Currently Loaded Modulefiles: 1) python/2.7-anaconda-2.1.0 3) cmake/3.0.0 2) papi/5.4.1 Discretization: RT0 MPI processes 2: solving... Compiling form form00 Compiler stage 1: Analyzing form(s) ----------------------------------- Geometric dimension: 3 Number of cell subdomains: 0 Rank: 2 Arguments: '(v_0, v_1)' Number of coefficients: 1 Coefficients: '[Coordinates]' Unique elements: 'RT1(?), Vector<3 x CG1(?)>' Unique sub elements: 'RT1(?), Vector<3 x CG1(?)>, CG1(?)' representation: quadrature quadrature_degree: auto --> 2 quadrature_rule: auto --> default Compiler stage 1 finished in 0.0274231 seconds. Compiler stage 2: Computing intermediate representation ------------------------------------------------------- Computing representation of integrals Computing quadrature representation Transforming cell integral Compiler stage 2 finished in 0.128273 seconds. Compiler stage 3: Optimizing intermediate representation -------------------------------------------------------- Skipping optimizations, add -O to optimize Compiler stage 3 finished in 0.00029707 seconds. Compiler stage 4 finished in 0.019155 seconds. FFC finished in 0.177397 seconds. Compiling form form01 Compiler stage 1: Analyzing form(s) ----------------------------------- Geometric dimension: 3 Number of cell subdomains: 0 Rank: 2 Arguments: '(v_0, v_1)' Number of coefficients: 1 Coefficients: '[Coordinates]' Unique elements: 'RT1(?), DG0(?), Vector<3 x CG1(?)>' Unique sub elements: 'RT1(?), DG0(?), Vector<3 x CG1(?)>, CG1(?)' representation: quadrature quadrature_degree: auto --> 1 quadrature_rule: auto --> default Compiler stage 1 finished in 0.0231221 seconds. Compiler stage 2: Computing intermediate representation ------------------------------------------------------- Computing representation of integrals Computing quadrature representation Transforming cell integral Compiler stage 2 finished in 0.0208521 seconds. Compiler stage 3: Optimizing intermediate representation -------------------------------------------------------- Skipping optimizations, add -O to optimize Compiler stage 3 finished in 0.000285864 seconds. Compiler stage 4 finished in 0.00608015 seconds. FFC finished in 0.05071 seconds. Compiling form form10 Compiler stage 1: Analyzing form(s) ----------------------------------- Geometric dimension: 3 Number of cell subdomains: 0 Rank: 2 Arguments: '(v_0, v_1)' Number of coefficients: 1 Coefficients: '[Coordinates]' Unique elements: 'DG0(?), RT1(?), Vector<3 x CG1(?)>' Unique sub elements: 'DG0(?), RT1(?), Vector<3 x CG1(?)>, CG1(?)' representation: quadrature quadrature_degree: auto --> 1 quadrature_rule: auto --> default Compiler stage 1 finished in 0.0230188 seconds. Compiler stage 2: Computing intermediate representation ------------------------------------------------------- Computing representation of integrals Computing quadrature representation Transforming cell integral Compiler stage 2 finished in 0.0197461 seconds. Compiler stage 3: Optimizing intermediate representation -------------------------------------------------------- Skipping optimizations, add -O to optimize Compiler stage 3 finished in 0.000277042 seconds. Compiler stage 4 finished in 0.00754809 seconds. FFC finished in 0.050946 seconds. Compiling form form11 Compiler stage 1: Analyzing form(s) ----------------------------------- Geometric dimension: 3 Number of cell subdomains: 0 Rank: 2 Arguments: '(v_0, v_1)' Number of coefficients: 1 Coefficients: '[Coordinates]' Unique elements: 'DG0(?), Vector<3 x CG1(?)>' Unique sub elements: 'DG0(?), Vector<3 x CG1(?)>, CG1(?)' representation: quadrature quadrature_degree: auto --> 0 quadrature_rule: auto --> default Compiler stage 1 finished in 0.0213521 seconds. Compiler stage 2: Computing intermediate representation ------------------------------------------------------- Computing representation of integrals Computing quadrature representation Transforming cell integral Compiling form form00 Compiler stage 1: Analyzing form(s) ----------------------------------- Geometric dimension: 3 Number of cell subdomains: 0 Rank: 1 Arguments: '(v_0)' Number of coefficients: 2 Coefficients: '[Coordinates, function_10]' Unique elements: 'RT1(?), Vector<3 x CG1(?)>, DG0(?)' Unique sub elements: 'RT1(?), Vector<3 x CG1(?)>, DG0(?), CG1(?)' representation: quadrature quadrature_degree: auto --> 1 quadrature_rule: auto --> default Compiler stage 1 finished in 0.00957394 seconds. Compiler stage 2: Computing intermediate representation ------------------------------------------------------- Computing representation of integrals Computing quadrature representation Transforming cell integral Compiling form form10 Compiler stage 1: Analyzing form(s) ----------------------------------- Geometric dimension: 3 Number of cell subdomains: 0 Rank: 1 Arguments: '(v_0)' Number of coefficients: 2 Coefficients: '[Coordinates, function_10]' Unique elements: 'DG0(?), Vector<3 x CG1(?)