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cogenda / Genius-TCAD-Open

Open-source version of the Genius Semiconductor Device Simulator
http://www.cogenda.com
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Genius is not compiled with XML VTK support, skip VTK export... #18

Open pinkchalk opened 10 years ago

pinkchalk commented 10 years ago

I have installed Genius open source on my Ubuntu 13.10. While compiling any input test file genius gives an error

"Genius is not compiled with XML VTK support, skip VTK export..."

and hence no vtk files are generated. I have vtk 5.4.2 installed on my system and I am pretty sure that I had specified the correct paths while building Genius.

lutherthecat commented 10 years ago

Please see my install note: https://github.com/lutherthecat/Genius-TCAD-Open/blob/2b7f74b44ce11c81118f487186ed3e13111b3b6d/myinstall.txt

This version still uses waf. Later version use cmake instead on my fork.

pinkchalk commented 10 years ago

Oh, I figured it out. It was to do with specifying the VTK_DATA_ROOT while configuring vtk. Thanks anyways.

lutherthecat commented 10 years ago

Sounds good. With my instructions, it is possible to avoid compiling vtk.

pinkchalk commented 10 years ago

Great, I'll surely have a look at it. However, can you please tell me how to add -fPIC to CFLAGS while configuring vtk. There is this silly error I'm getting

/usr/bin/ld: /usr/local/lib/vtk-5.4/libvtkIO.a(vtkXMLUnstructuredGridWriter.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/vtk-5.4/libvtkIO.a: error adding symbols: Bad value collect2: error: ld returned 1 exit status

Hoping to hear from you soon. Regards

lutherthecat commented 10 years ago

Look at setting CMAKE_CXX_FLAGS and CMAKE_C_FLAGS in your CMakeCache.txt. According to this: http://vtk.1045678.n5.nabble.com/Compile-and-build-VTK-with-shared-libraries-enabled-td5721521.html you may be able to set BUILD_SHARED_LIBS=ON

pinkchalk commented 10 years ago

Thanks buddy. My first day on Git and issues have started to solve faster. Regards

lutherthecat commented 10 years ago

You're welcome. Sounds like you are well on your way. Any issues with cmake or vtk are best handled on their mailing lists.

