The issue is: > csg_get_property: No value for 'cg.inverse.scriptpath' found in settings.xml, > trying /usr/local/votca/share/votca/xml/csg_defaults.xml > Ramons-MacBook-Air:atomistic ramongonzalezperez$ csg_get_property > cg.inverse.log_filedyld: Library not loaded: > @loader_path/../lib/libgromacs.4.dylib > Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib > Reason: image not found > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 181: > 45917 Abort trap: 6 "$@"
It basically cannot find your gromacs library. Like I said in an earlier email you need to run "export DYLD_LIBRARY_PATH=/usr/local/gromacs/lib" before sourcing VOTCARC.bash ( For convenience you can also add this line to your VOTCARC.bash somewhere in the top.) And you will have to do this for every new terminal you open unless you add these commands to your ~/.bashrc Alternatively you can change LD_LIBRARY_PATH to DYLD_LIBRARY_PATH in /usr/local/gromacs/bin/GMXRC.bash and source GMXRC.bash before VOTCARC.bash. As a second alternative you can install gromacs and votca in the same prefix path. Also, didn't we have the exact same discussion on this mailing list a year ago already: https://groups.google.com/d/topic/votca/QpoDsXf56bg/discussion ? I looked up the solution myself right there. Christoph On Sat, Apr 4, 2020 at 8:45 AM Ramon Gonzalez Perez <[email protected]> wrote: > > Hello, > > I get a loop of this: > > dyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib > Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib > Reason: image not found > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 181: > 45909 Abort trap: 6 "$@" > > Callstack: > /usr/local/votca/bin/csg_call - linenumber 165 > csg_get_property - linenumber 338 in > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh > critical - linenumber 187 in > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh > die - linenumber 109 in > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh > ###################################################################################################### > # > # > # ERROR: > # > # critical: 'csg_property --file settings.xml --path cg.inverse.scriptpath > --short --print .' failed # > # Details can be found above > # > # > # > ###################################################################################################### > Terminated: 15 > csg_get_property: No value for 'cg.inverse.scriptpath' found in settings.xml, > trying /usr/local/votca/share/votca/xml/csg_defaults.xml > Ramons-MacBook-Air:atomistic ramongonzalezperez$ csg_get_property > cg.inverse.log_filedyld: Library not loaded: > @loader_path/../lib/libgromacs.4.dylib > Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib > Reason: image not found > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 181: > 45917 Abort trap: 6 "$@" > > Callstack: > /usr/local/votca/bin/csg_call - linenumber 165 > csg_get_property - linenumber 344 in > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh > critical - linenumber 187 in > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh > die - linenumber 109 in > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh > ########################################################################################################################################### > # > # > # ERROR: > # > # critical: 'csg_property --file > /usr/local/votca/share/votca/xml/csg_defaults.xml --path > cg.inverse.scriptpath --short --print .' failed # > # Details can be found above > # > # > # > ########################################################################################################################################### > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line 136: > kill: (45887) - No such process > > Ramón > > On Saturday, April 4, 2020 at 7:38:22 AM UTC-6, Christoph Junghans wrote: >> >> Try to run "csg_call --debug --options settings.xml function >> csg_get_property cg.inverse.log_file" ? And post the output here. >> >> Christoph >> >> On Fri, Apr 3, 2020 at 8:35 PM Ramon Gonzalez Perez >> <[email protected]> wrote: >> > >> > Actually, I don't know what changed but I tried it again and the output is: >> > >> > + [[ --debug = \-\-\h\e\l\p ]] >> > + source /usr/local/votca/share/votca/scripts/inverse/start_framework.sh >> > ++ '[' --debug = --help ']' >> > ++ [[ -n /usr/local/votca/share/votca ]] >> > ++ [[ -d /usr/local/votca/share/votca ]] >> > ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> > ++ [[ -f /usr/local/votca/share/votca/scripts/inverse/inverse.sh ]] >> > ++ [[ -f /usr/local/votca/share/votca/scripts/inverse/functions_common.sh >> > ]] >> > ++ source /usr/local/votca/share/votca/scripts/inverse/functions_common.sh >> > +++ [[ --debug = \-\-\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=11337 >> > ++ CSG_MASTER_PID=11337 >> > ++ export >> > CSG_MAINDIR=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all >> > ++ >> > CSG_MAINDIR=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all >> > ++ [[ -n '' ]] >> > ++ export >> > VOTCA_CSG_DEFAULTS=/usr/local/votca/share/votca/xml/csg_defaults.xml >> > ++ VOTCA_CSG_DEFAULTS=/usr/local/votca/share/votca/xml/csg_defaults.xml >> > ++ [[ -f /usr/local/votca/share/votca/xml/csg_defaults.xml ]] >> > ++ add_to_csgshare --at-the-end >> > /usr/local/votca/share/votca/scripts/inverse >> > ++ local dir end=no >> > ++ [[ --at-the-end = \-\-\a\t\-\t\h\e\-\e\n\d ]] >> > ++ end=yes >> > ++ shift >> > ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]] >> > ++ for dirlist in '"$@"' >> > ++ old_IFS=' >> > ' >> > ++ IFS=: >> > ++ for dir in '$dirlist' >> > ++ eval dir=/usr/local/votca/share/votca/scripts/inverse >> > +++ dir=/usr/local/votca/share/votca/scripts/inverse >> > ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> > +++ globalize_dir /usr/local/votca/share/votca/scripts/inverse >> > +++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]] >> > +++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> > +++ cd /usr/local/votca/share/votca/scripts/inverse >> > +++ pwd >> > ++ dir=/usr/local/votca/share/votca/scripts/inverse >> > ++ [[ yes = \y\e\s ]] >> > ++ export CSGSHARE=/usr/local/votca/share/votca/scripts/inverse >> > ++ CSGSHARE=/usr/local/votca/share/votca/scripts/inverse >> > ++ export PERL5LIB=/usr/local/votca/share/votca/scripts/inverse >> > ++ PERL5LIB=/usr/local/votca/share/votca/scripts/inverse >> > ++ IFS=' >> > ' >> > ++ check_path_variable CSGSHARE PERL5LIB >> > ++ local old_IFS dir >> > ++ [[ -z CSGSHARE ]] >> > ++ for var in '"$@"' >> > ++ [[ -z CSGSHARE ]] >> > ++ old_IFS=' >> > ' >> > ++ IFS=: >> > ++ for dir in '${!var}' >> > ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]] >> > ++ [[ /usr/local/votca/share/votca/scripts/inverse = *votca* ]] >> > ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> > ++ IFS=' >> > ' >> > ++ for var in '"$@"' >> > ++ [[ -z PERL5LIB ]] >> > ++ old_IFS=' >> > ' >> > ++ IFS=: >> > ++ for dir in '${!var}' >> > ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]] >> > ++ [[ /usr/local/votca/share/votca/scripts/inverse = *votca* ]] >> > ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> > ++ IFS=' >> > ' >> > + do_iterations= >> > + waittime=10 >> > + unset CSGXMLFILE CSGENDING CSGDEBUG >> > + shopt -s extglob >> > + [[ -debug != --debug ]] >> > + [[ debug = --debug ]] >> > + case $1 in >> > + export CSGDEBUG=yes >> > + CSGDEBUG=yes >> > + shift >> > + [[ -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/Desktop/csg-tutorials/hexane/ibi_all/settings.xml >> > + export >> > CSGXMLFILE=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml >> > + >> > CSGXMLFILE=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml >> > + shift 2 >> > + [[ '' != '' ]] >> > + [[ -z >> > /Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all/settings.xml >> > ]] >> > + [[ '' = \c\l\e\a\n ]] >> > + enable_logging >> > + local log >> > + [[ -z '' ]] >> > ++ csg_get_property cg.inverse.log_file >> > Terminated: 15 >> > >> > >> > >> > On Friday, April 3, 2020 at 8:30:16 PM UTC-6, Ramon Gonzalez Perez wrote: >> >> >> >> Yes, here's what I get if I do «ls -l»: >> >> >> >> -rw-r--r-- 1 ramongonzalezperez staff 4536 Apr 3 12:11 settings.xml >> >> >> >> Ramón >> >> >> >> On Friday, April 3, 2020 at 8:21:49 PM UTC-6, Christoph Junghans wrote: >> >>> >> >>> On Fri, Apr 3, 2020 at 7:44 PM Ramon Gonzalez Perez >> >>> <[email protected]> wrote: >> >>> > >> >>> > Yes, I meant csg_inverse. Here's the output: >> >>> > >> >>> > + [[ --debug = \-\-\h\e\l\p ]] >> >>> > + source >> >>> > /usr/local/votca/share/votca/scripts/inverse/start_framework.sh >> >>> > ++ '[' --debug = --help ']' >> >>> > ++ [[ -n /usr/local/votca/share/votca ]] >> >>> > ++ [[ -d /usr/local/votca/share/votca ]] >> >>> > ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > ++ [[ -f /usr/local/votca/share/votca/scripts/inverse/inverse.sh ]] >> >>> > ++ [[ -f >> >>> > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh ]] >> >>> > ++ source >> >>> > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh >> >>> > +++ [[ --debug = \-\-\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=65637 >> >>> > ++ CSG_MASTER_PID=65637 >> >>> > ++ export >> >>> > CSG_MAINDIR=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all >> >>> > ++ >> >>> > CSG_MAINDIR=/Users/ramongonzalezperez/Desktop/csg-tutorials/hexane/ibi_all >> >>> > ++ [[ -n '' ]] >> >>> > ++ export >> >>> > VOTCA_CSG_DEFAULTS=/usr/local/votca/share/votca/xml/csg_defaults.xml >> >>> > ++ VOTCA_CSG_DEFAULTS=/usr/local/votca/share/votca/xml/csg_defaults.xml >> >>> > ++ [[ -f /usr/local/votca/share/votca/xml/csg_defaults.xml ]] >> >>> > ++ add_to_csgshare --at-the-end >> >>> > /usr/local/votca/share/votca/scripts/inverse >> >>> > ++ local dir end=no >> >>> > ++ [[ --at-the-end = \-\-\a\t\-\t\h\e\-\e\n\d ]] >> >>> > ++ end=yes >> >>> > ++ shift >> >>> > ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > ++ for dirlist in '"$@"' >> >>> > ++ old_IFS=' >> >>> > ' >> >>> > ++ IFS=: >> >>> > ++ for dir in '$dirlist' >> >>> > ++ eval dir=/usr/local/votca/share/votca/scripts/inverse >> >>> > +++ dir=/usr/local/votca/share/votca/scripts/inverse >> >>> > ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > +++ globalize_dir /usr/local/votca/share/votca/scripts/inverse >> >>> > +++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > +++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > +++ cd /usr/local/votca/share/votca/scripts/inverse >> >>> > +++ pwd >> >>> > ++ dir=/usr/local/votca/share/votca/scripts/inverse >> >>> > ++ [[ yes = \y\e\s ]] >> >>> > ++ export CSGSHARE=/usr/local/votca/share/votca/scripts/inverse >> >>> > ++ CSGSHARE=/usr/local/votca/share/votca/scripts/inverse >> >>> > ++ export PERL5LIB=/usr/local/votca/share/votca/scripts/inverse >> >>> > ++ PERL5LIB=/usr/local/votca/share/votca/scripts/inverse >> >>> > ++ IFS=' >> >>> > ' >> >>> > ++ check_path_variable CSGSHARE PERL5LIB >> >>> > ++ local old_IFS dir >> >>> > ++ [[ -z CSGSHARE ]] >> >>> > ++ for var in '"$@"' >> >>> > ++ [[ -z CSGSHARE ]] >> >>> > ++ old_IFS=' >> >>> > ' >> >>> > ++ IFS=: >> >>> > ++ for dir in '${!var}' >> >>> > ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > ++ [[ /usr/local/votca/share/votca/scripts/inverse = *votca* ]] >> >>> > ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > ++ IFS=' >> >>> > ' >> >>> > ++ for var in '"$@"' >> >>> > ++ [[ -z PERL5LIB ]] >> >>> > ++ old_IFS=' >> >>> > ' >> >>> > ++ IFS=: >> >>> > ++ for dir in '${!var}' >> >>> > ++ [[ -z /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > ++ [[ /usr/local/votca/share/votca/scripts/inverse = *votca* ]] >> >>> > ++ [[ -d /usr/local/votca/share/votca/scripts/inverse ]] >> >>> > ++ IFS=' >> >>> > ' >> >>> > + do_iterations= >> >>> > + waittime=10 >> >>> > + unset CSGXMLFILE CSGENDING CSGDEBUG >> >>> > + shopt -s extglob >> >>> > + [[ -debug != --debug ]] >> >>> > + [[ debug = --debug ]] >> >>> > + case $1 in >> >>> > + export CSGDEBUG=yes >> >>> > + CSGDEBUG=yes >> >>> > + shift >> >>> > + [[ -options != --options ]] >> >>> > + [[ options = --options ]] >> >>> > + case $1 in >> >>> > + CSGXMLFILE= >> >>> > + [[ -f '' ]] >> >>> > + die 'options xml file '\'''\'' not found' >> >>> > + local pid pids c place >> >>> > + echo -e '\nCallstack:' >> >>> > >> >>> > Callstack: >> >>> > + show_callstack >> >>> > + local space line >> >>> > + [[ -n '' ]] >> >>> > + space= >> >>> > + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = >> >>> > *\b\a\s\h ]] >> >>> > + echo '/usr/local/votca/share/votca/scripts/inverse/inverse.sh - >> >>> > linenumber 82' >> >>> > /usr/local/votca/share/votca/scripts/inverse/inverse.sh - linenumber 82 >> >>> > + (( c=3-1 )) >> >>> > + (( c>0 )) >> >>> > + [[ main = main ]] >> >>> > + continue >> >>> > + (( c-- )) >> >>> > + (( c>0 )) >> >>> > + [[ die = main ]] >> >>> > + space+=' ' >> >>> > + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = >> >>> > *csg_call ]] >> >>> > + [[ /usr/local/votca/share/votca/scripts/inverse/inverse.sh = >> >>> > *inverse.sh ]] >> >>> > + echo ' die - linenumber 109 in >> >>> > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh' >> >>> > die - linenumber 109 in >> >>> > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh >> >>> > + (( c-- )) >> >>> > + (( c>0 )) >> >>> > + [[ '' = \-\-\e\x\t\r\a ]] >> >>> > + return 0 >> >>> > + [[ -z '' ]] >> >>> > + place='Details can be found above' >> >>> > ++ csg_banner ERROR: 'options xml file '\'''\'' not found' 'Details >> >>> > can be found above' >> >>> > ++ list=() >> >>> > ++ local i l=0 list >> >>> > ++ [[ -z ERROR: ]] >> >>> > ++ for i in '"$@"' >> >>> > ++ [[ -n ERROR: ]] >> >>> > ++ [[ -z ERROR: ]] >> >>> > ++ list[$l]=ERROR: >> >>> > ++ (( l++ )) >> >>> > ++ for i in '"$@"' >> >>> > ++ [[ -n options xml file '' not found ]] >> >>> > ++ [[ -z options xml file '' not found ]] >> >>> > ++ list[$l]='options xml file '\'''\'' not found' >> >>> > ++ (( l++ )) >> >>> > ++ for i in '"$@"' >> >>> > ++ [[ -n Details can be found above ]] >> >>> > ++ [[ -z Details can be found above ]] >> >>> > ++ list[$l]='Details can be found above' >> >>> > ++ (( l++ )) >> >>> > ++ l=1 >> >>> > ++ for i in '"${list[@]}"' >> >>> > ++ [[ 1 -lt 6 ]] >> >>> > ++ l=ERROR: >> >>> > ++ for i in '"${list[@]}"' >> >>> > ++ [[ 6 -lt 29 ]] >> >>> > ++ l='options xml file '\'''\'' not found' >> >>> > ++ for i in '"${list[@]}"' >> >>> > ++ [[ 29 -lt 26 ]] >> >>> > ++ echo '#################################' >> >>> > ++ echo '# #' >> >>> > ++ for i in '"${list[@]}"' >> >>> > ++ printf '# %-29s #\n' ERROR: >> >>> > ++ for i in '"${list[@]}"' >> >>> > ++ printf '# %-29s #\n' 'options xml file '\'''\'' not found' >> >>> > ++ for i in '"${list[@]}"' >> >>> > ++ printf '# %-29s #\n' 'Details can be found above' >> >>> > ++ echo '# #' >> >>> > ++ echo '#################################' >> >>> > + msg --color red --to-stderr '################################# >> >>> > # # >> >>> > # ERROR: # >> >>> > # options xml file '\'''\'' not found # >> >>> > # Details can be found above # >> >>> > # # >> >>> > #################################' >> >>> > + local color 'colors=blue cyan cyann green red purp' >> >>> > + [[ -z '' ]] >> >>> > + local 'blue=' >> >>> > + local 'cyan=' >> >>> > + local 'cyann=' >> >>> > + local 'green=' >> >>> > + local 'red=' >> >>> > + local 'purp=' >> >>> > + local 'off=' >> >>> > + [[ --color = \-\-\c\o\l\o\r ]] >> >>> > + [[ -z red ]] >> >>> > + is_part red 'blue cyan cyann green red purp' >> >>> > + [[ -z red ]] >> >>> > + [[ -z blue cyan cyann green red purp ]] >> >>> > + [[ blue cyan cyann green red purp = *\ \r\e\d\ * ]] >> >>> > + color='' >> >>> > + shift 2 >> >>> > + [[ --to-stderr = \-\-\t\o\-\s\t\d\e\r\r ]] >> >>> > + shift >> >>> > + [[ -z ################################# # # # ERROR: # # options xml >> >>> > file '' not found # # Details can be found above # # # >> >>> > ################################# ]] >> >>> > + [[ -n '' ]] >> >>> > + echo -e '################################# >> >>> > # # >> >>> > # ERROR: # >> >>> > # options xml file '\'''\'' not found # >> >>> > # Details can be found above # >> >>> > # # >> >>> > #################################' >> >>> > ################################# >> >>> > # # >> >>> > # ERROR: # >> >>> > # options xml file '' not found # >> >>> > # Details can be found above # >> >>> > # # >> >>> > ################################# >> >>> > + [[ -n 65637 ]] >> >>> > + pid=65637 >> >>> > + pids=65637 >> >>> > + c=0 >> >>> > + [[ 65637 -eq 65637 ]] >> >>> > + [[ -n '' ]] >> >>> > + kill 65637 >> >>> > Terminated: 15 >> >>> The error is "options xml file '' not found", between '' should be the >> >>> filename. I am really not sure why that is. >> >>> Is the settings.xml file there and readable? >> >>> >> >>> Christoph >> >>> >> >>> > >> >>> > On Friday, April 3, 2020 at 7:40:54 PM UTC-6, Christoph Junghans wrote: >> >>> >> >> >>> >> On Fri, Apr 3, 2020 at 6:49 PM Ramon Gonzalez Perez >> >>> >> <[email protected]> wrote: >> >>> >> > >> >>> >> > Hello, >> >>> >> > >> >>> >> > I'm using GROMACS 2019. >> >>> >> > >> >>> >> > I did "export >> >>> >> > DYLD_LIBRARY_PATH=/usr/local/votca/lib:/usr/local/gromacs/lib" and >> >>> >> > csg_stat and csg_map seem to work but when I run "csg_settings >> >>> >> > --options settings.xml" on the hexane/ibi_all tutorial I get: >> >>> >> Do you mean csg_inverse? Try "csg_inverse --debug --options >> >>> >> settings.xml" and post the end of the output here. >> >>> >> >> >>> >> Christoph >> >>> >> > >> >>> >> > Terminated: 15 >> >>> >> > >> >>> >> > Thanks, >> >>> >> > >> >>> >> > Ramón >> >>> >> > >> >>> >> > On Friday, April 3, 2020 at 11:36:55 AM UTC-6, Christoph Junghans >> >>> >> > wrote: >> >>> >> >> >> >>> >> >> On Fri, Apr 3, 2020 at 11:29 AM Ramon Gonzalez Perez >> >>> >> >> <[email protected]> wrote: >> >>> >> >> > >> >>> >> >> > Hello, >> >>> >> >> > >> >>> >> >> > I added -DENABLE_RPATH_INJECT=ON and moved from zsh to bash but >> >>> >> >> > got a new error when running make: >> >>> >> >> > >> >>> >> >> > error: >> >>> >> >> > no member named 'nmolblock' in 'gmx_mtop_t' >> >>> >> >> > for(int iblock=0; iblock<mtop.nmolblock; ++iblock) >> >>> >> >> > ~~~~ ^ >> >>> >> >> Yea, VOTCA-1.4* doesn't support newer versions of gromacs. What >> >>> >> >> version of gromacs are you using? >> >>> >> >> >> >>> >> >> > >> >>> >> >> > I tried the stable version and the installation seemed to work >> >>> >> >> > but when running csg_stat it says: >> >>> >> >> > >> >>> >> >> > dyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib >> >>> >> >> > Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib >> >>> >> >> > Reason: image not found >> >>> >> >> > Abort trap: 6 >> >>> >> >> Did you source VOTCARC.bash and GMXRC.bash? >> >>> >> >> >> >>> >> >> Alternatively, do "export >> >>> >> >> DYLD_LIBRARY_PATH=/usr/local/votca/lib:/usr/local/gromacs/lib" >> >>> >> >> >> >>> >> >> Christoph >> >>> >> >> >> >>> >> >> >> >>> >> >> > >> >>> >> >> > This is the procedure I'm following: >> >>> >> >> > >> >>> >> >> > sudo rm -rf /usr/local/votca >> >>> >> >> > sudo rm -rf votca >> >>> >> >> > prefix=/usr/local/votca >> >>> >> >> > version=stable >> >>> >> >> > 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_SQLITE3=OFF -DWITH_GMX=ON >> >>> >> >> > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include >> >>> >> >> > -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.4.dylib >> >>> >> >> > -DENABLE_RPATH_INJECT=ON >> >>> >> >> > -DYLD_LIBRARY_PATH=/usr/local/votca/lib/libvotca_csg.6.dylib .. >> >>> >> >> > make -j5 >> >>> >> >> > sudo make install >> >>> >> >> > source /usr/local/votca/bin/VOTCARC.bash >> >>> >> >> > >> >>> >> >> > And this is the content of the directories where the libraries >> >>> >> >> > are located: >> >>> >> >> > >> >>> >> >> > ls /usr/local/gromacs/lib/ >> >>> >> >> > libgromacs.4.0.0.dylib libgromacs.4.dylib libgromacs.dylib >> >>> >> >> > pkgconfig >> >>> >> >> > >> >>> >> >> > ls /usr/local/votca/lib/ >> >>> >> >> > cmake libvotca_csg.6.dylib libvotca_csg.dylib >> >>> >> >> > libvotca_tools.6.dylib libvotca_tools.dylib >> >>> >> >> > >> >>> >> >> > Am I missing something? >> >>> >> >> > >> >>> >> >> > Ramón >> >>> >> >> > >> >>> >> >> > On Wednesday, April 1, 2020 at 8:41:08 PM UTC-6, Christoph >> >>> >> >> > Junghans wrote: >> >>> >> >> >> >> >>> >> >> >> On Wed, Apr 1, 2020 at 2:52 PM Christoph Junghans >> >>> >> >> >> <[email protected]> wrote: >> >>> >> >> >> > >> >>> >> >> >> > On Wed, Apr 1, 2020 at 2:36 PM Ramon Gonzalez Perez >> >>> >> >> >> > <[email protected]> wrote: >> >>> >> >> >> > > >> >>> >> >> >> > > I'm also getting that file. Did the installation work, then? >> >>> >> >> >> > > >> >>> >> >> >> > > Because when I try to use csg_stat I get the following >> >>> >> >> >> > > message: >> >>> >> >> >> > > >> >>> >> >> >> > > dyld: Library not loaded: @rpath/libmkl_core.dylib >> >>> >> >> >> > > Referenced from: /usr/local/votca/bin/csg_stat >> >>> >> >> >> > You could try to adding -DENABLE_RPATH_INJECT=ON on your >> >>> >> >> >> > cmake comment. >> >>> >> >> >> > Alternatively, set the DYLD_LIBRARY_PATH variable to where >> >>> >> >> >> > your libmkl >> >>> >> >> >> > is located. >> >>> >> >> >> > >> >>> >> >> >> > > Reason: image not found >> >>> >> >> >> > > zsh: abort csg_stat >> >>> >> >> >> > Oh, you are using zsh, so the VOTCA.bash won't work for you >> >>> >> >> >> > as it is for bash. >> >>> >> >> >> > I guess, you could try "setopt NULL_GLOB" in zsh to make the >> >>> >> >> >> > bash file work. >> >>> >> >> >> Also fixed in the next release: >> >>> >> >> >> https://github.com/votca/tools/pull/220 >> >>> >> >> >> >> >>> >> >> >> Christoph >> >>> >> >> >> > >> >>> >> >> >> > Christoph >> >>> >> >> >> > > >> >>> >> >> >> > > On Wednesday, April 1, 2020 at 1:56:05 PM UTC-6, Christoph >> >>> >> >> >> > > Junghans wrote: >> >>> >> >> >> > >> >> >>> >> >> >> > >> On Wed, Apr 1, 2020 at 1:30 PM Ramon Gonzalez Perez >> >>> >> >> >> > >> <[email protected]> wrote: >> >>> >> >> >> > >> > >> >>> >> >> >> > >> > v1.4.1 through: >> >>> >> >> >> > >> > >> >>> >> >> >> > >> > 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_SQLITE3=OFF >> >>> >> >> >> > >> > -DWITH_GMX=ON >> >>> >> >> >> > >> > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include >> >>> >> >> >> > >> > -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.dylib >> >>> >> >> >> > >> > .. >> >>> >> >> >> > >> > >> >>> >> >> >> > >> > sudo make -j5 >> >>> >> >> >> > >> No sudo needed here. >> >>> >> >> >> > >> > >> >>> >> >> >> > >> > sudo make install >> >>> >> >> >> > >> I did exactly that on Linux and I get the following file: >> >>> >> >> >> > >> >> >>> >> >> >> > >> $ ls /usr/local/votca/share/votca/rc/ >> >>> >> >> >> > >> csg-completion.bash >> >>> >> >> >> > >> >> >>> >> >> >> > >> Christoph >> >>> >> >> >> > >> > >> >>> >> >> >> > >> > >> >>> >> >> >> > >> > On Wednesday, April 1, 2020 at 1:23:14 PM UTC-6, >> >>> >> >> >> > >> > Christoph Junghans wrote: >> >>> >> >> >> > >> >> >> >>> >> >> >> > >> >> On Wed, Apr 1, 2020 at 1:14 PM Ramon Gonzalez Perez >> >>> >> >> >> > >> >> <[email protected]> wrote: >> >>> >> >> >> > >> >> > >> >>> >> >> >> > >> >> > Hello, >> >>> >> >> >> > >> >> > >> >>> >> >> >> > >> >> > I installed VOTCA on macOS but when I source >> >>> >> >> >> > >> >> > /usr/local/votca/bin/VOTCARC.bash I get this error: >> >>> >> >> >> > >> >> > >> >>> >> >> >> > >> >> > /usr/local/votca/bin/VOTCARC.bash:29: no matches >> >>> >> >> >> > >> >> > found: /usr/local/votca/share/votca/rc/*rc.bash >> >>> >> >> >> > >> >> How did you install VOTCA? What version? >> >>> >> >> >> > >> >> >> >>> >> >> >> > >> >> Christoph >> >>> >> >> >> > >> >> > >> >>> >> >> >> > >> >> > Thanks, >> >>> >> >> >> > >> >> > >> >>> >> >> >> > >> >> > Ramón >> >>> >> >> >> > >> >> > >> >>> >> >> >> > >> >> > -- >> >>> >> >> >> > >> >> > 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/c19d41b6-7295-41d3-8fac-1366431f7601%40googlegroups.com. >> >>> >> >> >> > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> > >> >> >> >>> >> >> >> > >> >> -- >> >>> >> >> >> > >> >> 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 view this discussion on the web visit >> >>> >> >> >> > >> > https://groups.google.com/d/msgid/votca/10085817-cd1a-45e6-8054-8e570f7ec1ea%40googlegroups.com. >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> >> >>> >> >> >> > >> -- >> >>> >> >> >> > >> 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 view this discussion on the web visit >> >>> >> >> >> > > https://groups.google.com/d/msgid/votca/23598d8a-56eb-4a45-a796-5e95a13c469d%40googlegroups.com. >> >>> >> >> >> > >> >>> >> >> >> > >> >>> >> >> >> > >> >>> >> >> >> > -- >> >>> >> >> >> > Christoph Junghans >> >>> >> >> >> > Web: http://www.compphys.de >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> -- >> >>> >> >> >> 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 view this discussion on the web visit >> >>> >> >> > https://groups.google.com/d/msgid/votca/9fb7768d-cc06-4e3b-bf93-5c9d227c49ff%40googlegroups.com. >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> -- >> >>> >> >> 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 view this discussion on the web visit >> >>> >> > https://groups.google.com/d/msgid/votca/c80e6e02-10c2-4cb6-a871-de091895798e%40googlegroups.com. >> >>> >> >> >>> >> >> >>> >> >> >>> >> -- >> >>> >> 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 view this discussion on the web visit >> >>> > https://groups.google.com/d/msgid/votca/218b0088-3272-4c9e-ad5f-7e92942ac3e5%40googlegroups.com. >> >>> >> >>> >> >>> >> >>> -- >> >>> 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 view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/f43e6426-fe77-4745-a39a-c6f2a6924864%40googlegroups.com. >> >> >> >> -- >> 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/9390608a-d38e-4053-8cc6-051b8bf5bbe7%40googlegroups.com. -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e6dwGBx2O34CuPQmXyF58nHzZd20YM1%2BztBgzr45WkRjg%40mail.gmail.com.
