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opensecura/3p/lowrisc/opentitan/5aba85ae4b645f7cf3bb592dd522e88c5b659bfa/./util/dvsim/qsubopts.py
blob: c94c1c1e8055eb1c0700d276113ff0a377ee280e [file]
#!/usr/bin/env python
# Copyright lowRISC contributors.
# Licensed under the Apache License, Version 2.0, see LICENSE for details.
# SPDX-License-Identifier: Apache-2.0
# -*- coding: utf-8 -*-
# ----------------------------------
# qsubOptions Class
# ----------------------------------
"""A helper class designed to handle the managment of options and
positional arguments to qsub and related Grid Engine executables.
Contains functions to write the requested execution string either
to the command line or to a script file.
"""
import argparse
class qsubOptions():
"A data type meant to collect qsub options. See man qsub for information"
def __init__(self, optstring='', prog='qsub'):
# Which SGE command are we going to work with?
self.prog = prog
sge_program_names = [
'qsub', 'qrsh', 'qsh', 'qlogin', 'qalter', 'qresub', 'qmake'
]
assert self.prog in sge_program_names, 'Unsupported SGE command: ' + prog + \
'not one of ' + ', '.join(sge_program_names)
if prog == 'qmake' and '-pe' in optstring:
prog = 'qsub'
else:
prog = 'qrsh'
# SUPPRESS = If not specified, do not generate variable in namespace
self.parser = argparse.ArgumentParser(
description='Options to pass to qsub',
formatter_class=argparse.RawTextHelpFormatter,
argument_default=argparse.SUPPRESS,
epilog="""The following is scraped from the qsub manpage for GE \
6.2u5 dated 2009/12/01 12:24:06""")
# BEGIN SGE OPTION PARSER
# BUG if help still begins with a line with -option, have cosmetic bug where
# metavar cannot be specified correctly
yesno = ['y', 'yes', 'n', 'no']
if prog in ['qsub', 'qrsh', 'qsh', 'qlogin']:
self.parser.add_argument('-@',
metavar='optionfile',
help="""\
Forces qsub, qrsh, qsh, or qlogin to use the options contained
in optionfile. The indicated file may contain all
valid options. Comment lines must start with a "#" sign.""")
if prog in ['qsub', 'qalter']:
self.parser.add_argument('-a',
metavar='date_time',
help="""\
Available for qsub and qalter only.
Defines or redefines the time and date at which a job is eligible
for execution. Date_time conforms to [[CC]]YY]MMDDhhmm[.SS],
for the details, please see Date_time in: sge_types(1).
If this option is used with qsub or if a corresponding value is specified
in qmon then a parameter named a and the value in the format CCYYMMDDhhmm.SS
will be passed to the defined JSV instances (see -jsv option below or
find more information concerning JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-ac',
metavar='variable[=value]',
action='append',
help=""" -ac variable[=value],...
Available for qsub, qsh, qrsh, qlogin and qalter only.
Adds the given name/value pair(s) to the job's context. Value may be omitted.
Grid Engine appends the given argument to the list of context variables for the job.
Multiple -ac, -dc, and -sc options may be given. The order is important here.
The outcome of the evaluation of all -ac, -dc, and -sc options or
corresponding values in qmon is passed to defined JSV instances as parameter
with the name ac. (see -jsv option below or find more information concerning
JSV in jsv(1)) QALTER allows changing this option even while the job executes."""
)
if prog in ['qsub', 'qalter', 'qrsh', 'qsh', 'qlogin']:
self.parser.add_argument('-ar',
metavar='ar_id',
help="""\
Available for qsub, qalter, qrsh, qsh, or qlogin only.
Assigns the submitted job to be a part of an existing Advance Reservation.
The complete list of existing
Advance Reservations can be obtained using the qrstat(1) command.
Note that the -ar option adds implicitly the -w e option if not otherwise requested.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job however.
If this option or a corresponding value in qmon is specified
then this value will be passed to defined JSV instances as parameter
with the name ar. (see -jsv option below or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-A',
metavar='account_string',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Identifies the account to which the resource consumption of the
job should be charged. The account_string should
conform to the name definition in M sge_types 1 .
In the absence of this parameter Grid Engine will place the
default account string "ge" in the accounting record of the job.
Qalter allows changing this option even while the job executes.
If this option or a corresponding value in qmon is specified
then this value will be passed to defined JSV instances as parameter with the name A.
(see -jsv option below or find more information concerning JSV in jsv(1))"""
)
self.parser.add_argument('-binding',
nargs='+',
metavar=('binding_instance',
'binding_strategy'),
help="""\
-binding [ binding_instance ] binding_strategy
A job can request a specific processor core binding (processor affinity)
with this parameter. This request is neither a hard nor a soft request,
it is a hint for the execution host to do this if possible. Please note that
the requested binding strategy is not used for resource selection within
Grid Engine. As a result an execution host might be selected where Grid Engine
does not even know the hardware topology and therefore is not able
to apply the requested binding.
To enforce Grid Engine to select hardware on which the binding can be applied
please use the -l switch in combination with the complex attribute m_topology.
binding_instance is an optional parameter.
It might either be env, pe or set depending on which instance should
accomplish the job to core binding. If the value for binding_instance
is not specified then set will be used.
env means that the environment variable SGE_BINDING will be exported
to the job environment of the job. This variable contains the selected
operating system internal processor numbers. They might be more than selected
cores in presence of SMT or CMT because each core could be represented
by multiple processor identifiers. The processor numbers are space separated.
pe means that the information about the selected cores appears in
the fourth column of the pe_hostfile. Here the logical core and
socket numbers are printed (they start at 0 and have no holes)
in colon separated pairs (i.e. 0,0:1,0 which means core 0 on socket 0 and
core 0 on socket 1). For more information about the $pe_hostfile
check ge_pe(5)
set (default if nothing else is specified). The binding strategy is applied
by Grid Engine. How this is achieved depends on the underlying hardware
architecture of the execution host where the submitted job will be started.
On Solaris 10 hosts a processor set will be created where the job can
exclusively run in. Because of operating system limitations at least
one core must remain unbound. This resource could of course used by an unbound job.
On Linux hosts a processor affinity mask will be set to restrict the job
to run exclusively on the selected cores.
The operating system allows other unbound processes to use these cores.
Please note that on Linux the binding requires a Linux kernel
version of 2.6.16 or greater. It might be even possible to use a kernel with
lower version number but in that case additional kernel patches have to be
applied. The loadcheck tool in the utilbin directory can be used to check
if the hosts capabilities. You can also use the -sep in combination with
-cb of qconf(5) command to identify if Grid Engine is able to recognize the
hardware topology.
Possible values for binding_strategy are as follows:
linear:<amount>[:<socket>,<core>]
striding:<amount>:<n>[:<socket>,<core>]
explicit:[<socket>,<core>;...]<socket>,<core>
For the binding strategy linear and striding there is an optional
socket and core pair attached.
These denotes the mandatory starting point for the first core to bind on.
linear means that Grid Engine tries to bind the job on amount successive cores.
