[CIG-SEISMO] Specfem Cartesian 2.1 Example issues

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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