Open MPI logo

Open MPI User's Mailing List Archives

  |   Home   |   Support   |   FAQ   |   all Open MPI User's mailing list

Subject: Re: [OMPI users] MPI_Allgather problem
From: Brett Tully (brett.tully_at_[hidden])
Date: 2012-01-27 05:12:03


Looking at the change log for 1.5.1 I see:
- Use memmove (instead of memcpy) when necessary (e.g., source
and destination overlap).

It seems as though this might be a likely candidate for a change that might
fix my problems if I am indeed using 1.5.3 following the installation of
OpenFOAM?

On Fri, Jan 27, 2012 at 10:02 AM, Brett Tully wrote:

> Interesting. In the same set of updates, I installed OpenFOAM from their
> Ubuntu deb package and it claims to ship with openmpi. I just downloaded
> their Third-party source tar and unzipped it to see what version of openmpi
> they are using, and it is 1.5.3. However, when I do man openmpi, or
> ompi_info, I get the same version as before (1.4.3). How do I determine for
> sure what is being included when I compile something using mpicc?
>
> Thanks,
> Brett.
>
>
>
> On Thu, Jan 26, 2012 at 10:05 PM, Jeff Squyres <jsquyres_at_[hidden]> wrote:
>
>> What version did you upgrade to? (we don't control the Ubuntu packaging)
>>
>> I see a bullet in the soon-to-be-released 1.4.5 release notes:
>>
>> - Fix obscure cases where MPI_ALLGATHER could crash. Thanks to Andrew
>> Senin for reporting the problem.
>>
>> But that would be surprising if this is what fixed your issue, especially
>> since it's not released yet. :-)
>>
>>
>>
>> On Jan 26, 2012, at 5:24 AM, Brett Tully wrote:
>>
>> > As of two days ago, this problem has disappeared and the tests that I
>> had written and run each night are now passing. Having looked through the
>> update log of my machine (Ubuntu 11.10) it appears as though I got a new
>> version of mpi-default-dev (0.6ubuntu1). I would like to understand this
>> problem in more detail -- is it possible to see what changed in this update?
>> > Thanks,
>> > Brett.
>> >
>> >
>> >
>> > On Fri, Dec 9, 2011 at 6:43 PM, teng ma <tma_at_[hidden]> wrote:
>> > I guess your output is from different ranks. YOu can add rank infor
>> inside print to tell like follows:
>> >
>> > (void) printf("rank %d: gathered[%d].node = %d\n", rank, i,
>> gathered[i].node);
>> >
>> > From my side, I did not see anything wrong from your code in Open MPI
>> 1.4.3. after I add rank, the output is
>> > rank 5: gathered[0].node = 0
>> > rank 5: gathered[1].node = 1
>> > rank 5: gathered[2].node = 2
>> > rank 5: gathered[3].node = 3
>> > rank 5: gathered[4].node = 4
>> > rank 5: gathered[5].node = 5
>> > rank 3: gathered[0].node = 0
>> > rank 3: gathered[1].node = 1
>> > rank 3: gathered[2].node = 2
>> > rank 3: gathered[3].node = 3
>> > rank 3: gathered[4].node = 4
>> > rank 3: gathered[5].node = 5
>> > rank 1: gathered[0].node = 0
>> > rank 1: gathered[1].node = 1
>> > rank 1: gathered[2].node = 2
>> > rank 1: gathered[3].node = 3
>> > rank 1: gathered[4].node = 4
>> > rank 1: gathered[5].node = 5
>> > rank 0: gathered[0].node = 0
>> > rank 0: gathered[1].node = 1
>> > rank 0: gathered[2].node = 2
>> > rank 0: gathered[3].node = 3
>> > rank 0: gathered[4].node = 4
>> > rank 0: gathered[5].node = 5
>> > rank 4: gathered[0].node = 0
>> > rank 4: gathered[1].node = 1
>> > rank 4: gathered[2].node = 2
>> > rank 4: gathered[3].node = 3