If socket and core is omitted then Grid Engine first allocates successive cores
on the first empty socket found. Empty means that there are
no jobs bound to the socket by Grid Engine. If this is not possible or is
not sufficient Grid Engine tries to
find (further) cores on the socket with the most unbound cores and so on.
If the amount of allocated cores is
lower than requested cores, no binding is done for the job.
If socket and core is specified then Grid Engine
tries to find amount of empty cores beginning with this starting point.
If this is not possible then binding is not done.
striding means that Grid Engine tries to find cores with a certain offset.
It will select amount of empty cores with a offset of n -1 cores in between.
Start point for the search algorithm is socket 0 core 0. As soon as
amount cores are found they will be used to do the job binding.
If there are not enough empty cores or if correct offset cannot be
achieved then there will be no binding done.
explicit binds the specified sockets and cores that are mentioned
in the provided socket/core list. Each socket/core pair has to
be specified only once.If a socket/core pair is already in use by a different job the
whole binding request will be ignored.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is specified then these values
will be passe to defined JSV instances as parameters with the names binding_strategy,
binding_type, binding_amount, binding_step, binding_socket,
binding_core, binding_exp_n, binding_exp_socket<id>, binding_exp_core<id>.
Please note that the length of the socket/core value list of the explicit binding is
reported as binding_exp_n.
<id> will be replaced by the position of the socket/core pair within the explicit
list (0 <= id < binding_exp_n). The first socket/core pair of the explicit
binding will be reported with the parameter names bind-
ing_exp_socket0 and binding_exp_core0.
Values that do not apply for the specified binding will not be reported to JSV.
E.g. binding_step will only be
reported for the striding binding and all binding_exp_* values will passed to
JSV if explicit binding was speci‐
fied. (see -jsv option below or find more information concerning
JSV in jsv(1))""")
if prog in ['qsub', 'qrsh']:
self.parser.add_argument('-b',
choices=yesno,
help="""\
Available for qsub, qrsh only. Qalter does not allow changing this option.
This option cannot be embedded in the script file itself.
Gives the user the possibility to indicate explicitly whether command should be
treated as binary or script. If the value of -b is 'y', then command may be a
binary or script. The command might not be accessible from the
submission host. Nothing except the path of the command will be
transferred from the submission host to the
execution host. Path aliasing will be applied to the path of command
before command will be executed.
If the value of -b is 'n' then command needs to be a script and it will
be handled as script. The script file
has to be accessible by the submission host.
It will be transferred to the execution host. qsub/qrsh will search
directive prefixes within script.
qsub will implicitly use -b n whereas qrsh will apply the -b y option
if nothing else is specified.
The value specified with this option or the corresponding value
specified in qmon will only be passed to defined
JSV instances if the value is yes. The name of the parameter will be b.
The value will be y also when then long
form yes was specified during submission.
(see -jsv option below or find more information concerning JSV in
jsv(1))
Please note that submission of command as script (-b n) can have a
significant performance impact,especially for short running jobs and big job scripts.
Script submission adds a number of operations to the submission
process: The job script needs to be
- parsed at client side (for special comments)
- transferred from submit client to qmaster
- spooled in qmaster
- transferred to execd at job execution
- spooled in execd
- removed from spooling both in execd and qmaster once the job is done
If job scripts are available on the execution nodes, e.g. via NFS, binary
submission can be the better choice.""")
if prog in ['qsub', 'qalter']:
self.parser.add_argument('-c',
metavar='occasion_specifier',
help="""\
Available for qsub and qalter only.
Defines or redefines whether the job should be checkpointed, and if so,
under what circumstances. The specifica‐
tion of the checkpointing occasions with this option overwrites the
definitions of the when parameter in the
checkpointing environment (see checkpoint(5)) referenced by the qsub
-ckpt switch. Possible values for occa‐
sion_specifier are
n no checkpoint is performed.
s checkpoint when batch server is shut down.
m checkpoint at minimum CPU interval.
x checkpoint when job gets suspended.
<interval> checkpoint in the specified time interval.
The minimum CPU interval is defined in the queue configuration (see
queue_conf(5) for details). <interval> has
to be specified in the format hh:mm:ss.
The maximum of <interval> and the queue's minimum CPU interval is used
if <interval> is specified. This is done to ensure that a machine is not
overloaded by checkpoints being generated too frequently.
The value specified with this option or the corresponding value specified
in qmon will be passed to defined JSV
instances. The <interval> will be available as parameter with the name c_interval.
The character sequence
specified will be available as parameter with the name c_occasion.
Please note that if you change c_occasion via
JSV then the last setting of c_interval will be overwritten and vice versa.
(see -jsv option below or find more
information concerning JSV in jsv(1))""")
if prog in ['qsub', 'qalter']:
self.parser.add_argument('-ckpt',
metavar='ckpt_name',
help="""\
Available for qsub and qalter only.
Selects the checkpointing environment (see checkpoint(5)) to be used
for checkpointing the job. Also declares the job to be a checkpointing job.
If this option or a corresponding value in qmon is specified then this
value will be passed to defined JSV
instances as parameter with the name ckpt. (see -jsv option below or
find more information concerning JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin']:
self.parser.add_argument('-clear',
action='store_true',
help="""\
Available for qsub, qsh, qrsh, and qlogin only.
Causes all elements of the job to be reset to the initial default
status prior to applying any modifications (if
any) appearing in this specific command.""")
if prog in ['qsub', 'qsh', 'qrsh', 'qalter']:
self.parser.add_argument('-cwd',
action='store_true',
help="""\
Available for qsub, qsh, qrsh and qalter only.
Execute the job from the current working directory.
This switch will activate Grid Engine's path aliasing
facility, if the corresponding configuration files are present (see ge_aliases(5)).
In the case of qalter, the previous definition of the current working
directory will be overwritten if qalter is
executed from a different directory than the preceding qsub or qalter.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is specified
then this value will be passed to defined JSV
instances as parameter with the name cwd. The value of this parameter
will be the absolute path to the current
working directory. JSV scripts can remove the path from jobs during the
verification process by setting the
value of this parameter to an empty string.
As a result the job behaves as if -cwd was not specified during job
submission. (see -jsv option below or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qrsh']:
self.parser.add_argument('-C',
metavar='prefix_string',
help="""\
Available for qsub and qrsh with script submission (-b n).
Prefix_string defines the prefix that declares a directive in the job's command.
The prefix is not a job
attribute, but affects the behavior of qsub and qrsh.
If prefix is a null string, the command will not be
scanned for embedded directives.
The directive prefix consists of two ASCII characters which,
when appearing in the first two bytes of a script
line, indicate that what follows is an Grid Engine command. The default is "#$".
The user should be aware that changing the first delimiting character
can produce unforeseen side effects. If
the script file contains anything other than a "#" character in the first byte
position of the line, the shell
processor for the job will reject the line and may exit the job prematurely.
If the -C option is present in the script file, it is ignored."""
)
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-dc',
action='append',
metavar='variable',
help="""\
-dc variable,...
Available for qsub, qsh, qrsh, qlogin and qalter only.
Removes the given variable(s) from the job's context. Multiple -ac, -dc, and
-sc options may be given. The order is important.
Qalter allows changing this option even while the job executes.
