Hi Scott, thanks for your response.
I've tried with GNU compilers, OpenMPI and HDF5 (1.8.15, 1.8.16, 1.18.17), but in a local scope or small cluster, not in Marenostrum. Ok, I'm going to try to compile all this tools to reproduce this environment and I will tell you if there are some news. Can you report the compilation errors you are talking about? I can help you in this point or fix any issue! Thank you again for your effort! Víctor. 2016-07-26 16:41 GMT+02:00 Scot Breitenfeld <[email protected]>: > I suspect that it is an issue with the impi implementation. I have not > been able to compile your code on our systems due to various compilation > errors (this is using a different compiler as I don’t have access to impi). > Have you tried using mpich (or some other mpi implementation) instead to > see if that works? Also, have you tried using 1.10.0? > > Scot > > > On Jul 23, 2016, at 1:12 PM, victor sv <[email protected]> wrote: > > Hi again, > > In order to help to understand what is happening, I've implemented and > example using the HDF5 library. > > You can see it in the following link: > > https://github.com/victorsndvg/XH5For/blob/master/src/examples/hdf5_performance_test/ch_unstructured_hexahedron_perf.f90 > > I've compiled and launched it reproducing the previous mail and I'm > getting the same behavior/errors with the new code. > > I also compiled and linked against HDF5 1.8.17 by myself with the same > results. > > I'm not using any tunning hint ... this could be the problem? > > Thanks! > Víctor > > > > 2016-07-19 11:08 GMT+02:00 victor sv <[email protected]>: > >> Hi all, >> >> I'm developing XH5For <https://github.com/victorsndvg/XH5For>, an OO >> fortran light-weight XDMF/HDF5 layer, and now I would like to test its >> scalability, but I'm lost with an issue that i'm getting. >> >> I'm going to try to explain it as best as I can. >> >> I'm performing some weak scalability tests on Marenostrum III >> <http://www.bsc.es/user-support/mn3.php> (GPFS file system) using >> Collective Writing with the Contiguous HyperSlab strategy. I'm running >> tests with 1, 16, 32, 64, 128, 256, 512, 1024 and 2048 MPI tasks. >> >> All seems to work as expected except for the 2048 MPI tasks test, where I >> think I'm getting an MPI interlock (it's still running without doing >> anything till the job time exceeds and the job is killed). >> >> After that, i try to reproduce an error with a number of MPI tasks >> between 1024-2048, and I could get the following error message while >> launching a smaller size job, with 1164 MPI tasks: >> >> HDF5-DIAG: Error detected in HDF5 (1.8.16) MPI-process 1009: >>> #000: H5Dio.c line 271 in H5Dwrite(): can't prepare for writing data >>> major: Dataset >>> minor: Write failed >>> #001: H5Dio.c line 352 in H5D__pre_write(): can't write data >>> major: Dataset >>> minor: Write failed >>> #002: H5Dio.c line 789 in H5D__write(): can't write data >>> major: Dataset >>> minor: Write failed >>> #003: H5Dmpio.c line 529 in H5D__contig_collective_write(): couldn't >>> finish shared collective MPI-IO >>> major: Low-level I/O >>> minor: Write failed >>> >> >> I have used the following libraries/versions during compilation stage: >> >> - intel/16.0.1 >> - impi/5.1.2.150 >> - HDF5/1.8.16-mpi >> >> Here you can see how I open the HDF5 file for Collective Writing: >> >> https://github.com/victorsndvg/XH5For/blob/master/src/lib/hdf5_handler/hdf5_handler.f90#L531 >> >> And here, how I write HyperSlabs: >> >> https://github.com/victorsndvg/XH5For/blob/master/src/lib/hdf5_handler/contiguous_hyperslab/hdf5_contiguous_hyperslab_handler.f90#L102 >> >> Note: ENABLE_MPI, ENABLE_HDF5. ENABLE_PARALLEL_HDF5 definition flags are >>> enabled >>> >> >> Could anyone give me some ligth about this? >> >> I would greatly appreciate your help! >> >> Thank you in advance, >> Víctor. >> >> >> > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 > > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 >
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