[MacPorts] #36911: petsc @ petsc-3.3-p3 +openmpi configure failure
#36911: petsc @ petsc-3.3-p3 +openmpi configure failure -----------------------+-------------------------------- Reporter: dustman@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Keywords: | Port: -----------------------+-------------------------------- 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 -- Ticket URL: <https://trac.macports.org/ticket/36911> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36911: petsc @ petsc-3.3-p3 +openmpi configure failure ------------------------+--------------------- Reporter: dustman@… | Owner: mmoll@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: petsc | ------------------------+--------------------- Changes (by ryandesign@…): * owner: macports-tickets@… => mmoll@… * port: => petsc Old description:
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
New description: 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 }}} -- -- Ticket URL: <https://trac.macports.org/ticket/36911#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36911: petsc @ petsc-3.3-p3 +openmpi configure failure ------------------------+--------------------- Reporter: dustman@… | Owner: mmoll@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: petsc | ------------------------+--------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/36911#comment:2> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36911: petsc @ petsc-3.3-p3 +openmpi configure failure ------------------------+--------------------- Reporter: dustman@… | Owner: mmoll@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: petsc | ------------------------+--------------------- Comment (by mmoll@…): 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. -- Ticket URL: <https://trac.macports.org/ticket/36911#comment:3> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36911: petsc @ petsc-3.3-p3 +openmpi configure failure ------------------------+--------------------- Reporter: dustman@… | Owner: mmoll@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: | Keywords: Port: petsc | ------------------------+--------------------- Comment (by 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. -- Ticket URL: <https://trac.macports.org/ticket/36911#comment:4> MacPorts <http://www.macports.org/> Ports system for Mac OS
#36911: petsc @ petsc-3.3-p3 +openmpi configure failure ------------------------+--------------------- Reporter: dustman@… | Owner: mmoll@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.1.2 Resolution: fixed | Keywords: Port: petsc | ------------------------+--------------------- Changes (by mmoll@…): * status: new => closed * resolution: => fixed Comment: should be fixed in r100485. -- Ticket URL: <https://trac.macports.org/ticket/36911#comment:5> MacPorts <http://www.macports.org/> Ports system for Mac OS
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