The outcome of the evaluation of all -ac, -dc, and -sc options or corresponding
values in qmon is passed to
defined JSV instances as parameter with the name ac. (see -jsv option below or
find more information concerning
JSV in jsv(1))""")
if prog in ['qsh', 'qrsh']:
self.parser.add_argument('-display',
metavar='display_specifier',
help="""\
Available for qsh and qrsh.
Directs xterm(1) to use display_specifier in order to contact the X server.
The display_specifier has to con‐
tain the hostname part of the display name (e.g. myhost:1).
Local display names (e.g. :0) cannot be used in
grid environments. Values set with the -display option overwrite settings
from the submission environment and
from -v command line options.
If this option or a corresponding value in qmon is specified then this
value will be passed to defined JSV
instances as parameter with the name display. This value will also be available
in the job environment which
might optionally be passed to JSV scripts. The variable name will be DISPLAY.
(see -jsv option below or find
more information concerning JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-dl',
metavar='date_time',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Specifies the deadline initiation time in [[CC]YY]MMDDhhmm[.SS] format (see -a
option above). The deadline ini‐
tiation time is the time at which a deadline job has to reach top priority to be
able to complete within a given
deadline. Before the deadline initiation time the priority of a deadline job
will be raised steadily until it
reaches the maximum as configured by the Grid Engine administrator.
This option is applicable only for users allowed to submit deadline jobs.
If this option or a corresponding value in qmon is specified then this
value will be passed to defined JSV
instances as parameter with the name dl. The format for the date_time value
is CCYYMMDDhhmm.SS (see -jsv option
below or find more information concerning JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-e',
metavar='path',
help="""\
-e [[hostname]:]path,...
Available for qsub, qsh, qrsh, qlogin and qalter only.
Defines or redefines the path used for the standard error stream of the job.
For qsh, qrsh and qlogin only the
standard error stream of prolog and epilog is redirected. If the path
constitutes an absolute path name, the
error-path attribute of the job is set to path, including the hostname.
If the path name is relative, Grid
Engine expands path either with the current working directory path
(if the -cwd switch (see above) is also spec‐
ified) or with the home directory path. If hostname is present,
the standard error stream will be placed in the
corresponding location only if the job runs on the specified host.
If the path contains a ":" without a host‐
name, a leading ":" has to be specified.
By default the file name for interactive jobs is /dev/null.
For batch jobs the default file name has the form
job_name.ejob_id and job_name.ejob_id.task_id for array job tasks (see -t option
below).
If path is a directory, the standard error stream of the job will be put
in this directory under the default
file name. If the pathname contains certain pseudo environment variables,
their value will be expanded at run‐
time of the job and will be used to constitute the standard error stream path name.
The following pseudo envi‐
ronment variables are supported currently:
$HOME home directory on execution machine
$USER user ID of job owner
$JOB_ID current job ID
$JOB_NAME current job name (see -N option)
$HOSTNAME name of the execution host
$TASK_ID array job task index number
Alternatively to $HOME the tilde sign "~" can be used as common in csh(1)
or ksh(1). Note, that the "~" sign
also works in combination with user names, so that "~<user>" expands to the
home directory of <user>. Using
another user ID than that of the job owner requires corresponding permissions,
of course.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is specified then this value
will be passed to defined JSV
instances as parameter with the name e. (see -jsv option below or
find more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-hard',
action='store_true',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Signifies that all -q and -l resource requirements following in the command
line will be hard requirements and
must be satisfied in full before a job can be scheduled.
As Grid Engine scans the command line and script file for Grid Engine options
and parameters it builds a list of
resources required by a job. All such resource requests are considered as
absolutely essential for the job to
commence. If the -soft option (see below) is encountered during the scan then
all following resources are desig‐
nated as "soft requirements" for execution, or "nice-to-have, but not essential".
If the -hard flag is encoun‐
tered at a later stage of the scan, all resource requests following it once again
become "essential". The -hard
and -soft options in effect act as "toggles" during the scan.
If this option or a corresponding value in qmon is specified then the corresponding
-q and -l resource require‐
ments will be passed to defined JSV instances as parameter with the names
q_hard and l_hard. Find for informa‐
tion in the sections describing -q and -l. (see -jsv option below or find
more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qrsh', 'qalter', 'qresub']:
# NOTE in SGE this is -h, here I have renamed it to -hold
# TODO check if multiple holds are parsed correctly
self.parser.add_argument('-hold',
choices='usonUOS',
help="""\
NOTE: Originally defined as -h, but changed to -hold here.
Available for qsub (only -h), qrsh, qalter and qresub (hold state is
removed when not set explicitly).
List of holds to place on a job, a task or some tasks of a job.
`u' denotes a user hold.
`s' denotes a system hold.
`o' denotes a operator hold.
`n' denotes no hold (requires manager privileges).
As long as any hold other than `n' is assigned to the job the job is
not eligible for execution. Holds can be
released via qalter and qrls(1). In case of qalter this is supported
by the following additional option speci‐
fiers for the -h switch:
`U' removes a user hold.
`S' removes a system hold.
`O' removes a operator hold.
Grid Engine managers can assign and remove all hold types,
Grid Engine operators can assign and remove user and
operator holds, and users can only assign or remove user holds.
In the case of qsub only user holds can be placed on a job and thus
only the first form of the option with the
-h switch alone is allowed. As opposed to this, qalter requires
the second form described above.
An alternate means to assign hold is provided by the qhold(1) facility.
If the job is a array job (see the -t option below), all tasks specified via
-t are affected by the -h operation
simultaneously.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option is specified with qsub or during the submission
of a job in qmon then the parameter h with the
value u will be passed to the defined JSV instances indicating that
the job will be in user hold after the sub‐
mission finishes. (see -jsv option below or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qrsh', 'qalter']:
self.parser.add_argument('-hold_jid',
nargs='+',
metavar='wc_job_list',
help="""\
Available for qsub, qrsh, and qalter only. See sge_types(1).
for wc_job_list definition.
Defines or redefines the job dependency list of the submitted job.
A reference by job name or pattern is only
accepted if the referenced job is owned by the same user as the referring job.
The submitted job is not eligible
for execution unless all jobs referenced in the comma-separated job id and/or
job name list have completed. If
any of the referenced jobs exits with exit code 100, the submitted
job will remain ineligible for execution.
With the help of job names or regular pattern one can specify a job
dependency on multiple jobs satisfying the
regular pattern or on all jobs with the requested name.
The name dependencies are resolved at submit time and
can only be changed via qalter. New jobs or name changes
of other jobs will not be taken into account.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is specified
then this value will be passed to defined JSV
instances as parameter with the name hold_jid.
(see -jsv option below or find more information concerning JSV
in jsv(1))""")
if prog in ['qsub', 'qrsh', 'qalter']:
self.parser.add_argument('-hold_jid_ad',
nargs='+',
metavar='wc_job_list',
help="""\
Available for qsub, qrsh, and qalter only. See sge_types(1).
for wc_job_list definition.
Defines or redefines the job array dependency list of
the submitted job. A reference by job name or pattern is
only accepted if the referenced job is owned by the same
user as the referring job. Each sub-task of the submit‐
ted job is not eligible for execution unless the corresponding
sub-tasks of all jobs referenced in the comma-
separated job id and/or job name list have completed.
