I just tried a of petsc-3.4 on centos-7.2 - and that went through fine. ./configure --with-clanguage=cxx --with-mpi-dir=/usr/lib64/openmpi/bin --with-c2html=0
Satish On Fri, 18 Nov 2016, Satish Balay wrote: > The stack says - the crash is OpenMPI's orterun [aka mpiexec]. > > Perhaps its broken? > > you can run PETSc examples without mpiexec as: > > cd src/ksp/ksp/examples/tutorials > make ex2 > ./ex2 > > I don't understand the tweak. Usually 'compat' packages are used by > precompiled binaries - that were compiled with old compilers. And > PETSc shouldn't need it. > > Also PETSc can use system blas/lapack - instead of > --download-f2cblaslapack=1 [but that shouldn't cause issues] > > Also gcc, openmpi are in the base CentOS 7.2 repo - so I'm not sure I > understand the reference to EPEL. > > Satish > > On Fri, 18 Nov 2016, Park, Joseph wrote: > > > 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! > > > >
