Re: max no. of observation per subject

From:Nick Holford Subject: Re: [NMusers] max no. of observation per subject Date:Fri, January 25, 2002 2:20 pm Sam, There is no maximum in theory. Increasing NO changes the dimension of fixed size arrays used by the NONMEM executable. The effect is to increase the memory requirements but does not directly affect execution speed of each subject. Execution speed does slow down however because the virtual memory exceed physical memory allocated to the NONMEM executable and more swapping between the pagefile on the hard disk and physical RAM must take place. You can check on the Memory Usage, Virtual Memory Size and Page Fault rate using the Task Manager (WinXP, Win2K, WinNT). You will need to use the View Select Columns menu to see VM Size and PF Delta. This will give you an idea of how much memory your NONMEM run is using and especially if it is causing a lot of page faults (ie. swapping memory between RAM and the hard disk). The memory swapping overhead may also depend on the compiler you use and how it requests memory from the OS e.g. the Watcom compiler uses a third part memory manager while the Compaq compiler seems more aware of the native Windows memory management. The default settings in NSIZES seem to be a pretty good optmization. Increasing the number of parameters and/or number of observations will slow down execution time. If time is important to you then I do not recommend routinely using larger settings for NONMEM unless your particular model/data combination calls for it. You say "NONMEM seems to become very slow, I have to interrupt it after 12 hours run.". Does this mean that each iteration takes longer and longer and eventually NONMEM seems to have stopped making any progress so you kill the task? I cannot explain this behaviour unless somehow there is a memory leak. I have not noticed that NONMEM has memory leaks although the Pharsight Trial Simulator 2.1.1. has a leak that causes this kind of problem with its execution when trying to simulate large data sets. If you check the Task Manager performance page you can watch if memory usage is increasing while NONMEM runs. Are you running other programs e.g. Visual NM that might be monitoring the NONMEM execution and perhaps are using up memory? [I know you sometimes use WFN but that does not run while NONMEM runs and so I cannot see that this would cause a problem]. Nick -- Nick Holford, Divn Pharmacology & Clinical Pharmacology University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand email:n.holford@auckland.ac.nz tel:+64(9)373-7599x6730 fax:373-7556 http://www.health.auckland.ac.nz/pharmacology/staff/nholford/