Shared Memory
Nathan S. Watson-Haigh schrieb:
I'm new to HPC and parallel programming but I've created my own R package which has a parallel (using Rmpi) and non-parallel implementation of the same algorithm. It works nicely, but I'm trying to better understand how/if Rmpi uses shared memory. Does/can Rmpi use shared memory? For instance, if each slave needs access to the same data matrix, does Rmpi create a copy of that data for each slave when I do: mpi.bcast.Robj2slave(myMatrix)
Yes
I think it does create a copy and I therefore currently pass a subset of the data matrix to each slave using: objList <- list(m=m[xMin:nrow(m), xMin:nrow(m)]) mpi.send.Robj(objList, slave_id, 1)
Yes, this works
myMatrix can be up to 24k x 24k in size. That's > 4Gb of RAM just to hold it in memory! I suppose I'm wondering if memory requirements are proportional to the number of slaves requested - if each slave has to have it's own copy of the data and if I can reduce this requirement by utilising the shared memory!?
Yes, you will get some memory problems. Using Rmpi I think there is no way to use shared memory. There is a great new package for shared memory sytems: multicore http://cran.r-project.org/web/packages/multicore/index.html I already tested it with 500 cores and there is a great performance (nearly linear!) Best Markus
Cheers, Nath
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Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4497