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Subject: Re: [OMPI users] Problems on large clusters
From: Thorsten Schuett (schuett_at_[hidden])
Date: 2011-06-22 03:13:35


Sure. It's an SGI ICE cluster with dual-rail IB. The HCAs are Mellanox
ConnectX IB DDR.

This is a 2040 cores job. I use 255 nodes with one MPI task on each node and
use 8-way OpenMP.

I don't need -np and -machinefile, because mpiexec picks up this information
from PBS.

Thorsten

On Tuesday, June 21, 2011, Gilbert Grosdidier wrote:
> Bonjour Thorsten,
>
> Could you please be a little bit more specific about the cluster
> itself ?
>
> G.
>
> Le 21 juin 11 à 17:46, Thorsten Schuett a écrit :
> > Hi,
> >
> > I am running openmpi 1.5.3 on a IB cluster and I have problems
> > starting jobs
> > on larger node counts. With small numbers of tasks, it usually
> > works. But now
> > the startup failed three times in a row using 255 nodes. I am using
> > 255 nodes
> > with one MPI task per node and the mpiexec looks as follows:
> >
> > mpiexec --mca btl self,openib --mca mpi_leave_pinned 0 ./a.out
> >
> > After ten minutes, I pulled a stracktrace on all nodes and killed
> > the job,
> > because there was no progress. In the following, you will find the
> > stack trace
> > generated with gdb thread apply all bt. The backtrace looks
> > basically the same
> > on all nodes. It seems to hang in mpi_init.
> >
> > Any help is appreciated,
> >
> > Thorsten
> >
> > Thread 3 (Thread 46914544122176 (LWP 28979)):
> > #0 0x00002b6ee912d9a2 in select () from /lib64/libc.so.6
> > #1 0x00002b6eeabd928d in service_thread_start (context=<value
> > optimized out>)
> > at btl_openib_fd.c:427
> > #2 0x00002b6ee835e143 in start_thread () from /lib64/libpthread.so.0
> > #3 0x00002b6ee9133b8d in clone () from /lib64/libc.so.6
> > #4 0x0000000000000000 in ?? ()
> >
> > Thread 2 (Thread 46916594338112 (LWP 28980)):
> > #0 0x00002b6ee912b8b6 in poll () from /lib64/libc.so.6
> > #1 0x00002b6eeabd7b8a in btl_openib_async_thread (async=<value
> > optimized
> > out>) at btl_openib_async.c:419
> > #2 0x00002b6ee835e143 in start_thread () from /lib64/libpthread.so.0
> > #3 0x00002b6ee9133b8d in clone () from /lib64/libc.so.6
> > #4 0x0000000000000000 in ?? ()
> >
> > Thread 1 (Thread 47755361533088 (LWP 28978)):
> > #0 0x00002b6ee9133fa8 in epoll_wait () from /lib64/libc.so.6
> > #1 0x00002b6ee87745db in epoll_dispatch (base=0xb79050, arg=0xb558c0,
> > tv=<value optimized out>) at epoll.c:215
> > #2 0x00002b6ee8773309 in opal_event_base_loop (base=0xb79050,
> > flags=<value
> > optimized out>) at event.c:838
> > #3 0x00002b6ee875ee92 in opal_progress () at runtime/
> > opal_progress.c:189
> > #4 0x0000000039f00001 in ?? ()
> > #5 0x00002b6ee87979c9 in std::ios_base::Init::~Init () at
> > ../../.././libstdc++-v3/src/ios_init.cc:123
> > #6 0x00007fffc32c8cc8 in ?? ()
> > #7 0x00002b6ee9d20955 in orte_grpcomm_bad_get_proc_attr (proc=<value
> > optimized out>, attribute_name=0x2b6ee88e5780 " \020322351n+",
> > val=0x2b6ee875ee92, size=0x7fffc32c8cd0) at grpcomm_bad_module.c:500
> > #8 0x00002b6ee86dd511 in ompi_modex_recv_key_value (key=<value
> > optimized
> > out>, source_proc=<value optimized out>, value=0xbb3a00, dtype=14
> > '\016') at
> > runtime/ompi_module_exchange.c:125
> > #9 0x00002b6ee86d7ea1 in ompi_proc_set_arch () at proc/proc.c:154
> > #10 0x00002b6ee86db1b0 in ompi_mpi_init (argc=15, argv=0x7fffc32c92f8,
> > requested=<value optimized out>, provided=0x7fffc32c917c) at
> > runtime/ompi_mpi_init.c:699
> > #11 0x00007fffc32c8e88 in ?? ()
> > #12 0x00002b6ee77f8348 in ?? ()
> > #13 0x00007fffc32c8e60 in ?? ()
> > #14 0x00007fffc32c8e20 in ?? ()
> > #15 0x0000000009efa994 in ?? ()
> > #16 0x0000000000000000 in ?? ()
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> --
> *---------------------------------------------------------------------*
> Gilbert Grosdidier Gilbert.Grosdidier_at_[hidden]
> LAL / IN2P3 / CNRS Phone : +33 1 6446 8909
> Faculté des Sciences, Bat. 200 Fax : +33 1 6446 8546
> B.P. 34, F-91898 Orsay Cedex (FRANCE)
> *---------------------------------------------------------------------*