Jan, I tried the new installation method and when it came to installing PETSc, it gave me this error:
2015/01/13 06:03:35 - INFO: [package:run_job] ******************************************************************************* 2015/01/13 06:03:35 - INFO: [package:run_job] UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): 2015/01/13 06:03:35 - INFO: [package:run_job] ------------------------------------------------------------------------------- 2015/01/13 06:03:35 - INFO: [package:run_job] Could not find a functional LAPACK. Run with --with-lapack-lib=<lib> to indicate the library containing LAPACK. 2015/01/13 06:03:35 - INFO: [package:run_job] Or --download-fblaslapack=1 to have one automatically downloaded and installed 2015/01/13 06:03:35 - INFO: [package:run_job] ******************************************************************************* 2015/01/13 06:03:35 - INFO: [package:run_job] 2015/01/13 06:03:35 - ERROR: [package:run_job] Command '[u'/bin/bash', '_hashdist/build.sh']' returned non-zero exit status 1 2015/01/13 06:03:35 - ERROR: [package:run_job] command failed (code=1); raising How do I set ./configure for PETSc such that it will link to the LAPACK that was already successfully installed? Thanks, Justin On Tue, Jan 13, 2015 at 3:59 AM, Jan Blechta <[email protected]> wrote: > On Mon, 12 Jan 2015 18:45:13 -0600 > Justin Chang <[email protected]> wrote: > > > Hi all, > > > > So I am attempting to install FEnics on our university's RHEL 6.6 > > cluster through the dorsal scripts. I normally use FEnics using > > Ubuntu's binary distribution so doing this kind of installation is > > uncharted territory so bear with me :) > > > > I had to modify the rhel6.platform file significantly and the final > > list of packages i needed were: > > > > PACKAGES=( > > blas > > boost > > lapack > > suitesparse > > pcre > > swig > > cmake > > vtkdata > > vtk > > parmetis > > scotch > > numpy > > trilinos > > petsc > > slepc > > armadillo > > mpfr > > cgal > > skip:scientificpython > > eigen > > fiat > > ferari > > ufl > > ffc > > viper > > instant > > dolfin > > ) > > > > Everything works until i get to installing dolfin and this is the > > error I am getting > > > > -- Build files have been written to: > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir > > make: Entering directory > > `/home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir' > > make[1]: Entering directory > > `/home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir' > > make[2]: Entering directory > > `/home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir' > > make[2]: Leaving directory > > `/home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir' > > make[2]: Entering directory > > `/home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir' > > [ 0%] Building CXX object > > dolfin/CMakeFiles/dolfin.dir/generation/UnitTetrahedronMesh.cpp.o > > In file included from /home/jchang23/FEniCS/include/petscsys.h:105, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/common/types.h:29, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/function/Function.h:34, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/ale/MeshDisplacement.h:28, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/mesh/Mesh.h:38, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/mesh/MeshPartitioning.h:35, > > from > > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/generation/UnitTetrahedronMesh.cpp:22: > > /share/apps/openmpi-1.8.3/include/mpi.h:324: error: conflicting > > declaration ‘typedef struct ompi_communicator_t* MPI_Comm’ > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/common/MPI.h:42: error: > > ‘MPI_Comm’ has a previous declaration as ‘typedef int MPI_Comm’ > > In file included from /home/jchang23/FEniCS/include/petscsys.h:1794, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/common/types.h:29, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/function/Function.h:34, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/ale/MeshDisplacement.h:28, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/mesh/Mesh.h:38, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/mesh/MeshPartitioning.h:35, > > from > > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/generation/UnitTetrahedronMesh.cpp:22: > > /home/jchang23/FEniCS/include/petsclog.h: In function ‘PetscErrorCode > > PetscMPITypeSizeComm(MPI_Comm, PetscLogDouble*, PetscMPIInt*, > > ompi_datatype_t*)’: > > /home/jchang23/FEniCS/include/petsclog.h:323: error: cast from > > ‘void*’ to ‘MPI_Comm’ loses precision > > /home/jchang23/FEniCS/include/petsclog.h:324: error: cast from > > ‘void*’ to ‘MPI_Comm’ loses precision > > In file included from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/common/types.h:29, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/function/Function.h:34, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/ale/MeshDisplacement.h:28, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/mesh/Mesh.h:38, > > from > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/mesh/MeshPartitioning.h:35, > > from > > > /home/jchang23/FEniCS/src/dolfin-1.4.0/dolfin/generation/UnitTetrahedronMesh.cpp:22: > > /home/jchang23/FEniCS/include/petscsys.h: In function ‘PetscErrorCode > > PetscCitationsRegister(const char*, PetscBool*)’: > > /home/jchang23/FEniCS/include/petscsys.h:2650: error: cast from > > ‘void*’ to ‘MPI_Comm’ loses precision > > /home/jchang23/FEniCS/include/petscsys.h:2651: error: cast from > > ‘void*’ to ‘MPI_Comm’ loses precision > > /home/jchang23/FEniCS/include/petscsys.h:2652: error: cast from > > ‘void*’ to ‘MPI_Comm’ loses precision > > make[2]: *** > > [dolfin/CMakeFiles/dolfin.dir/generation/UnitTetrahedronMesh.cpp.o] > > Error 1 make[2]: Leaving directory > > `/home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir' > > make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2 > > make[1]: Leaving directory > > `/home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir' > > make: *** [all] Error 2 > > make: Leaving directory > > `/home/jchang23/FEniCS/src/dolfin-1.4.0/dorsal_build_dir' > > Failure with exit status: 2 > > Exit message: There was a problem building dolfin-1.4.0. > > > > > > >From the looks of it it seems I already have an existing > > >installation of > > OpenMPI, but my question is what do I do to resolve this? > > This could happened because DOLFIN did not find MPI during configure > time and typedefed MPI_Comm to int which conflicts with MPI_Comm > indcluded from petscsys.h. Try adding > > -DMPI_CXX_COMPILER:FILEPATH=/share/apps/openmpi-1.8.3/bin/mpicxx > -DMPI_C_COMPILER:FILEPATH=/share/apps/openmpi-1.8.3/bin/mpicc > -DMPI_Fortran_COMPILER:FILEPATH=/share/apps/openmpi-1.8.3/bin/mpif90 > > (or other correct paths) to CONFOPTS in > <dorsal>/FEniCS/packages/dolfin.package > > Check <dolfin>/cmake/modules/FindMPI.cmake for more detailed > instrunctions how to configure DOLFIN with MPI. > > Note that Dorsal is going to be retired and you could succeed with new > installation method https://bitbucket.org/fenics-project/fenics-install > > Jan > > > > > Thanks, > > Justin > >
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