NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
On 01/27/2012 01:22 PM, Rob Latham wrote:
On Wed, Jan 25, 2012 at 10:06:59PM -0900, Constantine Khroulev wrote:Hello NetCDF developers, My apologies to list subscribers not interested in these (very) technical details.I'm interested! I hope you send more of these kinds of reports.When the collective parallel access mode is selected all processors in a communicator have to call H5Dread() (or H5Dwrite()) the same number of times. In nc_put_varm_*, NetCDF breaks data into contiguous segments that can be written one at a time (see NCDEFAULT_get_varm(...) in libdispatch/var.c, lines 479 and on). In some cases the number of these segments varies from one processor to the next. As a result as soon as one of the processors in a communicator is done writing its data the program locks up, because now only a subset of processors in this communicator are calling H5Dwrite(). (Unless all processors have the same number of "data segments" to write, that is.)Oh, that's definitely a bug. netcdf4 should call something like MPI_Allreduce with MPI_MAX to figure out how many "rounds" of I/O will be done (this is what we do inside ROMIO, for a slightly different reason)But here's the thing: I'm not sure this is worth fixing. The only reason to use collective I/O I can think of is for better performance, and then avoiding sub-sampled and mapped reading and writing is a good idea anyway.well, if varm and vars are the natural way to access the data, then the library should do what it can to do that efficiently. The fix appears to be straightforward. Collective I/O has a lot of advantages on some platforms: it will automatically select a subset of processors or automatically construct a file access most closely suited to the underlying file system. ==rob
Was this ever fixed? -- Orion Poplawski Technical Manager 303-415-9701 x222 NWRA, Boulder Office FAX: 303-415-9702 3380 Mitchell Lane orion@xxxxxxxx Boulder, CO 80301 http://www.nwra.com
netcdfgroup archives: