Hi, Angel de Vicente <[email protected]> writes: > I'm having a hard time trying to figure out what could be causing the > slow I/O behaviour that I see: the same code (in Fortran) run in three > different clusters behaves pretty similar in terms of I/O times, except > for one of the variables in the code, where I get two orders of > magnitude slower writes in one of machines (last timing data in the > e-mail). So I hope that somebody with more in-depth knowledge of > Parallel HDF5 can give me a hand with it.
regarding this issue, I extracted only the relevant parts of the code and I can reproduce the behaviour I was explaining in the previous e-mail with a very simple code, which you can see at: http://pastebin.com/HjnS82Gp (to compile it I just do h5pfc -o phdf5write timing.f90 phdf5write.f90, where timing.f90 is timing routine by Arjen Markus, available at http://pastebin.com/480RmNET) The code generates a 4D array with the relevant sizes, and writes the relevant part of the data to a file in three modes PMLX, PMLY, and PMLZ (these replicate the ranks that I would get for X,Y and Z planes respectively when creating a Cartesian topology with the relevant MPI routines). The clusters where I run this code all have 16 cores per node. When I run this test code in only 8 cores (nblocks set to 2), then the three clusters behave similarly and there is no penalty for writing the PMLZ. When I run it in 64 nodes, only PMLZ is heavily penalized, and only very badly in one cluster, while badly in the other one. It looks like there is some contention issue with the Parallel file system when the cores span a number of nodes, but I certainly don't understand why it only affects the PMLZ variable and not the PMLY, and why one of the clusters doesn't seem to be affected. Is there something in the code something that is calling for trouble? Any ideas/pointers/suggestions? Thanks a lot, -- Ángel de Vicente http://www.iac.es/galeria/angelv/ --------------------------------------------------------------------------------------------- ADVERTENCIA: Sobre la privacidad y cumplimiento de la Ley de Protecci�n de Datos, acceda a http://www.iac.es/disclaimer.php WARNING: For more information on privacy and fulfilment of the Law concerning the Protection of Data, consult http://www.iac.es/disclaimer.php?lang=en
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