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/CAHG27e4Pu39Fepxa937WXECedaGh%3D2xD4CRayqjpieyoPiEPww%40mail.gmail.com.
