[AMBER-Developers] [Fwd: Re: [mpich-discuss] MPICH2 with MPI-1 code]

From: Mark Williamson <mjw.sdsc.edu>
Date: Wed, 14 Apr 2010 13:36:10 -0700

Dear all,

I sought some clarification on this from the MPICH2 authors and I have a
conclusion. Section 2.2, page 7 of the MPI-1.3 standard [1] disallows
argument aliasing.

Mark Williamson, Post Doc
Walker Molecular Dynamics Group
Room 395E
San Diego Supercomputer Center
9500 Gilman Drive
La Jolla, CA 92093-0505
Email:  mjw at sdsc.edu
Office: 858-246-0827

attached mail follows:

On Apr 14, 2010, at 2:19 PM, Mark Williamson wrote:

> Looking closer into the fail, it pertained to this error message
> from a recent MPICH2 release:
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x6e51a4 src_=0x6e51a0
> len_=100
> Having researched this, it was related to an "Incorrect call to
> MPI_Gatherv"; the root process aliased the send buffer and the
> receive buffer alias to each other. This of course, can be resolved
> by using MPI_IN_PLACE. Interestingly, mpich2-1.0.7, with which we
> had used in the past, never complained about this.

We improve our error checking constantly; this is an example of such
error checking. Error checking like this is typically helpful both to
applications and to us when supporting applications.

The error message in this particular case is not helpful enough, but
that has already been rectified in the current code and a much clearer
error message will be elicited by similarly incorrect calls in future

> So, this brings me to my question. My understanding is that
> MPI_IN_PLACE is a MPI-2 specific argument value.

Correct. My copy of the MPI-1.3 standard does not mention MPI_IN_PLACE.

> The piece of AMBER code that I refer to in this discussion written
> within the a MPI-1 standard. As stated on the MPICH2 home page,
> "MPICH2 is a high-performance and widely portable implementation of
> the Message Passing Interface (MPI) standard (*BOTH* MPI-1 and
> MPI-2)". If I use MPI_IN_PLACE, the code will not be MPI-1 standard,
> so how to I specific instruct MPICH2's mpif90 or mpirun that one is
> using a MPI-1 code, hence avoiding this error?

This was not valid MPI code in the MPI-1 standard either. Section
2.2, page 7 of the MPI-1.3 standard [1] disallows argument aliasing.
You have at least three options:

1) As another poster suggested, disable assertions and keep your code
as-is. Your code isn't strictly portable MPI, so you might have
trouble with it on other MPI implementations, including later versions
of MPICH2.

2) Use separate input and output buffers. This is the only valid way
to fix this in strict MPI-1.

3) Make the jump to modest usage of MPI-2 features, specifically
MPI_IN_PLACE. Basic MPI-2 support isn't hard to come by at this
point, so I consider this to be a reasonable option. Your specific
circumstances (access to machines, need to use particular MPI
implementations, etc) will dictate whether this is practical for you.


[1] http://www.mpi-forum.org/docs/mpi-1.3/mpi-report-1.3-2008-05-30.pdf

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