[petsc-users] petsc 3.4.5 on CentOS 7.2.511

Park, Joseph joseph_park at nps.gov
Mon Nov 21 08:08:48 CST 2016 

Thank you!  I tried the suggested invocation, but with a different result:

./configure --with-clanguage=cxx --with-mpi-dir=/usr/lib64/openmpi/bin
--with-c2html=0
===============================================================================
             Configuring PETSc to compile on your system

===============================================================================
TESTING: check from
config.libraries(config/BuildSystem/config/libraries.py:145)

 *******************************************************************************
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for
details):
-------------------------------------------------------------------------------
--with-mpi-dir=/usr/lib64/openmpi/bin did not work
*******************************************************************************

The configure.log ends with a self-referral suggestion and generation of
the above error message, while the first error message tracing back from
the end of configure.log provides:

                        Pushing language CXX
                        Popping language CXX
sh: g++  -o /tmp/petsc-HWuXr9/config.libraries/conftest    -Wall
-Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g
 /tmp/petsc-HWuXr9/config.libraries/conftest.o
 /usr/lib64/openmpi/bin/lib64/i386/msmpi.lib
-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -ldl -lgcc_s -ldl
Executing: g++  -o /tmp/petsc-HWuXr9/config.libraries/conftest    -Wall
-Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g
 /tmp/petsc-HWuXr9/config.libraries/conftest.o
 /usr/lib64/openmpi/bin/lib64/i386/msmpi.lib
-Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.8.5
-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -ldl -lgcc_s -ldl
sh:
Possible ERROR while running linker: g++: error:
/usr/lib64/openmpi/bin/lib64/i386/msmpi.lib: No such file or directory
 output: ret = 256
error message = {g++: error: /usr/lib64/openmpi/bin/lib64/i386/msmpi.lib:
No such file or directory
}

Indeed, there is no /usr/lib64/openmpi/bin/lib64, but i'm not clear as to
whether this is a 'possible' or the realised error.

Perhaps this all boils down to an incomplete development environment.



On Fri, Nov 18, 2016 at 4:03 PM, Satish Balay <balay at mcs.anl.gov> wrote:

> 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!
> > >
> >
> >
>
>
>
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