I am using the Ubuntu package, the dolfin version is 1.2.0 (1.2.0+dfsg-1build2~ppa1~saucy1).
/Henrik Garde ________________________________________ Fra: [email protected] [[email protected]] på vegne af [email protected] [[email protected]] Sendt: 28. november 2013 10:12 Til: [email protected] Emne: fenics-support Digest, Vol 7, Issue 12 Send fenics-support mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://fenicsproject.org/mailman/listinfo/fenics-support or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of fenics-support digest..." Today's Topics: 1. Re: Scientific Linux configuration problem SOLVED (Mike Sussman) 2. Segmentation fault (core dumped) when evaluating at a point (Henrik Garde) 3. Re: Segmentation fault (core dumped) when evaluating at a point (Garth N. Wells) 4. Binary Install for Mac 10.9 (Reuben Kraft) 5. Dolfin: compilation error (Tianyi LI) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Nov 2013 10:01:58 -0500 From: Mike Sussman <[email protected]> To: Johannes Ring <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [FEniCS-support] Scientific Linux configuration problem SOLVED Message-ID: <[email protected]> Content-Type: text/plain; format=flowed; charset=UTF-8 On 11/27/2013 04:10 AM, Johannes Ring wrote: > On Tue, Nov 26, 2013 at 7:51 PM, Mike Sussman <[email protected]> wrote: >> Folks, >> >> I have just installed FEniCS on my Scientific Linux 6 (derivative of >> RHEL6) box. The installation SEEMS to be correct (after some tweaking), >> but I cannot get the environment correct to actually run an example. The >> installation is done in my home directory ~/Installs/FEniCS >> >> I am trying to run examples-1.0/stationary/poisson/d1_p2D.py but it never >> actually gets running. I set the environment variables using >> share/dolfin/dolfin.conf, but it complains that it cannot find swig. >> The swig executable is in my path, and the answer to "which swig" is >> "~/Installs/FEniCS/bin/swig" and according to "swig -version" its version >> number is 2.0.3. This is the version downloaded as part of the FEniCS >> install. >> >> BUT here is what I get: >> $ python d1_p2D.py >> Reading DOLFIN parameters from file "dolfin_parameters.xml". >> *** ------------------------------------------------------------------------- >> *** Warning: UnitSquare has been deprecated in DOLFIN version 1.1.0. >> *** The class UnitSquare has been replaced by UnitSquareMesh. >> *** ------------------------------------------------------------------------- >> >> Traceback (most recent call last): >> File "d1_p2D.py", line 15, in <module> >> V = FunctionSpace(mesh, 'Lagrange', 1) >> File >> "/home/mike/Installs/FEniCS/lib64/python2.6/site-packages/dolfin/functions/functionspace.py", >> line 390, in __init__ >> FunctionSpaceBase.__init__(self, mesh, element, constrained_domain) >> File >> "/home/mike/Installs/FEniCS/lib64/python2.6/site-packages/dolfin/functions/functionspace.py", >> line 84, in __init__ >> ufc_element, ufc_dofmap = jit(self._ufl_element) >> File >> "/home/mike/Installs/FEniCS/lib64/python2.6/site-packages/dolfin/compilemodules/jit.py", >> line 66, in mpi_jit >> return local_jit(*args, **kwargs) >> File >> "/home/mike/Installs/FEniCS/lib64/python2.6/site-packages/dolfin/compilemodules/jit.py", >> line 102, in jit >> raise OSError, "Could not find swig installation. Pass an existing "\ >> OSError: Could not find swig installation. Pass an existing swig binary or >> install SWIG version 2.0 or higher. > The problem is in dolfin_parameters.xml. Remove any swig related line > in this file and it should work. > > Johannes Thank you, Johannes, that solved the problem. -- Mike Sussman [email protected] ------------------------------ Message: 2 Date: Thu, 28 Nov 2013 08:07:51 +0000 From: Henrik Garde <[email protected]> To: "[email protected]" <[email protected]> Subject: [FEniCS-support] Segmentation fault (core dumped) when evaluating at a point Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" Hi, I am getting a "Segmentation fault (core dumped)" error when I try to evaluate a function at a point in python. Simple example: from dolfin import * mesh = UnitCircleMesh(20) V = FunctionSpace(mesh, 'CG', 1) u = Function(V) print u((0,0)) This simply gives the output "Segmentation fault (core dumped)", nothing else. I have tried reinstalling fenics, updating, and also running instant-clean. I am running Ubuntu 13.10, and I have not noticed this error before as I have not needed to evaluate at other points than at the grid-points until now, and everything else seems to work. /Henrik Garde ------------------------------ Message: 3 Date: Thu, 28 Nov 2013 