toil.batchSystems.lsfHelper

Attributes

LSB_PARAMS_FILENAME
LSF_CONF_FILENAME
LSF_CONF_ENV
DEFAULT_LSF_UNITS
DEFAULT_RESOURCE_UNITS
LSF_JSON_OUTPUT_MIN_VERSION
logger

Functions

find(basedir, string)	walk basedir and return all files matching string
find_first_match(basedir, string)	return the first file that matches string starting from basedir
get_conf_file(filename, env)
apply_conf_file(fn, conf_filename)
per_core_reserve_from_stream(stream)
get_lsf_units_from_stream(stream)
tokenize_conf_stream(conf_handle)	convert the key=val pairs in a LSF config stream to tuples of tokens
apply_bparams(fn)	apply fn to each line of bparams, returning the result
apply_lsadmin(fn)	apply fn to each line of lsadmin, returning the result
get_lsf_units([resource])	check if we can find LSF_UNITS_FOR_LIMITS in lsadmin and lsf.conf
parse_mem_and_cmd_from_output(output)	Use regex to find "MAX MEM" and "Command" inside of an output.
get_lsf_version()	Get current LSF version
check_lsf_json_output_supported()	Check if the current LSF system supports bjobs json output.
parse_memory(mem)	Parse memory parameter.
per_core_reservation()	returns True if the cluster is configured for reservations to be per core,

Module Contents

toil.batchSystems.lsfHelper.LSB_PARAMS_FILENAME = 'lsb.params'

toil.batchSystems.lsfHelper.LSF_CONF_FILENAME = 'lsf.conf'

toil.batchSystems.lsfHelper.LSF_CONF_ENV = ['LSF_CONFDIR', 'LSF_ENVDIR']

toil.batchSystems.lsfHelper.DEFAULT_LSF_UNITS = 'KB'

toil.batchSystems.lsfHelper.DEFAULT_RESOURCE_UNITS = 'MB'

toil.batchSystems.lsfHelper.LSF_JSON_OUTPUT_MIN_VERSION = '10.1.0.2'

toil.batchSystems.lsfHelper.logger

toil.batchSystems.lsfHelper.find(basedir, string)

walk basedir and return all files matching string

toil.batchSystems.lsfHelper.find_first_match(basedir, string)

return the first file that matches string starting from basedir

toil.batchSystems.lsfHelper.get_conf_file(filename, env)

toil.batchSystems.lsfHelper.apply_conf_file(fn, conf_filename)

toil.batchSystems.lsfHelper.per_core_reserve_from_stream(stream)

toil.batchSystems.lsfHelper.get_lsf_units_from_stream(stream)

toil.batchSystems.lsfHelper.tokenize_conf_stream(conf_handle)

convert the key=val pairs in a LSF config stream to tuples of tokens

toil.batchSystems.lsfHelper.apply_bparams(fn)

apply fn to each line of bparams, returning the result

toil.batchSystems.lsfHelper.apply_lsadmin(fn)

apply fn to each line of lsadmin, returning the result

toil.batchSystems.lsfHelper.get_lsf_units(resource=False)

check if we can find LSF_UNITS_FOR_LIMITS in lsadmin and lsf.conf files, preferring the value in bparams, then lsadmin, then the lsf.conf file

Parameters:

resource (bool)

Return type:

str

toil.batchSystems.lsfHelper.parse_mem_and_cmd_from_output(output)

Use regex to find “MAX MEM” and “Command” inside of an output.

Parameters:

output (str)

toil.batchSystems.lsfHelper.get_lsf_version()

Get current LSF version

toil.batchSystems.lsfHelper.check_lsf_json_output_supported()

Check if the current LSF system supports bjobs json output.

toil.batchSystems.lsfHelper.parse_memory(mem)

Parse memory parameter.

Parameters:

mem (float)

Return type:

str

toil.batchSystems.lsfHelper.per_core_reservation()

returns True if the cluster is configured for reservations to be per core, False if it is per job