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] <javascript:>>
> 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] <javascript:>.
> > To post to this group, send email to [email protected]
> <javascript:>.
> > 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
>
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