Provided by:
gridengine-client_6.2~beta2-2_i386 
NAME
sge_submit.1 - Job submission commands for SGE
qsub - submit a batch job to Grid Engine.
qsh - submit an interactive X-windows session to Grid Engine.
qlogin - submit an interactive login session to Grid Engine.
qrsh - submit an interactive rsh session to Grid Engine.
qalter - modify a pending batch job of Grid Engine.
qresub - submit a copy of an existing Grid Engine job.
SYNTAX
qsub [ options ] [ command | -- [ command_args ]]
qsh [ options ] [ -- xterm_args ]
qlogin [ options ]
qrsh [ options ] [ command [ command_args ]]
qalter [ options ] wc_job_range_list [ -- [ command_args ]]
qalter [ options ] -u user_list | -uall [ -- [ command_args ]]
qresub [ options ] job_id_list
DESCRIPTION
Qsub submits batch jobs to the Grid Engine queuing system. Grid Engine
supports single- and multiple-node jobs. Command can be a path to a
binary or a script (see -b below) which contains the commands to be run
by the job using a shell (for example, sh(1) or csh(1)). Arguments to
the command are given as command_args to qsub . If command is handled
as a script then it is possible to embed flags in the script. If the
first two characters of a script line either match ’#$’ or are equal to
the prefix string defined with the -C option described below, the line
is parsed for embedded command flags.
Qsh submits an interactive X-windows session to Grid Engine. An
xterm(1) is brought up from the executing machine with the display
directed either to the X-server indicated by the DISPLAY environment
variable or as specified with the -display qsh option. Interactive jobs
are not spooled if no resource is available to execute them. They are
either dispatched to a suitable machine for execution immediately or
the user submitting the job is notified by qsh that appropriate
resources to execute the job are not available. xterm_args are passed
to the xterm(1) executable. Note, however, that the -e and -ls xterm
options do not work with qsh .
Qlogin is similar to qsh in that it submits an interactive job to the
queueing system. It does not open an xterm(1) window on the X display,
but uses the current terminal for user I/O. Usually, qlogin establishes
a telnet(1) connection with the remote host, using standard client- and
server-side commands. These commands can be configured with the
qlogin_daemon (server-side, Grid Engine telnetd if not set, otherwise
something like /usr/sbin/in.telnetd) and qlogin_command (client-side,
Grid Engine telnet if not set, otherwise something like
/usr/bin/telnet) parameters in the global and local configuration
settings of ge_conf(5). The client side command is automatically
parameterized with the remote host name and port number to which to
connect, resulting in an invocation like
/usr/bin/telnet my_exec_host 2442
for example. Qlogin is invoked exactly like qsh and its jobs can only
run on INTERACTIVE queues. Qlogin jobs can only be used if the
ge_execd(8) is running under the root account.
Qrsh is similar to qlogin in that it submits an interactive job to the
queuing system. It uses the current terminal for user I/O. Usually,
qrsh establishes a rsh(1) connection with the remote host. If no
command is given to qrsh, an rlogin(1) session is established. The
server-side commands used can be configured with the rsh_daemon and
rlogin_daemon parameters in the global and local configuration settings
of ge_conf(5). An Grid Engine rshd or rlogind is used if the
parameters are not set. If the parameters are set, they should be set
to something like /usr/sbin/in.rshd or /usr/sbin/in.rlogind. On the
client-side, the rsh_command and rlogin_command parameters can be set
in the global and local configuration settings of ge_conf(5). If they
are not set, special Grid Engine rsh(1) and rlogin(1) binaries
delivered with Grid Engine are used. Use the cluster configuration
parameters to integrate mechanisms like ssh or the rsh(1) and rlogin(1)
facilities supplied with the operating system.
Qrsh jobs can only run in INTERACTIVE queues unless the option -now no
is used (see below). They can also only be run, if the ge_execd(8) is
running under the root account.
Qrsh provides an additional useful feature for integrating with
interactive tools providing a specific command shell. If the
environment variable QRSH_WRAPPER is set when qrsh is invoked, the
command interpreter pointed to by QRSH_WRAPPER will be executed to run
qrsh commands instead of the users login shell or any shell specified
in the qrsh command-line. The options -cwd, -v, -V, and -display
only apply to batch jobs.
