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?
Thanks,
Justin
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