pinkchalk commented 10 years ago

Another error now,

/usr/bin/ld: warning: libvtkNetCDF.so.5.4, needed by /usr/local/lib/vtk-5.4/libvtkIO.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libvtkmetaio.so.5.4, needed by /usr/local/lib/vtk-5.4/libvtkIO.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libvtksqlite.so.5.4, needed by /usr/local/lib/vtk-5.4/libvtkIO.so, not found (try using -rpath or -rpath-link) /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaImage::HeaderSize() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MetaImage::Modality() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_get_vara_double' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_sync' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_column_name' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_open' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_close' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_get_att_short' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaImage::ElementToIntensityFunctionOffset() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_def_var' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_prepare_v2' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_get_vara_schar' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_put_vara_uchar' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_errmsg' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaImage::DimSize(int) const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_get_att_uchar' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_close' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MetaObject::Position(int) const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_column_int' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MetaImage::MetaImage()' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_put_att_double' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_put_vara_double' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_column_count' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_inq' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_errcode' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_finalize' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_get_att_text' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MET_SystemByteOrderMSB()' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_get_vara_uchar' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_inq_att' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_open' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MetaImage::ElementByteOrderFix()' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MET_SizeOfType(vtkmetaio::MET_ValueEnumType, int*)' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_column_bytes' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_get_att_double' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MetaImage::ElementToIntensityFunctionSlope() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_put_att_text' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MetaImage::ElementNumberOfChannels() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_get_att_int' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_exec' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_put_att_int' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_inq_dim' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_strerror' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_reset' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_inq_attname' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_inq_var' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_bind_double' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_put_vara_short' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_def_dim' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_column_type' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaImage::ElementDataFileName(char const*)' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_get_att_float' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_column_blob' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_bind_int' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaObject::Position(double const*)' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MetaObject::CompressedData(bool)' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaObject::NDims() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_put_vara_int' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_get_vara_short' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_inq_varid' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_column_double' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_clear_bindings' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_netcdf_nc_get_vara_int' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_create' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_bind_blob' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_sqlite3_column_text' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_bind_text' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_get_vara_float' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaObject::DistanceUnits() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtkmetaio::MetaObject::AnatomicalOrientationAcronym() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaImage::ElementType() const' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_put_vara_float' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtk_sqlite3_step' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference tovtk_netcdf_nc_put_vara_schar' /usr/local/lib/vtk-5.4/libvtkIO.so: undefined reference to vtkmetaio::MetaObject::ElementSpacing(int) const' collect2: error: ld returned 1 exit status Waf: Leaving directory/home/pinkchalk/Downloads/Genius-TCAD-Open-master/build/default' Build failed -> task failed (exit status 1): {task 28798608: cxxprogram ANN.cpp.0.o,bd_fix_rad_search.cpp.0.o,bd_pr_search.cpp.0.o,bd_search.cpp.0.o,bd_tree.cpp.0.o,brute.cpp.0.o,kd_dump.cpp.0.o,kd_fix_rad_search.cpp.0.o,kd_pr_search.cpp.0.o,kd_search.cpp.0.o,kd_split.cpp.0.o,kd_tree.cpp.0.o,kd_util.cpp.0.o,perf.cpp.0.o,csa.cc.1.o,svd.c.1.o,expr.cc.1.o,expr_datalist.cc.1.o,expr_except.cc.1.o,expr_func.cc.1.o,expr_funclist.cc.1.o,expr_node.cc.1.o,expr_parser.cc.1.o,expr_vallist.cc.1.o,schur_solver.cc.1.o,spice_ckt.cc.1.o,tif3d.cc.1.o,UFconfig.c.1.o,amd_1.c.1.o,amd_2.c.1.o,amd_aat.c.1.o,amd_control.c.1.o,amd_defaults.c.1.o,amd_dump.c.1.o,amd_global.c.1.o,amd_info.c.1.o,amd_order.c.1.o,amd_post_tree.c.1.o,amd_postorder.c.1.o,amd_preprocess.c.1.o,amd_valid.c.1.o,btf_maxtrans.c.1.o,btf_order.c.1.o,btf_strongcomp.c.1.o,colamd.c.1.o,colamd_global.c.1.o,klu.c.1.o,klu_analyze.c.1.o,klu_analyze_given.c.1.o,klu_defaults.c.1.o,klu_diagnostics.c.1.o,klu_dump.c.1.o,klu_extract.c.1.o,klu_factor.c.1.o,klu_free_numeric.c.1.o,klu_free_symbolic.c.1.o,klu_kernel.c.1.o,klu_memory.c.1.o,klu_refactor.c.1.o,klu_scale.c.1.o,klu_solve.c.1.o,klu_sort.c.1.o,klu_tsolve.c.1.o,MXMLUtil.cpp.1.o,mxml-attr.c.1.o,mxml-entity.c.1.o,mxml-file.c.1.o,mxml-index.c.1.o,mxml-node.c.1.o,mxml-private.c.1.o,mxml-search.c.1.o,mxml-set.c.1.o,mxml-string.c.1.o,delaunay.cc.1.o,istack.cc.1.o,lpi.cc.1.o,spline.cc.1.o,triangle.c.1.o,tif_tool.cc.2.o,medici.cc.1.o,silvaco.cc.1.o,stanford.cc.1.o,suprem.cc.1.o,dfise.cc.2.o,dfise_grid.cc.2.o,trex.c.1.o,dof_object.cc.2.o,genius_env.cc.2.o,log.cc.2.o,perf_log.cc.2.o,boundary_condition.cc.2.o,boundary_condition_collector.cc.2.o,boundary_mos_channel_elem.cc.2.o,boundary_nearest_point.cc.2.o,fe.cc.2.o,fe_base.cc.2.o,fe_boundary.cc.2.o,fe_hermite.cc.2.o,fe_hermite_shape_1D.cc.2.o,fe_hermite_shape_2D.cc.2.o,fe_hermite_shape_3D.cc.2.o,fe_lagrange.cc.2.o,fe_lagrange_shape_0D.cc.2.o,fe_lagrange_shape_1D.cc.2.o,fe_lagrange_shape_2D.cc.2.o,fe_lagrange_shape_3D.cc.2.o,fe_map.cc.2.o,number_lookups.cc.2.o,edge.cc.2.o,edge_edge2.cc.2.o,edge_edge2_fvm.cc.2.o,elem.cc.2.o,elem_refinement.cc.2.o,face_cy_quad4_fvm.cc.2.o,face_cy_tri3_fvm.cc.2.o,face_quad.cc.2.o,face_quad4.cc.2.o,face_quad4_fvm.cc.2.o,face_tri.cc.2.o,face_tri3.cc.2.o,face_tri3_fvm.cc.2.o,node_elem.cc.2.o,plane.cc.2.o,polygon.cc.2.o,polygon_usample.cc.2.o,sphere.cc.2.o,interpolation_1d_linear.cc.2.o,interpolation_1d_spline.cc.2.o,interpolation_2d_csa.cc.2.o,interpolation_2d_nn.cc.2.o,interpolation_3d_nbtet.cc.2.o,interpolation_3d_qshep.cc.2.o,adolc_init.cc.2.o,dense_matrix.cc.2.o,dense_matrix_base.cc.2.o,dense_vector.cc.2.o,dense_vector_base.cc.2.o,expr_evaluate.cc.2.o,numeric_vector.cc.2.o,petsc_matrix.cc.2.o,petsc_type.cc.2.o,petsc_utils.cc.2.o,petsc_vector.cc.2.o,sparse_matrix.cc.2.o,symbolic_matrix.cc.2.o,type_tensor.cc.2.o,type_vector.cc.2.o,boundary_info.cc.2.o,boundary_mesh.cc.2.o,mesh_base.cc.2.o,mesh_communication.cc.2.o,mesh_modification.cc.2.o,mesh_refinement.cc.2.o,mesh_refinement_flagging.cc.2.o,mesh_refinement_smoothing.cc.2.o,mesh_tools.cc.2.o,serial_mesh.cc.2.o,serial_mesh_iterators.cc.2.o,unstructured_mesh.cc.2.o,mesh_generation.cc.2.o,mesh_generation_quad4.cc.2.o,mesh_generation_tri3.cc.2.o,file_include.cc.2.o,parser.cc.2.o,parser_card.cc.2.o,parser_parameter.cc.2.o,pattern.cc.2.o,pattern_xml.cc.2.o,linear_partitioner.cc.2.o,metis_partitioner.cc.2.o,parmetis_partitioner.cc.2.o,partitioner.cc.2.o,quadrature.cc.2.o,quadrature_build.cc.2.o,quadrature_conical.cc.2.o,quadrature_conical_2D.cc.2.o,quadrature_conical_3D.cc.2.o,quadrature_gauss.cc.2.o,quadrature_gauss_1D.cc.2.o,quadrature_gauss_2D.cc.2.o,quadrature_gauss_3D.cc.2.o,quadrature_jacobi_1D.cc.2.o,cgns_io.cc.2.o,conductor_region.cc.2.o,control.cc.2.o,dfise_io.cc.2.o,external_circuit.cc.2.o,external_circuit_pi.cc.2.o,external_circuit_rcl.cc.2.o,external_circuit_rct.cc.2.o,fvm_cell_data.cc.2.o,fvm_node_data.cc.2.o,fvm_node_info.cc.2.o,gdml_io.cc.2.o,insulator_region.cc.2.o,location_io.cc.2.o,pml_region.cc.2.o,resistance_region.cc.2.o,semiconductor_region.cc.2.o,simulation_region.cc.2.o,simulation_system.cc.2.o,solution_define.cc.2.o,stanford_io.cc.2.o,tif3d_io.cc.2.o,tif_io.cc.2.o,vacuum_region.cc.2.o,variable_define.cc.2.o,vtk_io.cc.2.o,ddm1.cc.2.o,ddm1_boundary_ei_interface.cc.2.o,ddm1_boundary_float_metal.cc.2.o,ddm1_boundary_gate.cc.2.o,ddm1_boundary_hetero_interface.cc.2.o,ddm1_boundary_homo_interface.cc.2.o,ddm1_boundary_ii_interface.cc.2.o,ddm1_boundary_ir_interface.cc.2.o,ddm1_boundary_is_interface.cc.2.o,ddm1_boundary_ohmic.cc.2.o,ddm1_boundary_resistance_ohmic.cc.2.o,ddm1_boundary_resistance_schottky.cc.2.o,ddm1_boundary_rr_interface.cc.2.o,ddm1_boundary_schottky.cc.2.o,ddm1_boundary_simple_gate.cc.2.o,ddm1_boundary_solderpad.cc.2.o,ddm1_conductor.cc.2.o,ddm1_conductor_hanging_node.cc.2.o,ddm1_insulator.cc.2.o,ddm1_insulator_hanging_node.cc.2.o,ddm1_resistance.cc.2.o,ddm1_resistance_hanging_node.cc.2.o,ddm1_semiconductor.cc.2.o,ddm1_semiconductor_hanging_node.cc.2.o,ddm1r.cc.2.o,ddm1r_boundary_ir_interface.cc.2.o,ddm1r_boundary_resistance_ohmic.cc.2.o,ddm1r_boundary_resistance_schottky.cc.2.o,ddm1r_boundary_rr_interface.cc.2.o,ddm1r_boundary_solderpad.cc.2.o,ddm1r_resistance.cc.2.o,ddm1r_resistance_hanging_node.cc.2.o,ddm2.cc.2.o,ddm2_boundary_ei_interface.cc.2.o,ddm2_boundary_ev.cc.2.o,ddm2_boundary_float_metal.cc.2.o,ddm2_boundary_gate.cc.2.o,ddm2_boundary_hetero_interface.cc.2.o,ddm2_boundary_homo_interface.cc.2.o,ddm2_boundary_ii_interface.cc.2.o,ddm2_boundary_ir_interface.cc.2.o,ddm2_boundary_is_interface.cc.2.o,ddm2_boundary_iv.cc.2.o,ddm2_boundary_neumann.cc.2.o,ddm2_boundary_ohmic.cc.2.o,ddm2_boundary_resistance_ohmic.cc.2.o,ddm2_boundary_resistance_schottky.cc.2.o,ddm2_boundary_rr_interface.cc.2.o,ddm2_boundary_schottky.cc.2.o,ddm2_boundary_simple_gate.cc.2.o,ddm2_boundary_solderpad.cc.2.o,ddm2_conductor.cc.2.o,ddm2_conductor_hanging_node.cc.2.o,ddm2_insulator.cc.2.o,ddm2_insulator_hanging_node.cc.2.o,ddm2_resistance.cc.2.o,ddm2_resistance_hanging_node.cc.2.o,ddm2_semiconductor.cc.2.o,ddm2_semiconductor_hanging_node.cc.2.o,ddm_ac.cc.2.o,ddmac_boundary_ei_interface.cc.2.o,ddmac_boundary_ev.cc.2.o,ddmac_boundary_float_metal.cc.2.o,ddmac_boundary_gate.cc.2.o,ddmac_boundary_hetero_interface.cc.2.o,ddmac_boundary_homo_interface.cc.2.o,ddmac_boundary_ii_interface.cc.2.o,ddmac_boundary_ir_interface.cc.2.o,ddmac_boundary_is_interface.cc.2.o,ddmac_boundary_iv.cc.2.o,ddmac_boundary_neumann.cc.2.o,ddmac_boundary_ohmic.cc.2.o,ddmac_boundary_resistance_ohmic.cc.2.o,ddmac_boundary_rr_interface.cc.2.o,ddmac_boundary_schottky.cc.2.o,ddmac_boundary_simple_gate.cc.2.o,ddmac_boundary_solderpad.cc.2.o,ddmac_conductor.cc.2.o,ddmac_insulator.cc.2.o,ddmac_resistance.cc.2.o,ddmac_semiconductor.cc.2.o,charge_integral.cc.2.o,ddm_solver.cc.2.o,gate_current.cc.2.o,inter_connect.cc.2.o,mixA_solver.cc.2.o,mix_inter_connect.cc.2.o,mix_solver.cc.2.o,mob_semiconductor.cc.2.o,dg.cc.2.o,dg_boundary_homo_interface.cc.2.o,dg_boundary_is_interface.cc.2.o,dg_boundary_ohmic.cc.2.o,dg_boundary_resistance_ohmic.cc.2.o,dg_conductor.cc.2.o,dg_insulator.cc.2.o,dg_resistance.cc.2.o,dg_semiconductor.cc.2.o,doping_analytic.cc.2.o,doping_fun.cc.2.o,ebm3.cc.2.o,ebm3_boundary_ei_interface.cc.2.o,ebm3_boundary_ev.cc.2.o,ebm3_boundary_float_metal.cc.2.o,ebm3_boundary_gate.cc.2.o,ebm3_boundary_hetero_interface.cc.2.o,ebm3_boundary_homo_interface.cc.2.o,ebm3_boundary_ii_interface.cc.2.o,ebm3_boundary_ir_interface.cc.2.o,ebm3_boundary_is_interface.cc.2.o,ebm3_boundary_iv.cc.2.o,ebm3_boundary_neumann.cc.2.o,ebm3_boundary_ohmic.cc.2.o,ebm3_boundary_resistance_ohmic.cc.2.o,ebm3_boundary_resistance_schottky.cc.2.o,ebm3_boundary_rr_interface.cc.2.o,ebm3_boundary_schottky.cc.2.o,ebm3_boundary_simple_gate.cc.2.o,ebm3_boundary_solderpad.cc.2.o,ebm3_conductor.cc.2.o,ebm3_conductor_hanging_node.cc.2.o,ebm3_insulator.cc.2.o,ebm3_insulator_hanging_node.cc.2.o,ebm3_resistance.cc.2.o,ebm3_resistance_hanging_node.cc.2.o,ebm3_semiconductor.cc.2.o,ebm3_semiconductor_hanging_node.cc.2.o,ebm3_semiconductor_jacob.cc.2.o,emfem2d.cc.2.o,fem_linear_solver.cc.2.o,fem_pde_solver.cc.2.o,fvm_explicit_solver.cc.2.o,fvm_linear_solver.cc.2.o,fvm_nonlinear_solver.cc.2.o,fvm_pde_solver.cc.2.o,hall.cc.2.o,hall_conductor.cc.2.o,hall_insulator.cc.2.o,hall_resistance.cc.2.o,hall_semiconductor.cc.2.o,hdm.cc.2.o,hdm_boundary_neumann.cc.2.o,hdm_boundary_ohmic.cc.2.o,hdm_semiconductor.cc.2.o,linear_poisson.cc.2.o,linear_poisson_boundary_ohmic.cc.2.o,linear_poisson_conductor.cc.2.o,linear_poisson_insulator.cc.2.o,linear_poisson_semiconductor.cc.2.o,mix1.cc.2.o,mix1_boundary_gate.cc.2.o,mix1_boundary_ohmic.cc.2.o,mix1_boundary_schottky.cc.2.o,mix1_boundary_solderpad.cc.2.o,mixA1.cc.2.o,mixA1_boundary_gate.cc.2.o,mixA1_boundary_ohmic.cc.2.o,mixA1_boundary_schottky.cc.2.o,mixA1_boundary_solderpad.cc.2.o,mixA2.cc.2.o,mixA2_boundary_gate.cc.2.o,mixA2_boundary_ohmic.cc.2.o,mixA2_boundary_schottky.cc.2.o,mixA2_boundary_solderpad.cc.2.o,mixA3.cc.2.o,mixA3_boundary_gate.cc.2.o,mixA3_boundary_ohmic.cc.2.o,mixA3_boundary_schottky.cc.2.o,mixA3_boundary_solderpad.cc.2.o,mole_analytic.cc.2.o,poisson.cc.2.o,poisson_boundary_ei_interface.cc.2.o,poisson_boundary_float_metal.cc.2.o,poisson_boundary_gate.cc.2.o,poisson_boundary_hetero_interface.cc.2.o,poisson_boundary_homo_interface.cc.2.o,poisson_boundary_ii_interface.cc.2.o,poisson_boundary_ir_interface.cc.2.o,poisson_boundary_is_interface.cc.2.o,poisson_boundary_ohmic.cc.2.o,poisson_boundary_resistance_ohmic.cc.2.o,poisson_boundary_resistance_schottky.cc.2.o,poisson_boundary_rr_interface.cc.2.o,poisson_boundary_schottky.cc.2.o,poisson_boundary_simple_gate.cc.2.o,poisson_boundary_solderpad.cc.2.o,poisson_conductor.cc.2.o,poisson_conductor_hanging_node.cc.2.o,poisson_insulator.cc.2.o,poisson_insulator_hanging_node.cc.2.o,poisson_resistance.cc.2.o,poisson_resistance_hanging_node.cc.2.o,poisson_semiconductor.cc.2.o,poisson_semiconductor_hanging_node.cc.2.o,light_thread.cc.2.o,object_tree.cc.2.o,ray_tracing.cc.2.o,solver_base.cc.2.o,solver_specify.cc.2.o,stress_solver.cc.2.o,electrical_source.cc.2.o,field_source.cc.2.o,isource.cc.2.o,light_lenses.cc.2.o,light_source.cc.2.o,particle_source.cc.2.o,vsource.cc.2.o,waveform.cc.2.o,dose_rate.cc.2.o,error_vector.cc.2.o,extend_to_3d.cc.2.o,location_maps.cc.2.o,mat_analysis.cc.2.o,monot_cubic_interpolator.cc.2.o,nearest_node_locator.cc.2.o,octree.cc.2.o,point_locator_base.cc.2.o,point_locator_list.cc.2.o,point_locator_tree.cc.2.o,show_mesh_2d.cc.2.o,statistics.cc.2.o,surface_locator_base.cc.2.o,surface_locator_hub.cc.2.o,surface_locator_list.cc.2.o,surface_locator_sphere.cc.2.o,sync_file.cc.2.o,tree.cc.2.o,tree_node.cc.2.o,PMI.cc.2.o,material.cc.2.o,material_define.cc.2.o,physical_unit.cc.2.o,dlhook.cc.1.o,main.cc.3.o -> genius.LINUX} ['/usr/bin/g++', 'src/contrib/ann/ANN.cpp.0.o', 'src/contrib/ann/bd_fix_rad_search.cpp.0.o', 'src/contrib/ann/bd_pr_search.cpp.0.o', 'src/contrib/ann/bd_search.cpp.0.o', 'src/contrib/ann/bd_tree.cpp.0.o', 'src/contrib/ann/brute.cpp.0.o', 'src/contrib/ann/kd_dump.cpp.0.o', 'src/contrib/ann/kd_fix_rad_search.cpp.0.o', 'src/contrib/ann/kd_pr_search.cpp.0.o', 'src/contrib/ann/kd_search.cpp.0.o', 'src/contrib/ann/kd_split.cpp.0.o', 'src/contrib/ann/kd_tree.cpp.0.o', 'src/contrib/ann/kd_util.cpp.0.o', 'src/contrib/ann/perf.cpp.0.o', 'src/contrib/csabathy/csa.cc.1.o', 'src/contrib/csabathy/svd.c.1.o', 'src/contrib/expreval/expr.cc.1.o', 'src/contrib/expreval/expr_datalist.cc.1.o', 'src/contrib/expreval/expr_except.cc.1.o', 'src/contrib/expreval/expr_func.cc.1.o', 'src/contrib/expreval/expr_funclist.cc.1.o', 'src/contrib/expreval/expr_node.cc.1.o', 'src/contrib/expreval/expr_parser.cc.1.o', 'src/contrib/expreval/expr_vallist.cc.1.o', 'src/contrib/spice/schur_solver.cc.1.o', 'src/contrib/spice/spice_ckt.cc.1.o', 'src/contrib/tif3d/tif3d.cc.1.o', 'src/contrib/klu/UFconfig.c.1.o', 'src/contrib/klu/amd_1.c.1.o', 'src/contrib/klu/amd_2.c.1.o', 'src/contrib/klu/amd_aat.c.1.o', 'src/contrib/klu/amd_control.c.1.o', 'src/contrib/klu/amd_defaults.c.1.o', 'src/contrib/klu/amd_dump.c.1.o', 'src/contrib/klu/amd_global.c.1.o', 'src/contrib/klu/amd_info.c.1.o', 'src/contrib/klu/amd_order.c.1.o', 'src/contrib/klu/amd_post_tree.c.1.o', 'src/contrib/klu/amd_postorder.c.1.o', 'src/contrib/klu/amd_preprocess.c.1.o', 'src/contrib/klu/amd_valid.c.1.o', 'src/contrib/klu/btf_maxtrans.c.1.o', 'src/contrib/klu/btf_order.c.1.o', 'src/contrib/klu/btf_strongcomp.c.1.o', 'src/contrib/klu/colamd.c.1.o', 'src/contrib/klu/colamd_global.c.1.o', 'src/contrib/klu/klu.c.1.o', 'src/contrib/klu/klu_analyze.c.1.o', 'src/contrib/klu/klu_analyze_given.c.1.o', 'src/contrib/klu/klu_defaults.c.1.o', 'src/contrib/klu/klu_diagnostics.c.1.o', 'src/contrib/klu/klu_dump.c.1.o', 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'src/solver/poisson/poisson_boundary_solderpad.cc.2.o', 'src/solver/poisson/poisson_conductor.cc.2.o', 'src/solver/poisson/poisson_conductor_hanging_node.cc.2.o', 'src/solver/poisson/poisson_insulator.cc.2.o', 'src/solver/poisson/poisson_insulator_hanging_node.cc.2.o', 'src/solver/poisson/poisson_resistance.cc.2.o', 'src/solver/poisson/poisson_resistance_hanging_node.cc.2.o', 'src/solver/poisson/poisson_semiconductor.cc.2.o', 'src/solver/poisson/poisson_semiconductor_hanging_node.cc.2.o', 'src/solver/ray_tracing/light_thread.cc.2.o', 'src/solver/ray_tracing/object_tree.cc.2.o', 'src/solver/ray_tracing/ray_tracing.cc.2.o', 'src/solver/solver_base.cc.2.o', 'src/solver/solver_specify.cc.2.o', 'src/solver/stress_solver/stress_solver.cc.2.o', 'src/source/electrical_source.cc.2.o', 'src/source/field_source.cc.2.o', 'src/source/isource.cc.2.o', 'src/source/light_lenses.cc.2.o', 'src/source/light_source.cc.2.o', 'src/source/particle_source.cc.2.o', 'src/source/vsource.cc.2.o', 'src/source/waveform.cc.2.o', 'src/utils/dose_rate.cc.2.o', 'src/utils/error_vector.cc.2.o', 'src/utils/extend_to_3d.cc.2.o', 'src/utils/location_maps.cc.2.o', 'src/utils/mat_analysis.cc.2.o', 'src/utils/monot_cubic_interpolator.cc.2.o', 'src/utils/nearest_node_locator.cc.2.o', 'src/utils/octree.cc.2.o', 'src/utils/point_locator_base.cc.2.o', 'src/utils/point_locator_list.cc.2.o', 'src/utils/point_locator_tree.cc.2.o', 'src/utils/show_mesh_2d.cc.2.o', 'src/utils/statistics.cc.2.o', 'src/utils/surface_locator_base.cc.2.o', 'src/utils/surface_locator_hub.cc.2.o', 'src/utils/surface_locator_list.cc.2.o', 'src/utils/surface_locator_sphere.cc.2.o', 'src/utils/sync_file.cc.2.o', 'src/utils/tree.cc.2.o', 'src/utils/tree_node.cc.2.o', 'src/material/PMI.cc.2.o', 'src/material/material.cc.2.o', 'src/material/material_define.cc.2.o', 'src/material/physical_unit.cc.2.o', 'src/hook/dlhook.cc.1.o', 'src/main.cc.3.o', '-o', '/home/pinkchalk/Downloads/Genius-TCAD-Open-master/build/default/src/genius.LINUX', '-Wl,-Bstatic', '-Wl,-Bdynamic', '-lcgns', '-lvtkRendering', '-lvtkGraphics', '-lvtkImaging', '-lvtkIO', '-lvtkFiltering', '-lvtkCommon', '-lvtksys', '-lvtkDICOMParser', '-lvtkpng', '-lvtktiff', '-lvtkzlib', '-lvtkjpeg', '-lvtkexpat', '-lvtkftgl', '-lvtkfreetype', '-lpthread', '-ldl', '-Wl,--export-dynamic', '-lpetsc', '-L/home/pinkchalk/petsc-3.1-p8/linux-gnu-c-debug/lib', '-lcmumps', '-ldmumps', '-lsmumps', '-lzmumps', '-lmumps_common', '-lpord', '-lscalapack', '-lblacs', '-lsuperlu_dist_2.4', '-lparmetis', '-lmetis', '-lsuperlu_4.0', '-lflapack', '-lfblas', '-lnsl', '-lrt', '-lm', '-lmpich', '-lpthread', '-lgfortran', '-lquadmath', '-Wl,-Bdynamic', '-lpetsc', '-L/home/pinkchalk/petsc-3.1-p8/linux-gnu-c-debug/lib', '-lcmumps', '-ldmumps', '-lsmumps', '-lzmumps', '-lmumps_common', '-lpord', '-lscalapack', '-lblacs', '-lsuperlu_dist_2.4', '-lparmetis', '-lmetis', '-lsuperlu_4.0', '-lflapack', '-lfblas', '-lnsl', '-lrt', '-lm', '-L/home/pinkchalk/petsc-3.1-p8/linux-gnu-c-debug/lib', '-lmpich', '-lpthread', '-lrt', '-lgfortran', '-lquadmath', '-Wl,-Bdynamic', '', '-L/usr/local/lib/vtk-5.4']