Qalter can be used to change the attributes of pending jobs. For array
jobs with a mix of running and pending tasks (see the -t option below),
modification with qalter only affects the pending tasks. Qalter can
change most of the characteristics of a job (see the corresponding
statements in the OPTIONS section below), including those which were
defined as embedded flags in the script file (see above). Some submit
options, such as the job script, cannot be changed with I. qalter.
Qresub allows the user to create jobs as copies of existing pending or
running jobs. The copied jobs will have exactly the same attributes as
the ones from which they were copied, except with a new job ID. The
only modification to the copied jobs supported by qresub is assignment
of a hold state with the -h option. This option can be used to first
copy a job and then change its attributes via qalter.
Only a manager can use qresub on jobs submitted by another user.
Regular users can only use qresub on their own jobs.
For qsub, qsh, qrsh, and qlogin the administrator and the user may
define default request files (see ge_request(5)) which can contain any
of the options described below. If an option in a default request file
is understood by qsub and qlogin but not by qsh the option is silently
ignored if qsh is invoked. Thus you can maintain shared default request
files for both qsub and qsh.
A cluster wide default request file may be placed under
$GE_ROOT/$GE_CELL/common/ge_request. User private default request
files are processed under the locations $HOME/.ge_request and
$cwd/.ge_request. The working directory local default request file has
the highest precedence, then the home directory located file and then
the cluster global file. The option arguments, the embedded script
flags and the options in the default request files are processed in the
following order:
left to right in the script line,
left to right in the default request files,
from top to bottom of the script file (qsub only),
from top to bottom of default request files,
from left to right of the command line.
In other words, the command line can be used to override the embedded
flags and the default request settings. The embedded flags, however,
will override the default settings.
Note, that the -clear option can be used to discard any previous
settings at any time in a default request file, in the embedded script
flags, or in a command-line option. It is, however, not available with
qalter.
The options described below can be requested either hard or soft. By
default, all requests are considered hard until the -soft option (see
below) is encountered. The hard/soft status remains in effect until its
counterpart is encountered again. If all the hard requests for a job
cannot be met, the job will not be scheduled. Jobs which cannot be run
at the present time remain spooled.
OPTIONS
-@ optionfile
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.
-a date_time
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).
-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.
QALTER allows changing this option even while the job executes.
-ar AR_id
Available for qsub, qalter qrsh, qsh, or qloginP only.
The AR_id AR_is is required. 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.
-ar option adds implicitly the -w e option if not otherwise requested.
Qalter allows the AR_id of a pending job to be changed. The AR_id of a
running job cannot be changed.
-A account_string
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.
-b y[es]|n[o]
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.
-c occasion_specifier
Available for qsub and qalter only.
Defines or redefines whether the job should be checkpointed, and
if so, under what circumstances. The specification 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 occasion_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.
-ckpt ckpt_name
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.
-clear 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.
-cwd 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.
-C prefix_string
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.
-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.
-display display_specifier
Available for qsh only.
Directs xterm(1) to use display_specifier in order to contact
the X server. The display_specifier has to contain 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.
-dl date_time
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 initiation 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.
-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
specified) 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 hostname, 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 runtime of the job and will be
used to constitute the standard error stream path name. The
following pseudo environment 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.
-hard Available for qsub, qsh, qrsh, qlogin and qalter only.
Signifies that all 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 designated as "soft requirements" for
execution, or "nice-to-have, but not essential". If the -hard
flag 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.
-h | -h {u|s|o|n|U|O|S}...
Available for qsub, qsh, qrsh, qlogin, qalter and qresub.
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.
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 specifiers 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.
-help Prints a listing of all options.
-hold_jid wc_job_list
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.
-hold_jid_ad wc_job_list
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 submitted 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.
-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 relative, 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.
-inherit
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.
-j y[es]|n[o]
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.
-js job_share
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 distribution 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 policies, and the tickets
independently derived in each of them are added to the total
number of tickets for each job.
-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 effective after a restart or migration
of the job.
-m b|e|a|s|n,...
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.
-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.
-masterq wc_queue_list
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.
-notify
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. 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.
-now y[es]|n[o]
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.
-N name
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.
