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