Re: [votca] ld: symbol(s) not found for architecture x86_64 on macOS Mojave 10.14.3 with GROMACS 2019.1

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Christoph Junghans

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Feb 26, 2019, 10:00:16 PM2/26/19
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On Tue, Feb 26, 2019 at 19:57 <gonzale...@licifug.ugto.mx> wrote:
Hello, 

I'm trying to install VOTCA on macOS Mojave 10.14.3 with GROMACS 2019.1 (also tried 2016) using:

cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} -DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs_d.dylib  ..


but I get this error:

...

[ 30%] Linking CXX shared library libvotca_tools.dylib

ld: warning: ignoring file /Applications/VMD 1.9.4.app/Contents/vmd/libsqlite3.dylib, file was built for i386 which is not the architecture being linked (x86_64): /Applications/VMD 1.9.4.app/Contents/vmd/libsqlite3.dylib


This error says it all, the liqsqlite3 coming with vmd is 32-bit, but need a 64-bit version!

Christoph 

Undefined symbols for architecture x86_64:

  "_sqlite3_bind_double", referenced from:

      void votca::tools::Statement::Bind<double>(int, double const&) in statement.cc.o

  "_sqlite3_bind_int", referenced from:

      void votca::tools::Statement::Bind<int>(int, int const&) in statement.cc.o

  "_sqlite3_bind_text", referenced from:

      void votca::tools::Statement::Bind<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in statement.cc.o

  "_sqlite3_close", referenced from:

      votca::tools::Database::~Database() in database.cc.o

      votca::tools::Database::Close() in database.cc.o

      votca::tools::Database::~Database() in database.cc.o

  "_sqlite3_column_double", referenced from:

      double votca::tools::Statement::Column<double>(int) in statement.cc.o

  "_sqlite3_column_int", referenced from:

      int votca::tools::Statement::Column<int>(int) in statement.cc.o

  "_sqlite3_column_text", referenced from:

      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > votca::tools::Statement::Column<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(int) in statement.cc.o

  "_sqlite3_exec", referenced from:

      votca::tools::Database::Exec(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in database.cc.o

  "_sqlite3_finalize", referenced from:

      votca::tools::Statement::~Statement() in statement.cc.o

      votca::tools::Statement::~Statement() in statement.cc.o

  "_sqlite3_last_insert_rowid", referenced from:

      votca::tools::Database::LastInsertRowId() in database.cc.o

  "_sqlite3_open_v2", referenced from:

      votca::tools::Database::Open(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int) in database.cc.o

      votca::tools::Database::OpenHelper(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in database.cc.o

  "_sqlite3_prepare_v2", referenced from:

      votca::tools::Database::Prepare(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in database.cc.o

  "_sqlite3_reset", referenced from:

      votca::tools::Statement::Reset() in statement.cc.o

  "_sqlite3_step", referenced from:

      votca::tools::Statement::Step() in statement.cc.o

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make[2]: *** [tools/src/libtools/libvotca_tools.6.dylib] Error 1

make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2

make: *** [all] Error 2

[  0%] Built target votca_tools_manpages

Current git revision is 7e20a28

[  0%] Built target gitversion

[  1%] Linking CXX shared library libvotca_tools.dylib

ld: warning: ignoring file /Applications/VMD 1.9.4.app/Contents/vmd/libsqlite3.dylib, file was built for i386 which is not the architecture being linked (x86_64): /Applications/VMD 1.9.4.app/Contents/vmd/libsqlite3.dylib

Undefined symbols for architecture x86_64:

  "_sqlite3_bind_double", referenced from:

      void votca::tools::Statement::Bind<double>(int, double const&) in statement.cc.o

  "_sqlite3_bind_int", referenced from:

      void votca::tools::Statement::Bind<int>(int, int const&) in statement.cc.o

  "_sqlite3_bind_text", referenced from:

      void votca::tools::Statement::Bind<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in statement.cc.o

  "_sqlite3_close", referenced from:

      votca::tools::Database::~Database() in database.cc.o

      votca::tools::Database::Close() in database.cc.o

      votca::tools::Database::~Database() in database.cc.o

  "_sqlite3_column_double", referenced from:

      double votca::tools::Statement::Column<double>(int) in statement.cc.o

  "_sqlite3_column_int", referenced from:

      int votca::tools::Statement::Column<int>(int) in statement.cc.o

  "_sqlite3_column_text", referenced from:

      std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > votca::tools::Statement::Column<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(int) in statement.cc.o

  "_sqlite3_exec", referenced from:

      votca::tools::Database::Exec(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in database.cc.o

