[CIG-SEISMO] Specfem Cartesian 2.1 Example issues
胡喆骞
huzheqian at gmail.com
Sun Aug 2 19:30:33 PDT 2015
*Dear experts:*
*I used Specfem3D 2.0 before. *
*There are some issues when **I use specfem Cartesian version 2.1. When I
run example/homogeneous_halfspace following READEM like that below:*
[root at CentOS homogeneous_halfspace]# which mpirun
/opt/openmpi/bin/mpirun
[root at CentOS homogeneous_halfspace]# which gout
/app/20140625/specfem3d/src/decompose_mesh/scotch_5.1.12b/bin/gout
[root at CentOS homogeneous_halfspace]# ./run_this_example.sh
./run_this_example.sh >& run_this_example.sh.log
*Then ,the log show :*
running example: Sat Aug 1 17:41:10 CST 2015
(will take about 15 minutes)
setting up example...
## ---------------------------- ##
## setting up compilation flags ##
## ---------------------------- ##
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gfortran... gfortran
checking whether the Fortran compiler works... yes
checking for Fortran compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
configure: running /bin/sh ./flags.guess
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran...
-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7
-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64
-L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..
-lgfortranbegin -lgfortran -lm
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no
extra underscore
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag needed to accept free-form source... none
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking emmintrin.h usability... yes
checking emmintrin.h presence... yes
checking for emmintrin.h... yes
checking xmmintrin.h usability... yes
checking xmmintrin.h presence... yes
checking for xmmintrin.h... yes
## ------ ##
## SCOTCH ##
## ------ ##
checking for scotchfarchinit in -lscotch... no
checking whether Scotch is usable... no, using bundled scotch instead
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... none needed
checking whether yytext is a pointer... no
checking for bison... bison -y
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
pthread found
## ----------------- ##
## module extensions ##
## ----------------- ##
checking Fortran 90 module extension... mod
checking Fortran 90 module inclusion flag... -I
checking Fortran 90 module output flag... -J
## --- ##
## MPI ##
## --- ##
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
## ----------------------------------- ##
## setting up default simulation setup ##
## ----------------------------------- ##
configure: creating ./config.status
config.status: creating Makefile
config.status: creating setup/constants.h
config.status: creating setup/precision.h
config.status: creating ./src/decompose_mesh/scotch/src/Makefile.inc
config.status: creating setup/config.h
config.status: setup/config.h is unchanged
config.status: executing bin commands
config.status: executing obj commands
config.status: executing DATA commands
config.status: executing OUTPUT_FILES commands
config.status: executing DATABASES_MPI commands
## --------------- ##
## Specfem3D 2.1.0 ##
## --------------- ##
./configure has completed and set up a default configuration to build.
You may wish to modify the following files before running a simulation:
DATA/Par_file Set parameters affecting the simulation.
DATA/CMTSOLUTION Set the source parameters before running the
solver.
DATA/STATIONS Set the receiver stations before running the
solver.
cleaning by CLEAN not defined
rm -f ./obj/combine_surf_data.aux.o ./obj/combine_vol_data.aux.o
./obj/convolve_source_timefunction.aux.o
./obj/create_movie_shakemap_AVS_DX_GMT.aux.o ./obj/model_update.aux.o
./obj/save_external_bin_m_up.aux.o ./obj/smooth_vol_data.aux.o
./obj/sum_kernels.aux.o ./obj/specfem3D_par.spec.o ./obj/pml_par.spec.o
