[CIG-SHORT] pylith1.8.0-0/openmpi build failing on OS X

Tue Jan 29 16:52:27 PST 2013

Thanks, Brad and Matt.

MPICH didn't build correctly either, by simply selecting it.  There was a
problem that was fixed by changing a variable in the Makefile after
configuration:

line 305:   mpich_sharedarch=gcc changeed to mpich_sharedarch=osx-gcc

Now, the build is failing during the spatiadata/spatialdb tests:

spatialdata::spatialdb::TestSimpleGridDB::testDataIndex : OK
spatialdata::spatialdb::TestSimpleGridDBLine1D::testQueryNearesttestspatial(91490)
malloc: *** error for object 0xd000000000000000: pointer being freed was
not allocated
*** set a breakpoint in malloc_error_break to debug
/bin/sh: line 1: 91490 Abort trap: 6           ${dir}$tst
FAIL: testspatial
==================================
1 of 1 test failed
Please report to baagaard at usgs.gov
==================================
make[8]: *** [check-TESTS] Error 1
make[7]: *** [check-am] Error 2
make[6]: *** [check-recursive] Error 1
make[5]: *** [check-recursive] Error 1
make[4]: *** [check-recursive] Error 1
make[3]: *** [check-recursive] Error 1
make[2]: *** [spatialdata] Error 2
make[1]: *** [installed_spatialdata] Error 2
make: *** [installed_pylith] Error 2

I'm not sure what this might be related to, or what log files might contain
relevant info.  Please let me know if there's more info I can give.

Thanks,
Richard

On Tue, Jan 29, 2013 at 2:23 PM, Matthew Knepley <knepley at mcs.anl.gov>wrote:

> On Tue, Jan 29, 2013 at 2:00 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>
>> Richard,
>>
>> We have not encountered this problem you are describing with regards to
>> openmpi and darwin. I am still using 10.6 on my Mac; I am not sure if we
>> have tested building from source under 10.8.
>>
>> We didn't setup the pylith-installer configure to have openmpi options
>> because we didn't anticipate the user needing to customize the openmpi
>> options. For clusters and other computers where custom MPI settings are
>> used, we expect a sysadmin to install MPI in a system wide location.
>>
>> There are two easy workarounds to this problem:
>> (1) Install mpi yourself in a custom location that is in the path and
>> then don't install it using the pylith installer. You can customize the
>> mpi configure arguments to make them work on your machine.
>> (2) Manually adjust the openmpi configure options used by the pylith
>> installer by editing the install_openmpi target in the Makefile.
>>
>
> (3) Have it install MPICH instead.
>
>   Thanks,
>
>     Matt
>
>
>> Regards,
>> Brad
>>
>>
>> On 1/29/13 7:34 AM, Richard Styron wrote:
>> > Hi all,
>> >
>> > I am trying to build Pylith from source on a mac (OS X 10.8) following
>> > the install instructions for Darwin/CUDA:
>> >
>> >    mkdir -p $HOME/build/pylith
>> >    $HOME/src/pylith/pylith-installer-1.8.0-0/configure \
>> >      --enable-gcc=fortran \
>> >      --enable-python \
>> >      --enable-mpi=openmpi \
>> >      --with-fetch=curl \
>> >      --with-make-threads=2 \
>> >      --prefix=$HOME/pylith \
>> >      --with-cuda (<-- also tried without this.  CUDA is installed and
>> > functional on my machine.)
>> >
>> >
>> >
>> >
>> > However, OpenMPI fails when during the build:
>> >
>> > libtool: link: g++ -fopenmp -DVT_OMP -g -O2 -DMPICH_IGNORE_CXX_SEEK
>> > -fopenmp -o vtfilter vtfilter-vt_filter.o vtfilter-vt_filthandler.o
>> > vtfilter-vt_otfhandler.o vtfilter-vt_tracefilter.o ../../util/util.o
>> > -Wl,-bind_at_load
>> >
>> -L/Users/itchy/src/pylith/openmpi-build/ompi/contrib/vt/vt/extlib/otf/otflib/.libs
>> -L/Users/itchy/pylith/lib
>> -L/Users/itchy/src/pylith/openmpi-build/ompi/contrib/vt/vt/extlib/otf/otflib
>> /Users/itchy/src/pylith/openmpi-build/ompi/contrib/vt/vt/extlib/otf/otflib/.libs/libotf.a
>> -lz -lutil
>> > Undefined symbols for architecture x86_64:
>> >    "___builtin_expect", referenced from:
>> >        _main.omp_fn.0 in vtfilter-vt_tracefilter.o
>> >        _main.omp_fn.1 in vtfilter-vt_tracefilter.o
>> > ld: symbol(s) not found for architecture x86_64
>> > collect2: ld returned 1 exit status
>> > make[11]: *** [vtfilter] Error 1
>> > make[10]: *** [all-recursive] Error 1
>> > make[9]: *** [all-recursive] Error 1
>> > make[8]: *** [all] Error 2
>> > make[7]: *** [all-recursive] Error 1
>> > make[6]: *** [all-recursive] Error 1
>> > make[5]: *** [all-recursive] Error 1
>> > make[4]: *** [openmpi] Error 2
>> > make[3]: *** [installed_mpi] Error 2
>> > make[2]: *** [installed_hdf5] Error 2
>> > make[1]: *** [installed_netcdf] Error 2
>> > make: *** [installed_pylith] Error 2
>> >
>> > The error appears to be related to building VampirTrace, which may not
>> > be critical (?), and following this
>> > http://stackoverflow.com/questions/7785464/open-mpi-compilation-errorI'd like
>> > to disable VampirTrace during the build, but I don't know how to pass
>> > the 'disable-vt' flag during the pylith configuration process.  I tried
>> > building openmpi from the terminal using the configuration generated by
>> > autoconf during the Pylith install ($ ../openmpi-1.4.5/configure
>> > --prefix=/Users/itchy/pylith CPPFLAGS=-I/Users/itchy/pylith/include
>> >   LDFLAGS=-L/Users/itchy/pylith/lib  CFLAGS=-g -O2 CXXFLAGS=-g -O2
>> > -DMPICH_IGNORE_CXX_SEEK FCFLAGS= CC=gcc CXX=g++ FC=gfortran) plus
>> > '--disable-vt' but that doesn't work because many of the flags there
>> > aren't recognized as options from the command line.  I also tried adding
>> > '--mpi_options="--disable-vt" ' and '--openmpi_options="--disable-vt" '
>> > during pylith configuration (similar to what can be done with petsc) but
>> > those don't fly.
>> >
>> > The config.log files for both pylith and openmpi are attached.
>> >
>> > Has anyone dealt with this or a similar issue?
>> >
>> > Thanks,
>> > Richard
>> >
>> >
>> >
>> > _______________________________________________
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>> > CIG-SHORT at geodynamics.org
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>> >
>>
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>
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