Hi,
I builded libmesh again with netcdf and got the same error. Another problem
I ran into is associated with PETSC when running example case,
transient_ex1:
Mesh Information:
elem_dimensions()={2}
spatial_dimension()=2
n_nodes()=6273
n_local_nodes()=6273
n_elem()=13650
n_local_elem()=13650
n_active_elem()=10240
n_subdomains()=2
n_partitions()=1
n_processors()=1
n_threads()=1
processor_id()=0
EquationSystems
n_systems()=1
System #0, "Convection-Diffusion"
Type "TransientLinearImplicit"
Variables="u"
Finite Element Types="LAGRANGE"
Approximation Orders="FIRST"
n_dofs()=6273
n_local_dofs()=6273
n_constrained_dofs()=0
n_local_constrained_dofs()=0
n_vectors()=3
n_matrices()=1
DofMap Sparsity
Average On-Processor Bandwidth <= 7.57038
Average Off-Processor Bandwidth <= 0
Maximum On-Processor Bandwidth <= 9
Maximum Off-Processor Bandwidth <= 0
DofMap Constraints
Number of DoF Constraints = 0
Number of Node Constraints = 0
Warning: This MeshOutput subclass only supports meshes which have been
serialized!
Warning: This MeshOutput subclass only supports meshes which have been
serialized!
[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 see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X
to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------------- Stack Frames
------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR: INSTEAD the line number of the start of the function
[0]PETSC ERROR: is given.
*[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------*
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.6.4, Apr, 12, 2016
[0]PETSC ERROR: ./libmesh_ex on a gnu-c-debug named
j4ryans-MacBook-Pro.local by j4ryan Sat Jun 25 17:30:46 2016
[0]PETSC ERROR: Configure options --prefix=/opt/petsc-3.6.4
--with-shared-libraries --with-mpi-dir=/opt/mpich2/ --download-fblaslapack
--with-debugging=1
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
:
system msg for write_line failure : Bad file descriptor
------------------------------------------------------------------------------------------------------------------
| Time: Sat Jun 25 17:30:49 2016
|
| OS: Darwin
|
| HostName: j4ryans-MacBook-Pro.local
|
| OS Release: 14.5.0
|
| OS Version: Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT
2015; root:xnu-2782.40.9~1/RELEASE_X86_64 |
| Machine: x86_64
|
| Username: j4ryan
|
| Configuration: ./configure '--prefix=/opt/libmesh-1.0.0'
|
| '--disable-strict-lgpl'
|
| '--disable-ifem'
|
| '--with-mpi=/opt/mpich2'
|
| 'PETSC_DIR=/opt/petsc-3.6.4'
|
| '--enable-metis'
|
| '--enable-everything'
|
| '--enable-parmesh'
|
| '--enable-blocked-storage'
|
| 'HDF5_DIR=/usr/local/Cellar/hdf5'
|
| 'VTK_DIR=/usr/local/Cellar/vtk'
|
| 'VTK_INCLUDE=/usr/local/Cellar/vtk/7.0.0_1/include/vtk-7.0'
|
| '--with-vtk-lib=/usr/local/Cellar/vtk/7.0.0_1/lib'
|
| 'PETSC_ARCH=gnu-c-debug'
|
------------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------------------
| libMesh Performance: Alive time=3.07726, Active time=2.71201
|
---------------------------------------------------------------------------------------------------------------------------
| Event nCalls Total Time Avg
Time Total Time Avg Time % of Active Time |
| w/o Sub w/o
Sub With Sub With Sub w/o S With S |
|---------------------------------------------------------------------------------------------------------------------------|
|
|
|
|
| DofMap
|
| add_neighbors_to_send_list() 1 0.1358
0.135786 0.1358 0.135786 5.01 5.01 |
| build_sparsity() 1 0.0925
0.092506 0.2539 0.253927 3.41 9.36 |
| create_dof_constraints() 1 0.0232
0.023190 0.0232 0.023190 0.86 0.86 |
| distribute_dofs() 1 0.1581
0.158109 0.4951 0.495110 5.83 18.26 |
| dof_indices() 40960 0.6162
0.000015 0.6162 0.000015 22.72 22.72 |
| prepare_send_list() 2 0.0000
0.000007 0.0000 0.000007 0.00 0.00 |
| reinit() 1 0.2012
0.201210 0.2012 0.201210 7.42 7.42 |
|
|
| EquationSystems
|
| build_parallel_solution_vector() 1 0.1900
0.190048 0.3448 0.344840 7.01 12.72 |
| build_solution_vector() 1 0.0001
0.000080 0.3449 0.344920 0.00 12.72 |
|
|
| ExodusII_IO
|
| write_nodal_data() 1 0.0000
0.000000 0.0000 0.000000 0.00 0.00 |
|
|
| GenericProjector
|
| operator() 1 0.2483
0.248252 0.6311 0.631060 9.15 23.27 |
| project_edges 10240 0.0093
0.000001 0.0093 0.000001 0.34 0.34 |
| project_interior 10240 0.0127
0.000001 0.0127 0.000001 0.47 0.47 |
| project_nodes 10240 0.0390
0.000004 0.0390 0.000004 1.44 1.44 |
| project_sides 10240 0.0089
0.000001 0.0089 0.000001 0.33 0.33 |
|
|
| Mesh
|
| find_neighbors() 2 0.2172
0.108598 0.2172 0.108598 8.01 8.01 |
|
|
| MeshCommunication
|
| delete_remote_elements() 2 0.0697
0.034850 0.0697 0.034850 2.57 2.57 |
| make_elems_parallel_consistent() 5 0.0162
0.003249 0.0162 0.003249 0.60 0.60 |
| make_node_ids_parallel_consistent() 5 0.0135
0.002700 0.0135 0.002700 0.50 0.50 |
| make_node_proc_ids_parallel_consistent() 10 0.0220
0.002195 0.0220 0.002195 0.81 0.81 |
| make_node_unique_ids_parallel_consistent() 5 0.0036
0.000723 0.0036 0.000723 0.13 0.13 |
|
|
| MeshOutput
|
| write_equation_systems() 1 0.0488
0.048777 0.0000 0.000000 1.80 0.00 |
|
|
| MeshRefinement
|
| _refine_elements() 5 0.1725
0.034501 0.3973 0.079460 6.36 14.65 |
| add_node() 43648 0.1627
0.000004 0.1627 0.000004 6.00 6.00 |
|
|
| Parallel
|
| allgather() 9 0.0001
0.000008 0.0001 0.000008 0.00 0.00 |
|
|
| ParallelMesh
|
| renumber_nodes_and_elements() 4 0.2269
0.056726 0.2270 0.056743 8.37 8.37 |
|
|
| Partitioner
|
| set_node_processor_ids() 1 0.0002
0.000176 0.0002 0.000176 0.01 0.01 |
| single_partition() 2 0.0039
0.001929 0.0039 0.001929 0.14 0.14 |
|
|
| System
|
| project_fem_vector() 1 0.0046
0.004590 0.6357 0.635650 0.17 23.44 |
| project_vector(FunctionBase) 1 0.0000
0.000017 0.6357 0.635667 0.00 23.44 |
|
|
| TopologyMap
|
| init() 5 0.0145
0.002899 0.0145 0.002899 0.53 0.53 |
|
|
| XdrIO
|
| read() 1 0.0005
0.000489 0.0005 0.000489 0.02 0.02 |
---------------------------------------------------------------------------------------------------------------------------
| Totals: 125638 2.7120
100.00 |
---------------------------------------------------------------------------------------------------------------------------
Any advice?
Thanks.
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