[petsc-users] petsc 3.4.5 on CentOS 7.2.511

Matthew Knepley knepley at gmail.com
Mon Nov 21 08:16:22 CST 2016 

On Mon, Nov 21, 2016 at 8:08 AM, Park, Joseph <joseph_park at nps.gov> wrote:

> 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:
>

You HAVE to send the log with bug reports. Otherwise, we are just guessing.

   Matt


>                         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_top
>> ology_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!
>> > >
>> >
>> >
>>
>>
>>
>


-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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