[CIG-SHORT] pylith1.8.0-0/openmpi build failing on OS X
Brad Aagaard
baagaard at usgs.gov
Thu Jan 31 12:06:39 PST 2013
Richard,
Please try the updated installer (v1.8.0-1) posted on the PyLith webpage
http://www.geodynamics.org/cig/software/pylith/
I updated the spatialdata tarball that includes several bugfixes in the
SimpleGridDB unit tests.
To be safe you should remove everything from the previous installer
directory and the installed dependencies (i.e., where the PyLith
installer installed the packages).
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
> >
> >
> >
> > _______________________________________________
> > CIG-SHORT mailing list
> > CIG-SHORT at geodynamics.org <mailto:CIG-SHORT at geodynamics.org>
> > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >
>
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