-noshell
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’
-nostdin
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.
-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.
-ot override_tickets
Available for qalter only.
Changes the number of override tickets for the specified job.
Requires manager/operator privileges.
-P project_name
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)).
-p priority
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 dispatched by the Grid Engine
scheduler.
-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.
-pty y[es]|n[o]
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.
-q wc_queue_list
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.
-R y[es]|n[o]
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 reservation 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.
-r y[es]|n[o]
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.
-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 previously 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 variables are not
passed to the job’s execution context in its environment.
Qalter allows changing this option even while the job executes.
-shell y[es]|n[o]
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 executable 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.
-soft 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.
-sync y[es]|n[o]
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.
-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 execution 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.
-t n[-m[:s]]
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 further 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 environment
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.
-terse 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.
-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 â€â€™*â€â€™
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.
-v variable[=value],...
Available for qsub, qsh, qrsh 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, optionally, 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.
-verbose
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.
-verify
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.
-V Available for qsub, qsh, qrsh with command, qalter and qresub.
Specifies that all environment variables active within the qsub
utility be exported to the context of the job.
-w e|w|n|v
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 unavailable 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; the default for qrsh, qsh
and qlogin.
‘w’ warning - only a warning will be displayed
for invalid requests.
‘n’ none - switches off validation; the default for
qsub and qalter.
‘v’ verify - does not submit the job but prints an
extensive validation report.
Note, that the necessary checks are performance consuming and
hence the checking is switched off by default.
Note also, that the reasons for job requirements being invalid
with respect to resource availability of queues are displayed in
the "-w v" case using the format as described for the qstat(1)
-F option (see description of Full Format in section OUTPUT
FORMATS of the qstat(1) manual page.
-wd working_dir
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.
command
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.
command_args
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.
xterm_args
Available for qsh only.
Arguments to the xterm(1) executable, as defined in the
configuration. For details, refer to ge_conf(5)).
ENVIRONMENTAL VARIABLES
GE_ROOT Specifies the location of the Grid Engine standard
configuration files.
GE_CELL If set, specifies the default Grid Engine cell. To
address a Grid Engine cell qsub, qsh, qlogin or qalter
use (in the order of precedence):
The name of the cell specified in the environment
variable GE_CELL, if it is set.
The name of the default cell, i.e. default.
GE_DEBUG_LEVEL If set, specifies that debug information should be
written to stderr. In addition the level of detail in
which debug information is generated is defined.
GE_QMASTER_PORT
If set, specifies the tcp port on which ge_qmaster(8) is
expected to listen for communication requests. Most
installations will use a services map entry for the
service "sge_qmaster" instead to define that port.
DISPLAY For qsh jobs the DISPLAY has to be specified at job
submission. If the DISPLAY is not set by using the
-display or the -v switch, the contents of the DISPLAY
environment variable are used as default.
In addition to those environment variables specified to be exported to
the job via the -v or the -V option (see above) qsub, qsh, and qlogin
add the following variables with the indicated values to the variable
list:
GE_O_HOME the home directory of the submitting client.
GE_O_HOST the name of the host on which the submitting client is
running.
GE_O_LOGNAME the LOGNAME of the submitting client.
GE_O_MAIL the MAIL of the submitting client. This is the mail
directory of the submitting client.
GE_O_PATH the executable search path of the submitting client.
GE_O_SHELL the SHELL of the submitting client.
GE_O_TZ the time zone of the submitting client.
GE_O_WORKDIR the absolute path of the current working directory of
the submitting client.
Furthermore, Grid Engine sets additional variables into the job’s
environment, as listed below.
ARC
SGE_ARCH The Grid Engine architecture name of the node on which
the job is running. The name is compiled-in into the
ge_execd(8) binary.
GE_CKPT_ENV Specifies the checkpointing environment (as selected
with the -ckpt option) under which a checkpointing job
executes. Only set for checkpointing jobs.
GE_CKPT_DIR Only set for checkpointing jobs. Contains path ckpt_dir
(see checkpoint(5) ) of the checkpoint interface.
GE_STDERR_PATH the pathname of the file to which the standard error
stream of the job is diverted. Commonly used for
enhancing the output with error messages from prolog,
epilog, parallel environment start/stop or checkpointing
scripts.
