petsc @ petsc-3.3-p3 +openmpi configure failure

[dustman@…]

Installation of petsc fails during the configuration phase. Snippet of log message is (full log is attached):

:info:configure *******************************************************************************
:info:configure          UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):
:info:configure -------------------------------------------------------------------------------
:info:configure Incomplete LAPACK install? Perhaps lapack package is installed - but lapack-dev/lapack-devel is required.
:info:configure *******************************************************************************
:info:configure 
:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_petsc/petsc/work/petsc-3.3-p3" && ./configure --prefix=/opt/local --prefix=/opt/local/lib/petsc --with-mpi=1 --with-clanguage=C++ --download-ml --download-metis --download-parmetis --download-blacs --download-scalapack --download-mumps --download-ptscotch --with-hdf5-dir=/opt/local --with-yaml-dir=/opt/local --with-cc=/opt/local/bin/openmpicc --with-cxx=/opt/local/bin/openmpicxx --with-fc=/opt/local/bin/openmpif90 --with-mpiexec=/opt/local/bin/openmpiexec --COPTFLAGS="-O2" --CXXOPTFLAGS="-O2" --FOPTFLAGS="-O2" --LDFLAGS="-L/opt/local/lib" --CFLAGS="-O2" --CXXFLAGS="-O2" --FFLAGS="-lstdc++" 
:info:configure Exit code: 1
:error:configure org.macports.configure for port petsc returned: configure failure: command execution failed

[dustman@…]

/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_petsc/petsc/main.log

[dustman@…]

/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_petsc/petsc/work/petsc-3.3-p3/configure.log

[eschnett (Erik Schnetter)]

I see the same error. I believe this is caused by PETSc using openmpicc, whereas openmpicc uses /usr/bin/clang as compiler by default. I do not know whether this is an error in the openmpi or the petsc port. I have installed the gcc47 variant of openmpi, so I expected it to use gcc47 by default.

openmpicc uses gcc47 if the environment variable OMPI_CC is set to gcc (or gcc-mp-4.7). I assume that other OMPI_* variables then need to be set accordingly as well.

[mamoll (Mark Moll)]

Petsc builds just fine for me on Mountain Lion with the latest xcode. These are the versions of the dependencies I have installed:

  hdf5-18 @1.8.9_2+cxx+fortran+openmpi (active)
  openmpi @1.6.3_0+gcc47 (active)

I don't have atlas installed. Do you? From the log file it looks like the petsc build system has trouble figuring out how to use LAPACK.

It used to be that the +gccNN variants specified only the Fortran compiler, but it seems many people interpret them as applying to the whole compiler suite. This can be done.

[dustman@…]

Petsc now builds for me. It seems deactivating atlas did the trick.

I also installed openmpi @1.6.3_0+gcc47 (whereas before I had installed openmpi @1.6.3_0+gcc45) prior to deactivating atlas. The openmpi change did not make a difference though.

[mamoll (Mark Moll)]

should be fixed in r100485.