I did but no change. I was however able to get more from the error message loop. It refers to line 348 in the common_functions.sh all the time. I also tried to compile it on another machine that runs Linux mint 18.04 but it shows the same behavior as the Ubuntu 16.04.
Martin Am Donnerstag, 23. August 2018 14:49:53 UTC+2 schrieb Christoph Junghans: > > > > On Thu, Aug 23, 2018, 00:50 <[email protected] <javascript:>> wrote: > >> I am running Ubuntu 16.04.4 LTS >> >> The xml file is ok (no output from command) >> >> When I do either of the two csg_call commands the termiinal is stuck in a >> loop and tries to terminate a process that is not there I can only stop it >> with killall csg_call >> but I do get an error message: >> >> for the first one: >> >> >> ################################################################################################################################## >> # >> # >> # ERROR: >> # >> # critical: 'csg_property --file >> /usr/local/share/votca/xml/csg_defaults.xml --path cg.inverse.program >> --short --print .' failed # >> # Details can be found above >> # >> # >> # >> >> ################################################################################################################################## >> /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: >> kill: (11334) - No such process >> csg_property: error while loading shared libraries: libvotca_csg.so.5: >> cannot open shared object file: No such file or directory >> >> for the second one: >> >> >> ################################################################################################### >> # >> # >> # ERROR: >> # >> # critical: 'csg_property --file settings.xml --path cg.inverse.program >> --short --print .' failed # >> # Details can be found above >> # >> # >> # >> >> ################################################################################################### >> /usr/local/share/votca/scripts/inverse/functions_common.sh: line 136: >> kill: (14732) - No such process >> csg_get_property: No value for 'cg.inverse.program' found in >> settings.xml, trying /usr/local/share/votca/xml/csg_defaults.xml >> csg_property: error while loading shared libraries: libvotca_csg.so.5: >> cannot open shared object file: No such file or directory >> >> Maybe this can shed some light on the problem. >> > Try to "source VOTCARC.bash" first and rerun! > > Christoph > >> >> Greetings Martin >> >> >> >> Am Mittwoch, 22. August 2018 15:42:05 UTC+2 schrieb [email protected]: >>> >>> Ok I will do this tomorrow as I leave early today from work. >>> thank you so far for the quick replies :) >>> >>> Martin >>> >>> Am Mittwoch, 22. August 2018 15:01:28 UTC+2 schrieb Christoph Junghans: >>>> >>>> Hmm, one step closer. >>>> What Linux Distribution and what version of it are you using? >>>> >>>> Can you check that your xml file is valid, with >>>> $ xmlwf settings.xml >>>> (a good xml file should have no output) >>>> >>>> If that is the case, check what the output of: >>>> $ csg_call --options settings.xml function csg_get_property >>>> cg.inverse.log_file >>>> and >>>> $ csg_call --debug --options settings.xml function csg_get_property >>>> cg.inverse.log_file >>>> and post it. >>>> >>>> Christoph >>>> On Wed, Aug 22, 2018 at 6:42 AM <[email protected]> wrote: >>>> > >>>> > Ok this is the output: >>>> > >>>> > + [[ --debug = \-\-\h\e\l\p ]] >>>> > + source /usr/local/share/votca/scripts/inverse/start_framework.sh >>>> > ++ '[' --debug = --help ']' >>>> > ++ [[ -n /usr/local/share/votca ]] >>>> > ++ [[ -d /usr/local/share/votca ]] >>>> > ++ [[ -d /usr/local/share/votca/scripts/inverse ]] >>>> > ++ [[ -f /usr/local/share/votca/scripts/inverse/inverse.sh ]] >>>> > ++ [[ -f /usr/local/share/votca/scripts/inverse/functions_common.sh >>>> ]] >>>> > ++ source /usr/local/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 /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=7293 >>>> > ++ CSG_MASTER_PID=7293 >>>> > ++ export >>>> CSG_MAINDIR=/home/martin/votca/csg-tutorials/spce/ibi_lammps >>>> > ++ CSG_MAINDIR=/home/martin/votca/csg-tutorials/spce/ibi_lammps >>>> > ++ [[ -n '' ]] >>>> > ++ export >>>> VOTCA_CSG_DEFAULTS=/usr/local/share/votca/xml/csg_defaults.xml >>>> > ++ VOTCA_CSG_DEFAULTS=/usr/local/share/votca/xml/csg_defaults.xml >>>> > ++ [[ -f /usr/local/share/votca/xml/csg_defaults.xml ]] >>>> > ++ add_to_csgshare --at-the-end >>>> /usr/local/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/share/votca/scripts/inverse ]] >>>> > ++ for dirlist in '"$@"' >>>> > ++ old_IFS=' >>>> > ' >>>> > ++ IFS=: >>>> > ++ for dir in '$dirlist' >>>> > ++ eval dir=/usr/local/share/votca/scripts/inverse >>>> > +++ dir=/usr/local/share/votca/scripts/inverse >>>> > ++ [[ -d /usr/local/share/votca/scripts/inverse ]] >>>> > +++ globalize_dir /usr/local/share/votca/scripts/inverse >>>> > +++ [[ -z /usr/local/share/votca/scripts/inverse ]] >>>> > +++ [[ -d /usr/local/share/votca/scripts/inverse ]] >>>> > +++ cd /usr/local/share/votca/scripts/inverse >>>> > +++ pwd >>>> > ++ dir=/usr/local/share/votca/scripts/inverse >>>> > ++ [[ yes = \y\e\s ]] >>>> > ++ export CSGSHARE=/usr/local/share/votca/scripts/inverse >>>> > ++ CSGSHARE=/usr/local/share/votca/scripts/inverse >>>> > ++ export PERL5LIB=/usr/local/share/votca/scripts/inverse >>>> > ++ PERL5LIB=/usr/local/share/votca/scripts/inverse >>>> > ++ export >>>> PYTHONPATH=:/home/martin/gsd2xyz:/usr/local/share/votca/scripts/inverse >>>> > ++ >>>> PYTHONPATH=:/home/martin/gsd2xyz:/usr/local/share/votca/scripts/inverse >>>> > ++ IFS=' >>>> > ' >>>> > ++ check_path_variable CSGSHARE PERL5LIB PYTHONPATH >>>> > ++ local old_IFS dir >>>> > ++ [[ -z CSGSHARE ]] >>>> > ++ for var in '"$@"' >>>> > ++ [[ -z CSGSHARE ]] >>>> > ++ old_IFS=' >>>> > ' >>>> > ++ IFS=: >>>> > ++ for dir in '${!var}' >>>> > ++ [[ -z /usr/local/share/votca/scripts/inverse ]] >>>> > ++ [[ /usr/local/share/votca/scripts/inverse = *votca* ]] >>>> > ++ [[ -d /usr/local/share/votca/scripts/inverse ]] >>>> > ++ IFS=' >>>> > ' >>>> > ++ for var in '"$@"' >>>> > ++ [[ -z PERL5LIB ]] >>>> > ++ old_IFS=' >>>> > ' >>>> > ++ IFS=: >>>> > ++ for dir in '${!var}' >>>> > ++ [[ -z /usr/local/share/votca/scripts/inverse ]] >>>> > ++ [[ /usr/local/share/votca/scripts/inverse = *votca* ]] >>>> > ++ [[ -d /usr/local/share/votca/scripts/inverse ]] >>>> > ++ IFS=' >>>> > ' >>>> > ++ for var in '"$@"' >>>> > ++ [[ -z PYTHONPATH ]] >>>> > ++ old_IFS=' >>>> > ' >>>> > ++ IFS=: >>>> > ++ for dir in '${!var}' >>>> > ++ [[ -z '' ]] >>>> > ++ continue >>>> > ++ for dir in '${!var}' >>>> > ++ [[ -z /home/martin/gsd2xyz ]] >>>> > ++ [[ /home/martin/gsd2xyz = *votca* ]] >>>> > ++ continue >>>> > ++ for dir in '${!var}' >>>> > ++ [[ -z /usr/local/share/votca/scripts/inverse ]] >>>> > ++ [[ /usr/local/share/votca/scripts/inverse = *votca* ]] >>>> > ++ [[ -d /usr/local/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 /home/martin/votca/csg-tutorials/spce/ibi_lammps/settings.xml >>>> > + export >>>> CSGXMLFILE=/home/martin/votca/csg-tutorials/spce/ibi_lammps/settings.xml >>>> > + >>>> CSGXMLFILE=/home/martin/votca/csg-tutorials/spce/ibi_lammps/settings.xml >>>> > + shift 2 >>>> > + [[ '' != '' ]] >>>> > + [[ -z /home/martin/votca/csg-tutorials/spce/ibi_lammps/settings.xml >>>> ]] >>>> > + [[ '' = \c\l\e\a\n ]] >>>> > + enable_logging >>>> > + local log >>>> > + [[ -z '' ]] >>>> > ++ csg_get_property cg.inverse.log_file >>>> > Terminated >>>> > >>>> > >>>> > Am Mittwoch, 22. August 2018 14:32:26 UTC+2 schrieb Christoph >>>> Junghans: >>>> >> >>>> >> On Wed, Aug 22, 2018 at 5:54 AM <[email protected]> wrote: >>>> >> > >>>> >> > No it did not create an inverse.log >>>> >> Ok, try running: >>>> >> $ csg_inverse --debug --options settings.xml >>>> >> and post the output of that. >>>> >> >>>> >> Christoph >>>> >> > >>>> >> > Am Mittwoch, 22. August 2018 13:52:54 UTC+2 schrieb Christoph >>>> Junghans: >>>> >> >> >>>> >> >> >>>> >> >> >>>> >> >> On Wed, Aug 22, 2018 at 05:49 <[email protected]> wrote: >>>> >> >>> >>>> >> >>> Yes I tried that as well but then it just says: Terminated >>>> >> >> >>>> >> >> Does it have any output before that? >>>> >> >> >>>> >> >> Did it create an inverse.log? And if so what are the last couple >>>> of lines in there? >>>> >> >> >>>> >> >> Christoph >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> Am Mittwoch, 22. August 2018 13:15:41 UTC+2 schrieb Christoph >>>> Junghans: >>>> >> >>>> >>>> >> >>>> On Wed, Aug 22, 2018 at 4:59 AM <[email protected]> wrote: >>>> >> >>>> > >>>> >> >>>> > Hello, >>>> >> >>>> > I do not know why votca will not run this tutorial. I changed >>>> the settings.xml to point to the lammps executable but when I run the >>>> run.sh script: >>>> >> >>>> > running csg_inverse --options "settings.xml" >>>> >> >>>> > ./run.sh: line 4: 6983 Terminated csg_inverse >>>> --options settings.xml >>>> >> >>>> It there any output before that? Can you try to run >>>> "csg_inverse >>>> >> >>>> --options settings.xml" directly? >>>> >> >>>> >>>> >> >>>> > >>>> >> >>>> > this is what I get. I compiled the latest master version of >>>> votca with the following options sucessfully .cmake -DBUILD_CSGAPPS=ON >>>> -DBUILD_CTP=OFF -DBUILD_XTP=OFF -DWITH_SQLITE3=OFF -DWITH_GMX=OFF >>>> >> >>>> > >>>> >> >>>> > I noticed that in the settings.xml the file CG_CG.pot is >>>> mentioned but it is not in folder. >>>> >> >>>> That is correct, CG_CG.pot gets generated every iteration for >>>> IBI by VOTCA. >>>> >> >>>> >>>> >> >>>> Christoph >>>> >> >>>> > >>>> >> >>>> > Here is also the settings.xml >>>> >> >>>> > <cg> >>>> >> >>>> > <!-- example for a non-bonded interaction entry --> >>>> >> >>>> > <non-bonded> >>>> >> >>>> > <!-- name of the interaction --> >>>> >> >>>> > <name>CG-CG</name> >>>> >> >>>> > <!-- types involved in this interaction --> >>>> >> >>>> > <type1>1</type1> >>>> >> >>>> > <type2>1</type2> >>>> >> >>>> > <!