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

[Richard Styron]

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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