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

[Brad Aagaard]

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.

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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