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 "$comp" done unset comp fi And when I do the otool: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump: 'csg_property': No such file or directory On Wednesday, March 20, 2019 at 7:47:26 AM UTC-6, Christoph Junghans wrote: > > My guess is that. > > dyld: Library not loaded: @rpath/libvotca_csg.6.dylib > is the core of the problem. > > Can you try to run "csg_property --help" to check if it fails, too? > Additionally, can you post the content of your VOTCARC? ("cat > VOTCARC.bash") > And do a "otool -l csg_property" as well. > > Christoph > > On Tue, Mar 19, 2019 at 11:21 PM <gonzale...@licifug.ugto.mx <javascript:>> > wrote: > > > > The output is a loop of this message (can't cancel using ctrl + C): > > > > dyld: Library not loaded: @rpath/libvotca_csg.6.dylib > > > > Referenced from: /Users/ramongonzalezperez/VOTCA/bin/csg_property > > > > Reason: image not found > > > > > /Users/ramongonzalezperez/VOTCA/share/votca/scripts/inverse/functions_common.sh: > > line 181: 16817 Abort trap: 6 "$@" > > > > > > 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 <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 > >> > > >> > > >> > On Tuesday, March 19, 2019 at 8:59:31 PM UTC-6, Christoph Junghans > wrote: > >> >> > >> >> 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 > >> >> > > >> >> > On Tuesday, March 19, 2019 at 5:49:18 PM UTC-6, Christoph Junghans > wrote: > >> >> >> > >> >> >> 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 > >> >> >> > > >> >> >> > -- > >> >> >> > 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 votca+un...@googlegroups.com. > >> >> >> > To post to this group, send email to vo...@googlegroups.com. > >> >> >> > 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 votca+un...@googlegroups.com. > >> >> > To post to this group, send email to vo...@googlegroups.com. > >> >> > 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 votca+un...@googlegroups.com. > >> > To post to this group, send email to vo...@googlegroups.com. > >> > 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 votca+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <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 > -- 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
