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.
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
>>
>
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