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Subject: Re: [OMPI users] MPI_Init segfault on Ubuntu 8.04 version 1.2.7~rc2
From: Adam C Powell IV (hazelsct_at_[hidden])
Date: 2008-07-29 14:21:38


On Mon, 2008-07-28 at 20:01 -0500, Dirk Eddelbuettel wrote:
> On 24 July 2008 at 14:39, Adam C Powell IV wrote:
> | Greetings,
> |
> | I'm seeing a segfault in a code on Ubuntu 8.04 with gcc 4.2. I
> | recompiled the Debian lenny openmpi 1.2.7~rc2 package on Ubuntu, and
> | compiled the Debian lenny petsc and libmesh packages against that.
> |
> | Everything works just fine in Debian lenny (gcc 4.3), but in Ubuntu
> | hardy it fails during MPI_Init:
> |
> | [Thread debugging using libthread_db enabled]
> | [New Thread 0x7faceea6f6f0 (LWP 5376)]
> |
> | Program received signal SIGSEGV, Segmentation fault.
> | [Switching to Thread 0x7faceea6f6f0 (LWP 5376)]
> | 0x00007faceb265b8b in _int_malloc () from /usr/lib/libopen-pal.so.0
> | (gdb) backtrace
> | #0 0x00007faceb265b8b in _int_malloc () from /usr/lib/libopen-pal.so.0
> | #1 0x00007faceb266e58 in malloc () from /usr/lib/libopen-pal.so.0
> | #2 0x00007faceb248bfb in opal_class_initialize ()
> | from /usr/lib/libopen-pal.so.0
> | #3 0x00007faceb25ce2b in opal_malloc_init () from /usr/lib/libopen-pal.so.0
> | #4 0x00007faceb249d97 in opal_init_util () from /usr/lib/libopen-pal.so.0
> | #5 0x00007faceb249e76 in opal_init () from /usr/lib/libopen-pal.so.0
> | #6 0x00007faced05a723 in ompi_mpi_init () from /usr/lib/libmpi.so.0
> | #7 0x00007faced07c106 in PMPI_Init () from /usr/lib/libmpi.so.0
> | #8 0x00007facee144d92 in libMesh::init () from /usr/lib/libmesh.so.0.6.2
> | #9 0x0000000000411f61 in main ()
> |
> | libMesh::init() just has an assertion and command line check before
> | MPI_Init, so I think it's safe to conclude this is an OpenMPI problem.
> |
> | How can I help to test and fix this?
> |
> | This might be related to Vincent Rotival's problem in
> | http://www.open-mpi.org/community/lists/users/2008/04/5427.php or maybe
> | http://www.open-mpi.org/community/lists/users/2008/05/5668.php . On the
> | latter, I'm building the Debian package, which should have the
> | LDFLAGS="" fix. Hmm, nope, no LDFLAGS anywhere in the .diff.gz... The
> | OpenMPI top-level Makefile has
> | "LDFLAGS = -export-dynamic -Wl,-Bsymbolic-functions"
>
> What bit us in the second bug report you refer to there was that _Ubuntu_ set
> this LDFLAGS value in their binutils settings for hardy. We do (did?) not
> (or at least not yet) do that in Debian -- the binutils there do not add
> LDFLAGS which is why do not unset anything in the debian/rules for ompi.
>
> As I recall, updated packages for Ubuntu hardy have been fix, i.e. have been
> built without the bad LDFLAGS value.

Great.

I rebuilt 1.2.7 with LDFLAGS="" and that fixed libMesh.

Thanks,
-Adam

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