[CIG-SHORT] pylith1.8.0-0/openmpi build failing on OS X
Brad Aagaard
baagaard at usgs.gov
Tue Jan 29 17:14:32 PST 2013
Richard,
This is a memory bug that I fixed in Dec. I forgot to update the
pylith-installer to use this newer version. I will update the installer
and upload this new version tomorrow (and let you know).
Regards,
Brad
On 1/29/13 4:52 PM, Richard Styron wrote:
> 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 <mailto: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
> <mailto:knepley at mcs.anl.gov>> wrote:
>
> On Tue, Jan 29, 2013 at 2:00 PM, Brad Aagaard <baagaard at usgs.gov
> <mailto: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-error
> I'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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