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Subject: Re: [OMPI users] MPI_Init segfault on Ubuntu 8.04 version 1.2.7~rc2
From: Dirk Eddelbuettel (edd_at_[hidden])
Date: 2008-07-28 21:01:24


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.

Hope this helps, Dirk

|
| -Adam
| --
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