./obj/model_update.aux.o ./obj/initialize_simulation.spec.o
./obj/read_mesh_databases.spec.o ./obj/save_external_bin_m_up.aux.o
./obj/specfem3D_gpu_cuda_method_stubs.cudacc.o
./obj/specfem3D_adios_stubs.spec_noadios.o ./obj/sum_kernels.aux.o
./obj/smooth_vol_data.aux.o ./obj/combine_surf_data.aux.o
./obj/combine_vol_data.aux.o ./obj/combine_vol_data_impl.aux.o
./obj/combine_vol_data_adios_stubs.aux_noadios.o
./obj/create_movie_shakemap_AVS_DX_GMT.aux.o
./obj/combine_vol_data_mod.mod ./obj/combine_vtk.mod ./obj/sum_par.mod
./obj/combine_vol_data_adios_mod.mod ./bin/xcombine_surf_data
./bin/xcombine_vol_data ./bin/xconvolve_source_timefunction
./bin/xcreate_movie_shakemap_AVS_DX_GMT ./bin/xmodel_update
./bin/xsmooth_vol_data ./bin/xsum_kernels
./obj/check_mesh_quality_CUBIT_Abaqus.check.o
./obj/convert_skewness_to_angle.check.o
./obj/multiply_CUBIT_Abaqus_mesh_by_1000.check.o
./bin/xcheck_mesh_quality_CUBIT_Abaqus ./bin/xconvert_skewness_to_angle
./bin/xmultiply_CUBIT_Abaqus_mesh_by_1000 ./obj/check_fields_cuda.cuda.o
./obj/compute_add_sources_acoustic_cuda.cuda.o
./obj/compute_add_sources_viscoelastic_cuda.cuda.o
./obj/compute_coupling_cuda.cuda.o
./obj/compute_forces_acoustic_cuda.cuda.o
./obj/compute_forces_viscoelastic_cuda.cuda.o
./obj/compute_kernels_cuda.cuda.o ./obj/compute_stacey_acoustic_cuda.cuda.o
./obj/compute_stacey_viscoelastic_cuda.cuda.o ./obj/initialize_cuda.cuda.o
./obj/noise_tomography_cuda.cuda.o ./obj/prepare_mesh_constants_cuda.cuda.o
./obj/save_and_compare_cpu_vs_gpu.cudacc.o
./obj/transfer_fields_cuda.cuda.o ./obj/update_displacement_cuda.cuda.o
./obj/write_seismograms_cuda.cuda.o ./obj/check_fields_cuda.cuda.o
./obj/compute_add_sources_acoustic_cuda.cuda.o
./obj/compute_add_sources_viscoelastic_cuda.cuda.o
./obj/compute_coupling_cuda.cuda.o
./obj/compute_forces_acoustic_cuda.cuda.o
./obj/compute_forces_viscoelastic_cuda.cuda.o
./obj/compute_kernels_cuda.cuda.o ./obj/compute_stacey_acoustic_cuda.cuda.o
./obj/compute_stacey_viscoelastic_cuda.cuda.o ./obj/initialize_cuda.cuda.o
./obj/noise_tomography_cuda.cuda.o ./obj/prepare_mesh_constants_cuda.cuda.o
./obj/save_and_compare_cpu_vs_gpu.cudacc.o
./obj/transfer_fields_cuda.cuda.o ./obj/update_displacement_cuda.cuda.o
./obj/write_seismograms_cuda.cuda.o ./obj/part_decompose_mesh.dec.o
./obj/fault_scotch.dec.o ./obj/decompose_mesh.dec.o
./obj/program_decompose_mesh.dec.o ./obj/decompose_mesh.mod
./obj/fault_scotch.mod ./obj/part_decompose_mesh.mod ./bin/xscotch
./bin/xdecompose_mesh ./obj/generate_databases_par.gen.o
./obj/tomography_par.gen.o ./obj/calc_jacobian.gen.o
./obj/fault_generate_databases.gen.o ./obj/create_mass_matrices.gen.o
./obj/create_regions_mesh.gen.o ./obj/finalize_databases.gen.o
./obj/generate_databases.gen.o ./obj/get_absorbing_boundary.gen.o
./obj/get_coupling_surfaces.gen.o ./obj/get_model.gen.o ./obj/get_MPI.gen.o
./obj/get_perm_color.gen.o ./obj/model_1d_cascadia.gen.o
./obj/model_1d_prem.gen.o ./obj/model_1d_socal.gen.o
./obj/model_aniso.gen.o ./obj/model_default.gen.o
./obj/model_external_values.gen.o ./obj/model_ipati.gen.o
./obj/model_gll.gen.o ./obj/model_salton_trough.gen.o
./obj/model_tomography.gen.o ./obj/pml_set_local_dampingcoeff.gen.o
./obj/program_generate_databases.gen.o ./obj/read_partition_files.gen.o
./obj/save_arrays_solver.gen.o ./obj/setup_color_perm.gen.o
./obj/setup_mesh.gen.o ./obj/memory_eval.gen.o
./obj/generate_databases_adios_stubs.gen_noadios.o
./obj/create_regions_mesh_ext_par.mod ./obj/external_model.mod
./obj/fault_generate_databases.mod ./obj/generate_databases_par.mod
./obj/model_ipati_adios_mod.mod ./obj/salton_trough_par.mod
./obj/tomography_par.mod ./bin/xgenerate_databases
./obj/check_mesh_quality.mesh.o ./obj/compute_parameters.mesh.o
./obj/create_regions_mesh.mesh.o ./obj/create_visual_files.mesh.o