If any array task of the referenced jobs exits with exit
code 100, the dependent tasks of the submitted job will remain
ineligible for execution.
With the help of job names or regular pattern one can specify
a job dependency on multiple jobs satisfying the
regular pattern or on all jobs with the requested name.
The name dependencies are resolved at submit time and
can only be changed via qalter. New jobs or name changes of other
jobs will not be taken into account.
If either the submitted job or any job in wc_job_list are
not array jobs with the same range of sub-tasks (see
-t option below), the request list will be rejected and the
job create or modify operation will error.
qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is
specified then this value will be passed to defined JSV
instances as parameter with the name hold_jid_ad.
(see -jsv option below or find more information concerning
JSV in jsv(1))""")
if prog in ['qsub', 'qalter']:
self.parser.add_argument('-i',
metavar='file',
help="""\
-i [[hostname]:]file,...
Available for qsub, and qalter only.
Defines or redefines the file used for the standard input stream of
the job. If the file constitutes an absolute
filename, the input-path attribute of the job is set to path,
including the hostname. If the path name is rela‐
tive, Grid Engine expands path either with the current working
directory path (if the -cwd switch (see above) is
also specified) or with the home directory path. If hostname is present,
the standard input stream will be
placed in the corresponding location only if the job runs
on the specified host. If the path contains a ":"
without a hostname, a leading ":" has to be specified.
By default /dev/null is the input stream for the job.
It is possible to use certain pseudo variables, whose values
will be expanded at runtime of the job and will be
used to express the standard input stream as described in
the -e option for the standard error stream.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is specified then
this value will be passed to defined JSV
instances as parameter with the name i.
(see -jsv option below or find more information concerning JSV in
jsv(1))""")
if prog in ['qrsh', 'qmake']:
self.parser.add_argument('-inherit',
action='store_true',
help="""\
Available only for qrsh and qmake(1).
qrsh allows the user to start a task in an already scheduled parallel job.
The option -inherit tells qrsh to
read a job id from the environment variable JOB_ID and start the
specified command as a task in this job. Please
note that in this case, the hostname of the host where the command
will be executed must precede the command to
execute; the syntax changes to
qrsh -inherit [ other options ] hostname command [ command_args ]
Note also, that in combination with -inherit, most other command line
options will be ignored. Only the options
-verbose, -v and -V will be interpreted. As a replacement to option
-cwd please use -v PWD.
Usually a task should have the same environment (including the
current working directory) as the corresponding
job, so specifying the option -V should be suitable for most applications.
Note: If in your system the qmaster tcp port is not configured as a service,
but rather via the environment
variable GE_QMASTER_PORT, make sure that this variable is set in the
environment when calling qrsh or qmake with
the -inherit option. If you call qrsh or qmake with the
-inherit option from within a job script, export
GE_QMASTER_PORT with the option "-v GE_QMASTER_PORT" either as
a command argument or an embedded directive.
This parameter is not available in the JSV context.
(see -jsv option below or find more information concerning
JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-j',
choices=yesno,
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Specifies whether or not the standard error stream of the job
is merged into the standard output stream.
If both the -j y and the -e options are present,
Grid Engine sets but ignores the error-path attribute.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
The value specified with this option or the corresponding
value specified in qmon will only be passed to defined
JSV instances if the value is yes. The name of the parameter will be j.
The value will be y also when then long
form yes was specified during submission.
(see -jsv option below or find more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-js',
nargs='?',
type=int,
metavar='job_share',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Defines or redefines the job share of the job relative to other jobs.
Job share is an unsigned integer value.
The default job share value for jobs is 0.
The job share influences the Share Tree Policy and the Functional Policy.
It has no effect on the Urgency and
Override Policies (see share_tree(5), sched_conf(5) and the
Grid Engine Installation and Administration Guide
for further information on the resource management policies supported
by Grid Engine).
In case of the Share Tree Policy, users can distribute the tickets to
which they are currently entitled among
their jobs using different shares assigned via -js.
If all jobs have the same job share value, the tickets are
distributed evenly. Otherwise, jobs receive tickets relative
to the different job shares. Job shares are treated
like an additional level in the share tree in the latter case.
In connection with the Functional Policy, the job share can be
used to weight jobs within the functional job
category. Tickets are distributed relative to any uneven
job share distribution treated as a virtual share dis‐
tribution level underneath the functional job category.
If both the Share Tree and the Functional Policy are active,
the job shares will have an effect in both poli‐
cies, and the tickets independently derived in each of them are
added to the total number of tickets for each
job.
If this option or a corresponding value in qmon is specified
then this value will be passed to defined JSV
instances as parameter with the name js. (see -jsv option below or
find more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin']:
self.parser.add_argument('-jsv',
metavar='jsv_url',
help="""\
Available for qsub, qsh, qrsh and qlogin only.
Defines a client JSV instance which will be executed to
verify the job specification before the job is sent to
qmaster.
In contrast to other options this switch will not be overwritten
if it is also used in sge_request files.
Instead all specified JSV instances will be executed to verify
the job to be submitted.
The JSV instance which is directly passed with the commandline
of a client is executed as first to verify the
job specification. After that the JSV instance which might have
been defined in various sge_request files will
be triggered to check the job. Find more details
in man page jsv(1) and sge_request(5).
The syntax of the jsv_url is specified in sge_types(1).()""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-l',
metavar='keywords',
help="""\
-l resource=value,...
Available for qsub, qsh, qrsh, qlogin and qalter only.
Launch the job in a Grid Engine queue meeting the given resource
request list. In case of qalter the previous
definition is replaced by the specified one.
complex(5) describes how a list of available resources and their
associated valid value specifiers can be
obtained.
There may be multiple -l switches in a single command.
You may request multiple -l options to be soft or hard
both in the same command line. In case of a serial job multiple
-l switches refine the definition for the sought
queue.
Qalter allows changing the value of this option even while the
job is running, but only if the initial list of
resources does not contain a resource that is marked as consumable.
However the modification will only be effec‐
tive after a restart or migration of the job.
If this option or a corresponding value in qmon is specified the
these hard and soft resource requirements will
be passed to defined JSV instances as parameter with the names
l_hard and l_soft. If regular expressions will be
used for resource requests, then these expressions will
be passed as they are. Also shortcut names will not be
expanded. (see -jsv option above or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
# TODO check if multiple arguments are parsed correctly
self.parser.add_argument('-m',
nargs='+',
choices='beasn',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Defines or redefines under which circumstances mail
is to be sent to the job owner or to the users defined with
the -M option described below. The option arguments
have the following meaning:
`b' Mail is sent at the beginning of the job.
`e' Mail is sent at the end of the job.
`a' Mail is sent when the job is aborted or
rescheduled.
`s' Mail is sent when the job is suspended.
`n' No mail is sent.
Currently no mail is sent when a job is suspended.
Qalter allows changing the b, e, and a option arguments
even while the job executes. The modification of the b
option argument will only be in effect after a restart
or migration of the job, however.