I am really having a hard time now. Hoping to hear from you soon. Regards

lutherthecat commented 10 years ago

Hi,

These are missing: libvtkNetCDF.so.5.4 ibvtkmetaio.so.5.4 libvtksqlite.so.5.4

It looks like you need to add the missing libraries to the linker line in the part where you see: '-lvtkRendering', '-lvtkGraphics', '-lvtkImaging', '-lvtkIO', '-lvtkFiltering', '-lvtkCommon', '-lvtksys', '-lvtkDICOMParser', '-lvtkpng', '-lvtktiff', '-lvtkzlib', '-lvtkjpeg', '-lvtkexpat', '-lvtkftgl', '-lvtkfreetype'

You'd have to look through the wscript file and add them: https://github.com/cogenda/Genius-TCAD-Open/blob/master/wscript

def config_vtk(): libs = '''vtkRendering vtkGraphics vtkImaging vtkIO vtkFiltering vtkCommon vtksys vtkDICOMParser vtkpng vtktiff vtkzlib vtkjpeg vtkexpat vtkftgl vtkfreetype'''.split()

pinkchalk commented 10 years ago

Hi, Thanks for the help. I did what you told but now I get this error:

src/solution/vtk_io.cc.2.o: In function VTKIO::nodes_to_vtk(MeshBase const&, vtkUnstructuredGrid*)': vtk_io.cc:(.text+0x131): undefined reference tovtkPoints::New()' src/solution/vtk_io.cc.2.o: In function VTKIO::read(std::string const&)': vtk_io.cc:(.text+0xf7e): undefined reference tovtkXMLUnstructuredGridReader::New()' vtk_io.cc:(.text+0xfb9): undefined reference to vtkXMLUnstructuredGridReader::GetOutput()' vtk_io.cc:(.text+0x1318): undefined reference tovtkDataSetAttributes::GetScalars(char const_)' vtk_io.cc:(.text+0x1328): undefined reference to typeinfo for vtkFloatArray' vtk_io.cc:(.text+0x132f): undefined reference totypeinfo for vtkDataArray' vtkio.cc:(.text+0x134b): undefined reference to `vtkDataSetAttributes::GetScalars(char const)' vtk_io.cc:(.text+0x135b): undefined reference to typeinfo for vtkFloatArray' vtk_io.cc:(.text+0x1362): undefined reference totypeinfo for vtkDataArray' src/solution/vtk_io.cc.2.o: In function VTKIO::write_node_complex_solution(std::vector<unsigned int, std::allocator<unsigned int> > const&, std::vector<std::complex<float>, std::allocator<std::complex<float> > >&, std::string const&, vtkUnstructuredGrid*)': vtk_io.cc:(.text+0x3438): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x344a): undefined reference to vtkFloatArray::New()' vtk_io.cc:(.text+0x34ae): undefined reference tovtkDataArrayTemplate::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x3510): undefined reference to vtkDataArrayTemplate<float>::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x35af): undefined reference tovtkDataArrayTemplate::InsertValue(long long, float)' vtk_io.cc:(.text+0x35c1): undefined reference to vtkDataArrayTemplate<float>::InsertValue(long long, float)' vtk_io.cc:(.text+0x35ef): undefined reference tovtkFieldData::AddArray(vtkAbstractArray_)' vtkio.cc:(.text+0x3604): undefined reference to `vtkFieldData::AddArray(vtkAbstractArray)' src/solution/vtk_io.cc.2.o: In function VTKIO::write_node_scaler_solution(std::vector<unsigned int, std::allocator<unsigned int> > const&, std::vector<float, std::allocator<float> >&, std::string const&, vtkUnstructuredGrid*)': vtk_io.cc:(.text+0x3cd6): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x3cff): undefined reference to vtkDataArrayTemplate<float>::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x3d1c): undefined reference tovtkFieldData::AddArray(vtkAbstractArray_)' vtk_io.cc:(.text+0x3dea): undefined reference to vtkDataArrayTemplate<float>::InsertValue(long long, float)' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_node_vectorsolution(std::vector<unsigned int, std::allocator > const&, std::vector<float, std::allocator >&, std::vector<float, std::allocator >&, std::vector<float, std::allocator >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x3ee9): undefined reference to vtkFloatArray::New()' vtk_io.cc:(.text+0x401d): undefined reference tovtkFieldData::AddArray(vtkAbstractArray_)' src/solution/vtk_io.cc.2.o: In function VTKIO::write_cell_scaler_solution(std::vector<unsigned int, std::allocator<unsigned int> > const&, std::vector<float, std::allocator<float> >&, std::string const&, vtkUnstructuredGrid_)': vtk_io.cc:(.text+0x41f1): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x421b): undefined reference tovtkDataArrayTemplate<float>::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x4238): undefined reference tovtkFieldData::AddArray(vtkAbstractArray)' vtk_io.cc:(.text+0x42ea): undefined reference tovtkDataArrayTemplate<float>::InsertValue(long long, float)' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_cell_vector_solution(std::vector<unsigned int, std::allocator > const&, std::vector<float, std::allocator >&, std::vector<float, std::allocator >&, std::vector<float, std::allocator >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x4399): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x44cd): undefined reference tovtkFieldData::AddArray(vtkAbstractArray)' src/solution/vtk_io.cc.2.o: In functionVTKIO::cells_to_vtk(MeshBase const&, vtkUnstructuredGrid_)': vtk_io.cc:(.text+0x90e9): undefined reference tovtkIdList::New()' vtk_io.cc:(.text+0x9105): undefined reference tovtkIdList::SetNumberOfIds(long long)' vtk_io.cc:(.text+0x91ac): undefined reference tovtkUnstructuredGrid::InsertNextCell(int, vtkIdList_)' vtk_io.cc:(.text+0x9262): undefined reference to vtkIdList::New()' vtk_io.cc:(.text+0x927e): undefined reference tovtkIdList::SetNumberOfIds(long long)' vtk_io.cc:(.text+0x9332): undefined reference to `vtkUnstructuredGrid::InsertNextCell(int, vtkIdList)' src/solution/vtk_io.cc.2.o: In functionVTKIO::meshinfo_to_vtk(MeshBase const&, vtkUnstructuredGrid_)': vtk_io.cc:(.text+0x9be8): undefined reference tovtkIntArray::New()' vtk_io.cc:(.text+0x9bf0): undefined reference tovtkIntArray::New()' vtk_io.cc:(.text+0x9bf8): undefined reference tovtkIntArray::New()' vtk_io.cc:(.text+0x9c1a): undefined reference tovtkDataArrayTemplate<int>::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x9c39): undefined reference tovtkDataArrayTemplate::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x9c58): undefined reference tovtkDataArrayTemplate<int>::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x9e0a): undefined reference tovtkFieldData::AddArray(vtkAbstractArray_)' vtk_io.cc:(.text+0x9e1b): undefined reference to vtkFieldData::AddArray(vtkAbstractArray*)' vtk_io.cc:(.text+0x9e27): undefined reference tovtkFieldData::AddArray(vtkAbstractArray_)' src/solution/vtk_io.cc.2.o: In function VTKIO::write(std::string const&)': vtk_io.cc:(.text+0xdf19): undefined reference tovtkUnstructuredGrid::New()' vtk_io.cc:(.text+0xdf7e): undefined reference to vtkXMLUnstructuredGridWriter::vtkXMLUnstructuredGridWriter()' vtk_io.cc:(.text+0xdfb0): undefined reference tovtkXMLWriter::SetInput(vtkDataObject_)' vtk_io.cc:(.text+0xdff6): undefined reference to vtkXMLWriter::Write()' src/solution/vtk_io.cc.2.o: In functionvtkXMLUnstructuredGridWriter::NewInstanceInternal() const': vtk_io.cc:(.text._ZNK28vtkXMLUnstructuredGridWriter19NewInstanceInternalEv[_ZNK28vtkXMLUnstructuredGridWriter19NewInstanceInternalEv]+0x1): undefined reference to vtkXMLUnstructuredGridWriter::New()' src/solution/vtk_io.cc.2.o: In functionvtkXMLUnstructuredGridWriter::IsA(char const_)': vtk_io.cc:(.text._ZN28vtkXMLUnstructuredGridWriter3IsAEPKc[ZN28vtkXMLUnstructuredGridWriter3IsAEPKc]+0x70): undefined reference to `vtkObjectBase::IsTypeOf(char const)' src/solution/vtk_io.cc.2.o: In function VTKIO::XMLUnstructuredGridWriter::~XMLUnstructuredGridWriter()': vtk_io.cc:(.text._ZN5VTKIO25XMLUnstructuredGridWriterD2Ev[_ZN5VTKIO25XMLUnstructuredGridWriterD5Ev]+0x2e): undefined reference tovtkXMLUnstructuredGridWriter::~vtkXMLUnstructuredGridWriter()' src/solution/vtk_io.cc.2.o: In function VTKIO::XMLUnstructuredGridWriter::~XMLUnstructuredGridWriter()': vtk_io.cc:(.text._ZN5VTKIO25XMLUnstructuredGridWriterD0Ev[_ZN5VTKIO25XMLUnstructuredGridWriterD0Ev]+0x2e): undefined reference tovtkXMLUnstructuredGridWriter::~vtkXMLUnstructuredGridWriter()' src/solution/vtk_io.cc.2.o: In function vtkAlgorithm::GetInformation()': vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x10): undefined reference tovtkObject::GetDebug()' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x31): undefined reference to vtkObject::GetGlobalWarningDisplay()' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x40): undefined reference tovtkOStrStreamWrapper::vtkOStrStreamWrapper()' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x4c): undefined reference to vtkObjectBase::GetClassName() const' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x57): undefined reference tovtkObjectBase::GetClassName() const' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x69): undefined reference to vtkOStreamWrapper::operator<<(char const*)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x76): undefined reference tovtkOStreamWrapper::operator<<(int)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x85): undefined reference to vtkOStreamWrapper::operator<<(char const*)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x90): undefined reference tovtkOStreamWrapper::operator<<(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[ZN12vtkAlgorithm14GetInformationEv]+0x9f): undefined reference to `vtkOStreamWrapper::operator<<(char const)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0xaa): undefined reference to vtkOStreamWrapper::operator<<(void*)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0xb9): undefined reference tovtkOStreamWrapper::operator<<(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[ZN12vtkAlgorithm14GetInformationEv]+0xc4): undefined reference to `vtkOStreamWrapper::operator<<(char const)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0xd3): undefined reference to vtkOStreamWrapper::operator<<(char const*)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0xde): undefined reference tovtkOStreamWrapper::operator<<(void_)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[ZN12vtkAlgorithm14GetInformationEv]+0xed): undefined reference to `vtkOStreamWrapper::operator<<(char const)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0xf8): undefined reference to vtkOStreamWrapper::operator<<(void*)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x107): undefined reference tovtkOStreamWrapper::operator<<(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x10f): undefined reference to vtkOStrStreamWrapper::str()' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x117): undefined reference tovtkOutputWindowDisplayDebugText(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x11f): undefined reference to vtkOStrStreamWrapper::rdbuf()' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x129): undefined reference tovtkOStrStreamWrapper::freeze(int)' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x131): undefined reference to vtkOStrStreamWrapper::~vtkOStrStreamWrapper()' vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x141): undefined reference tovtkOStrStreamWrapper::~vtkOStrStreamWrapper()' src/solution/vtk_io.cc.2.o: In function vtkAlgorithm::SetAbortExecute(int)': vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x12): undefined reference tovtkObject::GetDebug()' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x41): undefined reference to vtkObject::GetGlobalWarningDisplay()' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x50): undefined reference tovtkOStrStreamWrapper::vtkOStrStreamWrapper()' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x58): undefined reference to vtkObjectBase::GetClassName() const' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x63): undefined reference tovtkObjectBase::GetClassName() const' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x75): undefined reference to vtkOStreamWrapper::operator<<(char const*)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x82): undefined reference tovtkOStreamWrapper::operator<<(int)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x91): undefined reference to vtkOStreamWrapper::operator<<(char const*)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x9c): undefined reference tovtkOStreamWrapper::operator<<(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[ZN12vtkAlgorithm15SetAbortExecuteEi]+0xab): undefined reference to `vtkOStreamWrapper::operator<<(char const)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0xb6): undefined reference to vtkOStreamWrapper::operator<<(void*)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0xc5): undefined reference tovtkOStreamWrapper::operator<<(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[ZN12vtkAlgorithm15SetAbortExecuteEi]+0xd0): undefined reference to `vtkOStreamWrapper::operator<<(char const)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0xdf): undefined reference to vtkOStreamWrapper::operator<<(char const*)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0xea): undefined reference tovtkOStreamWrapper::operator<<(void_)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[ZN12vtkAlgorithm15SetAbortExecuteEi]+0xf9): undefined reference to `vtkOStreamWrapper::operator<<(char const)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x103): undefined reference to vtkOStreamWrapper::operator<<(int)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x112): undefined reference tovtkOStreamWrapper::operator<<(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x11a): undefined reference to vtkOStrStreamWrapper::str()' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x122): undefined reference tovtkOutputWindowDisplayDebugText(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x12a): undefined reference to vtkOStrStreamWrapper::rdbuf()' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x134): undefined reference tovtkOStrStreamWrapper::freeze(int)' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x13c): undefined reference to vtkOStrStreamWrapper::~vtkOStrStreamWrapper()' vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x14c): undefined reference tovtkOStrStreamWrapper::~vtkOStrStreamWrapper()' src/solution/vtk_io.cc.2.o: In function vtkAlgorithm::GetAbortExecute()': vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x10): undefined reference tovtkObject::GetDebug()' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x31): undefined reference to vtkObject::GetGlobalWarningDisplay()' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x40): undefined reference tovtkOStrStreamWrapper::vtkOStrStreamWrapper()' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x4c): undefined reference to vtkObjectBase::GetClassName() const' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x57): undefined reference tovtkObjectBase::GetClassName() const' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x69): undefined reference to vtkOStreamWrapper::operator<<(char const*)' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x76): undefined reference tovtkOStreamWrapper::operator<<(int)' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x85): undefined reference to vtkOStreamWrapper::operator<<(char const*)' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x90): undefined reference tovtkOStreamWrapper::operator<<(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[ZN12vtkAlgorithm15GetAbortExecuteEv]+0x9f): undefined reference to `vtkOStreamWrapper::operator<<(char const)' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0xaa): undefined reference to vtkOStreamWrapper::operator<<(void*)' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0xb9): undefined reference tovtkOStreamWrapper::operator<<(char const_)' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[ZN12vtkAlgorithm15GetAbortExecuteEv]+0xc4): undefined reference to `vtkOStreamWrapper::operator<<(char const)' vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0xd3): undefined reference to

