Hello,
I recently updated my PETSc install to the 3.5.2 version, and tried to
recompile FEniCS after this.
Everything goes right up to the building phase, where I run into errors,
the first one being this one:
> [ 28%] Building CXX object
dolfin/CMakeFiles/dolfin.dir/la/PETScKrylovSolver.cpp.o
>
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:
> In member function ‘void
dolfin::PETScKrylovSolver::set_petsc_operators()’:
>
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:
> 528:62: erreur: ‘SAME_PRECONDITIONER’ was not declared in this scope
> ierr = KSPSetOperators(_ksp, _matA->mat(), _matP->mat(),
SAME_PRECONDITIONER);
The full dorsal output can be found below.
I would greatly appreciate a hint on what is the best way to go over
this problem.
Thank you very much,
Serge
---------------------
> ./dorsal.sh FEniCS/platforms/supported/opensuse11.3.platform
Found configuration for project FEniCS.
Skipping parmetis-4.0.2
Skipping SuiteSparse-4.0.2
Skipping scotch_6.0.0_esmumps
Skipping ScientificPython-2.8
Skipping fiat-1.4.0
Skipping ufl-1.4.0
Skipping ffc-1.4.0
Skipping instant-1.4.0
Fetching dolfin-1.4.0
Verifying dolfin-1.4.0
dolfin-1.4.0.tar.gz: OK
Unpacking dolfin-1.4.0
Building dolfin-1.4.0
-- The C compiler identification is GNU 4.9.1
-- The CXX compiler identification is GNU 4.9.1
-- Check for working C compiler: /home/zatopek/gcc/MyInstall/bin/gcc
-- Check for working C compiler: /home/zatopek/gcc/MyInstall/bin/gcc --
works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /home/zatopek/gcc/MyInstall/bin/g++
-- Check for working CXX compiler: /home/zatopek/gcc/MyInstall/bin/g++
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_STD_CPP11
-- Performing Test HAVE_STD_CPP11 - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler:
/home/zatopek/gcc/MyInstall/bin/gfortran
-- Check for working Fortran compiler:
/home/zatopek/gcc/MyInstall/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /home/zatopek/gcc/MyInstall/bin/gfortran supports
Fortran 90
-- Checking whether /home/zatopek/gcc/MyInstall/bin/gfortran supports
Fortran 90 -- yes
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of size_t
-- Check size of size_t - done
-- Found MPI_C:
/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
-- Found MPI_CXX:
/opt/openmpi/lib/libmpi_cxx.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
-- Found MPI_Fortran:
/opt/openmpi/lib/libmpi_f90.so;/opt/openmpi/lib/libmpi_f77.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Performing Test OPENMP_UINT_TEST_RUNS
-- Performing Test OPENMP_UINT_TEST_RUNS - Success
-- Boost version: 1.56.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- thread
-- iostreams
-- UFC version: 1.4.0
-- Found Eigen3: /home/zatopek/Eigen3/eigen-eigen-1306d75b4a21 (Required
is at least version "3.0.0")
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6")
-- Found PythonInterp: /home/zatopek/Python/MyInstall/bin/python (found
suitable version "2.7.8", minimum required is "2")
-- NumPy header version 1.8.1 found
-- Found SWIG: /home/zatopek/swig-2.0.12/MyInstall/bin/swig (found
version "2.0.12")
-- Checking for package 'PETSc'
-- PETSC_DIR is /home/zatopek/PETSc/petsc-3.5.2-opt
-- PETSC_ARCH is arch-linux2-c-opt
-- Found petscconf.h
-- Include directory /home/zatopek/PETSc/petsc-3.5.2/include does not exist
-- Include directory
/home/zatopek/PETSc/petsc-3.5.2/arch-linux2-c-opt/include does not exist
-- Performing test PETSC_TEST_RUNS - Success
-- Performing Test PETSC_CUSP_FOUND
-- Performing Test PETSC_CUSP_FOUND - Failed
-- PETSc configured without Cusp support
-- Found PETSc:
/home/zatopek/PETSc/petsc-3.5.2-opt/arch-linux2-c-opt/lib/libpetsc.so
(Required is at least version "3.3")
-- Checking for package 'SLEPc'
-- SLEPC_DIR is SLEPC_DIR-NOTFOUND
-- SLEPc could not be found. Be sure to set SLEPC_DIR, PETSC_DIR, and
PETSC_ARCH. (missing: SLEPC_LIBRARIES SLEPC_DIR SLEPC_INCLUDE_DIRS
SLEPC_TEST_RUNS SLEPC_VERSION SLEPC_VERSION_OK) (Required is at least
version "3.3")
-- Checking for package 'PETSc4Py'
-- petsc4py version 3.5 found
-- Performing Test PARMETIS_TEST_RUNS
-- Performing Test PARMETIS_TEST_RUNS - Success
-- Found ParMETIS:
/home/zatopek/FenicsProject/MyInstall/lib/libparmetis.so;/home/zatopek/FenicsProject/MyInstall/lib/libmetis.so
(Required is at least version "4.0.2")
-- Checking for package 'SCOTCH-PT'
-- Found SCOTCH (version 6.0.0)
-- Performing test SCOTCH_TEST_RUNS
-- Performing test SCOTCH_TEST_RUNS - Success
-- Found SCOTCH:
/home/zatopek/FenicsProject/MyInstall/lib/libptscotch.a;/home/zatopek/FenicsProject/MyInstall/lib/libscotch.a;/home/zatopek/FenicsProject/MyInstall/lib/libptscotcherr.a
-- Checking for package 'AMD'
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- Performing Test CHOLMOD_TEST_RUNS
-- Performing Test CHOLMOD_TEST_RUNS - Success
-- Performing Test UMFPACK_TEST_RUNS
-- Performing Test UMFPACK_TEST_RUNS - Success
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Found HDF5:
/usr/lib64/libhdf5.so;/usr/lib64/libpthread.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so
-- HDF5 has been found, but is missing parallel support. It will not be
enabled.
