Error faced during ibi_lammps tutorial
68 views
Skip to first unread message
Clement Koh
Sep 2, 2020, 12:17:01 AM9/2/20
to votca
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: #
######################################################
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
Clement Koh
Sep 2, 2020, 12:18:30 AM9/2/20
to votca
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
Christoph Junghans
Sep 2, 2020, 8:44:03 AM9/2/20
to vo...@googlegroups.com
On Tue, Sep 1, 2020, 22:18 Clement Koh <kfjcl...@gmail.com> 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: 1an 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
--
Join us on Slack: https://join.slack.com/t/votca/signup
---
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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/5a70f328-dd87-45a3-b195-08575cbe619an%40googlegroups.com.
Clement Koh
Sep 2, 2020, 12:53:48 PM9/2/20
to votca
Hi,
I tried it on one thread (--nt 1) and it gave me the same error.
Christoph Junghans
Sep 2, 2020, 1:04:10 PM9/2/20
to vo...@googlegroups.com
On Wed, Sep 2, 2020 at 10:53 AM Clement Koh <kfjcl...@gmail.com> 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
>
> Hi,
>
> I tried it on one thread (--nt 1) and it gave me the same error.
--
Christoph Junghans
Web: http://www.compphys.de
Christoph Junghans
Sep 2, 2020, 3:59:48 PM9/2/20
to vo...@googlegroups.com
On Wed, Sep 2, 2020 at 11:03 AM Christoph Junghans <jung...@votca.org> wrote:
>
> On Wed, Sep 2, 2020 at 10:53 AM Clement Koh <kfjcl...@gmail.com> 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
https://github.com/votca/csg/issues/594, in short it was a mismatch
>
> On Wed, Sep 2, 2020 at 10:53 AM Clement Koh <kfjcl...@gmail.com> 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
between the csg and csg-tutorials version.
Christoph
Clement Koh
Sep 2, 2020, 4:59:09 PM9/2/20
to votca
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
Reply all
Reply to author
Forward
0 new messages