... and this continues. Too long to be fully pasted. Hoping to hear from you soon. Regards

cogenda commented 10 years ago

The 20 or so lines before the first "undefined reference" will help.

shenchen

On 2014-02-15 16:06, Ashish Kumar wrote:

Hi, Thanks for the help. I did what you told but now I get this error:

src/solution/vtk_io.cc.2.o: In function VTKIO::nodes_to_vtk(MeshBase const&, vtkUnstructuredGrid*)': vtk_io.cc:(.text+0x131): undefined reference tovtkPoints::New()' src/solution/vtk_io.cc.2.o: In function VTKIO::read(std::string const&)': vtk_io.cc:(.text+0xf7e): undefined reference tovtkXMLUnstructuredGridReader::New()'

vtk_io.cc:(.text+0xfb9): undefined reference to vtkXMLUnstructuredGridReader::GetOutput()' vtk_io.cc:(.text+0x1318): undefined reference tovtkDataSetAttributes::GetScalars(char const*)'

vtk_io.cc:(.text+0x1328): undefined reference to typeinfo for vtkFloatArray' vtk_io.cc:(.text+0x132f): undefined reference totypeinfo for vtkDataArray' vtk_io.cc:(.text+0x134b): undefined reference to vtkDataSetAttributes::GetScalars(char const*)'

vtk_io.cc:(.text+0x135b): undefined reference totypeinfo for vtkFloatArray' vtk_io.cc:(.text+0x1362): undefined reference to typeinfo for vtkDataArray' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_node_complex_solution(std::vector > const&, std::vectorstd::complex, std::allocatorstd::complex > >&, std::string const&, vtkUnstructuredGrid*)': vtk_io.cc:(.text+0x3438): undefined reference to vtkFloatArray::New()' vtk_io.cc:(.text+0x344a): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x34ae): undefined reference to vtkDataArrayTemplate::SetNumberOfValues(long long)'

vtk_io.cc:(.text+0x3510): undefined reference tovtkDataArrayTemplate::SetNumberOfValues(long long)'

vtk_io.cc:(.text+0x35af): undefined reference to vtkDataArrayTemplate::InsertValue(long long, float)'

vtk_io.cc:(.text+0x35c1): undefined reference tovtkDataArrayTemplate::InsertValue(long long, float)'

vtkio.cc:(.text+0x35ef): undefined reference to vtkFieldData::AddArray(vtkAbstractArray)' vtkio.cc:(.text+0x3604): undefined reference tovtkFieldData::AddArray(vtkAbstractArray)'

src/solution/vtk_io.cc.2.o: In function VTKIO::write_node_scalersolution(std::vector > const&, std::vector >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x3cd6): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x3cff): undefined reference to vtkDataArrayTemplate::SetNumberOfValues(long long)' vtkio.cc:(.text+0x3d1c): undefined reference tovtkFieldData::AddArray(vtkAbstractArray)' vtk_io.cc:(.text+0x3dea): undefined reference to vtkDataArrayTemplate::InsertValue(long long, float)' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_node_vectorsolution(std::vector > const&, std::vector >&, std::vector >&, std::vector >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x3ee9): undefined reference to vtkFloatArray::New()' vtkio.cc:(.text+0x401d): undefined reference tovtkFieldData::AddArray(vtkAbstractArray)'

src/solution/vtk_io.cc.2.o: In function VTKIO::write_cell_scalersolution(std::vector > const&, std::vector >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x41f1): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x421b): undefined reference to vtkDataArrayTemplate::SetNumberOfValues(long long)' vtkio.cc:(.text+0x4238): undefined reference tovtkFieldData::AddArray(vtkAbstractArray)' vtk_io.cc:(.text+0x42ea): undefined reference to vtkDataArrayTemplate::InsertValue(long long, float)' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_cell_vectorsolution(std::vector > const&, std::vector >&, std::vector >&, std::vector >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x4399): undefined reference to vtkFloatArray::New()' vtkio.cc:(.text+0x44cd): undefined reference tovtkFieldData::AddArray(vtkAbstractArray)'

src/solution/vtk_io.cc.2.o: In function VTKIO::cells_to_vtk(MeshBase const&, vtkUnstructuredGrid*)': vtk_io.cc:(.text+0x90e9): undefined reference tovtkIdList::New()' vtk_io.cc:(.text+0x9105): undefined reference to vtkIdList::SetNumberOfIds(long long)'

vtk_io.cc:(.text+0x91ac): undefined reference tovtkUnstructuredGrid::InsertNextCell(int, vtkIdList*)'

vtk_io.cc:(.text+0x9262): undefined reference to vtkIdList::New()'

vtk_io.cc:(.text+0x927e): undefined reference tovtkIdList::SetNumberOfIds(long long)' vtkio.cc:(.text+0x9332): undefined reference to vtkUnstructuredGrid::InsertNextCell(int, vtkIdList)' src/solution/vtk_io.cc.2.o: In functionVTKIO::meshinfo_tovtk(MeshBase const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x9be8): undefined reference to vtkIntArray::New()' vtk_io.cc:(.text+0x9bf0): undefined reference tovtkIntArray::New()' vtk_io.cc:(.text+0x9bf8): undefined reference to vtkIntArray::New()' vtk_io.cc:(.text+0x9c1a): undefined reference tovtkDataArrayTemplate::SetNumberOfValues(long long)'

vtk_io.cc:(.text+0x9c39): undefined reference to vtkDataArrayTemplate::SetNumberOfValues(long long)'

vtk_io.cc:(.text+0x9c58): undefined reference tovtkDataArrayTemplate::SetNumberOfValues(long long)'

vtkio.cc:(.text+0x9e0a): undefined reference to vtkFieldData::AddArray(vtkAbstractArray)' vtkio.cc:(.text+0x9e1b): undefined reference tovtkFieldData::AddArray(vtkAbstractArray)'

vtk_io.cc:(.text+0x9e27): undefined reference to vtkFieldData::AddArray(vtkAbstractArray*)' src/solution/vtk_io.cc.2.o: In functionVTKIO::write(std::string const&)':

vtk_io.cc:(.text+0xdf19): undefined reference to vtkUnstructuredGrid::New()' vtk_io.cc:(.text+0xdf7e): undefined reference tovtkXMLUnstructuredGridWriter::vtkXMLUnstructuredGridWriter()'

vtk_io.cc:(.text+0xdfb0): undefined reference to vtkXMLWriter::SetInput(vtkDataObject*)' vtk_io.cc:(.text+0xdff6): undefined reference tovtkXMLWriter::Write()'

src/solution/vtk_io.cc.2.o: In function vtkXMLUnstructuredGridWriter::NewInstanceInternal() const':

vtk_io.cc:(.text._ZNK28vtkXMLUnstructuredGridWriter19NewInstanceInternalEv[_ZNK28vtkXMLUnstructuredGridWriter19NewInstanceInternalEv]+0x1): undefined reference tovtkXMLUnstructuredGridWriter::New()'

src/solution/vtk_io.cc.2.o: In function vtkXMLUnstructuredGridWriter::IsA(char const*)':

vtk_io.cc:(.text._ZN28vtkXMLUnstructuredGridWriter3IsAEPKc[_ZN28vtkXMLUnstructuredGridWriter3IsAEPKc]+0x70): undefined reference tovtkObjectBase::IsTypeOf(char const*)'

src/solution/vtk_io.cc.2.o: In function VTKIO::XMLUnstructuredGridWriter::~XMLUnstructuredGridWriter()':

vtk_io.cc:(.text._ZN5VTKIO25XMLUnstructuredGridWriterD2Ev[_ZN5VTKIO25XMLUnstructuredGridWriterD5Ev]+0x2e): undefined reference tovtkXMLUnstructuredGridWriter::~vtkXMLUnstructuredGridWriter()'

src/solution/vtk_io.cc.2.o: In function VTKIO::XMLUnstructuredGridWriter::~XMLUnstructuredGridWriter()':

vtk_io.cc:(.text._ZN5VTKIO25XMLUnstructuredGridWriterD0Ev[_ZN5VTKIO25XMLUnstructuredGridWriterD0Ev]+0x2e): undefined reference tovtkXMLUnstructuredGridWriter::~vtkXMLUnstructuredGridWriter()'

src/solution/vtk_io.cc.2.o: In function vtkAlgorithm::GetInformation()':

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x10): undefined reference tovtkObject::GetDebug()'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x31): undefined reference to vtkObject::GetGlobalWarningDisplay()'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x40): undefined reference tovtkOStrStreamWrapper::vtkOStrStreamWrapper()'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x4c): undefined reference to vtkObjectBase::GetClassName() const'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x57): undefined reference tovtkObjectBase::GetClassName() const'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x69): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x85): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x9f): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0xb9): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0xd3): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0xed): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x107): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x117): undefined reference to vtkOutputWindowDisplayDebugText(char const*)'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x11f): undefined reference tovtkOStrStreamWrapper::rdbuf()'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x129): undefined reference to vtkOStrStreamWrapper::freeze(int)'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x131): undefined reference tovtkOStrStreamWrapper::~vtkOStrStreamWrapper()'

vtk_io.cc:(.text._ZN12vtkAlgorithm14GetInformationEv[_ZN12vtkAlgorithm14GetInformationEv]+0x141): undefined reference to vtkOStrStreamWrapper::~vtkOStrStreamWrapper()'

src/solution/vtk_io.cc.2.o: In functionvtkAlgorithm::SetAbortExecute(int)':

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x12): undefined reference to vtkObject::GetDebug()'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x41): undefined reference tovtkObject::GetGlobalWarningDisplay()'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x50): undefined reference to vtkOStrStreamWrapper::vtkOStrStreamWrapper()'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x58): undefined reference tovtkObjectBase::GetClassName() const'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x63): undefined reference to vtkObjectBase::GetClassName() const'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x75): undefined reference tovtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x91): undefined reference tovtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0xab): undefined reference tovtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0xc5): undefined reference tovtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0xdf): undefined reference tovtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0xf9): undefined reference tovtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x112): undefined reference tovtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x122): undefined reference tovtkOutputWindowDisplayDebugText(char const*)'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x12a): undefined reference to vtkOStrStreamWrapper::rdbuf()'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x134): undefined reference tovtkOStrStreamWrapper::freeze(int)'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x13c): undefined reference to vtkOStrStreamWrapper::~vtkOStrStreamWrapper()'

vtk_io.cc:(.text._ZN12vtkAlgorithm15SetAbortExecuteEi[_ZN12vtkAlgorithm15SetAbortExecuteEi]+0x14c): undefined reference tovtkOStrStreamWrapper::~vtkOStrStreamWrapper()'

src/solution/vtk_io.cc.2.o: In function vtkAlgorithm::GetAbortExecute()':

vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x10): undefined reference tovtkObject::GetDebug()'

vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x31): undefined reference to vtkObject::GetGlobalWarningDisplay()'

vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x40): undefined reference tovtkOStrStreamWrapper::vtkOStrStreamWrapper()'

vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x4c): undefined reference to vtkObjectBase::GetClassName() const'

vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x57): undefined reference tovtkObjectBase::GetClassName() const'

vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x69): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x85): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0x9f): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0xb9): undefined reference to vtkOStreamWrapper::operator< vtk_io.cc:(.text._ZN12vtkAlgorithm15GetAbortExecuteEv[_ZN12vtkAlgorithm15GetAbortExecuteEv]+0xd3): undefined reference to

... and this continues. Too long to be fully pasted. Hoping to hear from you soon. Regards

Reply to this email directly or view it on GitHub [1].

