On Tue, Apr 25, 2023 at 19:53 zongyun tsai <[email protected]> wrote:
> Dear Christoph, > The attachment is the error message and lines after adding --verbose > command. > Hmm, we test against gromacs-2023 all the time, but I don’t have enough experience with macOS and homebrew to help here. Two side notes: 1.) If you want to do coarse-graining you will need gromacs-2019 as gromacs-2023 doesn’t support tabulated interactions anymore. 2.) you could try to have votca build its own gromacs version with -DBUILD_OWN_GROMACS=On. Christoph > Sincerely, > Glenn > > Christoph Junghans <[email protected]> 於 2023年4月26日 週三 上午5:20寫道： > >> >> >> On Tue, Apr 25, 2023 at 00:47 zongyun tsai <[email protected]> >> wrote: >> >>> Dear Christoph, >>> >>> My gromacs version is 2023.1, and was built by myself using homebrew. >>> >> Can you do a verbose build (add —verbose) and post the error message and >> lines above again? >> >> Christoph >> >> >>> Glenn >>> >>> Christoph Junghans 在 2023年4月24日 星期一晚上11:40:24 [UTC+8] 的信中寫道： >>> >>>> On Sun, Apr 23, 2023 at 11:26 PM zongyun tsai <[email protected]> >>>> wrote: >>>> > >>>> > Dear Christoph >>>> > >>>> > >>>> > (base) glenntsai@GlenndeAir ~ % cmake --build builddir --parallel 8 >>>> > >>>> > [ 1%] Built target csg_inverse_manpage >>>> > >>>> > [ 2%] Built target csg_call_build >>>> > >>>> > [ 2%] Built target csg_call_manpage >>>> > >>>> > [ 2%] Built target csg_inverse_build >>>> > >>>> > [ 2%] Built target votca_tools_manpages >>>> > >>>> > [ 2%] Built target votca_csg_manpages >>>> > >>>> > Current git revision is b533e3901 >>>> > >>>> > [ 2%] Built target gitversion >>>> > >>>> > [ 17%] Built target votca_tools >>>> > >>>> > [ 17%] Built target votca_property >>>> > >>>> > [ 17%] Built target unit_test_correlate >>>> > >>>> > [ 17%] Built target unit_test_cubicspline >>>> > >>>> > [ 19%] Built target unit_test_datacollection >>>> > >>>> > [ 19%] Built target unit_test_crosscorrelate >>>> > >>>> > [ 19%] Built target unit_test_calculator >>>> > >>>> > [ 20%] Built target unit_test_constants >>>> > >>>> > [ 20%] Built target unit_test_edge_base >>>> > >>>> > [ 22%] Built target unit_test_floatingpointcomparison >>>> > >>>> > [ 22%] Built target unit_test_filesystem >>>> > >>>> > [ 23%] Built target unit_test_elements >>>> > >>>> > [ 25%] Built target unit_test_graphalgorithm >>>> > >>>> > [ 26%] Built target unit_test_edgecontainer >>>> > >>>> > [ 26%] Built target unit_test_graph_base >>>> > >>>> > [ 26%] Built target unit_test_graphdistvisitor >>>> > >>>> > [ 26%] Built target unit_test_graph_df_visitor >>>> > >>>> > [ 26%] Built target unit_test_graphvisitor >>>> > >>>> > [ 28%] Built target unit_test_histogramnew >>>> > >>>> > [ 29%] Built target unit_test_graph_bf_visitor >>>> > >>>> > [ 31%] Built target unit_test_graphnode >>>> > >>>> > [ 31%] Built target unit_test_identity >>>> > >>>> > [ 31%] Built target unit_test_name >>>> > >>>> > [ 32%] Built target unit_test_objectfactory >>>> > >>>> > [ 34%] Built target unit_test_property >>>> > >>>> > [ 34%] Built target unit_test_linalg >>>> > >>>> > [ 34%] Built target unit_test_optionshandler >>>> > >>>> > [ 35%] Built target unit_test_reducededge >>>> > >>>> > [ 35%] Built target unit_test_reducedgraph >>>> > >>>> > [ 37%] Built target unit_test_structureparameters >>>> > >>>> > [ 37%] Built target unit_test_thread >>>> > >>>> > [ 38%] Built target unit_test_tokenizer >>>> > >>>> > [ 38%] Built target unit_test_table >>>> > >>>> > [ 38%] Built target unit_test_random >>>> > >>>> > [ 40%] Built target unit_test_akimaspline >>>> > >>>> > [ 41%] Built target unit_test_linspline >>>> > >>>> > [ 43%] Built target unit_test_unitconverter >>>> > >>>> > [ 43%] Built target votca_property_manpage >>>> > >>>> > [ 43%] Built target unit_test_NDimVector >>>> > >>>> > [ 43%] Built target unit_test_eigenio_matrixmarket >>>> > >>>> > [ 43%] Linking CXX shared library libvotca_csg.dylib >>>> > >>>> > Undefined symbols for architecture arm64: >>>> > >>>> > "read_first_frame(gmx_output_env_t const*, t_trxstatus**, >>>> std::__1::__fs::filesystem::path