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 -- GPG fingerprint: D54D 1AEE B11C CE9B A02B C5DD 526F 01E8 564E E4B6 Engineering consulting with open source tools http://www.opennovation.com/
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