Error when installing VOTCA on macOS Ventura 13.0.1

[zongyun tsai]

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)

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

[Christoph Junghans]

On Sun, Apr 23, 2023 at 19:38 zongyun tsai <glenn....@gmail.com> 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

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Christoph Junghans
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[zongyun tsai]

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:

      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：

[Christoph Junghans]

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

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/3db772b3-1c44-4dad-ae1c-edea78357445n%40googlegroups.com.

[zongyun tsai]

Dear Christoph,

My gromacs version is 2023.1, and was built by myself using homebrew.

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：

[Christoph Junghans]

On Tue, Apr 25, 2023 at 00:47 zongyun tsai <glenn....@gmail.com> 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

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/2d28cdcd-9b3f-4d75-9dd8-f54ca7319e81n%40googlegroups.com.

[zongyun tsai]

Dear Christoph,

The attachment is the error message and lines after adding --verbose command.

Sincerely,

Glenn

Christoph Junghans <jung...@votca.org> 於 2023年4月26日 週三 上午5:20寫道：

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e4ZtqYZdBbsw4QpOZ5pZhKgawrJxs3Qqnn3Wov%3DqQ2wKw%40mail.gmail.com.

[Christoph Junghans]

On Tue, Apr 25, 2023 at 19:53 zongyun tsai <glenn....@gmail.com> 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

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAJs%3DatKxwXn563-bqJ_CPKOdDmqB9z_5ZkFymXX-AGoQ5tGS2A%40mail.gmail.com.

[zongyun tsai]

Dear Christoph,

Thank for your kind help.

My problem was solved after using gromacs-2019.

Best regards,

Glenn

Christoph Junghans <jung...@votca.org> 於 2023年4月27日 週四 上午12:23寫道：

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