-- PASTIX_LIBRARIES
PASTIX_LIBRARY-NOTFOUND;/usr/lib64/librt.so;/usr/lib64/libm.so
-- A library with BLAS API found.
-- PaStiX could not be found. Be sure to set PASTIX_DIR. (missing:
PASTIX_INCLUDE_DIRS PASTIX_TEST_RUNS PASTIX_VERSION PASTIX_VERSION_OK)
-- Checking for Trilinos
-- Unable to find Trilinos (>= 11.0.0)
-- Trilinos could not be found
-- Checking for package 'CGAL'
-- Performing Test CGAL_TEST_RUNS
-- Performing Test CGAL_TEST_RUNS - Failed
-- CGAL could not be found. Be sure to set CGAL_DIR (missing:
CGAL_TEST_RUNS) (Required is at least version "4.1")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
-- checking for module 'cppunit'
-- package 'cppunit' not found
-- CPPUNIT could not be found. Be sure to set CPPUNIT_DIR. (missing:
CPPUNIT_LIBRARIES CPPUNIT_INCLUDE_DIRS)
-- Checking for package 'Sphinx'
-- Found Sphinx: /home/zatopek/Sphinx/MyInstall/bin/sphinx-build
(Required is at least version "1.1.0")
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.6.3")
-- Found VTK: /home/zatopek/VTK/MyInstall/lib/cmake/vtk-6.1 (found
version "6.1")
--
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) PETSC4PY
-- (OK) UMFPACK
-- (OK) CHOLMOD
-- (OK) SCOTCH
-- (OK) PARMETIS
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) SPHINX
-- (OK) VTK
-- (OK) QT
--
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) SLEPC
-- (**) TRILINOS
-- (**) PASTIX
-- (**) CGAL
-- (**) HDF5
--
--
-- Generating SWIG interface.
-- --------------------------
-- Found Qt4: /usr/bin/qmake (found version "4.6.3")
-- Enabling generation of documentation.
-- Initializing sphinx projects
-- Enabling generation of html-documentation
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CGAL_DISABLE_ROUNDING_MATH_CHECK
-- Build files have been written to:
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
make: entrant dans le répertoire «
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
»
make[1]: entrant dans le répertoire «
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
»
make[2]: entrant dans le répertoire «
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
»
Scanning dependencies of target dolfin
make[2]: quittant le répertoire «
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
»
make[2]: entrant dans le répertoire «
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
»
[ 1%] Building CXX object
dolfin/CMakeFiles/dolfin.dir/generation/PolyhedronUtils.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/UnitTetrahedronMesh.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/ImplicitDomainMeshGenerator.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/CSGOperators.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/GeometryToCGALConverter.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/CSGCGALMeshGenerator3D.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/EllipseMesh.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/CSGGeometry.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/CSGPrimitives2D.cpp.o
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dolfin/CMakeFiles/dolfin.dir/generation/CSGGeometries3D.cpp.o
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dolfin/CMakeFiles/dolfin.dir/multistage/RKSolver.cpp.o
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dolfin/CMakeFiles/dolfin.dir/multistage/PointIntegralSolver.cpp.o
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dolfin/CMakeFiles/dolfin.dir/function/FunctionAXPY.cpp.o
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dolfin/CMakeFiles/dolfin.dir/function/CCFEMFunction.cpp.o
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dolfin/CMakeFiles/dolfin.dir/la/PETScBaseMatrix.cpp.o
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dolfin/CMakeFiles/dolfin.dir/la/PETScKrylovSolver.cpp.o
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:
In member function ‘void dolfin::PETScKrylovSolver::set_petsc_operators()’:
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:528:62:
erreur: ‘SAME_PRECONDITIONER’ was not declared in this scope
ierr = KSPSetOperators(_ksp, _matA->mat(), _matP->mat(),
SAME_PRECONDITIONER);
^
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:533:82:
erreur: too many arguments to function ‘PetscErrorCode
KSPSetOperators(KSP, Mat, Mat)’
ierr = KSPSetOperators(_ksp, _matA->mat(), _matP->mat(),
SAME_NONZERO_PATTERN);
^
In file included from
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScUserPreconditioner.h:29:0,
from
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:39:
/home/zatopek/PETSc/MyInstall/include/petscksp.h:260:29: note: declared here
PETSC_EXTERN PetscErrorCode KSPSetOperators(KSP,Mat,Mat);
^
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:539:53:
erreur: too many arguments to function ‘PetscErrorCode
KSPSetOperators(KSP, Mat, Mat)’
DIFFERENT_NONZERO_PATTERN);
^
In file included from
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScUserPreconditioner.h:29:0,
from
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:39:
/home/zatopek/PETSc/MyInstall/include/petscksp.h:260:29: note: declared here
PETSC_EXTERN PetscErrorCode KSPSetOperators(KSP,Mat,Mat);
^
make[2]: *** [dolfin/CMakeFiles/dolfin.dir/la/PETScKrylovSolver.cpp.o]
Erreur 1
make[2]: quittant le répertoire «
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
»
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Erreur 2
make[1]: quittant le répertoire «
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
»
make: *** [all] Erreur 2
make: quittant le répertoire «
/home/zatopek/FenicsProject/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
»
Failure with exit status: 2
Exit message: There was a problem building dolfin-1.4.0.
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