./obj/define_subregions.mesh.o ./obj/define_subregions_heuristic.mesh.o
./obj/define_superbrick.mesh.o ./obj/get_flags_boundaries.mesh.o
./obj/get_MPI_cutplanes_eta.mesh.o ./obj/get_MPI_cutplanes_xi.mesh.o
./obj/meshfem3D.mesh.o ./obj/program_meshfem3D.mesh.o
./obj/read_mesh_parameter_file.mesh.o
./obj/read_value_mesh_parameters.mesh.o ./obj/save_databases.mesh.o
./obj/store_boundaries.mesh.o ./obj/store_coords.mesh.o
./obj/meshfem3D_adios_stubs.mesh_noadios.o ./obj/createregmesh.mod
./obj/readparfile.mod ./bin/xmeshfem3D
./obj/assemble_MPI_scalar.shared.o ./obj/check_mesh_resolution.shared.o
./obj/constants_mod.shared_module.o ./obj/create_name_database.shared.o
./obj/create_serial_name_database.shared.o
./obj/define_derivation_matrices.shared.o ./obj/detect_surface.shared.o
./obj/exit_mpi.shared.o ./obj/force_ftz.cc.o
./obj/get_attenuation_model.shared.o ./obj/get_cmt.shared.o
./obj/get_element_face.shared.o ./obj/get_force.shared.o
./obj/get_global.shared.o ./obj/get_jacobian_boundaries.shared.o
./obj/get_shape2D.shared.o ./obj/get_shape3D.shared.o
./obj/gll_library.shared.o ./obj/hex_nodes.shared.o
./obj/lagrange_poly.shared.o ./obj/netlib_specfun_erf.shared.o
./obj/param_reader.cc.o ./obj/prepare_assemble_MPI.shared.o
./obj/read_parameter_file.shared.o ./obj/read_topo_bathy_file.shared.o
./obj/read_value_parameters.shared.o ./obj/recompute_jacobian.shared.o
./obj/safe_alloc_mod.shared.o ./obj/save_header_file.shared.o
./obj/sort_array_coordinates.shared.o ./obj/unused_mod.shared_module.o
./obj/utm_geo.shared.o ./obj/write_c_binary.cc.o
./obj/write_VTK_data.shared.o ./obj/parallel.sharedmpi.o
./obj/adios_manager_stubs.shared_noadios.o ./obj/constants.mod
./obj/safe_alloc_mod.mod ./obj/unused_mod.mod ./obj/adios_manager_mod.mod
./obj/assemble_MPI_scalar.shared.o ./obj/check_mesh_resolution.shared.o
./obj/constants_mod.shared_module.o ./obj/create_name_database.shared.o
./obj/create_serial_name_database.shared.o
./obj/define_derivation_matrices.shared.o ./obj/detect_surface.shared.o
./obj/exit_mpi.shared.o ./obj/force_ftz.cc.o
./obj/get_attenuation_model.shared.o ./obj/get_cmt.shared.o
./obj/get_element_face.shared.o ./obj/get_force.shared.o
./obj/get_global.shared.o ./obj/get_jacobian_boundaries.shared.o
./obj/get_shape2D.shared.o ./obj/get_shape3D.shared.o
./obj/gll_library.shared.o ./obj/hex_nodes.shared.o
./obj/lagrange_poly.shared.o ./obj/netlib_specfun_erf.shared.o
./obj/param_reader.cc.o ./obj/prepare_assemble_MPI.shared.o
./obj/read_parameter_file.shared.o ./obj/read_topo_bathy_file.shared.o
./obj/read_value_parameters.shared.o ./obj/recompute_jacobian.shared.o
./obj/safe_alloc_mod.shared.o ./obj/save_header_file.shared.o
./obj/sort_array_coordinates.shared.o ./obj/unused_mod.shared_module.o
./obj/utm_geo.shared.o ./obj/write_c_binary.cc.o
./obj/write_VTK_data.shared.o ./obj/parallel.sharedmpi.o
./obj/adios_manager_stubs.shared_noadios.o
./obj/assemble_MPI_vector.spec.o ./obj/check_stability.spec.o
./obj/fault_solver_common.spec.o ./obj/fault_solver_dynamic.spec.o
./obj/fault_solver_kinematic.spec.o ./obj/gravity_perturbation.spec.o
./obj/comp_source_time_function.spec.o
./obj/compute_add_sources_acoustic.spec.o
./obj/compute_add_sources_viscoelastic.spec.o
./obj/compute_add_sources_poroelastic.spec.o
./obj/compute_adj_source_frechet.spec.o ./obj/compute_arrays_source.spec.o
./obj/compute_boundary_kernel.spec.o
./obj/compute_coupling_acoustic_el.spec.o
./obj/compute_coupling_acoustic_po.spec.o
./obj/compute_coupling_viscoelastic_ac.spec.o
./obj/compute_coupling_viscoelastic_po.spec.o
./obj/compute_coupling_poroelastic_ac.spec.o
./obj/compute_coupling_poroelastic_el.spec.o
./obj/compute_forces_acoustic_calling_routine.spec.o
./obj/compute_forces_acoustic_noDev.spec.o
./obj/compute_forces_acoustic_Dev.spec.o
