[petsc-users] petsc 3.4.5 on CentOS 7.2.511

[Park, Joseph]

I'm having difficulty configuring petsc 3.4.5 on a CentOS 7.2 machine. I'm
forced to use petsc 3.4.5 until the application (C++) can be upgraded.  We
are restricted to EPEL packages for gcc, OpenMPI and all libraries.

The only 'tweak' is that EPEL package compat-openmpi16 is used instead
of openmpi, as the latter seems incompatible with petsc 3.4.2.

Petsc configures and builds fine via:

./configure --download-f2cblaslapack=1
--with-mpi-dir=/usr/lib64/compat-openmpi16 --with-debugging=1
--with-clanguage=cxx --with-fc=0

make PETSC_DIR=/opt/sfwmd_rsm/apps/petsc-3.4.5
PETSC_ARCH=arch-linux2-cxx-debug all

However, at test time:

make PETSC_DIR=/opt/sfwmd_rsm/apps/petsc-3.4.5
PETSC_ARCH=arch-linux2-cxx-debug test

Running test examples to verify correct installation
Using PETSC_DIR=/opt/sfwmd_rsm/apps/petsc-3.4.5 and
PETSC_ARCH=arch-linux2-cxx-debug
/usr/bin/sh: line 20: 24136 Segmentation fault
 /usr/lib64/compat-openmpi16/bin/mpiexec -n 1 ./ex19 -da_refine 3 -pc_type
mg -ksp_type fgmres > ex19_1.tmp 2>&1
Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI
process
See http://www.mcs.anl.gov/petsc/documentation/faq.html
[snailkite:24136] *** Process received signal ***
[snailkite:24136] Signal: Segmentation fault (11)
[snailkite:24136] Signal code: Address not mapped (1)
[snailkite:24136] Failing at address: (nil)
[snailkite:24136] [ 0] /lib64/libpthread.so.0(+0xf100) [0x7ff020de8100]
[snailkite:24136] [ 1] /lib64/libc.so.6(+0x85346) [0x7ff020a9c346]
[snailkite:24136] [ 2] /lib64/libhwloc.so.5(+0x7ccb) [0x7ff021206ccb]
[snailkite:24136] [ 3]
/lib64/libhwloc.so.5(hwloc__insert_object_by_cpuset+0xa7) [0x7ff021206e87]
[snailkite:24136] [ 4] /lib64/libhwloc.so.5(+0x2196e) [0x7ff02122096e]
[snailkite:24136] [ 5] /lib64/libhwloc.so.5(+0x22828) [0x7ff021221828]
[snailkite:24136] [ 6] /lib64/libhwloc.so.5(+0x228a3) [0x7ff0212218a3]
[snailkite:24136] [ 7] /lib64/libhwloc.so.5(hwloc_topology_load+0x13b)
[0x7ff0212098bb]
[snailkite:24136] [ 8]
/usr/lib64/compat-openmpi16/lib/libopen-rte.so.4(orte_odls_base_open+0x7ab)
[0x7ff021fa6dbb]
[snailkite:24136] [ 9]
/usr/lib64/compat-openmpi16/lib/openmpi/mca_ess_hnp.so(+0x2e54)
[0x7ff01f233e54]
[snailkite:24136] [10]
/usr/lib64/compat-openmpi16/lib/libopen-rte.so.4(orte_init+0x193)
[0x7ff021f7dd83]
[snailkite:24136] [11] /usr/lib64/compat-openmpi16/bin/mpiexec() [0x403dd5]
[snailkite:24136] [12] /usr/lib64/compat-openmpi16/bin/mpiexec() [0x403430]
[snailkite:24136] [13] /lib64/libc.so.6(__libc_start_main+0xf5)
[0x7ff020a38b15]
[snailkite:24136] [14] /usr/lib64/compat-openmpi16/bin/mpiexec() [0x403349]
[snailkite:24136] *** End of error message ***
/usr/bin/sh: line 20: 24139 Segmentation fault

Under gdb:

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff6647346 in __strcmp_sse2 () from /lib64/libc.so.6
(gdb)
(gdb) where
#0  0x00007ffff6647346 in __strcmp_sse2 () from /lib64/libc.so.6
#1  0x00007ffff6db1ccb in hwloc_obj_cmp () from /lib64/libhwloc.so.5
#2  0x00007ffff6db1e87 in hwloc__insert_object_by_cpuset () from
/lib64/libhwloc.so.5
#3  0x00007ffff6dcb96e in summarize () from /lib64/libhwloc.so.5
#4  0x00007ffff6dcc828 in hwloc_look_x86 () from /lib64/libhwloc.so.5
#5  0x00007ffff6dcc8a3 in hwloc_x86_discover () from /lib64/libhwloc.so.5
#6  0x00007ffff6db48bb in hwloc_topology_load () from /lib64/libhwloc.so.5
#7  0x00007ffff7b51dbb in orte_odls_base_open ()
   from /usr/lib64/compat-openmpi16/lib/libopen-rte.so.4
#8  0x00007ffff4ddee54 in rte_init () from
/usr/lib64/compat-openmpi16/lib/openmpi/mca_ess_hnp.so
#9  0x00007ffff7b28d83 in orte_init () from
/usr/lib64/compat-openmpi16/lib/libopen-rte.so.4
#10 0x0000000000403dd5 in orterun ()
#11 0x0000000000403430 in main ()

Any suggestions are most welcome!
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