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Subject: Re: [OMPI users] Fw: Re: Open MPI timeout problems.
From: Peter Diamessis (pjd38_at_[hidden])
Date: 2008-06-19 16:37:21


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)
> /<pasha_at_[hidden]>/* wrote:
>
> From: Pavel Shamis (Pasha) <pasha_at_[hidden]>
> Subject: Re: [OMPI users] Open MPI timeout problems.
> To: pjd38_at_[hidden], "Open MPI Users" <users_at_[hidden]>
> 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
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>

-- 
 
-------------------------------------------------------------
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
pjd38_at_[hidden] <mailto:pjd38_at_[hidden]>
http://www.cee.cornell.edu/faculty/pjd38