Links:

[1] https://github.com/cogenda/Genius-TCAD-Open/issues/18#issuecomment-35149976

pinkchalk commented 10 years ago

There were none. It just starts with these undefined references.

pinkchalk commented 10 years ago

What I understand is that all these issues are related to vtk. If possible can you please provide me with a step by step guide to build vtk? I am using version 5.4.2. Regards

cogenda commented 10 years ago

Below is the options I used for VTK, using static library

'-DCMAKE_BUILD_TYPE:STRING=RELEASE'

'-DCMAKE_INSTALL_PREFIX:PATH=${TGTDIR}'

'-DCMAKE_INCLUDE_PATH:PATH=${TGTDIR}/include'

'-DCMAKE_LIBRARY_PATH:PATH=${TGTDIR}/lib'

'-DBUILD_DOCUMENTATION:BOOL=OFF' '-DBUILD_EXAMPLES:BOOL=OFF'

'-DBUILD_TESTING:BOOL=OFF' '-DVTK_DEBUG_LEAKS:BOOL=OFF'

'-DVTK_USE_RPATH:BOOL=OFF' '-DVTK_USE_X:BOOL=OFF'

'-DVTK_USE_GUISUPPORT:BOOL=ON' '-DVTK_USE_INFOVIS:BOOL=ON'

'-DVTK_USE_PARALLEL:BOOL=OFF' '-DVTK_USE_RENDERING:BOOL=ON'

'-DVTK_USE_VIEWS:BOOL=ON' '-DVTK_USE_GL2PS:BOOL=OFF'

'-DVTK_USE_N_WAY_ARRAYS:BOOL=ON' '-DVTK_USE_TK:BOOL=OFF'

'-DVTK_WRAP_JAVA:BOOL=OFF' '-DVTK_WRAP_PYTHON:BOOL=OFF'

'-DVTK_WRAP_TCL:BOOL=OFF' '-DBUILD_SHARED_LIBS:BOOL=OFF'

'-DCMAKE_C_FLAGS:STRING=-O3 -DNDEBUG -fPIC'

'-DCMAKE_CXX_FLAGS:STRING=-O3 -DNDEBUG -fPIC'

As you see, a lot of VTK modules were disabled. You don't need the extra -l options in the wscript, as lutherthecat suggested.

We may switch to cmake at some point, since Petsc and VTK both uses cmake now, this will make compatibility easier.

regards, shenchen

On 2014-02-15 20:29, Ashish Kumar wrote:

What I understand is that all these issues are related to vtk. If possible can you please provide me with a step by step guide to build vtk? I am using version 5.4.2. Regards

Reply to this email directly or view it on GitHub [1].

Links:

[1] https://github.com/cogenda/Genius-TCAD-Open/issues/18#issuecomment-35155042

pinkchalk commented 10 years ago

I get the same error again. Have built vtk as directged but still.

