use of MPI derived types in Flexible API

[Wei-keng Liao]

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