Hi Pasha,
I appreciate the feedback. I'm assuming that this upgrade to the Open Fabric
driver is something that the System Admin. of the cluster should be
concerned with and not I ?
Thanks,
Peter
Peter Diamessis wrote:
--- On *Thu, 6/19/08, Pavel Shamis (Pasha)
/<pa...@dev.mellanox.co.il>/* wrote:
From: Pavel Shamis (Pasha) <pa...@dev.mellanox.co.il>
Subject: Re: [OMPI users] Open MPI timeout problems.
To: pj...@cornell.edu, "Open MPI Users" <us...@open-mpi.org>
Date: Thursday, June 19, 2008, 5:20 AM
Usually the retry exceed point to some network issue on your cluster. I
see from the logs that you still
use MVAPI. If i remember correct, MVAPI include IBADM application that
should be able to check and debug the network.
BTW I recommend you to update your MVAPI driver to latest OpenFabric driver.
Peter Diamessis wrote:
> Dear folks,
>
> I would appreciate your help on the following:
>
> I'm running a parallel CFD code on the Army Research Lab's MJM
Linux
> cluster, which uses Open-MPI. I've run the same code on other Linux
> clusters that use MPICH2 and had never run into this problem.
>
> I'm quite convinced that the bottleneck for my code is this data
> transposition routine, although I have not done any rigorous profiling
> to check on it. This is where 90% of the parallel communication takes
> place. I'm running a CFD code that uses a 3-D rectangular domain which
> is partitioned across processors in such a way that each processor
> stores vertical slabs that are contiguous in the x-direction but shared
> across processors in the y-dir. . When a 2-D Fast Fourier Transform
> (FFT) needs to be done, data is transposed such that the vertical slabs
> are now contiguous in the y-dir. in each processor.
>
> The code would normally be run for about 10,000 timesteps. In the
> specific case which blocks, the job crashes after ~200 timesteps and at
> each timestep a large number of 2-D FFTs are performed. For a domain
> with resolution of Nx * Ny * Nz points and P processors, during one FFT,
> each processor performs P Sends and P Receives of a message of size
> (Nx*Ny*Nz)/P, i.e. there are a total of 2*P^2 such Sends/Receives.
>
> I've focused on a case using P=32 procs with Nx=256, Ny=128, Nz=175.
You
> can see that each FFT involves 2048 communications. I totally rewrote my
> data transposition routine to no longer use specific blocking/non-
> blocking Sends/Receives but to use MPI_ALLTOALL which I would hope is
> optimized for the specific MPI Implementation to do data transpositions.
> Unfortunately, my code still crashes with time-out problems like before.
>
> This happens for P=4, 8, 16 & 32 processors. The same MPI_ALLTOALL
code
> worked fine on a smaller cluster here. Note that in the future I would
> like to work with resolutions of (Nx,Ny,Nz)=(512,256,533) and P=128 or
> 256 procs. which will involve an order of magnitude more communication.
>
> Note that I ran the job by submitting it to an LSF queue system. I've
> attached the script file used for that. I basically enter bsub -x <
> script_openmpi at the command line.
>
> When I communicated with a consultant at ARL, he recommended I use
> 3 specific script files which I've attached. I believe these enable
> control over some of the MCA parameters. I've experimented with values
> of btl_mvapi_ib_timeout = 14, 18, 20, 24 and 30 and I still have this
> problem. I am still in contact with this consultant but thought it would
> be good to contact you folks directly.
>
> Note:
> a) echo $PATH returns:
>
> /opt/mpi/x86_64/pgi/6.2/openmpi-1.2/bin:
> /opt/compiler/pgi/linux86-64/6.2/bin:/usr/lsf/6.2/linux2.6-glibc2.3-
> ia32e/bin:/usr/lsf/6.2/linux2.6-glibc2.3-
> ia32e/etc:/usr/cta/modules/3.1.6/bin:
> /usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/games:/opt/gnome/bin:
> .:/usr/lib/java/bin:/opt/gm/bin:/opt/mx/bin:/opt/PST/bin
>
> b) echo $LD_LIBRARY_PATH returns:
> /opt/mpi/x86_64/pgi/6.2/openmpi-1.2/lib:
> /opt/compiler/pgi/linux86-64/6.2/lib:
> /opt/compiler/pgi/linux86-64/6.2/libso:/usr/lsf/6.2/linux2.6-glibc2.3-
> ia32e/lib
>
> I've attached the following files:
> 1) Gzipped versions of the .out & .err files of the failed job.
> 2) ompi_info.log: The output of ompi_info -all
> 3) mpirun, mpirun.lsf, openmpi_wrapper: the three script files provided
> to me by the ARL consultant. I store these in my home directory and
> experimented with the MCA parameter btl_mvapi_ib_timeout in mpirun.
> 4) The script file script_openmpi that I use to submit the job.
>
> I am unable to provide you with the config.log file as I cannot find it
> in the top level Open MPI directory.
>
> I am also unable to provide you with details on the specific cluster
> that I'm running in terms of the network. I know they use Infiniband
and
> some more detail may be found on:
>
> http://www.arl.hpc.mil/Systems/mjm.html
>
> Some other info:
> a) uname -a returns:
> Linux l1 2.6.5-7.308-smp.arl-msrc #2 SMP Thu Jan 10 09:18:41 EST 2008
> x86_64 x86_64 x86_64 GNU/Linux
>
> b) ulimit -l returns: unlimited
>
> I cannot see a pattern as to which nodes are bad and which are good ...
>
>
> Note that I found in the mail archives that someone had a similar
> problem in transposing a matrix with 16 million elements. The only
> answer I found in the thread was to increase the value of
> btl_mvapi_ib_timeout to 14 or 16, something I've done already.
>
> I'm hoping that there must be a way out of this problem. I need to
> get my code running as I'm under pressure to produce results for a
> grant that's paying me.
>
> If you have any feedback I would be hugely grateful.
>
> Sincerely,
>
> Peter Diamessis
> Cornell University
>
>
>
> ------------------------------------------------------------------------
>
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--
-------------------------------------------------------------
Peter Diamessis
Assistant Professor
Environmental Fluid Mechanics & Hydrology
School of Civil and Environmental Engineering
Cornell University
Ithaca, NY 14853
Phone: (607)-255-1719 --- Fax: (607)-255-9004
pj...@cornell.edu <mailto:pj...@cornell.edu>
http://www.cee.cornell.edu/faculty/pjd38
