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
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