On Thu, Aug 23, 2018 at 2:39 PM <ifh...@gmail.com> wrote:
>
> 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.
Well the error was:
csg_property: error while loading shared libraries: libvotca_csg.so.5:
cannot open shared object file: No such file or directory
which means the directory which contains libvotca_csg.so.5 isn't in
your LD_LIBRARY_PATH and sourcing VOTCARC.bash should actually do
that!
Can you check your VOTCARC.bash and the value of LD_LIBRARY_PATH
before and after sourcing it?
Christoph
>
> Martin
>
> Am Donnerstag, 23. August 2018 14:49:53 UTC+2 schrieb Christoph Junghans:
>>
>>
>>
>> On Thu, Aug 23, 2018, 00:50 <ifh...@gmail.com> 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 ifh...@gmail.com:
>>>>
>>>> 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 <ifh...@gmail.com> 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 <ifh...@gmail.com> 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 <ifh...@gmail.com> 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 <ifh...@gmail.com> 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 votca+un...@googlegroups.com.
>>>>> >> >>>> > To post to this group, send email to vo...@googlegroups.com.
>>>>> >> >>>>
>>>>> >> >>>> > 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 votca+un...@googlegroups.com.
>>>>> >> >>> To post to this group, send email to vo...@googlegroups.com.
>>>>> >> >>> 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 votca+un...@googlegroups.com.
>>>>> >> > To post to this group, send email to vo...@googlegroups.com.
>>>>> >> > 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 votca+un...@googlegroups.com.
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>>>>> > For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Christoph Junghans
>>>>> Web: http://www.compphys.de
>>>
>>> --
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>
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