On Thu, Aug 23, 2018, 00:50 <[email protected]> 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]. > 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. > -- 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.
