use of MPI derived types in Flexible API

[Wei-keng Liao]

Do you have more error messages from the crash? coredump trace?
Could you send us a small program that can reproduce the crash?

Wei-keng

On Sep 26, 2014, at 4:34 PM, Jim Edwards wrote:

> 
> Making progress, but I sometimes have num=0 on some IO tasks, this is causing a crash in pnetcdf.   I also tried setting num=1 and count=0 with the same effect.   
> 
> On Fri, Sep 26, 2014 at 10:06 AM, Wei-keng Liao <wkliao at eecs.northwestern.edu> wrote:
> 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
> 
> 
> 
> 
> -- 
> Jim Edwards
> 
> CESM Software Engineer
> National Center for Atmospheric Research
> Boulder, CO