If this option or a corresponding value in qmon is
specified then this value will be passed to defined JSV
instances as parameter with the name m. (see -jsv option
above or find more information concerning JSV in""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-M',
metavar='user[@host]',
help="""\
-M user[@host],...
Available for qsub, qsh, qrsh, qlogin and qalter only.
Defines or redefines the list of users to which the server
that executes the job has to send mail, if the server
sends mail about the job. Default is the job owner at the originating host.
Qalter allows changing this option even while the job executes.
If this option or a corresponding value in qmon is specified then
this value will be passed to defined JSV
instances as parameter with the name M. (see -jsv option above or
find more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-masterq',
nargs='+',
metavar='wc_queue_list',
help="""\
Available for qsub, qrsh, qsh, qlogin and qalter. Only meaningful
for parallel jobs, i.e. together with the -pe option.
Defines or redefines a list of cluster queues, queue domains and
queue instances which may be used to become the
so called master queue of this parallel job. A more detailed
description of wc_queue_list can be found in
sge_types(1). The master queue is defined as the queue where
the parallel job is started. The other queues to
which the parallel job spawns tasks are called slave queues.
A parallel job only has one master queue.
This parameter has all the properties of a resource request
and will be merged with requirements derived from
the -l option described above.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is specified
the this hard resource requirement will be passed
to defined JSV instances as parameter with the name masterq.
(see -jsv option above or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qrsh', 'qalter']:
self.parser.add_argument('-notify',
action='store_true',
help="""\
Available for qsub, qrsh (with command) and qalter only.
This flag, when set causes Grid Engine to send "warning" signals
to a running job prior to sending the signals
themselves. If a SIGSTOP is pending, the job will receive
a SIGUSR1 several seconds before the SIGSTOP. If a
SIGKILL is pending, the job will receive a SIGUSR2 several
seconds before the SIGKILL. This option provides the
running job, before receiving the SIGSTOP or SIGKILL,
a configured time interval to do e.g. cleanup operations.
The amount of time delay is controlled by the notify parameter
in each queue configuration (see queue_conf(5)).
Note that the Linux operating system "misused" the user
signals SIGUSR1 and SIGUSR2 in some early Posix thread
implementations. You might not want to use the
-notify option if you are running multi-threaded applications in
your jobs under Linux, particularly on 2.0 or earlier kernels.
Qalter allows changing this option even while the job executes.
Only if this option is used the parameter named notify with
the value y will be passed to defined JSV instances.
(see -jsv option above or find more information concerning
JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin']:
self.parser.add_argument('-now',
choices=yesno,
help="""\
Available for qsub, qsh, qlogin and qrsh.
-now y tries to start the job immediately or not at all.
The command returns 0 on success, or 1 on failure (also
if the job could not be scheduled immediately).
For array jobs submitted with the -now option, if all tasks
cannot be immediately scheduled, no tasks are scheduled.
-now y is default for qsh, qlogin and qrsh
With the -now n option, the job will be put into the pending
queue if it cannot be executed immediately. -now n
is default for qsub.
The value specified with this option or the corresponding
value specified in qmon will only be passed to defined
JSV instances if the value is yes. The name of the
parameter will be now. The value will be y also when then
long form yes was specified during submission.
(see -jsv option above or find more information concerning JSV
in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-N',
metavar='name',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
The name of the job. The name should follow the "name"
definition in sge_types(1). Invalid job names will be
denied at submit time.
If the -N option is not present, Grid Engine assigns
the name of the job script to the job after any directory
pathname has been removed from the script-name.
If the script is read from standard input, the job name defaults
to STDIN.
In the case of qsh or qlogin with the -N option is absent,
the string `INTERACT' is assigned to the job.
In the case of qrsh if the -N option is absent, the resulting
job name is determined from the qrsh command line
by using the argument string up to the first
occurrence of a semicolon or whitespace and removing the directory
pathname.
Qalter allows changing this option even while the job executes.
The value specified with this option or the corresponding value
specified in qmon will be passed to defined JSV
instances as parameter with the name N. (see -jsv
option above or find more information concerning JSV in
jsv(1))""")
if prog in ['qrsh']:
self.parser.add_argument('-noshell',
action='store_true',
help="""\
Available only for qrsh with a command line.
Do not start the command line given to qrsh in a user's login shell,
i.e. execute it without the wrapping
shell.
This option can be used to speed up execution as some overhead,
like the shell startup and sourcing the shell
resource files, is avoided.
This option can only be used if no shell-specific command line
parsing is required. If the command line contains
shell syntax like environment variable substitution or (back) quoting,
a shell must be started. In this case,
either do not use the -noshell option or include the shell call in the command line.
Example:
qrsh echo '$HOSTNAME'
Alternative call with the -noshell option
qrsh -noshell /bin/tcsh -f -c 'echo $HOSTNAME'""")
if prog in ['qrsh']:
self.parser.add_argument('-nostdin',
action='store_true',
help="""\
Available only for qrsh.
Suppress the input stream STDIN - qrsh will pass the option -n
to the rsh(1) command. This is especially useful,
if multiple tasks are executed in parallel using qrsh, e.g.
in a make(1) process - it would be undefined, which
process would get the input.""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-o',
metavar='path',
help="""\
-o [[hostname]:]path,...
Available for qsub, qsh, qrsh, qlogin and qalter only.
The path used for the standard output stream of the job.
The path is handled as described in the -e option for
the standard error stream.
By default the file name for standard output has the
form job_name.ojob_id and job_name.ojob_id.task_id for
array job tasks (see -t option below).
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is
specified then this value will be passed to defined JSV
instances as parameter with the name o. (see -jsv option
above or find more information concerning JSV in
jsv(1))""")
if prog in ['qalter']:
self.parser.add_argument('-ot',
metavar='override_tickets',
help="""\
Available for qalter only.
Changes the number of override tickets for the specified job.
Requires manager/operator privileges.""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-P',
metavar='project_name',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Specifies the project to which this job is assigned.
The administrator needs to give permission to individual
users to submit jobs to a specific project. (see -aprj option to qconf(1)).
If this option or a corresponding value in qmon is specified then
this value will be passed to defined JSV
instances as parameter with the name ot. (see -jsv option
above or find more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-p',
metavar='priority',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Defines or redefines the priority of the job relative to other jobs.
Priority is an integer in the range -1023
to 1024. The default priority value for jobs is 0.
Users may only decrease the priority of their jobs.
Grid Engine managers and administrators may also increase
the priority associated with jobs. If a pending job has higher priority,
it is earlier eligible for being dis‐
patched by the Grid Engine scheduler.
If this option or a corresponding value in qmon is specified and
the priority is not 0 then this value will be
passed to defined JSV instances as parameter with the name p.
(see -jsv option above or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-slot',
metavar='slot',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Defines or redefines the priority of the job relative to other jobs.
Priority is an integer in the range -1023
to 1024. The default priority value for jobs is 0.
Users may only decrease the priority of their jobs.
Grid Engine managers and administrators may also increase
the priority associated with jobs. If a pending job has higher priority,
it is earlier eligible for being dis‐
patched by the Grid Engine scheduler.
If this option or a corresponding value in qmon is specified and
the priority is not 0 then this value will be
passed to defined JSV instances as parameter with the name p.