>' Unique sub elements: 'DG0(?), Vector<3 x CG1(?)>, CG1(?)' representation: quadrature quadrature_degree: auto --> 0 quadrature_rule: auto --> default Compiler stage 1 finished in 0.00945807 seconds. Compiler stage 2: Computing intermediate representation ------------------------------------------------------- Computing representation of integrals Computing quadrature representation Transforming cell integral Compiler stage 2 finished in 0.00732398 seconds. Compiler stage 3: Optimizing intermediate representation -------------------------------------------------------- Skipping optimizations, add -O to optimize Compiler stage 3 finished in 0.000273943 seconds. Compiler stage 4 finished in 0.00303102 seconds. FFC finished in 0.0204549 seconds. [0] pyop2:INFO Compiling wrapper... [0] pyop2:INFO Compiling wrapper...done Traceback (most recent call last): File "Compare_RT0.py", line 81, in solver = LinearSolver(A,solver_parameters=selfp_parameters,options_prefix="selfp_") File "/users/jychang48/.local/lib/python2.7/site-packages/firedrake/linear_solver.py", line 83, in __init__ self.ksp.setOperators(A=self.A.M.handle, P=self.P.M.handle) File "/users/jychang48/.local/lib/python2.7/site-packages/firedrake/matrix.py", line 145, in M self._M._force_evaluation() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 1565, in _force_evaluation _trace.evaluate(reads, writes) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 169, in evaluate comp._run() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 4031, in _run return self.compute() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 4072, in compute fun = self._jitmodule File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/utils.py", line 64, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/sequential.py", line 158, in _jitmodule direct=self.is_direct, iterate=self.iteration_region) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/host.py", line 706, in __init__ self.compile() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/host.py", line 804, in compile compiler=compiler.get('name')) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/compilation.py", line 269, in load dll = compiler.get_so(src, extension) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/compilation.py", line 186, in get_so return ctypes.CDLL(soname) File "/usr/projects/hpcsoft/toss2/common/anaconda/2.1.0-python-2.7/lib/python2.7/ctypes/__init__.py", line 365, in __init__ self._handle = _dlopen(self._name, mode) OSError: /tmp/pyop2-cache-uid25833/bd29bb408b4f81a331815956bbc1345d.so: cannot open shared object file: No such file or directory application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 [0] pyop2:INFO Compiling wrapper... /users/jychang48/.local/lib/python2.7/site-packages/pyop2_utils/prefork.py:78: UserWarning: Prefork server exiting upon apparent death of parent warn("%s exiting upon apparent death of %s" % (who, partner)) Traceback (most recent call last): File "Compare_RT0.py", line 11, in from firedrake import * RuntimeError: not holding the import lock [0] pyop2:INFO Compiling wrapper...done Traceback (most recent call last): File "Compare_RT0.py", line 81, in solver = LinearSolver(A,solver_parameters=selfp_parameters,options_prefix="selfp_") File "/users/jychang48/.local/lib/python2.7/site-packages/firedrake/linear_solver.py", line 83, in __init__ self.ksp.setOperators(A=self.A.M.handle, P=self.P.M.handle) File "/users/jychang48/.local/lib/python2.7/site-packages/firedrake/matrix.py", line 145, in M self._M._force_evaluation() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 1565, in _force_evaluation _trace.evaluate(reads, writes) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 169, in evaluate comp._run() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 4031, in _run return self.compute() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 4072, in compute fun = self._jitmodule File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/utils.py", line 64, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/sequential.py", line 158, in _jitmodule direct=self.is_direct, iterate=self.iteration_region) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/host.py", line 706, in __init__ self.compile() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/host.py", line 804, in compile compiler=compiler.get('name')) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/compilation.py", line 269, in load dll = compiler.get_so(src, extension) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/compilation.py", line 184, in get_so MPI.comm.barrier() File "Comm.pyx", line 859, in