Thanks for all the info! But still, can we get a copy of the test in C? That would make it significantly easier for us to tell if there is a problem with Open MPI -- mainly because we don't know anything about the internals of mpi4py.
On May 23, 2012, at 5:43 PM, Bennet Fauber wrote: > Thanks, Ralph, > > On Wed, 23 May 2012, Ralph Castain wrote: > >> I don't honestly think many of us have any knowledge of mpi4py. Does this >> test work with other MPIs? > > The mpi4py developers have said they've never seen this using mpich2. I have > not been able to test that myself. > >> 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. > > The actual test is included in the install bundle for mpi4py, along with the > C source code used to create the bindings. > > http://code.google.com/p/mpi4py/downloads/list > > The install is straightforward and simple. Unpack the tarball, make sure > that mpicc is in your path > > $ cd mpi4py-1.3 > $ python setup.py build > $ python setup.py install --prefix=/your/install > $ export PYTHONPATH=/your/install/lib/pythonN.M/site-packages > $ mpirun -np 5 python test/runtests.py \ > --verbose --no-threads --include cco_obj_inter > > where N.M are the major.minor numbers of your python distribution. > > What I find most puzzling is that, maybe, 1 out of 10 times it will run to > completion with -np 5, and it runs with all other numbers of processors I've > tested always. > > -- bennet > >> 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...@sirocco.math.lsa.umich.edu] Python 2.7 >>> (/home/bennet/epd7.2.2/bin/python) >>> [0...@sirocco.math.lsa.umich.edu] MPI 2.0 (Open MPI 1.3.0) >>> [0...@sirocco.math.lsa.umich.edu] mpi4py 1.3 >>> (build/lib.linux-x86_64-2.7/mpi4py) >>> [1...@sirocco.math.lsa.umich.edu] Python 2.7 >>> (/home/bennet/epd7.2.2/bin/python) >>> [1...@sirocco.math.lsa.umich.edu] MPI 2.0 (Open MPI 1.3.0) >>> [1...@sirocco.math.lsa.umich.edu] mpi4py 1.3 >>> (build/lib.linux-x86_64-2.7/mpi4py) >>> [2...@sirocco.math.lsa.umich.edu] Python 2.7 >>> (/home/bennet/epd7.2.2/bin/python) >>> [2...@sirocco.math.lsa.umich.edu] MPI 2.0 (Open MPI 1.3.0) >>> [2...@sirocco.math.lsa.umich.edu] mpi4py 1.3 >>> (build/lib.linux-x86_64-2.7/mpi4py) >>> [3...@sirocco.math.lsa.umich.edu] Python 2.7 >>> (/home/bennet/epd7.2.2/bin/python) >>> [3...@sirocco.math.lsa.umich.edu] MPI 2.0 (Open MPI 1.3.0) >>> [3...@sirocco.math.lsa.umich.edu] mpi4py 1.3 >>> (build/lib.linux-x86_64-2.7/mpi4py) >>> [4...@sirocco.math.lsa.umich.edu] Python 2.7 >>> (/home/bennet/epd7.2.2/bin/python) >>> [4...@sirocco.math.lsa.umich.edu] MPI 2.0 (Open MPI 1.3.0) >>> [4...@sirocco.math.lsa.umich.edu] 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...@host-rh6.engin.umich.edu] Python 2.6 (/usr/bin/python) >>> [4...@host-rh6.engin.umich.edu] MPI 2.1 (Open MPI 1.6.0) >>> [4...@host-rh6.engin.umich.edu] mpi4py 1.3 >>> (build/lib.linux-x86_64-2.6/mpi4py) >>> [2...@host-rh6.engin.umich.edu] Python 2.6 (/usr/bin/python) >>> [2...@host-rh6.engin.umich.edu] MPI 2.1 (Open MPI 1.6.0) >>> [2...@host-rh6.engin.umich.edu] mpi4py 1.3 >>> (build/lib.linux-x86_64-2.6/mpi4py) >>> [1...@host-rh6.engin.umich.edu] Python 2.6 (/usr/bin/python) >>> [1...@host-rh6.engin.umich.edu] MPI 2.1 (Open MPI 1.6.0) >>> [1...@host-rh6.engin.umich.edu] mpi4py 1.3 >>> (build/lib.linux-x86_64-2.6/mpi4py) >>> [0...@host-rh6.engin.umich.edu] Python 2.6 (/usr/bin/python) >>> [0...@host-rh6.engin.umich.edu] MPI 2.1 (Open MPI 1.6.0) >>> [0...@host-rh6.engin.umich.edu] mpi4py 1.3 >>> (build/lib.linux-x86_64-2.6/mpi4py) >>> [3...@host-rh6.engin.umich.edu] Python 2.6 (/usr/bin/python) >>> [3...@host-rh6.engin.umich.edu] MPI 2.1 (Open MPI 1.6.0) >>> [3...@host-rh6.engin.umich.edu] 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 >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
