Debugging IBI for simulation
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Satyen Dhamankar
Aug 9, 2021, 4:59:59 PM8/9/21
to votca
Hello,
I am running an IBI simulation for a CG bead in water. I have run csg_stat and csg_map on it without errors. I have a CG bead with residue name PNM and atom name COM.
I am trying to run csg_inverse on the distribution files generated using the above commands.
I ran:
csg_inverse --debug --options settings.xml > stderr.txt 2>&1
The stderr.txt file is attached to this message, and so is the settings.xml file.
Could anyone explain to me how to read the debug message over here? I do not where the error is located...
I would appreciate any advice you have for me.
The stderr.txt file is:
I am running an IBI simulation for a CG bead in water. I have run csg_stat and csg_map on it without errors. I have a CG bead with residue name PNM and atom name COM.
I am trying to run csg_inverse on the distribution files generated using the above commands.
I ran:
csg_inverse --debug --options settings.xml > stderr.txt 2>&1
The stderr.txt file is attached to this message, and so is the settings.xml file.
Could anyone explain to me how to read the debug message over here? I do not where the error is located...
I would appreciate any advice you have for me.
The stderr.txt file is:
+ [[ --debug = \-\-\h\e\l\p ]]
+ source /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/start_framework.sh
++ '[' --debug = --help ']'
++ [[ -n /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca ]]
++ [[ -d /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca ]]
++ [[ -d /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse ]]
++ [[ -f /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/inverse.sh ]]
++ [[ -f /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/functions_common.sh ]]
++ source /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/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=9540
++ CSG_MASTER_PID=9540
++ export CSG_MAINDIR=/tigress/satyend/pnipam_tigergpu/PNIPAM_SIMS/UNIQUE_INITIAL_CONFIG/1NIPAM/330K/CG/OneBead/ibi
++ CSG_MAINDIR=/tigress/satyend/pnipam_tigergpu/PNIPAM_SIMS/UNIQUE_INITIAL_CONFIG/1NIPAM/330K/CG/OneBead/ibi
+++ type -p csg_property
++ [[ -n /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/bin/csg_property ]]
++ csg_property --help
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.7) thread 0:
#000: H5T.c line 1708 in H5Tcopy(): not a datatype or dataset
major: Invalid arguments to routine
minor: Inappropriate type
++ [[ -n '' ]]
++ export VOTCA_CSG_DEFAULTS=/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/xml/csg_defaults.xml
++ VOTCA_CSG_DEFAULTS=/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/xml/csg_defaults.xml
++ [[ -f /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/xml/csg_defaults.xml ]]
++ add_to_csgshare --at-the-end /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
++ local dir end=no
++ [[ --at-the-end = \-\-\a\t\-\t\h\e\-\e\n\d ]]
++ end=yes
++ shift
++ [[ -z /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse ]]
++ for dirlist in '"$@"'
++ old_IFS='
'
++ IFS=:
++ for dir in '$dirlist'
++ eval dir=/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
+++ dir=/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
++ [[ -d /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse ]]
+++ globalize_dir /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
+++ [[ -z /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse ]]
+++ [[ -d /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse ]]
+++ cd /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
+++ pwd
++ dir=/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
++ [[ yes = \y\e\s ]]
++ export CSGSHARE=/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
++ CSGSHARE=/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
++ export PERL5LIB=/opt/rh/devtoolset-7/root//usr/lib64/perl5/vendor_perl:/opt/rh/devtoolset-7/root/usr/lib/perl5:/opt/rh/devtoolset-7/root//usr/share/perl5/vendor_perl:/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
++ PERL5LIB=/opt/rh/devtoolset-7/root//usr/lib64/perl5/vendor_perl:/opt/rh/devtoolset-7/root/usr/lib/perl5:/opt/rh/devtoolset-7/root//usr/share/perl5/vendor_perl:/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/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 /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse ]]
++ [[ /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse = *votca* ]]
++ [[ -d /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse ]]
++ IFS='
'
++ for var in '"$@"'
++ [[ -z PERL5LIB ]]
++ old_IFS='
'
++ IFS=:
++ for dir in '${!var}'
++ [[ -z /opt/rh/devtoolset-7/root//usr/lib64/perl5/vendor_perl ]]
++ [[ /opt/rh/devtoolset-7/root//usr/lib64/perl5/vendor_perl = *votca* ]]
++ continue
++ for dir in '${!var}'
++ [[ -z /opt/rh/devtoolset-7/root/usr/lib/perl5 ]]
++ [[ /opt/rh/devtoolset-7/root/usr/lib/perl5 = *votca* ]]
++ continue
++ for dir in '${!var}'
++ [[ -z /opt/rh/devtoolset-7/root//usr/share/perl5/vendor_perl ]]
++ [[ /opt/rh/devtoolset-7/root//usr/share/perl5/vendor_perl = *votca* ]]
++ continue
++ for dir in '${!var}'
++ [[ -z /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse ]]
++ [[ /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse = *votca* ]]
++ [[ -d /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/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 /tigress/satyend/pnipam_tigergpu/PNIPAM_SIMS/UNIQUE_INITIAL_CONFIG/1NIPAM/330K/CG/OneBead/ibi/settings.xml
+ export CSGXMLFILE=/tigress/satyend/pnipam_tigergpu/PNIPAM_SIMS/UNIQUE_INITIAL_CONFIG/1NIPAM/330K/CG/OneBead/ibi/settings.xml
+ CSGXMLFILE=/tigress/satyend/pnipam_tigergpu/PNIPAM_SIMS/UNIQUE_INITIAL_CONFIG/1NIPAM/330K/CG/OneBead/ibi/settings.xml
+ shift 2
+ [[ '' != '' ]]
+ [[ -z /tigress/satyend/pnipam_tigergpu/PNIPAM_SIMS/UNIQUE_INITIAL_CONFIG/1NIPAM/330K/CG/OneBead/ibi/settings.xml ]]
+ [[ '' = \c\l\e\a\n ]]
+ enable_logging
+ local log
+ [[ -z '' ]]
++ csg_get_property cg.inverse.log_file
Christoph Junghans
Aug 9, 2021, 5:12:19 PM8/9/21
to vo...@googlegroups.com
On Mon, Aug 9, 2021 at 15:00 Satyen Dhamankar <saty...@gmail.com> wrote:
Hello,
I am running an IBI simulation for a CG bead in water. I have run csg_stat and csg_map on it without errors. I have a CG bead with residue name PNM and atom name COM.
