Dear Christoph,
The attachment is the error message and lines after adding --verbose
command.
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.
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tools/src/tests/CMakeFiles/unit_test_floatingpointcomparison.dir/build
cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
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[ 20%] Built target unit_test_filesystem
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/Library/Developer/CommandLineTools/usr/bin/make -f
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/Library/Developer/CommandLineTools/usr/bin/make -f
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cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
cmake_depends "Unix Makefiles" /Users/glenntsai/votca
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cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
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[ 26%] Built target unit_test_graph_base
/Library/Developer/CommandLineTools/usr/bin/make -f
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cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
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cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
cmake_depends "Unix Makefiles" /Users/glenntsai/votca
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tools/src/tests/CMakeFiles/unit_test_optionshandler.dir/build.make
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cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
cmake_depends "Unix Makefiles" /Users/glenntsai/votca
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cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
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/Library/Developer/CommandLineTools/usr/bin/make -f
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`tools/src/tests/CMakeFiles/unit_test_identity.dir/build'.
cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
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[ 31%] Built target unit_test_identity
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`tools/src/tests/CMakeFiles/unit_test_linalg.dir/build'.
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cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
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cd /Users/glenntsai/builddir && /opt/homebrew/Cellar/cmake/3.26.3/bin/cmake -E
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/Library/Developer/CommandLineTools/usr/bin/make -f
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[ 43%] Linking CXX shared library libvotca_csg.dylib
cd /Users/glenntsai/builddir/csg/src/libcsg &&
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/opt/homebrew/lib/libboost_system-mt.dylib
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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
(base) glenntsai@GlenndeAir ~ %
