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Subject: Re: [OMPI users] parallel I/O on 64-bit indexed arays
From: Troels Haugboelle (haugboel_at_[hidden])
Date: 2011-06-07 04:53:55


> If I understand your question correctly, this is *exactly* one of the reasons that the MPI Forum has been arguing about the use of a new type, "MPI_Count", for certain parameters that can get very, very large.

Yes, that would help, but unfortunately only in the future.

> Sidenote: I believe that a workaround for you is to create some new MPI datatypes (e.g., of type contiguous) that you can then use to multiply to get to the offsets that you want. I.e., if you make a type contig datatype of 4 doubles, you can still only specify up to 2B of them, but that will now get you up to an offset of (2B * 4 * sizeof(double)) rather than (2B * sizeof(double)). Make sense?

In principle yes, but the problem is we have an unequal amount of
particles on each node, so the length of each array is not guaranteed to
be divisible by 2, 4 or any other number. If I have understood the
definition of MPI_TYPE_CREATE_SUBARRAY correctly the offset can be
64-bit, but not the global array size, so, optimally, what I am looking
for is something that has unequal size for each thread, simple vector,
and with 64-bit offsets and global array size.

Another possible workaround would be to identify subsections that do not
pass 2B elements, make sub communicators, and then let each of them dump
their elements with proper offsets. It may work. The problematic
architecture is a BG/P. On other clusters doing simple I/O, letting all
threads open the file, seek to their position, and then write their
chunk works fine, but somehow on BG/P performance drops dramatically. My
guess is that there is some file locking, or we are overwhelming the I/O
nodes..

> This ticket for the MPI-3 standard is a first step in the right direction, but won't do everything you need (this is more FYI):
>
> https://svn.mpi-forum.org/trac/mpi-forum-web/ticket/265
>
> See the PDF attached to the ticket; it's going up for a "first reading" in a month. It'll hopefully be part of the MPI-3 standard by the end of the year (Fab Tillier, CC'ed, has been the chief proponent of this ticket for the past several months).
>
> Quincey Koziol from the HDF group is going to propose a follow on to this ticket, specifically about the case you're referring to -- large counts for file functions and datatype constructors. Quincey -- can you expand on what you'll be proposing, perchance?

Interesting, I think something along the lines of the note would be very
useful and needed for large applications.

Thanks a lot for the pointers and your suggestions,

cheers,

Troels