  "_sqlite3_finalize", referenced from:

      votca::tools::Statement::~Statement() in statement.cc.o

      votca::tools::Statement::~Statement() in statement.cc.o

  "_sqlite3_last_insert_rowid", referenced from:

      votca::tools::Database::LastInsertRowId() in database.cc.o

  "_sqlite3_open_v2", referenced from:

      votca::tools::Database::Open(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int) in database.cc.o

      votca::tools::Database::OpenHelper(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in database.cc.o

  "_sqlite3_prepare_v2", referenced from:

      votca::tools::Database::Prepare(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in database.cc.o

  "_sqlite3_reset", referenced from:

      votca::tools::Statement::Reset() in statement.cc.o

  "_sqlite3_step", referenced from:

      votca::tools::Statement::Step() in statement.cc.o

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make[2]: *** [tools/src/libtools/libvotca_tools.6.dylib] Error 1

make[1]: *** [tools/src/libtools/CMakeFiles/votca_tools.dir/all] Error 2

make: *** [all] Error 2


Thanks,

Ramón González-Pérez

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Christoph Junghans
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Christoph Junghans

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Mar 19, 2019, 7:49:18 PM3/19/19
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On Tue, Mar 19, 2019 at 5:32 PM <gonzale...@licifug.ugto.mx> wrote:
>
> Hello,
>
> I get this output when I execute csg_inverse:
>
> running csg_inverse --options "settings.xml"
>
> ./run.sh: line 4: 42366 Terminated: 15 csg_inverse --options settings.xml
>
>
> What could be the problem?
What version of VOTCA is this?
Did you source VOTCARC?

Christoph
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Christoph Junghans

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Mar 19, 2019, 10:59:31 PM3/19/19
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On Tue, Mar 19, 2019 at 6:52 PM <gonzale...@licifug.ugto.mx> wrote:
>
> Yes, I sourced using
>
> source votca/bin/VOTCARC.bash
>
> The version is 1.6-dev.
Try to add "--debug" to csg_inverse call and post the output here.

Christoph
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Christoph Junghans

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Mar 19, 2019, 11:47:29 PM3/19/19
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Let's try to run the last command separately:
csg_call --options settings.xml function csg_get_property cg.inverse.log_file
and post the output.