I am trying to run csg_inverse on the distribution files generated using the above commands.
I ran:
csg_inverse --debug --options settings.xml > stderr.txt 2>&1
The stderr.txt file is attached to this message, and so is the settings.xml file.
Could anyone explain to me how to read the debug message over here? I do not where the error is located...
the debug option is really more a developer option and kind of a last resort if everything else fails.
I would start with looking at the inverse.log file first that has tons of information already.
What is the error message that you see when running csg_inverse without debug?
Christoph
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Satyen Dhamankar
Aug 9, 2021, 5:19:46 PM8/9/21
to votca
Thank you for your response, Christoph.
I ran csg_inverse without --debug, and I dont see an inverse.log file actually...
This is a copy of my settings.xml file:
<cg>
<non-bonded>
<name>COM-WT</name>
<!-- types of molecules involved in this interaction -->
<type1>COM</type1>
<type2>WT</type2>
<!-- dimensions + grid spacing of tables for calculations -->
<min>0</min>
<max>1.4</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf) -->
<target>COM-WT.dist.tgt</target>
<!-- update cycles -->
<do_potential>1</do_potential>
<!-- additional post processing of dU before added to potential -->
<post_update>scale smooth</post_update>
<post_update_options>
<scale>1</scale> <!-- scale the potentials before updating it -->
<smooth>
<iterations>2</iterations>
</smooth>
</post_update_options>
<post_add></post_add>
<gromacs>
<table>table_COM_WT.xvg<table>
</gromacs>
</inverse>
</non-bonded>
<non-bonded>
<name>WT-WT</name>
<type1>WT</type1>
<type2>WT</type2>
<min>0</min>
<max>1.4</max>
<step>0.01</step>
<inverse>
<target>WT-WT.dist.tgt</target>
<do_potential>1</do_potential>
<post_update>scale smooth</post_update>
<post_update_options>
<scale>1</scale>
<smooth>
<iterations>2</iterations>
</smooth>
</post_update_options>
<post_add></post_add>
<gromacs>
<table>table_WT_WT.xvg</table>
</gromacs>
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<kBT>2.7437883000</kBT>
<initial_configuration>maindir</initial_configuration>
<!-- use gromacs as the simulation program -->
<program>gromacs</program>
<gromacs>
<!-- trash so many frames at the beginning -->
<equi_time>500</equi_time>
<table_bins>0.002</table_bins>
<pot_max>1000000</pot_max>
<table_end>5.0</table_end>
<mdrun>
<opts>-nt 8</opts>
</mdrun>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top index.ndx table.xvg</filelist>
<!-- do so many iterations -->
<iterations_max>5</iterations_max>
<cleanlist>traj.xtc</cleanlist>
<method>ibi</method>
<log_file>inverse.log</log_file>
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>
Christoph Junghans
Aug 9, 2021, 5:43:27 PM8/9/21
to vo...@googlegroups.com
On Mon, Aug 9, 2021 at 3:19 PM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> Thank you for your response, Christoph.
>
> I ran csg_inverse without --debug, and I dont see an inverse.log file actually...
> This is a copy of my settings.xml file:
I would run "xmlwf settings.xml" to check for syntax errors in the xml file.
>
> Thank you for your response, Christoph.
>
> I ran csg_inverse without --debug, and I dont see an inverse.log file actually...
> This is a copy of my settings.xml file:
Another thing to try is to run "csg_property --help" and see if that
gives an error.
Christoph
Satyen Dhamankar
Aug 13, 2021, 3:24:07 PM8/13/21
to votca
Thanks Christoph, your advice helped run IBI!
Christoph Junghans
Aug 13, 2021, 3:41:10 PM8/13/21
to vo...@googlegroups.com
On Fri, Aug 13, 2021 at 13:24 Satyen Dhamankar <saty...@gmail.com> wrote:
Thanks Christoph, your advice helped run IBI!
what was the problem?
Christoph
To view this discussion on the web visit https://groups.google.com/d/msgid/votca/7f12a224-a719-424b-aeed-ab3c2d1d167an%40googlegroups.com.
Satyen Dhamankar
Aug 19, 2021, 9:26:49 PM8/19/21
to votca
Sorry for the late reply.
It was a combination of incorrectly assigned distribution functions while using csg_boltzmann!
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