On Tue, 10 Mar 2015 15:37:28 +0100 (CET) Birgitte Maria Elisabeth Brydso <[email protected]> wrote:
> >> /lap/openmpi/1.8.1/gcc-4.6/ > > > > Is this a module? In that case you should add "module load > > <modulename>" to PROLOGUE. See for instance some of the examples in > > hashstack. > > > > Yes. It's a module. > > > Some comments about your profile: > > > > - You should use openblas for blas and lapack since you build petsc > > and dolfin with openblas. > > - It looks like the PATH is not indented correctly. Is that on > > purpose? > > > > > > No, that was an error. > > After adding the module to prologue, using openblas, and indenting > the PATH, I got a bit longer. Fenics builds, I can import dolfin into > python, and I no longer get the ORTE error. It is using the correct > MPI version, so that is great, thanks! > > I now have a problem with incompatible versions of SWIG. The one > installed on the system is 2.0.4, and fenics seems to have built > 2.0.11. For some reason it then tries to use the system version > during running, I think? This is the error message I get when trying > to run a short test program bvp_01.py: > > Incompatible swig versions detected. UFC swig version is not the same > as extension module swig version: '2.0.11' != '2.0.4' > Traceback (most recent call last): > File "./bvp_01.py", line 119, in <module> > bvp_01 ( 8 ) > File "./bvp_01.py", line 47, in bvp_01 > V = FunctionSpace ( mesh, "Lagrange", 1 ) > File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/dolfin/functions/functionspace.py", > > line 456, in __init__ > FunctionSpaceBase.__init__(self, mesh, element, > constrained_domain) File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/dolfin/functions/functionspace.py", > > line 147, in __init__ > ufc_element, ufc_dofmap = jit(self._ufl_element) > File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", > > line 66, in mpi_jit > output = local_jit(*args, **kwargs) > File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", > > line 126, in jit > return jit_compile(form, parameters=p) > File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ffc/jitcompiler.py", > > line 75, in jit > return jit_element(ufl_object, parameters) > File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ffc/jitcompiler.py", > > line 186, in jit_element > compiled_form, module, form_data, prefix = jit_form(form, > parameters) File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ffc/jitcompiler.py", > > line 164, in jit_form > check_swig_version(module) > File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ffc/jitcompiler.py", > > line 86, in check_swig_version > (ufc.__swigversion__, compiled_module.swigversion)) > File "<string>", line 1, in <lambda> > File > "/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ufl/log.py", > > line 151, in error > raise self._exception_type(self._format_raw(*message)) > Exception: Incompatible swig versions detected. UFC swig version is > not the same as extension module swig version: '2.0.11' != '2.0.4' It is possible that you have a module JITted by some previous different install in the same cache ( ~/.instant/cache, ~/.instant/error by default, can be overriden by $INSTANT_CACHE_DIR, $INSTANT_ERROR_DIR at runtime; consider reading README in Instant source tree; there are also some relevant notes for cluster usage). As a workaround you can run intant-clean. Generally your $INSTANT_CACHE_DIR should depend on Python build, NumPy build, SWIG build and maybe others. (This is a know issue in FEniCS.) Jan > > > Also attaching the new version of my yaml file. > > Is there something I need to set differently in order for fenics to > run with the swig it has built? > > > Thanks, Birgitte > > > > > _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
