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 <[email protected]> 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
>
>
> On Tuesday, March 19, 2019 at 9:47:29 PM UTC-6, Christoph Junghans wrote:
>>
>> 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 <[email protected]> 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
>> >
>> >
>> > On Tuesday, March 19, 2019 at 8:59:31 PM UTC-6, Christoph Junghans wrote:
>> >>
>> >> On Tue, Mar 19, 2019 at 6:52 PM <[email protected]> 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
>> >> >
>> >> > On Tuesday, March 19, 2019 at 5:49:18 PM UTC-6, Christoph Junghans
>> >> > wrote:
>> >> >>
>> >> >> On Tue, Mar 19, 2019 at 5:32 PM <[email protected]> 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
>> >> >> >
>> >> >> > --
>> >> >> > 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 post to this group, send email to [email protected].
>> >> >> > Visit this group at https://groups.google.com/group/votca.
>> >> >> > For more options, visit https://groups.google.com/d/optout.
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Christoph Junghans
>> >> >> Web: http://www.compphys.de
>> >> >
>> >> > --
>> >> > 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 post to this group, send email to [email protected].
>> >> > Visit this group at https://groups.google.com/group/votca.
>> >> > For more options, visit https://groups.google.com/d/optout.
>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
>> > --
>> > 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 post to this group, send email to [email protected].
>> > Visit this group at https://groups.google.com/group/votca.
>> > For more options, visit https://groups.google.com/d/optout.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
> --
> 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 post to this group, send email to [email protected].
> Visit this group at https://groups.google.com/group/votca.
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--
Christoph Junghans
Web: http://www.compphys.de
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