RE: Simple parallel benchmark for Nonmem 7.2 with large Bayes problem

Hi Nick and Ron, During beta testing done by Exprimo it became clear that speed might not be the best heuristic to judge 7.2. First a tradeoff between consistency and speed that had to in the choice compiler options as some options resulted in different results between the MPI and NON-MPI runs. An added benefit is that using these option NONMEM 7.1 and NONMEM 7.2 produced IDENTICAL results. The "default" install of NONMEM has, as far as I know, rarely (if ever) produced identical results across version numbers. Putting the lingering issue of cross version consistency is in my option well worth waiting a few extra seconds. Second NONMEM 7.2 includes a semi-dynamic resizing step. This steps forces NONMEM to (re)compile a bigger part of the code before the actual NONMEM execution can take place. Here flexibly prevailed over speed. I certainly will not miss having to tweak the SIZES file and keeping reg, big, huge, etc... installations of NONMEM. Finally the speed increase of an MPI run is so dramatic that comparing speed moot for all but the simple models with limited data. For those the -trskip and -prskip options may help. (Untested) To add to the overall discussion on parallel NONMEM: - FPI should be avoided at all costs. Sharing data using files is far from efficient (Maybe for huge problems distributed over different geographical sites?) - The communication overhead for MPI executions over different machines will probably be extremely dependant on the ssh-settings (protocol used to communicate between two machines). - Hyperthreading* is open for debate and speculations... Critics will recommend not using it as it may give a false impression of having more resources than you actually have, add to the overhead, and requires specially designed code etc... Others -like me- will argue that having the hardware do some crude load balancing is better than leave it all to the OS. - Overall I would not recommend MPI over different machines, especially in a multi-user production environment. I am somewhat surprised that you did not see any difference when using multiple machines instead of one. To Ron I have a comment: I would not expect the big differences between FPi and MPI on a workstation but rather on a cluster. The reason is that on a workstation the working directories are locate on the local disk for both MPI and FPI. So on the one hand FPI will have slightly higher disk IO while MPI has an added overhead from the MPI daemon. The big difference would be in a cluster environment: FPI needs to use working directories located on a network drive while MPI can use local drives. Disk IO is distributed over the nodes when using MPI while it is centralized using FPI. I speculate that the performance of FPI will be strongly dependent on the IO of your cluster file system the network latency will be a defining factor for MPI. K. Regards, Xavier *Hyperthreading creates two virtual cores per physical... i7 with HT seem to have 8 cores although it only as 4 physical.