>> > rank 4: gathered[4].node = 4
>> > rank 4: gathered[5].node = 5
>> > rank 2: gathered[0].node = 0
>> > rank 2: gathered[1].node = 1
>> > rank 2: gathered[2].node = 2
>> > rank 2: gathered[3].node = 3
>> > rank 2: gathered[4].node = 4
>> > rank 2: gathered[5].node = 5
>> >
>> > Is that what you expected?
>> >
>> > On Fri, Dec 9, 2011 at 12:03 PM, Brett Tully <brett.tully_at_[hidden]>
>> wrote:
>> > Dear all,
>> >
>> > I have not used OpenMPI much before, but am maintaining a large legacy
>> application. We noticed a bug to do with a call to MPI_Allgather as
>> summarised in this post to Stackoverflow:
>> http://stackoverflow.com/questions/8445398/mpi-allgather-produces-inconsistent-results
>> >
>> > In the process of looking further into the problem, I noticed that the
>> following function results in strange behaviour.
>> >
>> > void test_all_gather() {
>> >
>> > struct _TEST_ALL_GATHER {
>> > int node;
>> > };
>> >
>> > int ierr, size, rank;
>> > ierr = MPI_Comm_size(MPI_COMM_WORLD, &size);
>> > ierr = MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>> >
>> > struct _TEST_ALL_GATHER local;
>> > struct _TEST_ALL_GATHER *gathered;
>> >
>> > gathered = (struct _TEST_ALL_GATHER*) malloc(size *
>> sizeof(*gathered));
>> >
>> > local.node = rank;
>> >
>> > MPI_Allgather(&local, sizeof(struct _TEST_ALL_GATHER), MPI_BYTE,
>> > gathered, sizeof(struct _TEST_ALL_GATHER), MPI_BYTE,
>> MPI_COMM_WORLD);
>> >
>> > int i;
>> > for (i = 0; i < numnodes; ++i) {
>> > (void) printf("gathered[%d].node = %d\n", i, gathered[i].node);
>> > }
>> >
>> > FREE(gathered);
>> > }
>> >
>> > At one point, this function printed the following:
>> > gathered[0].node = 2
>> > gathered[1].node = 3
>> > gathered[2].node = 2
>> > gathered[3].node = 3
>> > gathered[4].node = 4
>> > gathered[5].node = 5
>> >
>> > Can anyone suggest a place to start looking into why this might be
>> happening? There is a section of the code that calls MPI_Comm_split, but I
>> am not sure if that is related...
>> >
>> > Running on Ubuntu 11.10 and a summary of ompi_info:
>> > Package: Open MPI buildd_at_allspice Distribution
>> > Open MPI: 1.4.3
>> > Open MPI SVN revision: r23834
>> > Open MPI release date: Oct 05, 2010
>> > Open RTE: 1.4.3
>> > Open RTE SVN revision: r23834
>> > Open RTE release date: Oct 05, 2010
>> > OPAL: 1.4.3
>> > OPAL SVN revision: r23834
>> > OPAL release date: Oct 05, 2010
>> > Ident string: 1.4.3
>> > Prefix: /usr
>> > Configured architecture: x86_64-pc-linux-gnu
>> > Configure host: allspice
>> > Configured by: buildd
>> >
>> > Thanks!
>> > Brett
>> >
>> > _______________________________________________
>> > users mailing list
>> > users_at_[hidden]
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >
>> >
>> >
>> > --
>> > | Teng Ma Univ. of Tennessee |
>> > | tma_at_[hidden] Knoxville, TN |
>> > | http://web.eecs.utk.edu/~tma/ |
>> >
>> > _______________________________________________
>> > users mailing list
>> > users_at_[hidden]
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >
>> >
>> > _______________________________________________
>> > users mailing list
>> > users_at_[hidden]
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> --
>> Jeff Squyres
>> jsquyres_at_[hidden]
>> For corporate legal information go to:
>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>