On Mon, Aug 9, 2021 at 15:00 Satyen Dhamankar <[email protected]> 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
>
>
> 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
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
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> <https://groups.google.com/d/msgid/votca/6c50dbb4-7aa1-43bc-b2e3-88abed5649b5n%40googlegroups.com?utm_medium=email&utm_source=footer>
> .
>
--
Christoph Junghans
Web: http://www.compphys.de
--
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