3. apr. 2014 kl. 12:31 skrev Imran Ali <[email protected]>:
> On 2014-04-03 11:45, Johannes Ring wrote: >> On Thu, Apr 3, 2014 at 10:33 AM, Imran Ali >> <[email protected]> wrote: >>> Using Redhat Enterprise 6, I am installing following packages through dorsal >>> : >>> bzip2 boost cmake pcre swig glib2 libffi git vtkdata vtk cgal eigen mpfr ply >>> python numpy matplotlib scientificpython cython scipy ipython mpi4py hdf5 >>> h5py parmetis scotch blas lapack trilinos_intel petsc petsc4py slepc fiat >>> ferari ufc ufl ffc instant dolfin >> Note that the order you specify these packages is important for >> Dorsal. If the above list is what you have used, then for instance >> 'vtk' and 'ply' would be installed with system python (which I assume >> is version 2.6) because they come before 'python', while for instance >> 'numpy' will use the python built by Dorsal (which is version 2.7). >> You should therefor put 'python' early in the list to make sure all >> packages that depends on python are built with the same python. >>> I end up with two versions of python in my Work directory. I am guessing >>> that if I did not include the python package, I would only have 2.6. I >>> notice that both versions are used interchangeably when working with FEniCS >>> applications. Will this create any problems ? >> Yes, most likely. >> Johannes > > I just wanted to add the following warning I get when importing dolfin : > > import dolfin > /uio/hume/student-u29/imranal/Work/FEniCS/lib64/python2.6/site-packages/petsc4py/lib/__init__.py:64: > RuntimeWarning: compiletime version 2.6 of module 'petsc4py.PETSc' does not > match runtime version 2.7 > module = imp.load_module(fullname, fo, fn, stuff) > /uio/hume/student-u29/imranal/Work/FEniCS/lib64/python2.6/site-packages/petsc4py/lib/PETSc.so:4: > RuntimeWarning: compiletime version 2.6 of module 'libpetsc4py' does not > match runtime version 2.7 > > Thanks Johannes. I will try to fix my fenics install by rearranging those > packages. > > Imran I am afraid that simply worsened things. Installing Python first simply made dolfin unsuable. Importing dolfin generated error : No module named common. Reinstalling python2.7 only, I reverted back to the warning above. However, now PETSc crashes the ipython session : RuntimeWarning: compiletime version 2.6 of module 'petsc4py.PETSc' does not match runtime version 2.7 module = imp.load_module(fullname, fo, fn, stuff) /uio/hume/student-u29/imranal/Work/FEniCS/lib64/python2.6/site-packages/petsc4py/lib/PETSc.so:4: RuntimeWarning: compiletime version 2.6 of module 'libpetsc4py' does not match runtime version 2.7 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or seehttp://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: or tryhttp://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 59. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. --------------------------------------------------------------------------
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