Setting top to : /home/pinkchalk/Downloads/Genius-TCAD-Open-master Setting out to : /home/pinkchalk/Downloads/Genius-TCAD-Open-master/build/default Checking for 'icc' (c compiler) : not found Checking for 'gcc' (c compiler) : ok Checking for 'icpc' (c++ compiler) : not found Checking for 'g++' (c++ compiler) : ok Checking for 'ifort' (fortran compiler) : not found Checking for 'gfortran' (fortran compiler) : ok Checking for program git : not found Setting version string : 20140215 Detecting optimization options : -O2 -unroll -msse3 Checking for visibility flags : yes Checking for size of double : yes Checking for size of float : yes Checking for size of int : yes Checking for size of long int : yes Checking for size of long long int : yes Checking for size of short int : yes Checking for size of void * : yes Checking for header fcntl.h : yes Checking for header float.h : yes Checking for header fenv.h : yes Checking for header limits.h : yes Checking for header stddef.h : yes Checking for header stdlib.h : yes Checking for header string.h : yes Checking for header stdio.h : yes Checking for header assert.h : yes Checking for header sys/time.h : yes Checking for header sys/types.h : yes Checking for header sys/stat.h : yes Checking for header stdlib.h : yes Checking for header string.h : yes Checking for header memory.h : yes Checking for header strings.h : yes Checking for header inttypes.h : yes Checking for header stdint.h : yes Checking for header unistd.h : yes Checking for header tr1/unordered_map : yes Checking for header tr1/unordered_set : yes Checking for header unordered_map : not found Checking for header unordered_set : not found Checking for header limits : yes Checking for c++ namespaces : yes Checking for std::sstream : yes Checking for library m : yes Using Petsc version 3.1.0 Checking for header petscversion.h : yes Checking for MPI : yes Checking MPI library : ok Checking Fortran library : ok Checking for library Petsc : yes Checking for header nglib.h : no Checking for header nglib.h : no Checking for header nglib.h : no Checking for header nglib.h : no Checking for header nglib.h : no Checking for header cgnslib.h : yes Checking for library cgns : yes Checking for header vtkConfigure.h : no Checking for header vtkConfigure.h : no Checking for header vtkConfigure.h : yes Checking for libraries for VTK : no Checking for program flex : /usr/bin/flex Checking for program bison : /usr/bin/bison 'configure' finished successfully (7.434s) Waf: Entering directory /home/pinkchalk/Downloads/Genius-TCAD-Open-master/build/default' [587/587] cxxprogram: build/default/src/contrib/ann/ANN.cpp.0.o build/default/src/contrib/ann/bd_fix_rad_search.cpp.0.o build/default/src/contrib/ann/bd_pr_search.cpp.0.o build/default/src/contrib/ann/bd_search.cpp.0.o build/default/src/contrib/ann/bd_tree.cpp.0.o build/default/src/contrib/ann/brute.cpp.0.o build/default/src/contrib/ann/kd_dump.cpp.0.o build/default/src/contrib/ann/kd_fix_rad_search.cpp.0.o build/default/src/contrib/ann/kd_pr_search.cpp.0.o build/default/src/contrib/ann/kd_search.cpp.0.o build/default/src/contrib/ann/kd_split.cpp.0.o build/default/src/contrib/ann/kd_tree.cpp.0.o build/default/src/contrib/ann/kd_util.cpp.0.o build/default/src/contrib/ann/perf.cpp.0.o build/default/src/contrib/csabathy/csa.cc.1.o build/default/src/contrib/csabathy/svd.c.1.o build/default/src/contrib/expreval/expr.cc.1.o build/default/src/contrib/expreval/expr_datalist.cc.1.o build/default/src/contrib/expreval/expr_except.cc.1.o build/default/src/contrib/expreval/expr_func.cc.1.o build/default/src/contrib/expreval/expr_funclist.cc.1.o build/default/src/contrib/expreval/expr_node.cc.1.o build/default/src/contrib/expreval/expr_parser.cc.1.o build/default/src/contrib/expreval/expr_vallist.cc.1.o build/default/src/contrib/spice/schur_solver.cc.1.o build/default/src/contrib/spice/spice_ckt.cc.1.o build/default/src/contrib/tif3d/tif3d.cc.1.o build/default/src/contrib/klu/UFconfig.c.1.o build/default/src/contrib/klu/amd_1.c.1.o build/default/src/contrib/klu/amd_2.c.1.o build/default/src/contrib/klu/amd_aat.c.1.o build/default/src/contrib/klu/amd_control.c.1.o build/default/src/contrib/klu/amd_defaults.c.1.o build/default/src/contrib/klu/amd_dump.c.1.o build/default/src/contrib/klu/amd_global.c.1.o build/default/src/contrib/klu/amd_info.c.1.o build/default/src/contrib/klu/amd_order.c.1.o build/default/src/contrib/klu/amd_post_tree.c.1.o build/default/src/contrib/klu/amd_postorder.c.1.o build/default/src/contrib/klu/amd_preprocess.c.1.o build/default/src/contrib/klu/amd_valid.c.1.o build/default/src/contrib/klu/btf_maxtrans.c.1.o build/default/src/contrib/klu/btf_order.c.1.o build/default/src/contrib/klu/btf_strongcomp.c.1.o build/default/src/contrib/klu/colamd.c.1.o build/default/src/contrib/klu/colamd_global.c.1.o build/default/src/contrib/klu/klu.c.1.o build/default/src/contrib/klu/klu_analyze.c.1.o build/default/src/contrib/klu/klu_analyze_given.c.1.o build/default/src/contrib/klu/klu_defaults.c.1.o build/default/src/contrib/klu/klu_diagnostics.c.1.o build/default/src/contrib/klu/klu_dump.c.1.o build/default/src/contrib/klu/klu_extract.c.1.o build/default/src/contrib/klu/klu_factor.c.1.o build/default/src/contrib/klu/klu_free_numeric.c.1.o build/default/src/contrib/klu/klu_free_symbolic.c.1.o build/default/src/contrib/klu/klu_kernel.c.1.o build/default/src/contrib/klu/klu_memory.c.1.o build/default/src/contrib/klu/klu_refactor.c.1.o build/default/src/contrib/klu/klu_scale.c.1.o build/default/src/contrib/klu/klu_solve.c.1.o build/default/src/contrib/klu/klu_sort.c.1.o build/default/src/contrib/klu/klu_tsolve.c.1.o build/default/src/contrib/mxml/MXMLUtil.cpp.1.o build/default/src/contrib/mxml/mxml-attr.c.1.o build/default/src/contrib/mxml/mxml-entity.c.1.o build/default/src/contrib/mxml/mxml-file.c.1.o build/default/src/contrib/mxml/mxml-index.c.1.o build/default/src/contrib/mxml/mxml-node.c.1.o build/default/src/contrib/mxml/mxml-private.c.1.o build/default/src/contrib/mxml/mxml-search.c.1.o build/default/src/contrib/mxml/mxml-set.c.1.o build/default/src/contrib/mxml/mxml-string.c.1.o build/default/src/contrib/nn/delaunay.cc.1.o build/default/src/contrib/nn/istack.cc.1.o build/default/src/contrib/nn/lpi.cc.1.o build/default/src/contrib/spline/spline.cc.1.o build/default/src/contrib/triangle/triangle.c.1.o build/default/src/contrib/tif/tif_tool.cc.2.o build/default/src/contrib/stanford/medici.cc.1.o build/default/src/contrib/stanford/silvaco.cc.1.o build/default/src/contrib/stanford/stanford.cc.1.o build/default/src/contrib/stanford/suprem.cc.1.o build/default/src/contrib/dfise/dfise.cc.2.o build/default/src/contrib/dfise/dfise_grid.cc.2.o build/default/src/contrib/trex/trex.c.1.o build/default/src/base/dof_object.cc.2.o build/default/src/base/genius_env.cc.2.o build/default/src/base/log.cc.2.o build/default/src/base/perf_log.cc.2.o 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build/default/src/solver/mixA1/mixA1.cc.2.o build/default/src/solver/mixA1/mixA1_boundary_gate.cc.2.o build/default/src/solver/mixA1/mixA1_boundary_ohmic.cc.2.o build/default/src/solver/mixA1/mixA1_boundary_schottky.cc.2.o build/default/src/solver/mixA1/mixA1_boundary_solderpad.cc.2.o build/default/src/solver/mixA2/mixA2.cc.2.o build/default/src/solver/mixA2/mixA2_boundary_gate.cc.2.o build/default/src/solver/mixA2/mixA2_boundary_ohmic.cc.2.o build/default/src/solver/mixA2/mixA2_boundary_schottky.cc.2.o build/default/src/solver/mixA2/mixA2_boundary_solderpad.cc.2.o build/default/src/solver/mixA3/mixA3.cc.2.o build/default/src/solver/mixA3/mixA3_boundary_gate.cc.2.o build/default/src/solver/mixA3/mixA3_boundary_ohmic.cc.2.o build/default/src/solver/mixA3/mixA3_boundary_schottky.cc.2.o build/default/src/solver/mixA3/mixA3_boundary_solderpad.cc.2.o build/default/src/solver/mole_analytic/mole_analytic.cc.2.o build/default/src/solver/poisson/poisson.cc.2.o build/default/src/solver/poisson/poisson_boundary_ei_interface.cc.2.o build/default/src/solver/poisson/poisson_boundary_float_metal.cc.2.o build/default/src/solver/poisson/poisson_boundary_gate.cc.2.o build/default/src/solver/poisson/poisson_boundary_hetero_interface.cc.2.o build/default/src/solver/poisson/poisson_boundary_homo_interface.cc.2.o build/default/src/solver/poisson/poisson_boundary_ii_interface.cc.2.o build/default/src/solver/poisson/poisson_boundary_ir_interface.cc.2.o build/default/src/solver/poisson/poisson_boundary_is_interface.cc.2.o build/default/src/solver/poisson/poisson_boundary_ohmic.cc.2.o build/default/src/solver/poisson/poisson_boundary_resistance_ohmic.cc.2.o build/default/src/solver/poisson/poisson_boundary_resistance_schottky.cc.2.o build/default/src/solver/poisson/poisson_boundary_rr_interface.cc.2.o build/default/src/solver/poisson/poisson_boundary_schottky.cc.2.o build/default/src/solver/poisson/poisson_boundary_simple_gate.cc.2.o build/default/src/solver/poisson/poisson_boundary_solderpad.cc.2.o build/default/src/solver/poisson/poisson_conductor.cc.2.o build/default/src/solver/poisson/poisson_conductor_hanging_node.cc.2.o build/default/src/solver/poisson/poisson_insulator.cc.2.o build/default/src/solver/poisson/poisson_insulator_hanging_node.cc.2.o build/default/src/solver/poisson/poisson_resistance.cc.2.o build/default/src/solver/poisson/poisson_resistance_hanging_node.cc.2.o build/default/src/solver/poisson/poisson_semiconductor.cc.2.o build/default/src/solver/poisson/poisson_semiconductor_hanging_node.cc.2.o build/default/src/solver/ray_tracing/light_thread.cc.2.o build/default/src/solver/ray_tracing/object_tree.cc.2.o build/default/src/solver/ray_tracing/ray_tracing.cc.2.o build/default/src/solver/solver_base.cc.2.o build/default/src/solver/solver_specify.cc.2.o build/default/src/solver/stress_solver/stress_solver.cc.2.o build/default/src/source/electrical_source.cc.2.o build/default/src/source/field_source.cc.2.o build/default/src/source/isource.cc.2.o build/default/src/source/light_lenses.cc.2.o build/default/src/source/light_source.cc.2.o build/default/src/source/particle_source.cc.2.o build/default/src/source/vsource.cc.2.o build/default/src/source/waveform.cc.2.o build/default/src/utils/dose_rate.cc.2.o build/default/src/utils/error_vector.cc.2.o build/default/src/utils/extend_to_3d.cc.2.o build/default/src/utils/location_maps.cc.2.o build/default/src/utils/mat_analysis.cc.2.o build/default/src/utils/monot_cubic_interpolator.cc.2.o build/default/src/utils/nearest_node_locator.cc.2.o build/default/src/utils/octree.cc.2.o build/default/src/utils/point_locator_base.cc.2.o build/default/src/utils/point_locator_list.cc.2.o build/default/src/utils/point_locator_tree.cc.2.o build/default/src/utils/show_mesh_2d.cc.2.o build/default/src/utils/statistics.cc.2.o build/default/src/utils/surface_locator_base.cc.2.o build/default/src/utils/surface_locator_hub.cc.2.o build/default/src/utils/surface_locator_list.cc.2.o build/default/src/utils/surface_locator_sphere.cc.2.o build/default/src/utils/sync_file.cc.2.o build/default/src/utils/tree.cc.2.o build/default/src/utils/tree_node.cc.2.o build/default/src/material/PMI.cc.2.o build/default/src/material/material.cc.2.o build/default/src/material/material_define.cc.2.o build/default/src/material/physical_unit.cc.2.o build/default/src/hook/dlhook.cc.1.o build/default/src/main.cc.3.o -> build/default/src/genius.LINUX src/solution/vtk_io.cc.2.o: In functionVTKIO::nodes_tovtk(MeshBase const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x131): undefined reference to vtkPoints::New()' src/solution/vtk_io.cc.2.o: In functionVTKIO::read(std::string const&)': vtk_io.cc:(.text+0xf7e): undefined reference to vtkXMLUnstructuredGridReader::New()' vtk_io.cc:(.text+0xfb9): undefined reference tovtkXMLUnstructuredGridReader::GetOutput()' vtkio.cc:(.text+0x1318): undefined reference to `vtkDataSetAttributes::GetScalars(char const)' vtk_io.cc:(.text+0x1328): undefined reference to typeinfo for vtkFloatArray' vtk_io.cc:(.text+0x132f): undefined reference totypeinfo for vtkDataArray' vtk_io.cc:(.text+0x134b): undefined reference to vtkDataSetAttributes::GetScalars(char const*)' vtk_io.cc:(.text+0x135b): undefined reference totypeinfo for vtkFloatArray' vtk_io.cc:(.text+0x1362): undefined reference to typeinfo for vtkDataArray' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_node_complexsolution(std::vector<unsigned int, std::allocator > const&, std::vectorstd::complex<float, std::allocatorstd::complex >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x3438): undefined reference to vtkFloatArray::New()' vtk_io.cc:(.text+0x344a): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x34ae): undefined reference to vtkDataArrayTemplate<float>::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x3510): undefined reference tovtkDataArrayTemplate::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x35af): undefined reference to vtkDataArrayTemplate<float>::InsertValue(long long, float)' vtk_io.cc:(.text+0x35c1): undefined reference tovtkDataArrayTemplate::InsertValue(long long, float)' vtkio.cc:(.text+0x35ef): undefined reference to `vtkFieldData::AddArray(vtkAbstractArray)' vtk_io.cc:(.text+0x3604): undefined reference to vtkFieldData::AddArray(vtkAbstractArray*)' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_node_scalersolution(std::vector<unsigned int, std::allocator > const&, std::vector<float, std::allocator >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x3cd6): undefined reference to vtkFloatArray::New()' vtk_io.cc:(.text+0x3cff): undefined reference tovtkDataArrayTemplate::SetNumberOfValues(long long)' vtkio.cc:(.text+0x3d1c): undefined reference to `vtkFieldData::AddArray(vtkAbstractArray)' vtk_io.cc:(.text+0x3dea): undefined reference to vtkDataArrayTemplate<float>::InsertValue(long long, float)' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_node_vectorsolution(std::vector<unsigned int, std::allocator > const&, std::vector<float, std::allocator >&, std::vector<float, std::allocator >&, std::vector<float, std::allocator >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x3ee9): undefined reference to vtkFloatArray::New()' vtk_io.cc:(.text+0x401d): undefined reference tovtkFieldData::AddArray(vtkAbstractArray_)' src/solution/vtk_io.cc.2.o: In function VTKIO::write_cell_scaler_solution(std::vector<unsigned int, std::allocator<unsigned int> > const&, std::vector<float, std::allocator<float> >&, std::string const&, vtkUnstructuredGrid*)': vtk_io.cc:(.text+0x41f1): undefined reference tovtkFloatArray::New()' vtk_io.cc:(.text+0x421b): undefined reference to vtkDataArrayTemplate<float>::SetNumberOfValues(long long)' vtk_io.cc:(.text+0x4238): undefined reference tovtkFieldData::AddArray(vtkAbstractArray_)' vtk_io.cc:(.text+0x42ea): undefined reference to vtkDataArrayTemplate<float>::InsertValue(long long, float)' src/solution/vtk_io.cc.2.o: In functionVTKIO::write_cell_vectorsolution(std::vector<unsigned int, std::allocator > const&, std::vector<float, std::allocator >&, std::vector<float, std::allocator >&, std::vector<float, std::allocator >&, std::string const&, vtkUnstructuredGrid)': vtk_io.cc:(.text+0x4399): undefined reference to vtkFloatArray::New()' vtk_io.cc:(.text+0x44cd): undefined reference tovtkFieldData::AddArray(vtkAbstractArray*)'

Hoping to hear from you soon. Regards

pinkchalk commented 10 years ago

It seems to me that genius is not able to check for libraries of VTK as indicated by,

Checking for header vtkConfigure.h : yes Checking for libraries for VTK : no

thereby leading to these undefined references. The vtk libraries are however present at /usr/local/lib/vtk-5.4

Any ideas on how to correct this.

cogenda commented 10 years ago

The detailed error message is in the config.log file in the build/default/ directory.

It will try to link vtk libs from a few locations, if none of them works, it reports "no".

where is your vtk's .a or .so files located?

shenchen

On 2014-02-15 23:20, Ashish Kumar wrote:

It seems to me that genius is not able to check for libraries of VTK as indicated by,

Checking for header vtkConfigure.h : yes

Checking for libraries for VTK : no

thereby leading to these undefined references. The vtk libraries are however present at /usr/local/lib/vtk-5.4

Any ideas on how to correct this.

