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  1. Introduction to Parallel HDF5

    parallel I/O interface had to be portable to different platforms. With these requirements of HDF5 our initial target was to support MPI programming … : Parallel Programming with HDF5 This tutorial assumes that you are somewhat familiar with parallel programming with MPI (Message Passing Interface). If you
    HDF5Mar 02, 2018
  2. What performance can you expect from Parallel HDF5?

    HDF5 cannot do better than MPI I/O on your system. Usually HDF5 parallel applications have little overhead over MPI I/O applications on the same system. If MPI I/O performs well, then you should expect good performance from Parallel HDF5. If you want to compare the performance of MPI I/O and Parallel HDF5 on your
    HDF Knowledge BaseJul 14, 2017
  3. What do you need to run Parallel HDF5?

    performance. faq hdf5 kbarticle parallel mpi … You need an MPI library with MPII/O support installed on your system. If you use the MPIO VFD, the HDF5 library will use MPII/O for data access so MPII/O must
    HDF Knowledge BaseDec 14, 2017
  4. How do you set up HDF5 so only one MPI rank 0 process does I/O?

    Several scientific HDF5 applications use this approach, and we know it works very well. You should use the sequential HDF5 library. Pros: one HDF5 file Cons: Probably a lot of communications will be going on. faq hdf5 kbarticle parallel mpi
    HDF Knowledge BaseJul 13, 2017
  5. Parallel HDF5

    / https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/browse/releasedocs directory of the source code. Tutorials There are two HDF5 tutorials that will help in learning Parallel HDF5: Learning the Basics New users to HDF5 should work through this tutorial first. It does not cover parallel programming but contains basic information needed in order to use
    HDF5Oct 24, 2018
  6. How to pass hints to MPI from HDF5

    To set hints for MPI using HDF5, see: H5PSETFAPLMPIO You use the 'info' parameter to pass these kinds of lowlevel MPIIO tuning tweaks. In C, the calls are like this: MPIInfo info; MPIInfocreate(&info); / strange thing about MPI hints: the key and value are strings / MPIInfoset(info, "bgnodespset", "1"); H5Psetfaplmpio
    HDF Knowledge BaseDec 14, 2017
  7. How to improve performance with Parallel HDF5

    Tuning parallel HDF5 for a specific application on a specific system requires playing with a lot of tunable parameters many of which are specific to certain … Alignment properties: For MPI IO and other parallel systems, choose an alignment which is a multiple of the disk block size. See: H5PSETALIGNMENT MPIIO
    HDF Knowledge BaseDec 14, 2017
  8. Are serial HDF5 and Parallel HDF5 in the same source code?

    Yes, serial HDF5 and Parallel HDF5 (PHDF5) are part of the same HDF5 source code. Parallel HDF5 is a configure option that you can specify to build HDF5 with: ./configure enableparallel HDF5 "knows" certain parallel compilers and will automatically enable Parallel HDF5 if one of those compilers is specified in the CC
    HDF Knowledge BaseDec 14, 2017
  9. Problems installing Parallel HDF5 on IBM Regatta (with AIX5)

    to compile and run some simple MPIIO programs, both C and Fortran90, with the compilers, mpccr and mpxlfr, respectively. Once you get your MPI parallel environment set up, you can proceed with the instructions mentioned above. faq hdf5 kbarticle parallel
    HDF Knowledge BaseJul 13, 2017
  10. How to write and NOT to write compound datasets using F90 in Parallel HDF5

    Here are two examples of writing compound datatypes using F90 in Parallel HDF5: compoundpall.f90 … a compound dataset in parallel. hdf5 kbarticle parallel compounddatatypes howto
    HDF Knowledge BaseJul 10, 2019