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] <javascript:>> 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] <javascript:>. > > 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/ed7fb34f-a0f8-49f7-9adf-bc59c27fcf16%40googlegroups.com.
