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Subject: Re: [OMPI users] possible bug exercised by mpi4py
From: Ralph Castain (rhc_at_[hidden])
Date: 2012-05-23 17:02:20


I don't honestly think many of us have any knowledge of mpi4py. Does this test work with other MPIs?

MPI_Allgather seems to be passing our tests, so I suspect it is something in the binding. If you can provide the actual test, I'm willing to take a look at it.

On May 23, 2012, at 2:52 PM, Bennet Fauber wrote:

> I've installed the latest mpi4py-1.3 on several systems, and there is a repeated bug when running
>
> $ mpirun -np 5 python test/runtests.py
>
> where it throws an error on mpigather with openmpi-1.4.4 and hangs with openmpi-1.3.
>
> It runs to completion and passes all tests when run with -np of 2, 3, 4, 6, 7, 8, 9, 10, 11, and 12.
>
> There is a thread on this at
>
> http://groups.google.com/group/mpi4py/browse_thread/thread/509ac46af6f79973
>
> where others report being able to replicate, too.
>
> The compiler used first was gcc-4.6.2, with openmpi-1.4.4.
>
> These are all Red Hat machines, RHEL 5 or 6 and with multiple compilers and versions of openmpi 1.3.0 and 1.4.4.
>
> Lisandro who is the primary developer of mpi4py is able to replicate on Fedora 16.
>
> Someone else is able to reproduce with
>
> [ quoting from the groups.google.com page... ]
> ===============================================================
> It also happens with the current hg version of mpi4py and
> $ rpm -qa openmpi gcc python
> python-2.7.3-6.fc17.x86_64
> gcc-4.7.0-5.fc17.x86_64
> openmpi-1.5.4-5.fc17.1.x86_64
> ===============================================================
>
> So, I believe this is a bug to be reported. Per the advice at
>
> http://www.open-mpi.org/community/help/bugs.php
>
> If you feel that you do have a definite bug to report but are
> unsure which list to post to, then post to the user's list.
>
> Please let me know if there is additional information that you need to replicate.
>
> Some output is included below the signature in case it is useful.
>
> -- bennet
> --
> East Hall Technical Services
> Mathematics and Psychology Research Computing
> University of Michigan
> (734) 763-1182
>
> On RHEL 5, openmpi 1.3, gcc 4.1.2, python 2.7
>
> $ mpirun -np 5 --mca btl ^sm python test/runtests.py --verbose --no-threads --include cco_obj_inter
> [0_at_[hidden]] Python 2.7 (/home/bennet/epd7.2.2/bin/python)
> [0_at_[hidden]] MPI 2.0 (Open MPI 1.3.0)
> [0_at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.7/mpi4py)
> [1_at_[hidden]] Python 2.7 (/home/bennet/epd7.2.2/bin/python)
> [1_at_[hidden]] MPI 2.0 (Open MPI 1.3.0)
> [1_at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.7/mpi4py)
> [2_at_[hidden]] Python 2.7 (/home/bennet/epd7.2.2/bin/python)
> [2_at_[hidden]] MPI 2.0 (Open MPI 1.3.0)
> [2_at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.7/mpi4py)
> [3_at_[hidden]] Python 2.7 (/home/bennet/epd7.2.2/bin/python)
> [3_at_[hidden]] MPI 2.0 (Open MPI 1.3.0)
> [3_at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.7/mpi4py)
> [4_at_[hidden]] Python 2.7 (/home/bennet/epd7.2.2/bin/python)
> [4_at_[hidden]] MPI 2.0 (Open MPI 1.3.0)
> [4_at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.7/mpi4py)
> testAllgather (test_cco_obj_inter.TestCCOObjInter) ... testAllgather (test_cco_obj_inter.TestCCOObjInter) ... testAllgather (test_cco_obj_inter.TestCCOObjInter) ... testAllgather (test_cco_obj_inter.TestCCOObjInter) ... testAllgather (test_cco_obj_inter.TestCCOObjInter) ...
> [ hangs ]
>
> RHEL5
> ===================================================
> $ python
> Python 2.6.6 (r266:84292, Sep 12 2011, 14:03:14)
> [GCC 4.4.5 20110214 (Red Hat 4.4.5-6)] on linux2
>
> $ gcc -v
> Using built-in specs.
> COLLECT_GCC=gcc
> COLLECT_LTO_WRAPPER=/home/software/rhel6/gcc/4.7.0/libexec/gcc/x86_64-
> unknown-linux-gnu/4.7.0/lto-wrapper
> Target: x86_64-unknown-linux-gnu
> Configured with: ../gcc-4.7.0/configure --prefix=/home/software/rhel6/
> gcc/4.7.0 --with-mpfr=/home/software/rhel6/gcc/mpfr-3.1.0/ --with-mpc=/
> home/software/rhel6/gcc/mpc-0.9/ --with-gmp=/home/software/rhel6/gcc/
> gmp-5.0.5/ --disable-multilib
> Thread model: posix
> gcc version 4.7.0 (GCC)
>
> $ mpirun -np 5 python test/runtests.py --verbose --no-threads --include cco_obj_inter
> [4..._at_[hidden]] Python 2.6 (/usr/bin/python)
> [4..._at_[hidden]] MPI 2.1 (Open MPI 1.6.0)
> [4..._at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.6/mpi4py)
> [2..._at_[hidden]] Python 2.6 (/usr/bin/python)
> [2..._at_[hidden]] MPI 2.1 (Open MPI 1.6.0)
> [2..._at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.6/mpi4py)
> [1..._at_[hidden]] Python 2.6 (/usr/bin/python)
> [1..._at_[hidden]] MPI 2.1 (Open MPI 1.6.0)
> [1..._at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.6/mpi4py)
> [0..._at_[hidden]] Python 2.6 (/usr/bin/python)
> [0..._at_[hidden]] MPI 2.1 (Open MPI 1.6.0)
> [0..._at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.6/mpi4py)
> [3..._at_[hidden]] Python 2.6 (/usr/bin/python)
> [3..._at_[hidden]] MPI 2.1 (Open MPI 1.6.0)
> [3..._at_[hidden]] mpi4py 1.3 (build/lib.linux-x86_64-2.6/mpi4py)
> testAllgather (test_cco_obj_inter.TestCCOObjInter) ... testAllgather
> (test_cco_obj_inter.TestCCOObjInter) ... testAllgather
> (test_cco_obj_inter.TestCCOObjInter) ... testAllgather
> (test_cco_obj_inter.TestCCOObjInter) ... testAllgather
> (test_cco_obj_inter.TestCCOObjInter) ... ERROR
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