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/CAHG27e451L3gj%3DcmVKkUH44kVaeMpG%2BMNNHwVrzkDxGi1BMjuQ%40mail.gmail.com.
