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Tios user guide.
tios-config
#!irc usage: tios-config [-h] Create or modify the *tios* configuration file
tios-passwd
#!irc usage: tios-passwd [-h] Change you *tios* password
tios-ls
#!irc usage: tios-ls [-a] List simulations in the *tios* database Arguments: -a, --all List jobs for all users, not just yourself. Output: One line per job, Fields are: Job_id 6-character ID of the job, as set by tios-wrap. Title Descriptive title, as provided to tios-wrap. Timepoint Number of ps the simulation has been running for in total Username Name of the submitter as set by tios-config. Status Current status of the job. Last_update Last time the simulation data was updated.
tios-info
#!irc usage: tios-info [-h] id print information regarding a tios simulation positional arguments: id ID of tios simulation
tios-collect
#!irc usage: tios-collect [-h] [-o TRAJFILE] [-l LOGFILE] [-p PDB] [-v] [-t TIME_PERIOD] [-i INTERVAL] [-n FIRSTN] [-V] id Connect to a *tios* stream and download data positional arguments: id tios id of the job to collect data from optional arguments: -h, --help show this help message and exit -o TRAJFILE, --trajfile TRAJFILE name of trajectory file -l LOGFILE, --logfile LOGFILE name of log file -p PDB, --pdb PDB write a .pdb file to complement the trajectory -v, --verbose display info as collection progresses -t TIME_PERIOD, --time_period TIME_PERIOD time period over which to collect data (in ps or ns) -i INTERVAL, --interval INTERVAL time interval between snapshots (in ps or ns) -n FIRTSTN, --firstn FIRSTN include only these first N atoms in the trajectory file -V, --version show program's version number and exit
tios-download
#!irc usage: tios-download [-h] id Download copies of the simulation files (for Gromacs, .tpr and possibly .cpt files) positional arguments: id ID of *tios* simulation
tios-restart
#!irc usage: tios-restart ID [-p PREAMBLE] [-e EXTRA_ARGS] [-r TRATE] Connect to a stopped *tios* simulation and restart from where it left off. Arguments: ID The *tios* ID of the simulation to restart -p PREAMBLE, --preamble PREAMBLE preamble for command line (e.g. mpirun) -e EXTRA_ARGS, --extra_args EXTRA_ARGS extra arguments at end of command line (e.g. -maxh 24) -r TRATE, --trate TRATE Sampling interval in ps
tios-cp
#!irc usage: tios-cp ID [-t TITLE] Create a copy of a *tios* simulation (which may be currently running, or not), starting from the current coordinates Arguments: ID The *tios* ID of the simulation to clone from -t TITLE, --title TITLE New title for the cloned simulation (else the parent's title is used)
tios-stop
#!irc usage: tios-stop [-h] [-V] id Stop a *tios* simulation remotely positional arguments: id tios id of the job
tios-submit
Submit an MD simulation to tios.
#!irc usage: tios-submit [-h] [--title TITLE] [--selection SELECTION] [--trate TRATE] SIMCOMMAND Arguments: -t TITLE, --title TITLE descriptive title for the simulation -n FIRSTN, --firstn FIRSTN store the first N (most interesting atoms e.g. solute?) separately. Can improve receiver performance -r TRATE, --trate TRATE interval (in ps) between frames positional arguments: SIMCOMMAND The command that, by itself, would have been used to run the simulation job conventionally. Do not enclose this in quotes.
tios-config_admin
Requires administrator privileges to run. Configures the administrator account with details of the MongoDB server.
tios-add_user
Requires administrator privileges to run. Add a user account to the tios server.
#!irc usage: tios-add_user USERNAME PASSWORD
tios-remove_user
Requires administrator privileges to run. Remove a user account from the tios server.
#!irc usage: tios-remove_user USERNAME
tios-list_users
Requires administrator privileges to run. List the user accounts on the tios server.
tios-dockerhub_start
Start a local tios hub in a Docker container (required Docker installed).
#!irc usage: tios-dockerhub_start ADMIN_USERNAME ADMIN_PASSWORD
tios-dockerhub_stop
Stop a local tios hub running as a Docker container. Be aware this will delete all data!
#!irc usage: tios-dockerhub_stop
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