Easier than compiling VTK with PGI might be to disable it, unless you absolutely need it.
> On Oct 20, 2013, at 1:41 PM, Santiago Alonso Pérez Rubiano > <[email protected]> wrote: > > I'm trying to compile libmesh 0.9.2 with PGI 11.8 (I'm also trying more > recent PGI versions like 13.8). > > I deleted that section from include/base/libmesh_augment_**std_namespace.h > and now the problems went to linking. I get the trace shown below while > linking meshtool-opt. This seems to be a problem while linking against VTK > (which has been compiled using a different compiler) so I'll try to compile > VTK using PGI and try linking again. > > If you think the problem can be different please let me know. Thanks for > your help. > > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `__CPR409__write_nodal_data__Q2_7libMesh5VTKIOFRCQ2_3std78basic_string__tm__58_cQ2_3std20char_traits__tm__2_cQ2_3std18allocator__tm__2_cRCQ2_3std43vector__tm__29_dQ2_3std18allocator__tm__2_dRCQ2_3std218vector__tm__203_Q2_3stdJ45JQ2_3std105allocator__tm__88_Q2_3stdJ45J': > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:573: > undefined reference to `New__19vtkUnstructuredGridSFv' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:580: > undefined reference to `New__29vtkXMLPUnstructuredGridWriterSFv' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:583: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:584: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:587: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:592: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:592: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:597: > undefined reference to `New__14vtkDoubleArraySFv' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:597: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:597: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:598: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:598: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:84: > undefined reference to > `SetNumberOfValues__29vtkDataArrayTemplate__tm__2_dFL_v' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:601: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:601: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:608: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:608: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:619: > undefined reference to `vtkFieldData::AddArray(vtkAbstractArray *)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:619: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:619: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:620: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:620: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:620: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:636: > undefined reference to `vtkXMLWriter::SetInput(vtkDataObject *)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:638: > undefined reference to `vtkXMLWriter::SetDataModeToAscii(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:130: > undefined reference to `vtkXMLWriter::SetCompressorType(int)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:650: > undefined reference to `vtkXMLWriter::Write(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:653: > undefined reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `libMesh::VTKIO::read( > (std::basic_string<char,std::char_traits<char>,std::allocator<char>> const > &))': > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:413: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:416: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:419: > undefined reference to `vtkXMLUnstructuredGridReader::GetOutput(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:419: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:423: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:426: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:429: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:437: > undefined reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o):/home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:438: > more undefined references to `vtkSmartPointerBase::__dt(void)' follow > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `libMesh::VTKIO::nodes_to_vtk( (void))': > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:171: > undefined reference to `New__9vtkPointsSFv' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:172: > undefined reference to `New__14vtkDoubleArraySFv' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:172: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:172: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:173: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:173: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:174: > undefined reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o):/home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:174: > more undefined references to `vtkSmartPointerBase::__dt(void)' follow > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `libMesh::VTKIO::nodes_to_vtk( (void))': > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:66: > undefined reference to > `InsertNextTupleValue__29vtkDataArrayTemplate__tm__2_dFPCZ1Z_L' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:180: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:180: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:180: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:180: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:180: > undefined reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o):/home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:180: > more undefined references to `vtkSmartPointerBase::__dt(void)' follow > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `libMesh::VTKIO::cells_to_vtk( (void))': > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:210: > undefined reference to `New__12vtkCellArraySFv' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:211: > undefined reference to `New__9vtkIdListSFv' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:211: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:211: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:213: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:213: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:214: > undefined reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o):/home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:214: > more undefined references to `vtkSmartPointerBase::__dt(void)' follow > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `libMesh::VTKIO::cells_to_vtk( (void))': > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:222: > undefined reference to `SetNumberOfIds__9vtkIdListFL' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:222: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:222: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:225: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:225: > undefined reference to `vtkSmartPointerBase::__dt(void)' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:225: > undefined reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o):/home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:225: > more undefined references to `vtkSmartPointerBase::__dt(void)' follow > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `libMesh::VTKIO::cells_to_vtk( (void))': > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:262: > undefined reference to `InsertId__9vtkIdListFLT1' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:270: > undefined reference to `vtkUnstructuredGrid::SetCells(int *, vtkCellArray > *)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `libMesh::VTKIO::system_vectors_to_vtk( (libMesh::EquationSystems const &, > vtkUnstructuredGrid *&))': > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:306: > undefined reference to `New__14vtkDoubleArraySFv' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:84: > undefined reference to > `SetNumberOfValues__29vtkDataArrayTemplate__tm__2_dFL_v' > /home/user/software/libs/libmesh/libmesh-0.9.2/src/mesh/vtk_io.C:323: > undefined reference to `vtkFieldData::AddArray(vtkAbstractArray *)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkXMLWriter::SetCompressorTypeToZLib(void)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkXMLWriter.h:130: undefined > reference to `vtkXMLWriter::SetCompressorType(int)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `WritePointer__14vtkIdTypeArrayFLT1': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkIdTypeArray.h:129: undefined > reference to `WritePointer__29vtkDataArrayTemplate__tm__2_LFLT1_PZ1Z' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `InsertNextCell__12vtkCellArrayFLPCL': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkCellArray.h:248: undefined > reference to `WritePointer__29vtkDataArrayTemplate__tm__2_LFLT1_PZ1Z' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkCellArray::InsertNextCell(vtkIdList *)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkCellArray.h:286: undefined > reference to `WritePointer__29vtkDataArrayTemplate__tm__2_LFLT1_PZ1Z' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkDoubleArray::InsertNextTupleValue(double const *)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkDoubleArray.h:66: undefined > reference to `InsertNextTupleValue__29vtkDataArrayTemplate__tm__2_dFPCZ1Z_L' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `SetNumberOfValues__14vtkDoubleArrayFL': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkDoubleArray.h:84: undefined > reference to `SetNumberOfValues__29vtkDataArrayTemplate__tm__2_dFL_v' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `__ct__34vtkSmartPointer__tm__11_9vtkPointsFPZ1Z': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:36: undefined > reference to `vtkSmartPointerBase::__ct(vtkObjectBase *)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkSmartPointer<vtkPoints>::__dt(void)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:91: undefined > reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `__ct__40vtkSmartPointer__tm__17_14vtkDoubleArrayFPZ1Z': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:36: undefined > reference to `vtkSmartPointerBase::__ct(vtkObjectBase *)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkSmartPointer<vtkDoubleArray>::__dt(void)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:91: undefined > reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `__ct__38vtkSmartPointer__tm__15_12vtkCellArrayFPZ1Z': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:36: undefined > reference to `vtkSmartPointerBase::__ct(vtkObjectBase *)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkSmartPointer<vtkCellArray>::__dt(void)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:91: undefined > reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `__ct__34vtkSmartPointer__tm__11_9vtkIdListFPZ1Z': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:36: undefined > reference to `vtkSmartPointerBase::__ct(vtkObjectBase *)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkSmartPointer<vtkIdList>::__dt(void)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:91: undefined > reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `_Z1Z::New__54vtkSmartPointer__tm__31_28vtkXMLUnstructuredGridReaderSFv_26vtkSmartPointer__tm(void)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:113: undefined > reference to `New__28vtkXMLUnstructuredGridReaderSFv' > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:113: undefined > reference to > `__CPR83____ct__19vtkSmartPointerBaseFP13vtkObjectBaseRCQ2_J6J11NoReference' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `__ct__54vtkSmartPointer__tm__31_28vtkXMLUnstructuredGridReaderFPZ1ZRCQ2_19vtkSmartPointerBase11NoReference': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:163: undefined > reference to > `__CPR83____ct__19vtkSmartPointerBaseFP13vtkObjectBaseRCQ2_J6J11NoReference' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkSmartPointer<vtkXMLUnstructuredGridReader>::__dt(void)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:163: undefined > reference to `vtkSmartPointerBase::__dt(void)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `__ct__55vtkSmartPointer__tm__32_29vtkXMLPUnstructuredGridWriterFPZ1Z': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:36: undefined > reference to `vtkSmartPointerBase::__ct(vtkObjectBase *)' > ./.libs/libmesh_opt.a(libmesh_opt_la-vtk_io.o): In function > `vtkSmartPointer<vtkXMLPUnstructuredGridWriter>::__dt(void)': > /apps/rhel5/vtk-5.10.0/include/vtk-5.10/vtkSmartPointer.h:91: undefined > reference to `vtkSmartPointerBase::__dt(void)' > > > > > > > On Sun, Oct 20, 2013 at 9:34 AM, Roy Stogner <[email protected]>wrote: > >> >> On Sun, 20 Oct 2013, Santiago Alonso Pérez Rubiano wrote: >> >> Hi, I'm trying to compile libmesh with PGI using the instructions outlined >>> in >>> http://libmesh.sourceforge.**net/installation.php<http://libmesh.sourceforge.net/installation.php>but >>> I'm getting the >>> following error: >>> >>> "./include/libmesh/libmesh_**augment_std_namespace.h", line 59: error: >>> function >>> "std::abs(double)" conflicts with using-declaration of function >>> "abs(double)" >>> inline double abs(double a) >>> >>> Does anyone has a clue of how to solve this? >> >> Well, the code on those lines is actually invalid C++; it appears to >> be a workaround for some old PGI compiler that didn't correctly define >> std::abs(double). You can probably work around the problem by just >> deleting that function definition from >> include/base/libmesh_augment_**std_namespace.h >> >> Assuming that works, would you let us know exactly what version of PGI >> you're using? That way we can make the #ifdef there more specific and >> come up with a permanent fix. >> >> Thanks, >> --- >> Roy > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk > _______________________________________________ > Libmesh-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/libmesh-users ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
