On Sat, Apr 4, 2020, 09:10 Christoph Junghans <[email protected]> wrote:
> 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 "$@" > > It basically cannot find your gromacs library. Like I said in an > earlier email you need to run "export > DYLD_LIBRARY_PATH=/usr/local/gromacs/lib" > before sourcing VOTCARC.bash ( For convenience you can also add this > line to your VOTCARC.bash somewhere in the top.) > And you will have to do this for every new terminal you open unless > you add these commands to your ~/.bashrc > > Alternatively you can change LD_LIBRARY_PATH to DYLD_LIBRARY_PATH in > /usr/local/gromacs/bin/GMXRC.bash and That issue got fixed in gromacs: https://gitlab.com/gromacs/gromacs/-/merge_requests/49 Christoph source GMXRC.bash before > VOTCARC.bash. As a second alternative you can install gromacs and > votca in the same prefix path. > > Also, didn't we have the exact same discussion on this mailing list a > year ago already: > https://groups.google.com/d/topic/votca/QpoDsXf56bg/discussion ? > I looked up the solution myself right there. > > Christoph > > On Sat, Apr 4, 2020 at 8:45 AM Ramon Gonzalez Perez > <[email protected]> wrote: > > > > Hello, > > > > I get a loop of this: > > > > dyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib > > Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib > > Reason: image not found > > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh: line > 181: 45909 Abort trap: 6 "$@" > > > > 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 > -- Join us on Slack: https://join.slack.com/t/votca/signup --- 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/CAHG27e4THFfrni2NeS5tW9CEzMzKHsJ%2BzOkirTVqj17Zmp2KCQ%40mail.gmail.com.
