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From: Chris Reeves (chris.reeves_at_[hidden])
Date: 2007-06-19 09:18:23


(This time with attachments...)

Hi there,

I've had a look through the FAQ and searched the list archives and can't find
any similar problems to this one.

I'm running OpenMPI 1.2.2 on 10 Intel iMacs (Intel Core2 Duo CPU). I am
specifiying two slots per machine and starting my job with:
/Network/Guanine/csr201/local-i386/opt/openmpi/bin/mpirun -np 20 --hostfile
bhost.jobControl nice -19 /Network/Guanine/csr201/jobControl/run_torus.pl
/Network/Guanine/csr201/models-gap/torus/torus.ompiosx-intel

The config.log and output of 'ompi_info --all' are attached.

Also attached is a small patch that I wrote to work around some firewall
limitations on the nodes (I don't know if there's a better way to do this -
suggestions are welcome). The patch may or may not be relevant, but I'm not
ruling out network issues and a bit of peer review never goes amiss in case
I've done something very silly.

The programme that I'm trying to run is fairly hefty, so I'm afraid that I
can't provide you with a simple test case to highlight the problem. The best I
can do it provide you with a description of where I'm at and then ask for some
advice/suggestions...

The code itself has run in the past with various versions of MPI/LAM and
OpenMPI and hasn't, to my knowledge, undergone any significant changes
recently. I have noticed delays before, both on this system and on others,
when MPI_BARRIER is called but they don't always result in a permanent
'spinning' of the process.

The 20-node job that I'm running right now is using 90-100% of every CPU, but
hasn't made any progress for around 14 hours. I've used GDB to attach to each
of these processes and verified that every single one of them is sitting
inside a call to MPI_BARRIER. My understanding is that once every process hits
the barrier, they should then move on to the next part of the code.

Here's an example of what I see when I attach to one of these processes:
------------------------------------------------------------------------------

Attaching to program: `/private/var/automount/Network/Guanine/csr201/models-gap/torus/torus.ompiosx-intel', process 29578.
Reading symbols for shared libraries ..+++++.................................................................... done
0x9000121c in sigprocmask ()
(gdb) where
#0 0x9000121c in sigprocmask ()
#1 0x01c46f96 in opal_evsignal_recalc ()
#2 0x01c458c2 in opal_event_base_loop ()
#3 0x01c45d32 in opal_event_loop ()
#4 0x01c3e6f2 in opal_progress ()
#5 0x01b6083e in ompi_request_wait_all ()
#6 0x01ec68d8 in ompi_coll_tuned_sendrecv_actual ()
#7 0x01ecbf64 in ompi_coll_tuned_barrier_intra_bruck ()
#8 0x01b75590 in MPI_Barrier ()
#9 0x01aec47a in mpi_barrier__ ()
#10 0x0011c66c in MAIN_ ()
#11 0x002870f9 in main (argc=1, argv=0xbfffe6ec)
(gdb)

------------------------------------------------------------------------------

Does anyone have any suggestions as to what might be happening here? Is there
any way to 'tickle' the processes and get them to move on? What if some
packets went missing on the network? Surely TCP should take care of this an
resend? As implied by my line of questioning, my current thoughts are that
some messages between nodes have somehow gone missing. Could this happen? What
could cause this? All machines are on the same subnet.

I'm sorry my question is so open, but I don't know much about the internals of
OpenMPI and how it passes messages and I'm looking for some ideas on where to
start searching!

Thanks in advance for any help or suggestions that you can offer,
    Chris