08:51:43 +0000 From: "Garth N. Wells" <[email protected]> To: Henrik Garde <[email protected]> Cc: [email protected] Subject: Re: [FEniCS-support] Segmentation fault (core dumped) when evaluating at a point Message-ID: <[email protected]> Content-Type: text/plain; charset=UTF-8; format=flowed On 2013-11-28 08:07, Henrik Garde wrote: > Hi, > > I am getting a "Segmentation fault (core dumped)" error when I try to > evaluate a function at a point in python. Simple example: > > from dolfin import * > mesh = UnitCircleMesh(20) > V = FunctionSpace(mesh, 'CG', 1) > u = Function(V) > print u((0,0)) > > This simply gives the output "Segmentation fault (core dumped)", > nothing else. I have tried reinstalling fenics, updating, and also > running instant-clean. I am running Ubuntu 13.10, and I have not > noticed this error before as I have not needed to evaluate at other > points than at the grid-points until now, and everything else seems to > work. > Which version are you using, and are you building from source or using the Ubuntu package? Garth > /Henrik Garde > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support ------------------------------ Message: 4 Date: Wed, 27 Nov 2013 15:27:46 +0000 From: Reuben Kraft <[email protected]> To: "[email protected]" <[email protected]> Subject: [FEniCS-support] Binary Install for Mac 10.9 Message-ID: <263e134edfc33144ae7a4254d1a8cba3295ac...@engr2k10node2.engr.psu.edu> Content-Type: text/plain; charset="us-ascii" Hello, I was wondering if there is a binary build for FEniCS for Mac running 10.9? Thanks, Reuben Reuben Kraft. Ph.D. Shuman Assistant Professor of Mechanical Engineering Department of Mechanical & Nuclear Engineering The Pennsylvania State University 320 Leonhard Building University Park, PA 16802 Office: (814) 867-4570 Cell: (443) 417-4223 Email: [email protected] Web: http://www.mne.psu.edu/compbio -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://fenicsproject.org/pipermail/fenics-support/attachments/20131127/b0f56468/attachment.html> ------------------------------ Message: 5 Date: Wed, 27 Nov 2013 18:04:58 +0100 From: Tianyi LI <[email protected]> To: [email protected] Subject: [FEniCS-support] Dolfin: compilation error Message-ID: <cajjk5tep6opgvtg5f0enlexpo-czdqftsh09txuszmc4rpe...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi all, I'm having issues compiling myself Dolfin. All other dependencies have been installed (FFC, FIAT, Instant, UFL and UFC) and they can be successfully imported in my Python (~/.usr/local/bin/python). Below the cmake output: TL0E122N@dsp0647318:~/Bureau/dolfin/build$ cmake .. > -DEIGEN3_INCLUDE_DIR=/home/TL0E122N/.usr/local/include/eigen3 > -DPYTHON_EXECUTABLE=/home/TL0E122N/.usr/local/bin/python > -DPYTHON_LIBRARY=/home/TL0E122N/.usr/local/lib/libpython2.7.so.1 > -DCMAKE_INSTALL_PREFIX=/home/TL0E122N/.usr/local > -- The C compiler identification is GNU > -- The CXX compiler identification is GNU > -- Check for working C compiler: /usr/bin/gcc > -- Check for working C compiler: /usr/bin/gcc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > fatal: Not a git repository (or any parent up to mount parent ) > 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 > -- Performing Test HAVE_STD - 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: /usr/bin/gfortran > -- Check for working Fortran compiler: /usr/bin/gfortran -- works > -- Detecting Fortran compiler ABI info > -- Detecting Fortran compiler ABI info - done > -- Checking whether /usr/bin/gfortran supports Fortran 90 > -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes > -- Found MPI_C: > /usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/libdl.so;/usr/lib/libnsl.so;/usr/lib/libutil.so;/usr/lib/libm.so;/usr/lib/libdl.so > -- Found MPI_CXX: > /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/libdl.so;/usr/lib/libnsl.so;/usr/lib/libutil.so;/usr/lib/libm.so;/usr/lib/libdl.so > -- Found MPI_Fortran: > /usr/lib/openmpi/lib/libmpi_f90.so;/usr/lib/openmpi/lib/libmpi_f77.so;/usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/libdl.so;/usr/lib/libnsl.so;/usr/lib/libutil.so;/usr/lib/libm.so;/usr/lib/libdl.