to the SSE version of a PIII). Correct me if I'm wrong: I assume that with Linux the range of "standard" f77 / g77 compilers were used for the tests - with no support for SSE2 (sometimes even no SSE support). Therefore I would suggest to do some tests with the Intel Fortran Compiler 6.0 wich is available also for Linux. The options available in this versions will (surprisingly) work also on AMD CPUs. By the way: it would be really nice to see some data of the test Regards, Dirk Zeumer ******* From: José Javier Zarate Subject: Re: AW: [NMusers] NONMEM runtimes Date: Mon, 29 Apr 2002 23:17:54 +0200 Dear all I think that it is possible that you haven't activated your 32 bit access in your Linux installation (if I recall correctly some Linux distributions don't activate it by default) also try to check if you have DMA activated (it also improves disk performance) SSE and SSE2 are SIMD instruction sets that are only related to FPU work and the improvements described in the initial message of this thread appear to be related mainly to INT performance. Anyway Intel compilers increase performance of most applications (even for AMD processors if you don't apply specific P-4 optimizations) I tried the SIMD options on DEC Alpha microprocessors with Compa (DEC) compilers with not too much success. When changing some parameters I managed to improve performance by reducing disk usage. Take into account that Linux appears not to be too P-4 friendly (don't know the reasons) I think that this is a problem related to Linux behaviour and not compiler choice. I suspect that NONMEM would need to be substantially rewritten in order to get the benefits of using modern compilers and CPUs. Intel compilers haven't been listedas reccomended compilers for NONMEM. Other programs tested with V5.xx (e.g. POVRAY) caused erroneus results when some optimizations were applied: You should be careful with your results if you apply aggressive optimizations. Good luck JJ Zarate Departamento de Compras Clínica Universitaria de Navarra http://www.unav.es/cun/ *******