[Debichem-devel] Bug#531419: Bug#531419: gromacs: FTBFS: error: couldn't find library libmd_mpi_d_openmpi.so.5

[Nicholas Breen]

clone 531419 -1
reassign -1 libopenmpi-dev
retitle -1 libopenmpi-dev: mpicc segfaults under fakeroot
block 531419 by -1
thanks

Okay, it looks like the root cause is something that's appeared recently in
openmpi - it fails under 1.3.2-2, but works under 1.3-2.  Manuel, I'm cloning
the bug for tracking purposes, but I'm certainly not sure that it's actually an
OpenMPI bug at heart.  Have you seen anything else like this?

% echo "int main(void) { return 0; }" > test.c
% mpicc.openmpi test.c ; echo $?
0
% fakeroot mpicc.openmpi test.c ; echo $?
Segmentation fault
139

No failures with the other MPI implementations, nor with OpenMPI 1.3.  I can
put it under gdb but am missing some debugging libraries in the middle:

% fakeroot gdb mpicc.openmpi
[...]
(gdb) run test.c
Starting program: /usr/bin/mpicc.openmpi conftest.c
[Thread debugging using libthread_db enabled]
[New Thread 0xb7dc46c0 (LWP 6958)]

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0xb7dc46c0 (LWP 6958)]
__libc_calloc (n=1, elem_size=20) at malloc.c:3932
3932    malloc.c: No such file or directory.
        in malloc.c
(gdb) bt
#0  __libc_calloc (n=1, elem_size=20) at malloc.c:3932
#1  0xb7f83086 in _dlerror_run (operate=0xb7f82d90 <dlsym_doit>, args=0xbfd3002c) at dlerror.c:142
#2  0xb7f82d43 in __dlsym (handle=0xffffffff, name=0xb800f16a "open") at dlsym.c:71
#3  0xb800db73 in load_library_symbols () from /usr/lib/libfakeroot/libfakeroot-sysv.so
#4  0xb800e687 in tmp___xstat () from /usr/lib/libfakeroot/libfakeroot-sysv.so
#5  0xb800daa3 in __xstat () from /usr/lib/libfakeroot/libfakeroot-sysv.so
#6  0xb7fbcefc in ?? () from /usr/lib/libopen-pal.so.0
#7  0x00000003 in ?? ()
#8  0xb7fc948e in ?? () from /usr/lib/libopen-pal.so.0
#9  0xbfd300e4 in ?? ()
#10 0x00001b2e in ?? ()
#11 0xbfd300e4 in ?? ()
#12 0x00000003 in ?? ()
#13 0x00000003 in ?? ()
#14 0xbfd30164 in ?? ()
#15 0xb7f20ff4 in ?? () from /lib/i686/cmov/libc.so.6
#16 0x00000001 in ?? ()
#17 0xb7dc8d0c in ?? () from /lib/i686/cmov/libc.so.6
#18 0xbfd30148 in ?? ()
#19 0xb7ee4429 in *__GI__dl_addr (address=0xb7e34e70, info=0xbfd30184, mapp=0xbfd30194,
    symbolp=0xb7f2260c) at dl-addr.c:146
#20 0xb7e35096 in ptmalloc_init () at arena.c:571
#21 0xb7e386bc in malloc_hook_ini (sz=12, caller=0xb7f939ab) at hooks.c:37
#22 0xb7e38535 in *__GI___libc_malloc (bytes=12) at malloc.c:3546
#23 0xb7f939ab in opal_class_initialize () from /usr/lib/libopen-pal.so.0
#24 0xb7fb3227 in opal_output_init () from /usr/lib/libopen-pal.so.0
#25 0xb7f96205 in opal_init_util () from /usr/lib/libopen-pal.so.0
#26 0x08049b62 in main (argc=2, argv=0xbfd30404) at ../../../../../opal/tools/wrappers/opal_wrapper.c:480

I confess that the peculiar interactions of compilers, fakeroot, and (e)glibc
put me well out of my depth.

-- 
Nicholas Breen
nbreen at ofb.net