./obj/compute_forces_viscoelastic_calling_routine.spec.o
./obj/compute_forces_viscoelastic_Dev.spec.o
./obj/compute_forces_viscoelastic_noDev.spec.o
./obj/compute_forces_poro_fluid_part.spec.o
./obj/compute_forces_poroelastic_calling_routine.spec.o
./obj/compute_forces_poro_solid_part.spec.o ./obj/compute_gradient.spec.o
./obj/compute_interpolated_dva.spec.o ./obj/compute_kernels.spec.o
./obj/compute_stacey_acoustic.spec.o
./obj/compute_stacey_viscoelastic.spec.o
./obj/compute_stacey_poroelastic.spec.o ./obj/compute_total_energy.spec.o
./obj/create_color_image.spec.o ./obj/detect_mesh_surfaces.spec.o
./obj/finalize_simulation.spec.o ./obj/initialize_simulation.spec.o
./obj/iterate_time.spec.o ./obj/locate_receivers.spec.o
./obj/locate_source.spec.o ./obj/make_gravity.spec.o
./obj/multiply_arrays_source.spec.o ./obj/noise_tomography.spec.o
./obj/pml_allocate_arrays.spec.o ./obj/pml_output_VTKs.spec.o
./obj/pml_compute_accel_contribution.spec.o
./obj/pml_compute_memory_variables.spec.o ./obj/pml_par.spec.o
./obj/prepare_timerun.spec.o ./obj/program_specfem3D.spec.o
./obj/read_mesh_databases.spec.o ./obj/save_adjoint_kernels.spec.o
./obj/setup_GLL_points.spec.o ./obj/setup_movie_meshes.spec.o
./obj/setup_sources_receivers.spec.o ./obj/specfem3D.spec.o
./obj/specfem3D_par.spec.o ./obj/update_displacement_scheme.spec.o
./obj/write_movie_output.spec.o ./obj/write_output_ASCII.spec.o
./obj/write_output_SU.spec.o ./obj/write_seismograms.spec.o
./obj/specfem3D_gpu_cuda_method_stubs.cudacc.o
./obj/specfem3D_adios_stubs.spec_noadios.o ./obj/fault_solver_common.mod
./obj/fault_solver_dynamic.mod ./obj/fault_solver_kinematic.mod
./obj/gravity_perturbation.mod ./obj/image_pnm_par.mod ./obj/pml_par.mod
./obj/specfem_par.mod ./obj/specfem_par_acoustic.mod
./obj/specfem_par_elastic.mod ./obj/specfem_par_poroelastic.mod
./obj/specfem_par_movie.mod ./obj/user_noise_distribution.mod
./bin/xspecfem3D
decomposing mesh...
At line 357 of file src/decompose_mesh/decompose_mesh.F90
Fortran runtime error: End of file
total number of nodes:
nnodes = 43470
total number of spectral elements:
nspec = 39600
materials:
num_mat = 1
num_mat = 1
defined = 2 undefined = 0
running database generation on 4 processors...
--------------------------------------------------------------------------
mpirun has detected an attempt to run as root. This is *strongly*
discouraged as any mistake (e.g., in defining TMPDIR) or bug can
result in catastrophic damage to the OS file system, leaving
your system in an unusable state.
You can override this protection by adding the --allow-run-as-root
option to your cmd line. However, we reiterate our strong advice
against doing so - please do so at your own risk.
--------------------------------------------------------------------------
running solver on 4 processors...
--------------------------------------------------------------------------
mpirun has detected an attempt to run as root. This is *strongly*
discouraged as any mistake (e.g., in defining TMPDIR) or bug can
result in catastrophic damage to the OS file system, leaving
your system in an unusable state.
You can override this protection by adding the --allow-run-as-root
option to your cmd line. However, we reiterate our strong advice
against doing so - please do so at your own risk.
--------------------------------------------------------------------------
see results in directory: OUTPUT_FILES/
done
Sat Aug 1 17:41:52 CST 2015
*It is obviously that it does not work well , and the simulation does not
get the results .*
*I do not get how to solve the problem ,could you give me some suggestions
?*
*I am looking forward your reply. Thank you very much!*
*Sincerely Steve Hu*
--
---------------------------------------------
Steven Hu
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