Christoph

On Tue, Mar 19, 2019 at 9:05 PM <gonzale...@licifug.ugto.mx> wrote:
>
> running csg_inverse --options "settings.xml"
>
> + [[ --options = \-\-\h\e\l\p ]]
>
> + source /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/start_framework.sh
>
> ++ '[' --options = --help ']'
>
> ++ [[ -n /Users/ramongonzalezperez/VOTCA/share/votca ]]
>
> ++ [[ -d /Users/ramongonzalezperez/VOTCA/share/votca ]]
>
> ++ [[ -d /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> ++ [[ -f /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/inverse.sh ]]
>
> ++ [[ -f /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh ]]
>
> ++ source /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh
>
> +++ [[ --options = \-\-\h\e\l\p ]]
>
> +++ export BASH
>
> +++ shopt -s extglob
>
> +++ export -f msg
>
> +++ export -f show_callstack
>
> +++ unset -f die
>
> +++ export -f die
>
> +++ export -f cat_external
>
> +++ export -f do_external
>
> +++ export -f critical
>
> +++ export -f for_all
>
> +++ export -f csg_get_interaction_property
>
> +++ export -f csg_get_property
>
> +++ export -f trim_all
>
> +++ export -f mark_done
>
> +++ export -f is_done
>
> +++ export -f is_int
>
> +++ export -f to_int
>
> +++ export -f is_part
>
> +++ export -f has_duplicate
>
> +++ export -f remove_duplicate
>
> +++ export -f is_num
>
> +++ export -f get_stepname
>
> +++ export -f update_stepnames
>
> +++ export -f get_current_step_dir
>
> +++ export -f get_last_step_dir
>
> +++ export -f get_main_dir
>
> +++ export -f get_current_step_nr
>
> +++ export -f get_step_nr
>
> +++ export -f cp_from_main_dir
>
> +++ export -f cp_from_last_step
>
> +++ export -f get_time
>
> +++ export -f get_number_tasks
>
> +++ export -f get_table_comment
>
> +++ export -f csg_inverse_clean
>
> +++ export -f check_path_variable
>
> +++ export -f add_to_csgshare
>
> +++ export -f globalize_dir
>
> +++ export -f globalize_file
>
> +++ export -f source_function
>
> +++ export -f csg_banner
>
> +++ export -f csg_calc
>
> +++ export -f show_csg_tables
>
> +++ export -f get_command_from_csg_tables
>
> +++ export -f source_wrapper
>
> +++ export -f find_in_csgshare
>
> ++++ type -p mktemp
>
> +++ '[' -z /usr/bin/mktemp ']'
>
> +++ export -f enable_logging
>
> +++ export -f get_restart_file
>
> +++ export -f check_for_obsolete_xml_options
>
> +++ export -f command_not_found_handle
>
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
>
> +++ eval 'simulation_finish()' '{' command_not_found_handle 'simulation_finish;' '}'
>
> +++ eval export -f simulation_finish
>
> ++++ export -f simulation_finish
>
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
>
> +++ eval 'checkpoint_exist()' '{' command_not_found_handle 'checkpoint_exist;' '}'
>
> +++ eval export -f checkpoint_exist
>
> ++++ export -f checkpoint_exist
>
> +++ for i in simulation_finish checkpoint_exist get_simulation_setting
>
> +++ eval 'get_simulation_setting()' '{' command_not_found_handle 'get_simulation_setting;' '}'
>
> +++ eval export -f get_simulation_setting
>
> ++++ export -f get_simulation_setting
>
> +++ unset i
>
> ++ export CSG_MASTER_PID=67692
>
> ++ CSG_MASTER_PID=67692
>
> ++ export CSG_MAINDIR=/Users/ramongonzalezperez/votca/csg-tutorials/hexane/ibi_all
>
> ++ CSG_MAINDIR=/Users/ramongonzalezperez/votca/csg-tutorials/hexane/ibi_all
>
> ++ [[ -n '' ]]
>
> ++ export VOTCA_CSG_DEFAULTS=/Users/ramongonzalezperez/VOTCA/share/votca/xml/csg_defaults.xml
>
> ++ VOTCA_CSG_DEFAULTS=/Users/ramongonzalezperez/VOTCA/share/votca/xml/csg_defaults.xml
>
> ++ [[ -f /Users/ramongonzalezperez/VOTCA/share/votca/xml/csg_defaults.xml ]]
>
> ++ add_to_csgshare --at-the-end /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ local dir end=no
>
> ++ [[ --at-the-end = \-\-\a\t\-\t\h\e\-\e\n\d ]]
>
> ++ end=yes
>
> ++ shift
>
> ++ [[ -z /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> ++ for dirlist in '"$@"'
>
> ++ old_IFS='
>
> '
>
> ++ IFS=:
>
> ++ for dir in '$dirlist'
>
> ++ eval dir=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> +++ dir=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ [[ -d /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> +++ globalize_dir /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> +++ [[ -z /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> +++ [[ -d /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> +++ cd /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> +++ pwd
>
> ++ dir=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ [[ yes = \y\e\s ]]
>
> ++ export CSGSHARE=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ CSGSHARE=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ export PERL5LIB=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ PERL5LIB=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ export PYTHONPATH=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ PYTHONPATH=/Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse
>
> ++ IFS='
>
> '
>
> ++ check_path_variable CSGSHARE PERL5LIB PYTHONPATH
>
> ++ local old_IFS dir
>
> ++ [[ -z CSGSHARE ]]
>
> ++ for var in '"$@"'
>
> ++ [[ -z CSGSHARE ]]
>
> ++ old_IFS='
>
> '
>
> ++ IFS=:
>
> ++ for dir in '${!var}'
>
> ++ [[ -z /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> ++ [[ /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse = *votca* ]]
>
> ++ [[ -d /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> ++ IFS='
>
> '
>
> ++ for var in '"$@"'
>
> ++ [[ -z PERL5LIB ]]
>
> ++ old_IFS='
>
> '
>
> ++ IFS=:
>
> ++ for dir in '${!var}'
>
> ++ [[ -z /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> ++ [[ /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse = *votca* ]]
>
> ++ [[ -d /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> ++ IFS='
>
> '
>
> ++ for var in '"$@"'
>
> ++ [[ -z PYTHONPATH ]]
>
> ++ old_IFS='
>
> '
>
> ++ IFS=:
>
> ++ for dir in '${!var}'
>
> ++ [[ -z /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> ++ [[ /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse = *votca* ]]
>
> ++ [[ -d /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse ]]
>
> ++ IFS='
>
> '
>
> + do_iterations=
>
> + waittime=10
>
> + unset CSGXMLFILE CSGENDING CSGDEBUG
>
> + shopt -s extglob
>
> + [[ -options != --options ]]
>
> + [[ options = --options ]]
>
> + case $1 in
>
> + CSGXMLFILE=settings.xml
>
> + [[ -f settings.xml ]]
>
> ++ globalize_file settings.xml
>
> ++ [[ -z settings.xml ]]
>
> ++ [[ -f settings.xml ]]
>
> ++ local dir
>
> ++ [[ settings.xml = settings.xml ]]
>
> ++ dir=.
>
> +++ globalize_dir .
>
> +++ [[ -z . ]]
>
> +++ [[ -d . ]]
>
> +++ cd .
>
> +++ pwd
>
> ++ echo /Users/ramongonzalezperez/votca/csg-tutorials/hexane/ibi_all/settings.xml
>
> + export CSGXMLFILE=/Users/ramongonzalezperez/votca/csg-tutorials/hexane/ibi_all/settings.xml
>
> + CSGXMLFILE=/Users/ramongonzalezperez/votca/csg-tutorials/hexane/ibi_all/settings.xml
>
> + shift 2
>
> + [[ -debug != --debug ]]
>
> + [[ debug = --debug ]]
>
> + case $1 in
>
> + export CSGDEBUG=yes
>
> + CSGDEBUG=yes
>
> + shift
>
> + [[ '' != '' ]]
>
> + [[ -z /Users/ramongonzalezperez/votca/csg-tutorials/hexane/ibi_all/settings.xml ]]
>
> + [[ '' = \c\l\e\a\n ]]
>
> + enable_logging
>
> + local log
>
> + [[ -z '' ]]
>
> ++ csg_get_property cg.inverse.log_file
>
> ./run.sh: line 4: 67692 Terminated: 15 csg_inverse --options settings.xml --debug
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Christoph Junghans

