24. mai 2014 kl. 00:09 skrev Imran Ali <[email protected]>:
> On 2014-05-21 15:23, Johannes Ring wrote: >> On Wed, May 21, 2014 at 3:20 PM, Imran Ali >> <[email protected]> wrote: >>> On 2014-05-21 13:52, Johannes Ring wrote: >>>> On Wed, May 21, 2014 at 1:35 PM, Imran Ali >>>> <[email protected]> wrote: >>>>> On 2014-05-20 15:16, Johannes Ring wrote: >>>>>> On Tue, May 20, 2014 at 2:55 PM, Imran Ali >>>>>> <[email protected]> wrote: >>>>>>> I commented out the following in the cmake file : >>>>>>> ## Try to figure out PETSC_DIR by finding petsc.h >>>>>>> #find_path(PETSC_DIR include/petsc.h >>>>>>> # HINTS ${PETSC_DIR} $ENV{PETSC_DIR} >>>>>>> # PATHS ${petsc_dir_locations} >>>>>>> # DOC "PETSc directory") >>>>>>> message("Skipped find petsc") >>>>>>> # Report result of search for PETSC_DIR >>>>>>> if (DEFINED PETSC_DIR) >>>>>>> message(STATUS "PETSC_DIR is ${PETSC_DIR}") >>>>>>> else() >>>>>>> message(STATUS "PETSC_DIR is empty") >>>>>>> endif() >>>>>>> And the build went successfully, however without being able to find >>>>>>> PETSc. >>>>>>> Which I need. >>>>>> I was thinking more of disabling some of the try_run calls in >>>>>> FindPETSc.cmake. However, you can also try to turn off >>>>>> DOLFIN_SKIP_BUILD_TESTS and then apply the following patch to >>>>>> FindPETSc.cmake: >>>>>> # Build PETSc test program >>>>>> -if (DOLFIN_SKIP_BUILD_TESTS) >>>>>> +if (1) >>>>>> set(PETSC_TEST_RUNS TRUE) >>>>>> - set(PETSC_VERSION "UNKNOWN") >>>>>> + set(PETSC_VERSION "3.4.4") >>>>>> set(PETSC_VERSION_OK TRUE) >>>>>> elseif (FOUND_PETSC_CONF) >>>>>> Change the version number according to your PETSc version. >>>>>> Johannes >>>>> I added this in the PETSc cmake file (along with skip build in dolfin >>>>> script), however the build would crash with the following message >>>>> CMake Error at CMakeLists.txt:335 (if): >>>>> if given arguments: >>>>> "NOT" "(" "3" "EQUAL" "AND" "4" "EQUAL" ")" >>>>> Unknown arguments specified >>>> Haven't we already been through this? >>>> http://fenicsproject.org/pipermail/fenics-support/2014-May/000552.html >>>> Johannes >>> Thanks! That did it. The dolfin build went successfully. >> Good. However, the original problem was that you couldn't run the >> poisson demo. Does that work now? >> Johannes > > Hi and sorry for the delayed answer. I have reinstalled every thing from > beginning after removing the Work folder, and decided to go for python2.6. I forgot to mention that this was done after that the same error reoccured (after following the steps above). > > I ran the cpp demo, and get the following segmentation fault : > > $ ./demo_poisson > [bell:14359] *** Process received signal *** > [bell:14359] Signal: Segmentation fault (11) > [bell:14359] Signal code: Address not mapped (1) > [bell:14359] Failing at address: 0x1 > [bell:14359] [ 0] /lib64/libc.so.6[0x374fc329a0] > [bell:14359] [ 1] /lib64/libc.so.6(_IO_vfprintf+0x3e5c)[0x374fc4812c] > [bell:14359] [ 2] /lib64/libc.so.6(vasprintf+0xba)[0x374fc6f6da] > [bell:14359] [ 3] /lib64/libc.so.6(asprintf+0x88)[0x374fc4f648] > [bell:14359] [ 4] > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi.so.1(ompi_mpi_init+0x306)[0x7f853c87b9b6] > [bell:14359] [ 5] > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libmpi.so.1(MPI_Init_thread+0x184)[0x7f853c89f4e4] > [bell:14359] [ 6] > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libdolfin.so.1.3(_ZN6dolfin17SubSystemsManager8init_mpiEiPPci+0x9e)[0x7f85455bdaee] > [bell:14359] [ 7] > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libdolfin.so.1.3(_ZN6dolfin17SubSystemsManager8init_mpiEv+0x27)[0x7f85455bdcd7] > [bell:14359] [ 8] > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libdolfin.so.1.3(_ZN6dolfin3MPI13num_processesEv+0x9)[0x7f85455bc5d9] > [bell:14359] [ 9] > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libdolfin.so.1.3(_ZN6dolfin12MeshTopologyC1Ev+0xcf)[0x7f854573b41f] > [bell:14359] [10] > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libdolfin.so.1.3(_ZN6dolfin4MeshC2Ev+0xfa)[0x7f85456feeba] > [bell:14359] [11] > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/libdolfin.so.1.3(_ZN6dolfin13RectangleMeshC2EddddmmSs+0x40)[0x7f854537e650] > [bell:14359] [12] ./demo_poisson(main+0x6c)[0x40921c] > [bell:14359] [13] /lib64/libc.so.6(__libc_start_main+0xfd)[0x374fc1ed1d] > [bell:14359] [14] ./demo_poisson[0x409059] > [bell:14359] *** End of error message *** > Segmentation fault (core dumped) > > > While running the python demo, nothing happens...it simply hangs : > > $ python demo_poisson.py > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/python2.6/site-packages/numpy/oldnumeric/__init__.py:11: > ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy 1.9 > warnings.warn(_msg, ModuleDeprecationWarning) > Calling FFC just-in-time (JIT) compiler, this may take some time. > /mn/anatu/studenter-u1/imranal/Work/FEniCS/lib/python2.6/site-packages/numpy/linalg/linalg.py:520: > DeprecationWarning: Implicitly casting between incompatible kinds. In a > future numpy release, this will raise an error. Use casting="unsafe" if this > is intentional. > ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj) > Calling DOLFIN just-in-time (JIT) compiler, this may take some time. > Calling DOLFIN just-in-time (JIT) compiler, this may take some time. > > I tried some of the other cpp and python demos, and they all got stuck. > > Imran > >>> Imran >>>>> Using the if test if (DOLFIN_SKIP_BUILD_TESTS) instead of if(1), would >>>>> result in no error. However, then the dolfin build would not find PETSc : >>>>> -- Found petscconf.h >>>>> -- Performing test PETSC_TEST_RUNS - Failed >>>>> -- Performing test PETSC_TEST_3RD_PARTY_LIBS_RUNS - Failed >>>>> -- 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_TEST_RUNS) (Required is at least version "3.2") >>>>> And the build would continue without PETSc. >>>>> Imran > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support
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