Reply to this email directly or view it on GitHub [1].

Links:

[1] https://github.com/cogenda/Genius-TCAD-Open/issues/18#issuecomment-35158503

pinkchalk commented 10 years ago

/usr/local/lib

pinkchalk commented 10 years ago

Corrected the issue, edited the wscript file appropriately to include vtkNetCDF, vtkmetaio, vtksqlite instead of libvtkNetCDF, libvtkmetaio, libvtksqlite

Genius builds successfully. Now the problem arises when I try to run a test example.

pinkchalk@pinklet:~/Test/examples/PN_Diode/1D$ $GENIUS_DIR/bin/genius.LINUX -i pn1d.inp /home/pinkchalk/Genius/bin/genius.LINUX: error while loading shared libraries: libvtkIO.so.5.4: cannot open shared object file: No such file or directory

cogenda commented 10 years ago

Please check that the head/lib files are actually in

/usr/local/vtk/include/vtk-5.4

and

/usr/local/vtk/lib/vtk-5.4

respectively.

If not, please change your VTK configure scripts as I suggested in the previous message.

If this still doesn't work, please paste the relevant part of config.log file here.

shenchen

On 2014-02-15 23:38, Ashish Kumar wrote:

/usr/local/lib

Reply to this email directly or view it on GitHub [1].

Links:

[1] https://github.com/cogenda/Genius-TCAD-Open/issues/18#issuecomment-35158954

cogenda commented 10 years ago

do

export LD_LIBRARY_PATH=/usr/local/lib/vtk-5.4

before you run genius, so it can find the .so files.

shenchen

On 2014-02-15 23:46, Ashish Kumar wrote:

Corrected the issue, edited the wscript file appropriately to include vtkNetCDF, vtkmetaio, vtksqlite instead of libvtkNetCDF, libvtkmetaio, libvtksqlite

Genius builds successfully. Now the problem arises when I try to run a test example.

pinkchalk@pinklet:~/Test/examples/PN_Diode/1D$ $GENIUS_DIR/bin/genius.LINUX -i pn1d.inp

/home/pinkchalk/Genius/bin/genius.LINUX: error while loading shared libraries: libvtkIO.so.5.4: cannot open shared object file: No such file or directory

Reply to this email directly or view it on GitHub [1].

Links:

[1] https://github.com/cogenda/Genius-TCAD-Open/issues/18#issuecomment-35159151

pinkchalk commented 10 years ago

Thanks a lot. LD_LIBRARY_PATH did the trick. Genius is up and running..

Regards

lutherthecat commented 10 years ago

My fork of the software, https://github.com/lutherthecat/Genius-TCAD-Open builds using cmake using the instructions in myinstall.txt.

I recommend used the vtk packages in that file so that the program will run on any ubuntu system with those libraries preinstalled.

cogenda commented 10 years ago

I will definitely read your cmake code. Thank you for your participation and contribution in the project.

shenchen

On 2014-02-16 01:34, lutherthecat wrote:

My fork of the software, https://github.com/lutherthecat/Genius-TCAD-Open [1] builds using cmake using the instruction in myinstall.txt.

I recommend used the vtk packages in that file so that the program will run on any ubuntu system with those libraries preinstalled.

Reply to this email directly or view it on GitHub [2].

Links:

[1] https://github.com/lutherthecat/Genius-TCAD-Open [2] https://github.com/cogenda/Genius-TCAD-Open/issues/18#issuecomment-35162035

SlimeySlug commented 10 years ago

Anyone! Please Help! I have a very similar problem, Genius is installed and built but the first time I tried to run the diode example on Genius with:

$GENIUS_DIR/bin/genius.LINUX -i pn2d.inp

The following error is reported:

/home/sal/Genius/Genius-TCAD-Open-master/bin/genius.LINUX: error while loading shared libraries: libcgns.so: cannot open shared object file: No such file or directory

I deterred this by using Cogenda's suggestion:

export LD_LIBRARY_PATH=/path/to/cgnslib_2.5

This allowed Genius to compile/iterate successfully, however this prompted PinkChalk's error:

Genius is not compiled with XML VTK support, skip VTK export...

Disallowing the VTK file to pop up

I am relatively new to Linux, maybe my cgnslib files are in the wrong directory? Should they be in /usr/lib as well?

Does me having to declare the LD_LIBRARY_PATH for the cgnslib location prevent the use of VTK? Again I can't compile Genius LD_LIBRARY_PATH set to VTK due to the above error "cannot open shared object file: No such file or directory". Also, my BUILD_SHARED_LIBS is ON for VTK config

VTK is located in my /usr/local/lib

Thank you, I'm so close to get this running!

pinkchalk commented 10 years ago

This is to do with incorrect vtk installation. Did you specify VTK_DATA_ROOT while installation? Were the -fPIC flags set correctly?

This might come in handy.

http://thilinasameera.wordpress.com/2013/02/09/setting-up-vtk-and-itk-environments-for-ubuntu/

CMAKE_CXX_FLAGS and CMAKE_C_FLAGS need to be set to -fPIC while installation.

Regards

SlimeySlug commented 10 years ago

Thank you for your helpful response, I reconfigured VTK with the correct -fPIC flags, Shared Libraries ON, and VTK_DATA_ROOT set to my VTKData, reconfigured Genius then received this error again:

error while loading shared libraries: libcgns.so: cannot open shared object file: No such file or directory

after performing:

$GENIUS_DIR/bin/genius.LINUX -i pn2d.inp

I can get Genius to compile after this error only by:

export LD_LIBRARY_PATH=/path/to/cgnslib_2.5

Which renders VTK useless, any suggestions regarding this inability to find cngslib.so, because it seems I need to reserve the export LD_LIBRARY_PATH for finding VTK? Is there an easy way to use gnuplot or paraview instead of VTK?

Here is my VTK ccmake config window:

                                                Page 1 of 5

BUILD_DOCUMENTATION OFF
BUILD_EXAMPLES ON
BUILD_SHARED_LIBS ON
BUILD_TESTING ON
BZRCOMMAND BZRCOMMAND-NOTFOUND
CMAKE_BACKWARDS_COMPATIBILITY 2.4
CMAKE_BUILD_TYPE
CMAKE_COLOR_MAKEFILE ON
CMAKE_CXX_COMPILER /usr/bin/c++
CMAKE_CXX_FLAGS -fPIC
CMAKE_CXX_FLAGS_DEBUG -g
CMAKE_CXX_FLAGS_MINSIZEREL -Os -DNDEBUG
CMAKE_CXX_FLAGS_RELEASE -O3 -DNDEBUG
CMAKE_CXX_FLAGS_RELWITHDEBINFO -O2 -g -DNDEBUG
CMAKE_C_COMPILER /usr/bin/cc
CMAKE_C_FLAGS -fPIC
CMAKE_C_FLAGS_DEBUG -g
CMAKE_C_FLAGS_MINSIZEREL -Os -DNDEBUG
CMAKE_C_FLAGS_RELEASE -O3 -DNDEBUG
CMAKE_C_FLAGS_RELWITHDEBINFO -O2 -g -DNDEBUG
CMAKE_EXE_LINKER_FLAGS
CMAKE_EXE_LINKER_FLAGS_DEBUG
CMAKE_EXE_LINKER_FLAGS_MINSIZE
CMAKE_EXE_LINKER_FLAGS_RELEASE
CMAKE_EXE_LINKER_FLAGS_RELWITH
CMAKE_EXPORT_COMPILE_COMMANDS OFF
CMAKE_HP_PTHREADS OFF
CMAKE_INSTALL_PREFIX /usr/local
CMAKE_LINKER /usr/bin/ld
CMAKE_MAKE_PROGRAM /usr/bin/make
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
CMAKE_X_CFLAGS
CMAKE_X_LIBS /usr/lib/i386-linux-gnu/libSM.so;/usr/lib/i38 COVERAGE_COMMAND /usr/bin/gcov
COVERAGE_EXTRA_FLAGS -l
VTK_DATA_ROOT /home/sal/Genius/VTKData VTK_WRAP_JAVA OFF
VTK_WRAP_PYTHON OFF
VTK_WRAP_TCL OFF
X11_ICE_INCLUDE_PATH /usr/include
X11_ICE_LIB /usr/lib/i386-linux-gnu/libICE.so

lutherthecat commented 10 years ago

you can use a ":" to separate the paths: export LD_LIBRARY_PATH=/path/to/cgns:/path/to/vtk

SlimeySlug commented 10 years ago

I appreciate the support. I tried that as well, still would compile Genius but not export anything to VTK (mentioning I need xml support). Does cgnslib need to be located in /usr/local/lib or /usr/lib like VTK is?

lutherthecat commented 10 years ago

Are you sure that you have VTK enabled?

You need a command line like this: ./waf --prefix=$PWD --with-petsc-dir=/path/to/petsc --with-petsc-arch='' --with-cgns-dir=/path/to/cgns --with-vtk-dir=/path/to/vtk configure build install

SlimeySlug commented 10 years ago

I ran that command but I guess I'm confused about where each of these sub-directories should be stored. petsc, cgns, vtk, and Genius-TCAD-Open-master are all folders under my Genius directory. When I point petsc to anywhere other than $PETSC_DIR it gives me "Could not find petscversion.h, or it can not be parsed." An above user had VTK in /usr/local/lib/vtk-5.4 where mine is also stored, but do I set the path to that, or to /home/me/Genius/VTK? Thank you

pinkchalk commented 10 years ago

What happens when you start building genius? Do you see something like this?

Checking for header cgnslib.h : yes Checking for library cgns : yes

If no, then you have to specify the location where genius can find cgns. Also if VTK is installed in /usr/local/lib then this is the path that is to be specified and not /home/me/Genius/VTK which I understand is the VTK source.

SlimeySlug commented 10 years ago

Genius is installed but still won't run due libcgns.so not being found.

Checking for header nglib.h : no Checking for header cgnslib.h : yes Checking for library cgns : yes Checking for header vtkConfigure.h : no Checking for libraries for VTK : yes are a few key ones

after commanding

./waf --prefix=$PWD --with-petsc-dir=$PETSC_DIR --with-petsc-arch=$PETSC_ARCH configure build install

then I export GENIUS_DIR to Genius-TCAD-Open-master and run the example after cd'ing:

libcgns.so: cannot open shared object file: No such file or directory

Thank you again for your assistance!

lutherthecat commented 10 years ago

It looks like you would just need to set LD_LIBRARY_PATH to where the libcgns.so would be found. If you run "ldd", you can see which shared libraries that genius found and did not find. Then set LD_LIBRARY_PATH to the ":" delimited list of paths to find the libraries.

SlimeySlug commented 10 years ago

Thank you, the ldd on libcgns.so then setting LD_LIBRARY_PATH to this location as well as the /usr/local/lib/vtk did the trick. Now when I run the 2D PN Diode example it writes system to .vtu XML files which can only be accessed through a .dat text file, and to a Legacy VTK file pn2d.vtk which is a Dataset Unstructured Grid big text file. Is this the extent of the simulation, having to manually move and plot this text output?