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Mar 20, 2019, 9:47:26 AM3/20/19
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My guess is that.
> dyld: Library not loaded: @rpath/libvotca_csg.6.dylib
is the core of the problem.

Can you try to run "csg_property --help" to check if it fails, too?
Additionally, can you post the content of your VOTCARC? ("cat VOTCARC.bash")
And do a "otool -l csg_property" as well.

Christoph

On Tue, Mar 19, 2019 at 11:21 PM <gonzale...@licifug.ugto.mx> wrote:
>
> The output is a loop of this message (can't cancel using ctrl + C):
>
> dyld: Library not loaded: @rpath/libvotca_csg.6.dylib
>
> Referenced from: /Users/ramongonzalezperez/VOTCA/bin/csg_property
>
> Reason: image not found
>
> /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh: line 181: 16817 Abort trap: 6 "$@"
>
>
> Callstack:
>
> /Users/ramongonzalezperez/VOTCA/bin/csg_call - linenumber 165
>
> csg_get_property - linenumber 338 in /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh
>
> critical - linenumber 187 in /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh
>
> die - linenumber 109 in /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh
>
> ^[[31;01m######################################################################################################
>
> # #
>
> # ERROR: #
>
> # critical: 'csg_property --file settings.xml --path cg.inverse.scriptpath --short --print .' failed #
>
> # Details can be found above #
>
> # #
>
> ######################################################################################################^[[0m
>
> csg_get_property: No value for 'cg.inverse.scriptpath' found in settings.xml, trying /Users/ramongonzalezperez/VOTCA/share/votca/xml/csg_defaults.xml
>
> dyld: Library not loaded: @rpath/libvotca_csg.6.dylib
>
> Referenced from: /Users/ramongonzalezperez/VOTCA/bin/csg_property
>
> Reason: image not found
>
> /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh: line 181: 16825 Abort trap: 6 "$@"
>
>
> Callstack:
>
> /Users/ramongonzalezperez/VOTCA/bin/csg_call - linenumber 165
>
> csg_get_property - linenumber 344 in /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh
>
> critical - linenumber 187 in /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh
>
> die - linenumber 109 in /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh
>
> ^[[31;01m##########################################################################################################################################################
>
> # #
>
> # ERROR: #
>
> # critical: 'csg_property --file /Users/ramongonzalezperez/VOTCA/share/votca/xml/csg_defaults.xml --path cg.inverse.scriptpath --short --print .' failed #
>
> # Details can be found above #
>
> # #
>
> ##########################################################################################################################################################^[[0m
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Christoph Junghans

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Mar 20, 2019, 10:36:15 AM3/20/19
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That is strange, now is says:
dyld: Library not loaded: @loader_path/../lib/libgromacs_d.4.dylib
Referenced from: /Users/ramongonzalezperez/VOTCA/bin/csg_property
Reason: image not found

Before is said:
dyld: Library not loaded: @rpath/libvotca_csg.6.dylib
Referenced from: /Users/ramongonzalezperez/VOTCA/bin/csg_property
Reason: image not found

I am not 100% sure what you changed in your environment, but it seems
you hadn't sourced VOTCARC.bash before.

