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Subject: Re: [OMPI users] Bus Error in ompi_free_list_grow
From: Peter Cebull (peter.cebull_at_[hidden])
Date: 2008-11-14 13:14:08


Jeff Squyres wrote:
> Could this issue actually be related to:
>
> http://www.open-mpi.org/community/lists/devel/2008/11/4882.php
>
> (read through the thread to get to the error handling stuff)
You might be right that this issue is the problem. Our system has
diskless nodes, so /tmp uses a ramdisk. It was initially configured so
that /tmp could use up to 8 GB of the 16 GB of memory on each node. We
didn't notice until recently that something in the upgrade we made to
the system dropped the size of /tmp to 48 MB, so maybe that's the cause
of the problem. We've increased the size of /tmp again in the compute
node image, but I'll have to wait until we get a chance to push out the
new image before I can tell if that will fix our problem.

Thanks!
Peter
>
>
>
> On Nov 14, 2008, at 7:41 AM, Geraldo Veiga wrote:
>
>> Thanks Peter. Blocking the shared memory layer did the trick for our
>> program too.
>>
>> For the record, we also have SGI Propack 6 installed
>> (sgi-propack-release-6-sgi600r3).
>>
>> Is the on-node shared memory support completely blocked? What if the
>> MPI process calls a procedure that uses OpenMP threads, for instance?
>>
>>
>> On Thu, Nov 13, 2008 at 1:44 PM, Peter Cebull <peter.cebull_at_[hidden]>
>> wrote:
>> Geraldo,
>>
>> The previous message you saw was for our Altix ICE system. Since we
>> started seeing these errors after upgrading to SGI Propack 6, I
>> wonder if there's a bug somewhere in the Propack software or an
>> incompatibility between Open MPI and OFED 1.3 (we had no problems
>> under OFED 1.2). A workaround I stumbled across is to turn off the sm
>> component:
>>
>> mpirun --mca btl ^sm . . .
>>
>> That seems to allow our application to run, although I guess at the
>> expense of losing on-node shared memory support.
>>
>> Peter
>>
>> Geraldo Veiga wrote:
>> Hi to all,
>>
>> I am using the same subject of a recent message I found in the list
>> archives of this mailing list:
>>
>> http://www.open-mpi.org/community/lists/users/2008/10/7025.php
>>
>> There was no follow-up on that one, but will add this similar report
>> in case a list member can give us an idea of how to correct it. Or
>> whose bug this could be.
>>
>> My application behaves as expected when I run it in a single host and
>> multiple MPI nodes of our SGI Altix ICE 8200 cluster with in
>> InfiniBand. When I try the same with multiple hosts, using the PBS
>> batch system the program terminates with a segmentation fault:
>>
>> -------
>> [r1i0n9:09192] *** Process received signal ***
>> [r1i0n9:09192] Signal: Bus error (7)
>> [r1i0n9:09192] Signal code: (2)
>> [r1i0n9:09192] Failing at address: 0x2b67ca0c8c20
>> [r1i0n9:09192] [ 0] /lib64/libpthread.so.0 [0x2b67bfdb1c00]
>> [r1i0n9:09192] [ 1]
>> /sw/openmpi_intel/1.2.8/lib/libmpi.so.0(ompi_free_list_grow+0x14a)
>> [0x2b67bf499b38]
>> [r1i0n9:09192] [ 2]
>> /sw/openmpi_intel/1.2.8/lib/openmpi/mca_btl_sm.so(mca_btl_sm_alloc+0x321)
>> [0x2b67c3a43e15]
>> [r1i0n9:09192] [ 3]
>> /sw/openmpi_intel/1.2.8/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_start_copy+0x26d)
>> [0x2b67c34e9041]
>> [r1i0n9:09192] [ 4]
>> /sw/openmpi_intel/1.2.8/lib/openmpi/mca_pml_ob1.so(mca_pml_ob1_isend+0x540)
>> [0x2b67c34e17ec]
>> [r1i0n9:09192] [ 5]
>> /sw/openmpi_intel/1.2.8/lib/libmpi.so.0(PMPI_Isend+0x63)
>> [0x2b67bf4dcd1f]
>> [r1i0n9:09192] [ 6]
>> /sw/openmpi_intel/1.2.8/lib/libmpi_f77.so.0(pmpi_isend+0x8f)
>> [0x2b67bf36a03f]
>> [r1i0n9:09192] [ 7]
>> dsimpletest(dmumps_comm_buffer_mp_dmumps_519_+0x449) [0x53e19b]
>> [r1i0n9:09192] [ 8] dsimpletest(dmumps_load_mp_dmumps_512_+0x20b)
>> [0x54fda1]
>> [r1i0n9:09192] [ 9] dsimpletest(dmumps_251_+0x4995) [0x4d273b]
>> [r1i0n9:09192] [10] dsimpletest(dmumps_244_+0x808) [0x484e38]
>> [r1i0n9:09192] [11] dsimpletest(dmumps_142_+0x8717) [0x4bf5eb]
>> [r1i0n9:09192] [12] dsimpletest(dmumps_+0x1554) [0x43a720]
>> [r1i0n9:09192] [13] dsimpletest(MAIN__+0x50b) [0x41e4c3]
>> [r1i0n9:09192] [14] dsimpletest(main+0x3c) [0x683d4c]
>> [r1i0n9:09192] [15] /lib64/libc.so.6(__libc_start_main+0xf4)
>> [0x2b67bfeda184]
>> [r1i0n9:09192] [16] dsimpletest(dtrmv_+0xa1) [0x41df29]
>> [r1i0n9:09192] *** End of error message ***
>> ----
>>
>> Most of the software infrastructure is provided by the Intel
>> propack. Any hints of where to look further into this bug?
>>
>> Thanks in advance.
>>
>> --
>> Geraldo Veiga <gveiga_at_[hidden] <mailto:gveiga_at_[hidden]>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> --
>> Peter Cebull
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>>
>> --
>> Geraldo Veiga <gveiga_at_[hidden]>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>

-- 
Peter Cebull
Idaho National Laboratory
P.O. Box 1625, MS3605
Idaho Falls, ID 83415
Phone: 208-526-1909
Email: Peter.Cebull_at_[hidden]