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] <javascript:>> 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] <javascript:>.
> > 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
>
--
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