Re: [netcdf-hdf] using POSIX calls when configured for MPI-IO

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  • To: Quincey Koziol <koziol@xxxxxxxxxxxx>
  • Subject: Re: [netcdf-hdf] using POSIX calls when configured for MPI-IO
  • From: robl@xxxxxxxxxxx (Robert Latham)
  • Date: Mon, 17 Sep 2007 11:47:11 -0500
On Sat, Sep 15, 2007 at 07:03:06PM -0500, Quincey Koziol wrote:
> I think you might want the "MPI-POSIX" driver in HDF5 (look at
> H5Pset_fapl_mpiposix), but I don't know if the netCDF-4 library is
> exporting a way to use that in netCDF-4 applications.  Hmm, but re-
> reading your note again, I'm not certain.  Can you take a look at
> the  MPI-POSIX file driver and see if that's what you want?

Hi Quincey

That's close, but 

H5FD_mpio_read actually uses MPI_File_* calls, whereas
H5FD_mpiposix_read uses fread and such. 

What I'm asking for is an all MPI-IO path for applications to use.
This is already possible in HDF5.  

There are two reasons for this.  First, MPI_File_open does not
necessarily take a POSIX-style file name:

  "The format for specifying the file name in the filename argument is
  implementation dependent and must be documented by the

Second, by using all MPI-IO routines, there are opportunities for
performance tuning (through collective I/O or MPI_Info hints)
unavailable in the POSIX I/O case.  

I'm quite interested in an all MPI-IO path, because I made extensive
use  of this feature of HDF5 to track down bugs found by the HDF5
parallel tests last year.   Also, an all MPI-IO path allows us to make
full use of all the ROMIO optimizations we've worked on.  

You guys are so close to this, and that's why I'm sort of pushing.  It
looks like just a few tweaks to nc_get_file_version() and
nc_check_for_hdf5() get you there.


Rob Latham
Mathematics and Computer Science Division    A215 0178 EA2D B059 8CDF
Argonne National Lab, IL USA                 B29D F333 664A 4280 315B

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