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: 1.42.0 > -- Found the following Boost libraries: > -- filesystem > -- program_options > -- system > -- thread > -- iostreams > -- mpi > -- serialization > -- UFC version: 2.2.0+ > -- Found LibXml2: /usr/lib/libxml2.so > -- Found PythonInterp: /home/TL0E122N/.usr/local/bin/python > CMake Warning (dev) at CMakeLists.txt:306 (find_package): > Ignoring EXACT since no version is requested. > This warning is for project developers. Use -Wno-dev to suppress it. > > -- NumPy header version 1.7.1 found > -- Checking for package 'PETSc' > -- PETSC_DIR is /usr/lib/petscdir/3.1 > -- PETSC_ARCH is linux-gnu-c-opt > -- Found petscconf.h > -- Performing test PETSC_TEST_RUNS - Success > -- Performing Test PETSC_CUSP_FOUND > -- Performing Test PETSC_CUSP_FOUND - Failed > -- PETSc configured without Cusp support > -- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. > (missing: PETSC_VERSION_OK) > -- ParMETIS could not be found/configured. (missing: PARMETIS_LIBRARIES > PARMETIS_TEST_RUNS PARMETIS_INCLUDE_DIRS PARMETIS_VERSION > PARMETIS_VERSION_OK) > -- Checking for package 'SCOTCH-PT' > -- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing: > SCOTCH_INCLUDE_DIRS SCOTCH_TEST_RUNS) > -- Checking for package 'AMD' > -- Looking for Fortran dgemm > -- Looking for Fortran dgemm - found > -- Looking for include files CMAKE_HAVE_PTHREAD_H > -- Looking for include files CMAKE_HAVE_PTHREAD_H - found > -- Looking for pthread_create in pthreads > -- Looking for pthread_create in pthreads - not found > -- Looking for pthread_create in pthread > -- Looking for pthread_create in pthread - 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: > debug;/usr/lib/libhdf5_hl.so;/usr/lib/libhdf5.so;/usr/lib/libpthread.so;/usr/lib/libz.so;/usr/lib/libm.so;optimized;/usr/lib/libhdf5_hl.so;/usr/lib/libhdf5.so;/usr/lib/libpthread.so;/usr/lib/libz.so;/usr/lib/libm.so > -- HDF5 has been found, but is missing parallel support. It will not be > enabled. > -- PASTIX_LIBRARIES > PASTIX_LIBRARY-NOTFOUND;/usr/lib/librt.so;/usr/lib/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 - Success > -- Found CGAL: > /home/TL0E122N/.usr/local/lib/libCGAL.so;/usr/lib/libboost_thread-mt.so;/usr/lib/libboost_system-mt.so;/usr/lib/libgmp.so;/usr/lib/libmpfr.so > -- Found ZLIB: /usr/include > -- checking for module 'cppunit' > -- package 'cppunit' not found > -- Found CPPUNIT: /home/TL0E122N/.usr/local/lib/libcppunit.so > -- Checking for package 'Sphinx' > -- Found Sphinx: /usr/bin/sphinx-build > -- 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 Qt-Version 4.6.3 (using /usr/bin/qmake-qt4) > -- Found VTK: /usr/lib/vtk-5.4 (found version "5.4") > -- > -- The following optional packages were found: > -- ------------------------------------------- > -- (OK) OPENMP > -- (OK) MPI > -- (OK) UMFPACK > -- (OK) CHOLMOD > -- (OK) CGAL > -- (OK) ZLIB > -- (OK) PYTHON > -- (OK) SPHINX > -- (OK) VTK > -- (OK) QT > -- > -- The following optional packages were not found: > -- ----------------------------------------------- > -- (**) PETSC > -- (**) PETSC4PY > -- (**) SLEPC > -- (**) TAO > -- (**) TRILINOS > -- (**) PASTIX > -- (**) SCOTCH > -- (**) PARMETIS > -- (**) HDF5 > -- > -- > -- Generating SWIG interface. > -- -------------------------- > -- > -- Generating form files in demo, test, bench and dolfin directories. May > take some time... > -- > ---------------------------------------------------------------------------------------- > -- > -- Generating CMakeLists.txt files in demo, test and bench directories > -- ------------------------------------------------------------------- > -- > -- Download demo and test data. May take some time... > -- -------------------------------------------------- > -- > -- Copying demo and test data to build directory. > -- ---------------------------------------------- > -- Enabling generation of documentation. > -- Initializing sphinx projects > -- Enabling generation of html-documentation > -- Configuring done > -- Generating done > -- Build files have been written to: /home/TL0E122N/Bureau/dolfin2/build > However "make" gives at the end an error with "copy_swig_files". [ 94%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/refinement/ParallelRefinement2D.cpp.o > [ 95%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/refinement/refine.cpp.o > [ 95%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/refinement/RegularCutRefinement.cpp.o > [ 95%] Building CXX object > dolfin/CMakeFiles/dolfin.dir/refinement/LocalMeshRefinement.cpp.o > Linking CXX shared library libdolfin.so > [ 95%] Built target dolfin > Scanning dependencies of target copy_swig_files > [ 95%] Built target copy_swig_files > make[2]: *** Pas de r?gle pour fabriquer la cible ? copy_swig_files ?, > n?cessaire pour ? dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx ?. Arr?t. > make[1]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Erreur 2 > make: *** [all] Erreur 2 > I use a version 2.0.11 of swig. Thanks for your help. -------------- next part -------------- An HTML attachment was scrubbed... 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