use of MPI derived types in Flexible API

[Wei-keng Liao]

Hi, Jim

The C documentation is wrong. I will fix that. Thanks for catching the mistake.
Please use it as described in pnetcdf.h

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

FYI. There are a few examples in C and Fortran under examples:
  ./C/put_varn_float.c
./CXX/put_varn_float.cpp
./F77/put_varn_real.f
./F90/put_varn_real.f90


Wei-keng

On Sep 26, 2014, at 10:52 AM, Jim Edwards wrote:

> 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