use of MPI derived types in Flexible API

[Jim Edwards]

Wei-king,


There is a discrepancy between the documentation and the code with respect
to the varn functions.   The documentation at
http://cucis.ece.northwestern.edu/projects/PNETCDF/doc/pnetcdf-c/ncmpi_005fput_005fvarn_005f_003ctype_003e.html
has:

int ncmpi_put_varn_all        (int               ncid,
                               int               varid,
                               int               num,
                               const MPI_Offset  starts[num][],
                               const MPI_Offset  counts[num][],
                               const void       *bufs[num],
                               MPI_Offset        bufcounts[num],
                               MPI_Datatype      buftypes[num]);


While the source trunk has:


int ncmpi_put_varn_all(int ncid, int varid, int num, MPI_Offset* const
starts[],
              MPI_Offset* const counts[], const void *buf, MPI_Offset
bufcount,
              MPI_Datatype buftype);

The last three arguments are not arrays.

- Jim



On Wed, Sep 24, 2014 at 6:44 PM, Wei-keng Liao <wkliao at eecs.northwestern.edu
> wrote:

>
> If the data is contiguous in memory, then there is no need to use varm or
> flexible APIs.
>
> There is a new set of APIs named varn (available in PnetCDF version 1.4.0
> and later), eg.
>     ncmpi_put_varn_float_all()
> It allows a single API call to write a contiguous buffer to a set of
> noncontiguous places in file.
> Each noncontiguous place is specified by a (start, count) pair. The
> start-count pairs can be
> arbitrary in file offsets (i.e. unsorted order in offsets).
> Please note this API family is blocking. There is no nonblocking
> counterpart.
>
> In term of performance, this call is equivalent to making multiple iput or
> bput calls.
>
> Wei-keng
>
> On Sep 24, 2014, at 6:58 PM, Jim Edwards wrote:
>
> > Data is contiguous in memory but data on a given task maps to various
> non contiguous points in the file.   I can guarantee that the data in
> memory on a given mpi task is in monotonically increasing order with
> respect to offsets into the file, but not more than that.
> >
> > On Wed, Sep 24, 2014 at 3:43 PM, Wei-keng Liao <
> wkliao at eecs.northwestern.edu> wrote:
> > Hi, Jim
> >
> > Do you mean the local I/O buffer contains a list of non-contiguous data
> in memory?
> > Or do you mean "distributed" as data is partitioned across multiple MPI
> processes?
> >
> > The varm APIs and the "flexible" APIs that take an MPI derived datatype
> argument
> > are for users to describe non-contiguous data in the local I/O buffer.
> The imap
> > and MPI datatype argument has no effect to the data access in files. So,
> I need
> > to know which case you are referring to first.
> >
> > Thanks for pointing out the error in the user guide. It is fixed.
> >
> > Wei-keng
> >
> > On Sep 24, 2014, at 2:30 PM, Jim Edwards wrote:
> >
> > > I want to write a distributed variable to a file and the way the
> > > data is distributed is fairly random with respect to the ordering on
> the file.
> > >
> > > It seems like I can do several things from each task in order to write
> the data -
> > >
> > >       • I can specify several blocks of code using start and count and
> make mulitple calls on each task to ncmpi_bput_vara_all
> > >       • I can define an MPI derived type and make a single call to
> ncmpi_bput_var_all on each task
> > >       • I (think I) can use ncmpi_bput_varm_all and specify an imap
> (btw: the pnetcdf users guide has this interface wrong)
> > > Are any of these better from a performance standpoint?
> > >
> > > Thanks,
> > >
> > >
> > >
> > >
> > > --
> > > Jim Edwards
> > >
> > > CESM Software Engineer
> > > National Center for Atmospheric Research
> > > Boulder, CO
> >
> >
> >
> >
> > --
> > Jim Edwards
> >
> > CESM Software Engineer
> > National Center for Atmospheric Research
> > Boulder, CO
>
>


-- 
Jim Edwards

CESM Software Engineer
National Center for Atmospheric Research
Boulder, CO
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