(see -jsv option above or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qsh', 'qrsh', 'qlogin', 'qalter']:
self.parser.add_argument('-pe',
nargs=2,
metavar=('parallel_environment', 'n'),
help="""\
-pe parallel_environment n[-[m]]|[-]m,...
Available for qsub, qsh, qrsh, qlogin and qalter only.
Parallel programming environment (PE) to instantiate.
For more detail about PEs, please see the sge_types(1).
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is specified
then the parameters pe_name, pe_min and pe_max will
be passed to configured JSV instances where pe_name will be the
name of the parallel environment and the values
pe_min and pe_max represent the values n and m which have been
provided with the -pe option. A missing specifi‐
cation of m will be expanded as value 9999999 in JSV scripts
and it represents the value infinity. (see -jsv
option above or find more information concerning JSV in jsv(1))"""
)
if prog in ['qrsh', 'qlogin']:
self.parser.add_argument('-pty',
choices=yesno,
help="""\
Available for qrsh and qlogin only.
-pty yes enforces the job to be started in a pseudo terminal (pty).
If no pty is available, the job start fails.
-pty no enforces the job to be started without a pty.
By default, qrsh without a command and qlogin start the
job in a pty, qrsh with a command starts the job without a pty.
This parameter is not available in the JSV context.
(see -jsv option above or find more information concerning
JSV in jsv(1))""")
if prog in ['qsub', 'qrsh', 'qsh', 'qlogin', 'qalter']:
self.parser.add_argument('-q',
nargs='+',
metavar='wc_queue_list',
help="""\
Available for qsub, qrsh, qsh, qlogin and qalter.
Defines or redefines a list of cluster queues,
queue domains or queue instances which may be used to execute
this job. Please find a description of wc_queue_list in sge_types(1).
This parameter has all the properties of
a resource request and will be merged with requirements derived from the
-l option described above.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
If this option or a corresponding value in qmon is specified
the these hard and soft resource requirements will
be passed to defined JSV instances as parameters with the
names q_hard and q_soft. If regular expressions will
be used for resource requests, then these expressions will
be passed as they are. Also shortcut names will not
be expanded. (see -jsv option above or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qrsh', 'qsh', 'qlogin', 'qalter']:
self.parser.add_argument('-R',
choices=yesno,
help="""\
Available for qsub, qrsh, qsh, qlogin and qalter.
Indicates whether a reservation for this job should be done.
Reservation is never done for immediate jobs, i.e.
jobs submitted using the -now yes option. Please note that
regardless of the reservation request, job reserva‐
tion might be disabled using max_reservation in sched_conf(5)
and might be limited only to a certain number of
high priority jobs.
By default jobs are submitted with the -R n option.
The value specified with this option or the corresponding value
specified in qmon will only be passed to defined
JSV instances if the value is yes. The name of the parameter will be R.
The value will be y also when then long
form yes was specified during submission.
(see -jsv option above or find more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qalter']:
self.parser.add_argument('-r',
choices=yesno,
help="""\
Available for qsub and qalter only.
Identifies the ability of a job to be rerun or not.
If the value of -r is 'yes', the job will be rerun if the
job was aborted without leaving a consistent exit state.
(This is typically the case if the node on which the
job is running crashes). If -r is 'no',
the job will not be rerun under any circumstances.
Interactive jobs submitted with qsh, qrsh or qlogin are not rerunnable.
Qalter allows changing this option even while the job executes.
The value specified with this option or the corresponding value specified
in qmon will only be passed to defined
JSV instances if the value is yes. The name of the parameter will be r.
The value will be y also when then long
form yes was specified during submission. (see -jsv option above or
find more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qrsh', 'qsh', 'qlogin', 'qalter']:
self.parser.add_argument('-sc',
action='append',
metavar='variable[=value]',
help="""\
-sc variable[=value],...
Available for qsub, qsh, qrsh, qlogin and qalter only.
Sets the given name/value pairs as the job's context. Value may be omitted.
Grid Engine replaces the job's pre‐
viously defined context with the one given as the argument.
Multiple -ac, -dc, and -sc options may be given.
The order is important.
Contexts provide a way to dynamically attach and remove meta-information
to and from a job. The context vari‐
ables are not passed to the job's execution context in its environment.
Qalter allows changing this option even while the job executes.
The outcome of the evaluation of all -ac, -dc, and -sc options
or corresponding values in qmon is passed to
defined JSV instances as parameter with the name ac.
(see -jsv option above or find more information concerning
JSV in jsv(1))""")
if prog in ['qsub']:
self.parser.add_argument('-shell',
choices=yesno,
help="""\
Available only for qsub.
-shell n causes qsub to execute the command line directly,
as if by exec(2). No command shell will be executed
for the job. This option only applies when -b y is also used.
Without -b y, -shell n has no effect.
This option can be used to speed up execution as some overhead,
like the shell startup and sourcing the shell
resource files is avoided.
This option can only be used if no shell-specific command line parsing
is required. If the command line contains
shell syntax, like environment variable substitution or (back) quoting,
a shell must be started. In this case
either do not use the -shell n option or execute the shell as the
command line and pass the path to the exe‐
cutable as a parameter.
If a job executed with the -shell n option fails due to a user error,
such as an invalid path to the executable,
the job will enter the error state.
-shell y cancels the effect of a previous -shell n. Otherwise, it has no effect.
See -b and -noshell for more information.
The value specified with this option or the corresponding value
specified in qmon will only be passed to defined
JSV instances if the value is yes. The name of the parameter
will be shell. The value will be y also when then
long form yes was specified during submission.
(see -jsv option above or find more information concerning JSV
in jsv(1))""")
if prog in ['qsub', 'qrsh', 'qsh', 'qlogin', 'qalter']:
self.parser.add_argument('-soft',
action='store_true',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter only.
Signifies that all resource requirements following in the command
line will be soft requirements and are to be
filled on an "as available" basis.
As Grid Engine scans the command line and script file for
Grid Engine options and parameters, it builds a list
of resources required by the job. All such resource requests are
considered as absolutely essential for the job
to commence. If the -soft option is encountered during the
scan then all following resources are designated as
"soft requirements" for execution, or "nice-to-have, but not essential".
If the -hard flag (see above) is
encountered at a later stage of the scan, all resource requests following
it once again become "essential". The
-hard and -soft options in effect act as "toggles" during the scan.
If this option or a corresponding value in qmon is
specified then the corresponding -q and -l resource require‐
ments will be passed to defined JSV instances as parameter
with the names q_soft and l_soft. Find for informa‐
tion in the sections describing -q and -l. (see -jsv option
above or find more information concerning JSV in
jsv(1))""")
if prog in ['qsub']:
self.parser.add_argument('-sync',
choices=yesno,
help="""\
Available for qsub.
-sync y causes qsub to wait for the job to complete before exiting.
If the job completes successfully, qsub's
exit code will be that of the completed job.
If the job fails to complete successfully, qsub will print out a
error message indicating why the job failed and will have an exit code of 1.
If qsub is interrupted, e.g. with
CTRL-C, before the job completes, the job will be canceled.