Anyhow, I think now you forgot to source Gromacs' GMXRC.bash, you need
to source both, VOTCARC.bash and GMXRC.bash.

Christoph


On Wed, Mar 20, 2019 at 8:14 AM <gonzale...@licifug.ugto.mx> wrote:
>
> Here's the output when I run csg_property --help:
>
> dyld: Library not loaded: @loader_path/../lib/libgromacs_d.4.dylib
>
> Referenced from: /Users/ramongonzalezperez/VOTCA/bin/csg_property
>
> Reason: image not found
>
> Abort trap: 6
>
>
> The content of my VOTCARC:
>
> #!/usr/bin/env bash
>
> #
>
> # Copyright 2009-2017 The VOTCA Development Team (http://www.votca.org)
>
> #
>
> # Licensed under the Apache License, Version 2.0 (the "License");
>
> # you may not use this file except in compliance with the License.
>
> # You may obtain a copy of the License at
>
> #
>
> # http://www.apache.org/licenses/LICENSE-2.0
>
> #
>
> # Unless required by applicable law or agreed to in writing, software
>
> # distributed under the License is distributed on an "AS IS" BASIS,
>
> # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
>
> # See the License for the specific language governing permissions and
>
> # limitations under the License.
>
> #
>
>
> #path is never empty
>
> PATH="/Users/ramongonzalezperez/VOTCA/bin:${PATH}"
>
> #debian wants to have : at the end
>
> MANPATH="/Users/ramongonzalezperez/VOTCA/share/man:${MANPATH}"
>
> DYLD_LIBRARY_PATH="/Users/ramongonzalezperez/VOTCA/lib${DYLD_LIBRARY_PATH:+:}${DYLD_LIBRARY_PATH}"
>
> PKG_CONFIG_PATH="/Users/ramongonzalezperez/VOTCA/lib/pkgconfig${PKG_CONFIG_PATH:+:}${PKG_CONFIG_PATH}"
>
>
> VOTCASHARE="/Users/ramongonzalezperez/VOTCA/share/votca"
>
>
> export PATH MANPATH DYLD_LIBRARY_PATH PKG_CONFIG_PATH VOTCASHARE
>
>
> #votca rc files
>
> for rc in "${VOTCASHARE}"/rc/*rc.bash; do
>
> [ -r "$rc" ] && . "$rc"
>
> done
>
> unset rc
>
>
> #bash completion
>
> if [ -n "$BASH_VERSION" ]; then
>
> for comp in "${VOTCASHARE}"/rc/*completion.bash; do
>
> [ -r "$comp" ] && source "$comp"
>
> done
>
> unset comp
>
> fi
>
>
> And when I do the otool:
>
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump: 'csg_property': No such file or directory
Message has been deleted

Christoph Junghans

unread,
Mar 28, 2019, 2:22:47 PM3/28/19
to vo...@googlegroups.com


On Thu, Mar 28, 2019 at 11:50 <gonzale...@licifug.ugto.mx> wrote:
Hello,

I double checked and I have been sourced both .bash correctly, I even added to my bash_profile:

source votca/bin/VOTCARC.bash
source /usr/local/gromacs/bin/GMXRC.bash

I've tried it on another computer (macOS High Sierra) and the 'csg_property --help' option works but the 'csg_inverse' command also gives:

run.sh: line 4: 96084 Terminated: 15          csg_inverse --options settings.xml


The output of 'csg_call --options settings.xml function csg_get_property cg.inverse.log_file' is also a loop message that can't be be cancel using ctrl + C and starts with:

dyld: Library not loaded: @rpath/libvotca_csg.6.dylib
.6 is the library of the development version, if you have multiple votca versions installed, you have to ensure to source the corresponding VOTCARC.

Alternatively you can also set DYLD_LIBRARY_PATH by hand to point to location of libvotca. Running csg_property itself or inside csg_inverse should make no difference.

Christoph 


This is the script I'm using to install VOTCA (I have tried v1.4.1, stable and master versions):

sudo rm -rf /usr/local/votca

prefix=/usr/local/votca

version=v1.4.1

git clone -b ${version} --recursive https://github.com/votca/votca.git

cd votca

mkdir build

cd build

cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} -DWITH_GMX=ON -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.dylib -DEIGEN3_INCLUDE_DIR=/usr/local/Cellar/eigen/3.3.5/include/eigen3 -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON ..

sudo make -j5

sudo make install

source votca/bin/VOTCARC.bash

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--
Christoph Junghans
Web: http://www.compphys.de

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