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Subject: Re: [OMPI users] Problems on large clusters
From: Thorsten Schuett (schuett_at_[hidden])
Date: 2011-06-22 09:43:59


Thanks for the tip. I can't tell yet whether it helped or not. However, with
your settings I get the following warning:
WARNING: Open MPI will create a shared memory backing file in a
directory that appears to be mounted on a network filesystem.

I repeated the run with my settings and I noticed that on at least one node my
app didn't came up. I can see an orted daemon on this node, but no other
process. And this was 30 minutes after the app started.

orted -mca ess tm -mca orte_ess_jobid 125894656 -mca orte_ess_vpid 63 -mc
a orte_ess_num_procs 255 --hnp-uri ...

Thorsten

On Wednesday, June 22, 2011, Gilbert Grosdidier wrote:
> Bonjour Thorsten,
>
> I'm not surprised about the cluster type, indeed,
> but I do not remember getting such specific hang up you mention.
>
> Anyway, I suspect SGI Altix is a little bit special for OpenMPI,
> and I usually run with the following setup:
> - there is need to create for each job a specific tmp area,
> like "/scratch/ggg/uuu/run/tmp/pbs.${PBS_JOBID}"
> - then use something like that:
>
> setenv TMPDIR "/scratch/ggg/uuu/run/tmp/pbs.${PBS_JOBID}"
> setenv OMPI_PREFIX_ENV "/scratch/ggg/uuu/run/tmp/pbs.${PBS_JOBID}"
> setenv OMPI_MCA_mpi_leave_pinned_pipeline 1
>
> - then, for running, many of these -mca options are probably useless
> with your app,
> while many of them may show to be useful. Your own way ...
>
> mpiexec -mca coll_tuned_use_dynamic_rules 1 -hostfile $PBS_NODEFILE -
> mca rmaps seq -mca btl_openib_rdma_pipeline_send_length 65536 -mca
> btl_openib_rdma_pipeline_frag_size 65536 -mca
> btl_openib_min_rdma_pipeline_size 65536 -mca
> btl_self_rdma_pipeline_send_length 262144 -mca
> btl_self_rdma_pipeline_frag_size 262144 -mca plm_rsh_num_concurrent
> 4096 -mca mpi_paffinity_alone 1 -mca mpi_leave_pinned_pipeline 1 -mca
> btl_sm_max_send_size 128 -mca
> coll_tuned_pre_allocate_memory_comm_size_limit 1048576 -mca
> btl_openib_cq_size 128 -mca btl_ofud_rd_num 128 -mca
> mpi_preconnect_mpi 0 -mca mpool_sm_min_size 131072 -mca btl
> sm,openib,self -mca btl_openib_want_fork_support 0 -mca
> opal_set_max_sys_limits 1 -mca osc_pt2pt_no_locks 1 -mca
> osc_rdma_no_locks 1 YOUR_APP
>
> (Watch the step : only one line only ...)
>
> This should be suitable for up to 8k cores.
>
>
> HTH, Best, G.
>
> Le 22 juin 11 à 09:13, Thorsten Schuett a écrit :
> > 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)
> >>
> >> *---------------------------------------------------------------------*
> >
> > _______________________________________________
> > 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)
> *---------------------------------------------------------------------*