const&, t_trxframe*, int)", referenced >>>> from: >>>> Hmm, this means something is wrong with the linking against gromacs? >>>> >>>> 0.) Do you need gromacs at all? - Otherwise switch it off. >>>> 1.) What gromacs version are you using? >>>> 2.) Did you build gromacs yourself? >>>> >>>> Christoph >>>> >>>> > >>>> > votca::csg::GMXTrajectoryReader::FirstFrame(votca::csg::Topology&) in >>>> gmxtrajectoryreader.cc.o >>>> > >>>> > "open_trx(std::__1::__fs::filesystem::path const&, char const*)", >>>> referenced from: >>>> > >>>> > votca::csg::GMXTrajectoryWriter::Open(std::__1::basic_string<char, >>>> std::__1::char_traits<char>, std::__1::allocator<char> >, bool) in >>>> gmxtrajectorywriter.cc.o >>>> > >>>> > "read_tpx(std::__1::__fs::filesystem::path const&, t_inputrec*, float >>>> (*) [3], int*, float (*) [3], float (*) [3], gmx_mtop_t*)", referenced >>>> from: >>>> > >>>> > >>>> votca::csg::GMXTopologyReader::ReadTopology(std::__1::basic_string<char, >>>> std::__1::char_traits<char>, std::__1::allocator<char> >, >>>> votca::csg::Topology&) in gmxtopologyreader.cc.o >>>> > >>>> > ld: symbol(s) not found for architecture arm64 >>>> > >>>> > clang: error: linker command failed with exit code 1 (use -v to see >>>> invocation) >>>> > >>>> > make[2]: *** [csg/src/libcsg/libvotca_csg.2024.dylib] Error 1 >>>> > >>>> > make[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2 >>>> > >>>> > make: *** [all] Error 2 >>>> > >>>> > >>>> > >>>> > Glenn >>>> > >>>> > >>>> > Christoph Junghans 在 2023年4月24日 星期一上午11:51:51 [UTC+8] 的信中寫道： >>>> >> >>>> >> On Sun, Apr 23, 2023 at 19:38 zongyun tsai <[email protected]> >>>> wrote: >>>> >>> >>>> >>> Hello, >>>> >>> I encountered an Error message while when running the following >>>> command: >>>> >>> cmake --build builddirThe error shown in the terminal states that >>>> >>> >>>> >>> clang: error: linker command failed with exit code 1 (use -v to see >>>> invocation) >>>> >> >>>> >> can you post the lines above this error? >>>> >> >>>> >> Christoph >>>> >>> >>>> >>> make[2]: *** [csg/src/libcsg/libvotca_csg.2024.dylib] Error 1 >>>> >>> >>>> >>> make[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2 >>>> >>> >>>> >>> make: *** [all] Error 2 >>>> >>> >>>> >>> Can you please suggest some ways to correct this error? >>>> >>> Thank you,Glenn >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> Join us on Slack: https://join.slack.com/t/votca/signup >>>> >>> --- >>>> >>> You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> >>> To unsubscribe from this group and stop receiving emails from it, >>>> send an email to [email protected]. >>>> >>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/60a4e6f3-51d2-49a2-ad60-5b6df3d064d2n%40googlegroups.com. >>>> >>>> >> >>>> >> -- >>>> >> Christoph Junghans >>>> >> Web: http://www.compphys.de >>>> > >>>> > -- >>>> > Join us on Slack: https://join.slack.com/t/votca/signup >>>> > --- >>>> > You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> > To unsubscribe from this group and stop receiving emails from it, >>>> send an email to [email protected]. >>>> >>> > To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/3db772b3-1c44-4dad-ae1c-edea78357445n%40googlegroups.com. >>>> >>>> >>>> >>>> >>>> -- >>>> Christoph Junghans >>>> Web: http://www.compphys.de >>>> >>> -- >>> Join us on Slack: https://join.slack.com/t/votca/signup >>> --- >>> You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/2d28cdcd-9b3f-4d75-9dd8-f54ca7319e81n%40googlegroups.com >>> <https://groups.google.com/d/msgid/votca/2d28cdcd-9b3f-4d75-9dd8-f54ca7319e81n%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e4ZtqYZdBbsw4QpOZ5pZhKgawrJxs3Qqnn3Wov%3DqQ2wKw%40mail.gmail.com >> <https://groups.google.com/d/msgid/votca/CAHG27e4ZtqYZdBbsw4QpOZ5pZhKgawrJxs3Qqnn3Wov%3DqQ2wKw%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAJs%3DatKxwXn563-bqJ_CPKOdDmqB9z_5ZkFymXX-AGoQ5tGS2A%40mail.gmail.com > <https://groups.google.com/d/msgid/votca/CAJs%3DatKxwXn563-bqJ_CPKOdDmqB9z_5ZkFymXX-AGoQ5tGS2A%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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