Hi,
Thanks for all your help so far! I'm now trying to run the ibi_lammps
tutorial on my local cluster (Votca version 1.6.2). But it gets terminated
right away:
running csg_inverse --options "settings.xml"
run.sh: line 4: 66850 Terminated csg_inverse --options
settings.xml
I tried running the command csg_inverse with the debug option and it gave
the following output.
+ [[ hB != hxB ]]
+ XTRACE_STATE=-x
+ [[ hxB != hxB ]]
+ VERBOSE_STATE=+v
+ set +xv
+ unset XTRACE_STATE VERBOSE_STATE
+ [[ --debug = \-\-\h\e\l\p ]]
+ source
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse/start_framework.sh
++ '[' --debug = --help ']'
++ [[ -n /moto/home/cfk2120/packages/votca_build/share/votca ]]
++ [[ -d /moto/home/cfk2120/packages/votca_build/share/votca ]]
++ [[ -d
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse ]]
++ [[ -f
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse/inverse.sh
]]
++ [[ -f
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse/functions_common.sh
]]
++ source
/moto/home/cfk2120/packages/votca_build/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=55748
++ CSG_MASTER_PID=55748
++ export
CSG_MAINDIR=/moto/home/cfk2120/packages/votca/csg-tutorials/spce/ibi_lammps
++
CSG_MAINDIR=/moto/home/cfk2120/packages/votca/csg-tutorials/spce/ibi_lammps
++ [[ -n '' ]]
++ export
VOTCA_CSG_DEFAULTS=/moto/home/cfk2120/packages/votca_build/share/votca/xml/csg_defaults.xml
++
VOTCA_CSG_DEFAULTS=/moto/home/cfk2120/packages/votca_build/share/votca/xml/csg_defaults.xml
++ [[ -f
/moto/home/cfk2120/packages/votca_build/share/votca/xml/csg_defaults.xml ]]
++ add_to_csgshare --at-the-end
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
++ local dir end=no
++ [[ --at-the-end = \-\-\a\t\-\t\h\e\-\e\n\d ]]
++ end=yes
++ shift
++ [[ -z
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse ]]
++ for dirlist in '"$@"'
++ old_IFS='
'
++ IFS=:
++ for dir in '$dirlist'
++ eval
dir=/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
+++ dir=/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
++ [[ -d
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse ]]
+++ globalize_dir
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
+++ [[ -z
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse ]]
+++ [[ -d
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse ]]
+++ cd /moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
+++ pwd
++ dir=/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
++ [[ yes = \y\e\s ]]
++ export
CSGSHARE=/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
++
CSGSHARE=/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
++ export
PERL5LIB=/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse
++
PERL5LIB=/moto/home/cfk2120/packages/votca_build/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
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse ]]
++ [[ /moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse =
*votca* ]]
++ [[ -d
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse ]]
++ IFS='
'
++ for var in '"$@"'
++ [[ -z PERL5LIB ]]
++ old_IFS='
'
++ IFS=:
++ for dir in '${!var}'
++ [[ -z
/moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse ]]
++ [[ /moto/home/cfk2120/packages/votca_build/share/votca/scripts/inverse =
*votca* ]]
++ [[ -d
/moto/home/cfk2120/packages/votca_build/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
/moto/home/cfk2120/packages/votca/csg-tutorials/spce/ibi_lammps/settings.xml
+ export
CSGXMLFILE=/moto/home/cfk2120/packages/votca/csg-tutorials/spce/ibi_lammps/settings.xml
+
CSGXMLFILE=/moto/home/cfk2120/packages/votca/csg-tutorials/spce/ibi_lammps/settings.xml
+ shift 2
+ [[ '' != '' ]]
+ [[ -z
/moto/home/cfk2120/packages/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
On Wednesday, September 2, 2020 at 1:04:10 PM UTC-4 Christoph Junghans
wrote:
> On Wed, Sep 2, 2020 at 10:53 AM Clement Koh <[email protected]> wrote:
> >
> > Hi,
> >
> > I tried it on one thread (--nt 1) and it gave me the same error.
> Can you open an issue on GitHub: https://github.com/votca/csg/issues/new
>
> Christoph
> >
> > On Wednesday, September 2, 2020 at 8:44:03 AM UTC-4 Christoph Junghans
> wrote:
> >>
> >>
> >>
> >> On Tue, Sep 1, 2020, 22:18 Clement Koh <[email protected]> wrote:
> >>>
> >>> If I just run the csg_stat on its own I get the following error:
> >>>
> >>> begin to calculate distribution functions
> >>> # of bonded interactions: 0
> >>> # of non-bonded interactions: 1
> >>> an error occurred:
> >>> input format not supported: spce.data
> >>
> >> The data reader is built-in and cannot be disabled, so this is a bit
> strange.
> >>
> >> Can you run it on one thread (--nt 1)?
> >>
> >> Christoph
> >>>
> >>>
> >>> On Wednesday, September 2, 2020 at 12:17:01 AM UTC-4 Clement Koh wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> I ran the ibi_lammps tutorial and this error occurred and I'm not
> sure what is causing it. Can someone help please?
> >>>>
> >>>> For a more verbose log see: inverse.log
> >>>> We are doing Method: ibi
> >>>> Prepare (dir step_000)
> >>>> Using initial guess from dist CG-CG.dist.tgt for CG-CG
> >>>> ######################################################
> >>>> # WARNING using this simulator is still experimental #
> >>>> # If you find a problem report it under: #
> >>>> # https://github.com/votca/csg #
> >>>> ######################################################
> >>>> step 0 done
> >>>> Doing iteration 1 (dir step_001)
> >>>> Simulation with lammps
> >>>> Make update for ibi
> >>>> Calculating rdfs with csg_stat using 12 tasks
> >>>>
> ################################################################################################################################################################
> >>>> # #
> >>>> # ERROR: #
> >>>> # critical: 'csg_stat --nt 12 --options
> /home/cfk2120/Desktop/lammps/ibi_lammps/settings.xml --top spce.data --trj
> traj.dump --begin 0 --first-frame 0' failed #
> >>>> # For details see the logfile
> /home/cfk2120/Desktop/lammps/ibi_lammps/inverse.log #
> >>>> # #
> >>>>
> ################################################################################################################################################################
> >>>>
> >>>> I can provide the verbose log from inverse.log if necessary!
> >>>>
> >>>> Best,
> >>>> Clement
> >>>
> >>> --
> >>> Join us on Slack: https://join.slack.com/t/votca/signup
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> .
> >
> > --
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> .
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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