soprano.hpc.submitter.castep

Definition of CastepSubmitter class.

A basic “rolling” submitter for Castep calculations, grabbing from one folder and depositing results in another.

Classes

CastepSubmitter(name, queue, submit_script)

Initialize the Submitter object

class soprano.hpc.submitter.castep.CastepSubmitter(name, queue, submit_script, max_jobs=4, check_time=10, max_time=3600, temp_folder=None, remote_workdir=None, remote_getfiles=['*.*'], ssh_timeout=1.0, continuation=False)

Bases: Submitter

Initialize the Submitter object

Args:

name (str): name to be used for this Submitter (two Submitters

with the same name can’t be launched in the same

working directory)

queue (QueueInterface): object describing the properties of the

interface to the queue system in use

submit_script (str): text of the script to use when submitting a

job to the queue. All tags of the form <name>

will be replaced with the job’s name, and all

similar tags of the form <[arg]> will be

replaced if the argument name is present in

the job’s args dictionary

max_jobs (Optional[int]): maximum number of jobs to submit at a

given time. Default is 4

check_time (Optional[float]): time in seconds between consecutive

checks for the queue status and

attempts to submit new jobs. Default

is 10

max_time (Optional[float]): time in seconds the Submitter will run

for before shutting down. If set to

zero the thread won’t stop until

killed with Submitter.stop.

temp_folder (Optional[str]): where to store the temporary folders

for the calculations. By default it’s

the current folder.

remote_workdir (Optional[str]): if present, uses a directory on a

remote machine by logging in via

SSH. Must be in the format

<host>:<path/to/directory>.

Host must be defined in the user’s

~/.ssh/config file - check the

docs for RemoteTarget for more

information. It is possible to

omit the colon and directory, that

will use the home directory of the

given folder; that is HEAVILY

DISCOURAGED though. Best practice

would be to create an empty

directory on the remote machine

and use that, to avoid accidental

overwriting/deleting of important

files.

remote_getfiles (Optional[list(str)]): list of files to be

downloaded from the remote

copy of the job’s temporary

directory. By default, all

of them. Can be a list

using specific names,

wildcards etc. Filenames

can also use the

placeholder {name} to

signify the job name, as

well as any other element

from the arguments.

ssh_timeout (Optional[float]): connection timeout in seconds

(default is 1 second)

continuation (Optional[bool]): if True, when the Submitter is

stopped it will not terminate the

current jobs; rather, it will store

the list in a pickle file.

If the submitter is ran from the

same folder then it will “pick up

from where it left” and try

recovering those jobs, then

restart. If one wishes for

additional values to be saved and

restored, the save_state and

load_state methods need to be

defined.

_main_loop()

Main loop run as separate thread. Should not be edited when inheriting from the class

_putjob_remote(njob)

Copy the files generated for a job to a remote work directory

add_signal(command, callback)

Add a signal listener to this submitter. Unix systems only allow for up to TWO user-defined signals to be specified.

Args:

command (str): command that should be used to call this signal.

This would be used as:

python -m soprano.hpc.submitter <command> <file>

and will trigger the callback’s execution

callback (function<self> => None): method of the user defined

Submitter class to use as a callback when the

given signal is sent. Should accept and return

nothing.

check_job(job_id, name, args, folder)

Checks if given job is complete or not

finish_job(name, args, folder)

Save required output files to the output folder

finish_run()

Try removing the temporary keywords directory

load_state(loaded)

Replace attributes from loaded data in dictionary form

next_job()

Grab the next job from folder_in

remove_signal(command)

Remove a previously defined custom signal by its assigned command.

Args:

command (str): command assigned to the signal handler to remove.

save_state()

Return a dictionary containing serialisable data to be saved from one run to the next

set_parameters(folder_in, folder_out, castep_command, castep_path=None, copy_extensions=['.castep'], pspot_files=[], dryrun_test=False)

Set the parameters of the CASTEP Submitter

Args:

folder_in (str): path of the folder to extract cell files from

folder_out (str): path of the folder where the results will be

saved

castep_command (str): command used to call the CASTEP executable

on this system

castep_path (Optional[str]): folder where the CASTEP executable is

located (if not part of the system

PATH)

pspot_files (Optional[list[str]]): additional pseudopotential

files to be copied in the input

temporary folders

copy_extensions (Optional[list[str]]): extensions of output files

to copy to the output

folder (by default only

.castep file)

dryrun_test (Optional[bool]): run a dryrun test on files before

actually running the calculation.

Off by default.

setup_job(name, args, folder)

Copy files to temporary folder to prepare for execution

start_run()

Operations to perform when the daemon thread starts running

static stop(fname, subname)

Stop Submitter process from filename and name, return False if failed