-- dimension + grid spacing of tables for calculations >>>> --> >>>> >> >>>> > <min>0.0</min> >>>> >> >>>> > <max>0.9</max> >>>> >> >>>> > <step>0.01</step> >>>> >> >>>> > <inverse> >>>> >> >>>> > <!-- target distribution (rdf) --> >>>> >> >>>> > <target>CG-CG.dist.tgt</target> >>>> >> >>>> > <lammps> >>>> >> >>>> > <!-- name of the table for lammps run --> >>>> >> >>>> > <table>CG_CG.pot</table> >>>> >> >>>> > <table_begin>0.20</table_begin> >>>> >> >>>> > <table_bins>0.002</table_bins> >>>> >> >>>> > </lammps> >>>> >> >>>> > </inverse> >>>> >> >>>> > </non-bonded> >>>> >> >>>> > >>>> >> >>>> > <!-- general options for inverse script --> >>>> >> >>>> > <inverse> >>>> >> >>>> > <!-- 300*0.00831451 lammps units --> >>>> >> >>>> > <kBT>2.49435</kBT> >>>> >> >>>> > <!-- use lammps as simulation program --> >>>> >> >>>> > <program>lammps</program> >>>> >> >>>> > <!-- lammps specific options --> >>>> >> >>>> > <lammps> >>>> >> >>>> > <command>/usr/bin/lammps-daily</command> >>>> >> >>>> > <!-- lammps script to run !--> >>>> >> >>>> > <script>spce.in</script> >>>> >> >>>> > <!-- topology to be used by csg_stat !--> >>>> >> >>>> > <topol>spce.data</topol> >>>> >> >>>> > <!-- traj file created by lammps !--> >>>> >> >>>> > <traj>traj.dump</traj> >>>> >> >>>> > </lammps> >>>> >> >>>> > <initial_configuration>maindir</initial_configuration> >>>> >> >>>> > <!-- these files are copied for each new run --> >>>> >> >>>> > <filelist>spce.data spce.in</filelist> >>>> >> >>>> > <!-- do so many iterations --> >>>> >> >>>> > <iterations_max>300</iterations_max> >>>> >> >>>> > <!-- ibi: inverse biltzmann imc: inverse monte carlo --> >>>> >> >>>> > <method>ibi</method> >>>> >> >>>> > </inverse> >>>> >> >>>> > </cg> >>>> >> >>>> > >>>> >> >>>> > Any help would be great. >>>> >> >>>> > Thank you >>>> >> >>>> > >>>> >> >>>> > -- >>>> >> >>>> > 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 post to this group, send email to [email protected]. >>>> >> >>>> >>>> >> >>>> > Visit this group at https://groups.google.com/group/votca. >>>> >> >>>> > For more options, visit https://groups.google.com/d/optout. >>>> >> >>>> >>>> >> >>>> >>>> >> >>>> >>>> >> >>>> -- >>>> >> >>>> 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 post to this group, send email to [email protected]. >>>> >> >>> Visit this group at https://groups.google.com/group/votca. >>>> >> >>> For more options, visit https://groups.google.com/d/optout. >>>> >> >> >>>> >> >> -- >>>> >> >> 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 post to this group, send email to [email protected]. >>>> >> > Visit this group at https://groups.google.com/group/votca. >>>> >> > For more options, visit https://groups.google.com/d/optout. >>>> >> >>>> >> >>>> >> >>>> >> -- >>>> >> 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 post to this group, send email to [email protected]. >>>> > Visit this group at https://groups.google.com/group/votca. >>>> > For more options, visit https://groups.google.com/d/optout. >>>> >>>> >>>> >>>> -- >>>> 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 post to this group, send email to [email protected] <javascript:> >> . >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> > -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