With the -sync n option, qsub will exit with an exit code of 0 as soon as the
job is submitted successfully.
-sync n is default for qsub.
If -sync y is used in conjunction with -now y, qsub will behave
as though only -now y were given until the job
has been successfully scheduled, after which time qsub will behave
as though only -sync y were given.
If -sync y is used in conjunction with -t n[-m[:i]], qsub will
wait for all the job's tasks to complete before
exiting. If all the job's tasks complete successfully, qsub's
exit code will be that of the first completed job
tasks with a non-zero exit code, or 0 if all job tasks exited
with an exit code of 0. If any of the job's tasks
fail to complete successfully, qsub will print out an
error message indicating why the job task(s) failed and
will have an exit code of 1. If qsub is interrupted,
e.g. with CTRL-C, before the job completes, all of the
job's tasks will be canceled.
Information that this switch was specified during
submission is not available in the JSV context. (see -jsv
option above or find more information concerning JSV in jsv(1))"""
)
if prog in ['qsub', 'qsh', 'qalter']:
self.parser.add_argument('-S',
metavar='pathname',
help="""\
-S [[hostname]:]pathname,...
Available for qsub, qsh and qalter.
Specifies the interpreting shell for the job.
Only one pathname component without a host specifier is valid and
only one path name for a given host is allowed.
Shell paths with host assignments define the interpreting shell
for the job if the host is the execution host.
The shell path without host specification is used if the execu‐
tion host matches none of the hosts in the list.
Furthermore, the pathname can be constructed with pseudo
environment variables as described for the -e option
above.
In the case of qsh the specified shell path is used to
execute the corresponding command interpreter in the
xterm(1) (via its -e option) started on behalf of the interactive job.
Qalter allows changing this option even
while the job executes. The modified parameter will only be in effect
after a restart or migration of the job,
however.
If this option or a corresponding value in qmon is
specified then this value will be passed to defined JSV
instances as parameter with the name S. (see -jsv option
above or find more information concerning JSV in
jsv(1))""")
if True or prog in ['qsub', 'qalter']:
self.parser.add_argument('-t',
metavar='n[-m[:s]]',
help="""\
Available for qsub and qalter only.
Submits a so called Array Job, i.e. an array of identical
tasks being differentiated only by an index number and
being treated by Grid Engine almost like a series of jobs.
The option argument to -t specifies the number of
array job tasks and the index number which will be associated with the tasks.
The index numbers will be exported
to the job tasks via the environment variable GE_TASK_ID.
The option arguments n, m and s will be available
through the environment variables GE_TASK_FIRST,
GE_TASK_LAST and GE_TASK_STEPSIZE.
Following restrictions apply to the values n and m:
1 <= n <= MIN(2^31-1, max_aj_tasks)
1 <= m <= MIN(2^31-1, max_aj_tasks)
n <= m
max_aj_tasks is defined in the cluster configuration (see sge_conf(5))
The task id range specified in the option argument may be a single
number, a simple range of the form n-m or a
range with a step size. Hence, the task id range specified by
2-10:2 would result in the task id indexes 2, 4,
6, 8, and 10, for a total of 5 identical tasks, each with
the environment variable GE_TASK_ID containing one of
the 5 index numbers.
All array job tasks inherit the same resource requests and
attribute definitions as specified in the qsub or
qalter command line, except for the -t option.
The tasks are scheduled independently and, provided enough
resources exist, concurrently, very much like separate jobs.
However, an array job or a sub-array there of can
be accessed as a single unit by commands like qmod(1) or qdel(1).
See the corresponding manual pages for fur‐
ther detail.
Array jobs are commonly used to execute the same type of operation
on varying input data sets correlated with
the task index number. The number of tasks in a array job is unlimited.
STDOUT and STDERR of array job tasks will be written into different
files with the default location
<jobname>.['e'|'o']<job_id>'.'<task_id>
In order to change this default, the -e and -o options (see above)
can be used together with the pseudo environ‐
ment variables $HOME, $USER, $JOB_ID, $JOB_NAME, $HOSTNAME, and $GE_TASK_ID.
Note, that you can use the output redirection to divert the output
of all tasks into the same file, but the
result of this is undefined.
If this option or a corresponding value in qmon is specified
then this value will be passed to defined JSV
instances as parameters with the name t_min, t_max and t_step
(see -jsv option above or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qalter']:
self.parser.add_argument('-tc',
type=int,
metavar='max_running_tasks',
help="""\
-allow users to limit concurrent array job task
execution. Parameter max_running_tasks specifies maximum number
of simultaneously running tasks. For example we have
running SGE with 10 free slots. We call qsub -t 1-100 -tc
2 jobscript. Then only 2 tasks will be scheduled to run even
when 8 slots are free.""")
if prog in ['qsub']:
self.parser.add_argument('-terse',
action='store_true',
help="""\
Available for qsub only.
-terse causes the qsub to display only the job-id of the
job being submitted rather than the regular "Your job
..." string. In case of an error the error is reported on stderr as usual.
This can be helpful for scripts which need to parse qsub output to get the job-id.
Information that this switch was specified during submission
is not available in the JSV context. (see -jsv
option above or find more information concerning JSV in jsv(1))"""
)
if prog in ['qalter']:
self.parser.add_argument('-u',
metavar='username',
help="""\
-u username,...
Available for qalter only. Changes are only made
on those jobs which were submitted by users specified in the
list of usernames. For managers it is possible to use
the qalter -u '*' command to modify all jobs of all
users.
If you use the -u switch it is not permitted to
specify an additional wc_job_range_list.""")
if prog in ['qsub', 'qrsh', 'qalter']:
self.parser.add_argument('-v',
metavar='variable[=value]',
help="""\
-v variable[=value],...
Available for qsub, qrsh (with command argument) and qalter.
Defines or redefines the environment
variables to be exported to the execution context of the job. If the -v
option is present Grid Engine will add the
environment variables defined as arguments to the switch and, option‐
ally, values of specified variables, to the execution context of the job.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
All environment variables specified with -v, -V or the
DISPLAY variable provided with -display will be exported
to the defined JSV instances only optionally when this is
requested explicitly during the job submission verifi‐
cation. (see -jsv option above or find more information concerning JSV in jsv(1))"""
)
if prog in ['qrsh', 'qmake']:
self.parser.add_argument('-verbose',
action='store_true',
help="""\
Available only for qrsh and qmake(1).
Unlike qsh and qlogin, qrsh does not output any
informational messages while establishing the session, compliant
with the standard rsh(1) and rlogin(1) system calls.
If the option -verbose is set, qrsh behaves like the qsh
and qlogin commands, printing information about the
process of establishing the rsh(1) or rlogin(1) session.""")
if prog in ['qsub', 'qrsh', 'qsh', 'qlogin', 'qalter']:
self.parser.add_argument('-verify',
action='store_true',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter.
Instead of submitting a job, prints detailed information
about the would-be job as though qstat(1) -j were used,
including the effects of command-line parameters and
the external environment.""")
if prog in ['qsub', 'qrsh', 'qsh', 'qlogin', 'qalter']:
# TODO parse acceptability of qrsh argument properly
self.parser.add_argument('-V',
action='store_true',
help="""\
Available for qsub, qsh, qrsh with command and qalter.
