Hi Leigh, Yes, it is only a small difference in code between collective and independent mode for the MPI-IO VFD. To enable collective I/O, you pass a dataset transfer property list to H5Dwrite like this:
dxpl_id = H5Pcreate(H5P_DATASET_XFER);H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE); H5Dwrite(dset_id, H5T_NATIVE_FLOAT, memspace, filespace, dxpl_id, somedata0); One additional constraint with collective I/O, though, is that all MPI tasks must call H5Dwrite. If not, your program will stall in a barrier. In contrast, with independent I/O you can execute writes with no coordination among MPI tasks. If you do want only a subset of MPI tasks to write in collective mode, you can pass an empty selection to H5Dwrite for the non-writing tasks. Mark On Tue, Jan 18, 2011 at 12:45 AM, Leigh Orf <[email protected]> wrote: > Elena, > > That is good news, indeed this was with 1.8.5-patch1. > > Is code written with using independent IO structured significantly > different than with collective IO? I would like to get moving with pHDF5 and > as I am currently not too familiar with it, want to make sure that I am not > going to have to do a rewrite after the collective code works. It does seem > to all occur behind the scenes with the h5dwrite command, so I presume I am > safe. > > Thanks, > > Leigh > > On Mon, Jan 17, 2011 at 4:59 PM, Elena Pourmal <[email protected]>wrote: > >> Leigh, >> >> I am writing to confirm that the bug you reported does exist in >> 1.8.5-patch1, but is fixed in 1.8.6 (coming soon). >> >> Elena >> On Jan 16, 2011, at 3:47 PM, Leigh Orf wrote: >> >> I managed to build pHDF5 on blueprint.ncsa.uiuc.edu (IBM AIX Power 6). I >> compiled the hyperslab_by_chunk.f90 test program found at >> http://www.hdfgroup.org/HDF5/Tutor/phypechk.html without error. When I >> run it, however, I get the following output: >> >> ATTENTION: 0031-408 4 tasks allocated by LoadLeveler, continuing... >> ERROR: 0032-110 Attempt to free a predefined datatype (2) in >> MPI_Type_free, task 0 >> ERROR: 0032-110 Attempt to free a predefined datatype (2) in >> MPI_Type_free, task 1 >> ERROR: 0032-110 Attempt to free a predefined datatype (2) in >> MPI_Type_free, task 2 >> ERROR: 0032-110 Attempt to free a predefined datatype (2) in >> MPI_Type_free, task 3 >> HDF5: infinite loop closing library >> >> >> D,S,T,D,S,F,D,G,S,T,F,AC,FD,P,FD,P,FD,P,E,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL >> HDF5: infinite loop closing library >> >> The line which causes the grief is: >> >> CALL h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, data, dimsfi, error, & >> file_space_id = filespace, mem_space_id = memspace, >> xfer_prp = plist_id) >> >> If I replace that call with the one that is commented out in the program, >> it runs without a problem. That line is: >> >> CALL h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, data, dimsfi,error, & >> file_space_id = filespace, mem_space_id = memspace) >> >> Any ideas? I definitely want to take advantage of doing collective I/O if >> possible. >> >> Leigh >> >> -- >> Leigh Orf >> Associate Professor of Atmospheric Science >> Department of Geology and Meteorology >> Central Michigan University >> Currently on sabbatical at the National Center for Atmospheric Research >> in Boulder, CO >> NCAR office phone: (303) 497-8200 >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >> >> >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >> >> > > > -- > Leigh Orf > Associate Professor of Atmospheric Science > Department of Geology and Meteorology > Central Michigan University > Currently on sabbatical at the National Center for Atmospheric Research > in Boulder, CO > NCAR office phone: (303) 497-8200 > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org > >
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