mpi4py.MPI.Comm.barrier (src/mpi4py.MPI.c:73008) File "pickled.pxi", line 531, in mpi4py.MPI.PyMPI_barrier (src/mpi4py.MPI.c:32715) mpi4py.MPI.Exception: Other MPI error, error stack: PMPI_Barrier(425).........: MPI_Barrier(MPI_COMM_WORLD) failed MPIR_Barrier_impl(331)....: Failure during collective MPIR_Barrier_impl(313)....: MPIR_Barrier_intra(83)....: dequeue_and_set_error(596): Communication error with rank 1 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 /users/jychang48/.local/lib/python2.7/site-packages/pyop2_utils/prefork.py:78: UserWarning: Prefork server exiting upon apparent death of parent warn("%s exiting upon apparent death of %s" % (who, partner)) Traceback (most recent call last): File "Compare_RT0.py", line 11, in from firedrake import * RuntimeError: not holding the import lock ================= SEED 30 ================= Discretization: RT0 MPI processes 2: solving... [0] pyop2:INFO Compiling wrapper... [0] pyop2:INFO Compiling wrapper...done Traceback (most recent call last): File "Compare_RT0.py", line 81, in solver = LinearSolver(A,solver_parameters=selfp_parameters,options_prefix="selfp_") File "/users/jychang48/.local/lib/python2.7/site-packages/firedrake/linear_solver.py", line 83, in __init__ self.ksp.setOperators(A=self.A.M.handle, P=self.P.M.handle) File "/users/jychang48/.local/lib/python2.7/site-packages/firedrake/matrix.py", line 145, in M self._M._force_evaluation() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 1565, in _force_evaluation _trace.evaluate(reads, writes) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 169, in evaluate comp._run() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 4031, in _run return self.compute() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/base.py", line 4072, in compute fun = self._jitmodule File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/utils.py", line 64, in __get__ obj.__dict__[self.__name__] = result = self.fget(obj) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/sequential.py", line 158, in _jitmodule direct=self.is_direct, iterate=self.iteration_region) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/host.py", line 706, in __init__ self.compile() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/host.py", line 804, in compile compiler=compiler.get('name')) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/compilation.py", line 269, in load dll = compiler.get_so(src, extension) File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/compilation.py", line 186, in get_so return ctypes.CDLL(soname) File "/usr/projects/hpcsoft/toss2/common/anaconda/2.1.0-python-2.7/lib/python2.7/ctypes/__init__.py", line 365, in __init__ self._handle = _dlopen(self._name, mode) OSError: /tmp/pyop2-cache-uid25833/bd29bb408b4f81a331815956bbc1345d.so: cannot open shared object file: No such file or directory application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 /users/jychang48/.local/lib/python2.7/site-packages/pyop2_utils/prefork.py:78: UserWarning: Prefork server exiting upon apparent death of parent warn("%s exiting upon apparent death of %s" % (who, partner)) Traceback (most recent call last): File "Compare_RT0.py", line 11, in from firedrake import * RuntimeError: not holding the import lock Traceback (most recent call last): File "Compare_RT0.py", line 82, in solver.solve(solution,b) File "/users/jychang48/.local/lib/python2.7/site-packages/firedrake/linear_solver.py", line 136, in solve with b.dat.vec_ro as rhs: File "/usr/projects/hpcsoft/toss2/common/anaconda/2.1.0-python-2.7/lib/python2.7/contextlib.py", line 17, in __enter__ return self.gen.next() File "/users/jychang48/.local/lib/python2.7/site-packages/pyop2/petsc_base.py", line 296, in vecscatter self._vec.setUp() File "PETSc/Vec.pyx", line 309, in petsc4py.PETSc.Vec.setUp (src/petsc4py.PETSc.c:90287) petsc4py.PETSc.Error: error code 1 [0] VecSetUp() line 1584 in /tmp/pip-_4fFDW-build/src/vec/vec/interface/vector.c [0] VecSetType() line 53 in /tmp/pip-_4fFDW-build/src/vec/vec/interface/vecreg.c [0] VecCreate_MPI() line 244 in /tmp/pip-_4fFDW-build/src/vec/vec/impls/mpi/pbvec.c [0] VecCreate_MPI_Private() line 195 in /tmp/pip-_4fFDW-build/src/vec/vec/impls/mpi/pbvec.c [0] PetscLayoutSetUp() line 147 in /tmp/pip-_4fFDW-build/src/vec/is/utils/pmap.c [0] PetscSplitOwnership() line 84 in /tmp/pip-_4fFDW-build/src/sys/utils/psplit.c application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 /users/jychang48/.local/lib/python2.7/site-packages/pyop2_utils/prefork.py:78: UserWarning: Prefork server exiting upon apparent death of parent warn("%s exiting upon apparent death of %s" % (who, partner)) Traceback (most recent call last): File "Compare_RT0.py", line 11, in from firedrake import * RuntimeError: not holding the import lock