Specifies that all environment variables active within
the qsub utility be exported to the context of the job.
All environment variables specified with -v, -V or the DISPLAY
variable provided with -display will be exported
to the defined JSV instances only optionally when this is
requested explicitly during the job submission verifi‐
cation. (see -jsv option above or find more information
concerning JSV in jsv(1))""")
if prog in ['qsub', 'qrsh', 'qsh', 'qlogin', 'qalter']:
self.parser.add_argument('-w',
choices='ewnpv',
help="""\
Available for qsub, qsh, qrsh, qlogin and qalter.
Specifies a validation level applied to the job to be submitted
(qsub, qlogin, and qsh) or the specified queued
job (qalter). The information displayed indicates whether the
job can possibly be scheduled assuming an empty
system with no other jobs. Resource requests exceeding the
configured maximal thresholds or requesting unavail‐
able resource attributes are possible causes for jobs to fail this validation.
The specifiers e, w, n and v define the following validation modes:
`e' error - jobs with invalid requests will be
rejected.
`w' warning - only a warning will be displayed
for invalid requests.
`n' none - switches off validation; the default for
qsub, qalter, qrsh, qsh
and qlogin.
`p' poke - does not submit the job but prints a
validation report based on a cluster as is with
all resource utilizations in place.
`v' verify - does not submit the job but prints a
validation report based on an empty cluster.
Note, that the necessary checks are performance consuming
and hence the checking is switched off by default. It
should also be noted that load values are not taken
into account with the verification since they are assumed to
be too volatile. To cause -w e verification to be passed
at submission time, it is possible to specify non-
volatile values (non-consumables) or maximum values
(consumables) in complex_values.""")
if prog in ['qsub', 'qrsh', 'qsh', 'qalter']:
self.parser.add_argument('-wd',
metavar='working_dir',
help="""\
Available for qsub, qsh, qrsh and qalter only.
Execute the job from the directory specified in working_dir.
This switch will activate Grid Engine's path
aliasing facility, if the corresponding configuration files are present
(see ge_aliases(5)).
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
The parameter value will be available in defined JSV
instances as parameter with the name cwd (see -cwd switch above or
find more information concerning JSV in
jsv(1))""")
if prog in ['qsub', 'qrsh']:
self.parser.add_argument('command',
help="""\
Available for qsub and qrsh only.
The job's scriptfile or binary. If not present or if the operand
is the single-character string '-', qsub reads
the script from standard input.
The command will be available in defined JSV instances as parameter
with the name CMDNAME (see -jsv option above
or find more information concerning JSV in jsv(1))""")
if prog in ['qsub', 'qrsh', 'qalter']:
self.parser.add_argument('command_args',
nargs='*',
help="""\
Available for qsub, qrsh and qalter only.
Arguments to the job. Not valid if the script is entered from standard input.
Qalter allows changing this option even while the job executes.
The modified parameter will only be in effect
after a restart or migration of the job, however.
The number of command arguments is provided to configured
JSV instances as parameter with the name CMDARGS. Also
the argument values can by accessed. Argument names
have the format CMDARG<number> where <number> is a integer
between 0 and CMDARGS - 1. (see -jsv option above or
find more information concerning JSV in jsv(1))""")
if prog in ['qsh']:
self.parser.add_argument('xterm_args',
nargs='*',
help="""\
Available for qsh only.
Arguments to the xterm(1) executable, as defined in the configuration.
For details, refer to ge_conf(5)).
Information concerning xterm_args will be available in JSV context as
parameters with the name CMDARGS and
CMDARG<number>. Find more information above in section command_args.
(see -jsv option above or find more infor‐
mation concerning JSV in jsv(1))""")
# END SGE OPTION PARSER
# Initialize with defaults
self.parse('-cwd -V -j y -terse -pe lammpi 1 echo')
def parse(self, inputstring=''):
"""Helper method: parses a string"""
return self.parse_args(inputstring.split())
def parse_args(self, args=None):
"""Helper method: parses a list"""
if args is None:
self.args = self.parser.parse_args() # default is sys.argv[1:]
else:
self.args = self.parser.parse_args(args)
return self.args
def write_qsub_script(self, filename, echo=False):
"""
Writes the entire command line to a qsub script
filename: name of file to write
echo : echo contents of script to stdout. Default: False
"""
buf = ['#!/usr/bin/env qsub', '# Written using SGE module']
for option, value in self.args.__dict__.items():
if value is True:
value = ''
if option not in ['command', 'command_args', 'xterm_args']:
if isinstance(value, list):
val = ' '.join(value)
else:
val = str(value)
buf.append(' '.join(['#', '-' + option, val]))
args = getattr(self.args, 'command_args', [])
args = getattr(self.args, 'xterm_args', args)
buf.append(' '.join([self.args.command] + args))
if echo:
print('\n'.join(buf))
f = open(filename, 'w')
f.write('\n'.join(buf))
f.close()
def execute(self, mode='local', path=''):
"""
Executes qsub
known modes: local - run locally
echo - echoes out execution string only
path: path to qsub/... executable: Default = nothing
"""
# Form execution string
import random
test_id = ''
if "build.log" in self.args.o:
test_id = self.args.o.split("/")[-2]
elif "run.log" in self.args.o:
test_id = self.args.o.split("/")[-3]
if test_id == '':
test_id = str(random.randint(1, 9999))
import os
program = os.path.join(path, self.prog)
options = []
for option, value in self.args.__dict__.items():
if value is True:
value = ''
if isinstance(value, list):
val = ' '.join(value)
else:
val = str(value)
if option not in ['command', 'command_args', 'xterm_args']:
options.append('-' + option + ' ' + val)
args = getattr(self.args, 'command_args', [])
args = getattr(self.args, 'xterm_args', args)
# ---------------- command file -------------
cwd = os.getcwd()
command_file = cwd + '/command_file_' + str(os.getpid()) + '_' + test_id
try:
with open(command_file, 'w') as f_command:
command_temp = str(self.args.command)
command_temp = command_temp.replace('"', '')
f_command.write(command_temp + "\n/bin/rm -f " + command_file)
except IOError:
error_msg = 'Error: problem with open File: ' + str(f_command)
raise IOError(error_msg)
os.chmod(command_file, 0o0777)
exestring = ' '.join([program] + options + [command_file] + args)
exestring = exestring.replace('-pe lammpi 1', '')
exestring = exestring.replace('-slot', '-pe make')
exestring = exestring.replace('-ll ', '-l ')
exestring = exestring.replace('-t 0', '')
# exestring = exestring.replace('-j y','')
print('INFO: sge command file = ' + command_file)
if mode == 'echo':
return (exestring)
elif mode == 'local':
import subprocess
p = subprocess.Popen(command_file,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
shell=True)
print(p.stdout.read())
if __name__ == '__main__':
print('Attempting to validate qsub arguments using argparse')
o = qsubOptions()
o.parse_args()
o.args.t = '1-1000'
print('I will now print the script')
o.write_qsub_script('/dev/null', echo=True)
print('*' * 70)
print('I will now print the command line')
o.execute(mode='echo')