GE_STDOUT_PATH the pathname of the file to which the standard output
stream of the job is diverted. Commonly used for
enhancing the output with messages from prolog, epilog,
parallel environment start/stop or checkpointing
scripts.
GE_STDIN_PATH the pathname of the file from which the standard input
stream of the job is taken. This variable might be used
in combination with GE_O_HOST in prolog/epilog scripts
to transfer the input file from the submit to the
execution host.
GE_JOB_SPOOL_DIR
The directory used by ge_shepherd(8) to store job
related data during job execution. This directory is
owned by root or by a Grid Engine administrative account
and commonly is not open for read or write access to
regular users.
GE_TASK_ID The index number of the current array job task (see -t
option above). This is an unique number in each array
job and can be used to reference different input data
records, for example. This environment variable is set
to "undefined" for non-array jobs. It is possible to
change the predefined value of this variable with -v or
-V (see options above).
GE_TASK_FIRST The index number of the first array job task (see -t
option above). It is possible to change the predefined
value of this variable with -v or -V (see options
above).
GE_TASK_LAST The index number of the last array job task (see -t
option above). It is possible to change the predefined
value of this variable with -v or -V (see options
above).
GE_TASK_STEPSIZE
The step size of the array job specification (see -t
option above). It is possible to change the predefined
value of this variable with -v or -V (see options
above).
ENVIRONMENT The ENVIRONMENT variable is set to BATCH to identify
that the job is being executed under Grid Engine
control.
HOME The user’s home directory path from the passwd(5) file.
HOSTNAME The hostname of the node on which the job is running.
JOB_ID A unique identifier assigned by the ge_qmaster(8) when
the job was submitted. The job ID is a decimal integer
in the range 1 to 99999.
JOB_NAME The job name. For batch jobs or jobs submitted by qrsh
with a command, the job name is built as basename of the
qsub script filename resp. the qrsh command. For
interactive jobs it is set to ‘INTERACTIVE’ for qsh
jobs, ‘QLOGIN’ for qlogin jobs and ‘QRLOGIN’ for qrsh
jobs without a command.
This default may be overwritten by the -N. option.
LOGNAME The user’s login name from the passwd(5) file.
NHOSTS The number of hosts in use by a parallel job.
NQUEUES The number of queues allocated for the job (always 1 for
serial jobs).
NSLOTS The number of queue slots in use by a parallel job.
PATH A default shell search path of:
/usr/local/bin:/usr/ucb:/bin:/usr/bin
SGE_BINARY_PATH
The path where the Grid Engine binaries are installed.
The value is the concatenation of the cluster
configuration value binary_path and the architecture
name $SGE_ARCH environment variable.
PE The parallel environment under which the job executes
(for parallel jobs only).
PE_HOSTFILE The path of a file containing the definition of the
virtual parallel machine assigned to a parallel job by
Grid Engine. See the description of the $pe_hostfile
parameter in ge_pe(5) for details on the format of this
file. The environment variable is only available for
parallel jobs.
QUEUE The name of the cluster queue in which the job is
running.
REQUEST Available for batch jobs only.
The request name of a job as specified with the -N
switch (see above) or taken as the name of the job
script file.
RESTARTED This variable is set to 1 if a job was restarted either
after a system crash or after a migration in case of a
checkpointing job. The variable has the value 0
otherwise.
SHELL The user’s login shell from the passwd(5) file. Note:
This is not necessarily the shell in use for the job.
TMPDIR The absolute path to the job’s temporary working
directory.
TMP The same as TMPDIR; provided for compatibility with NQS.
TZ The time zone variable imported from ge_execd(8) if set.
USER The user’s login name from the passwd(5) file.
RESTRICTIONS
There is no controlling terminal for batch jobs under Grid Engine, and
any tests or actions on a controlling terminal will fail. If these
operations are in your .login or .cshrc file, they may cause your job
to abort.
Insert the following test before any commands that are not pertinent to
batch jobs in your .login:
if ( $?JOB_NAME) then
echo "Grid Engine spooled job"
exit 0
endif
Don’t forget to set your shell’s search path in your shell start-up
before this code.
EXIT STATUS
The following exit values are returned:
0 Operation was executed successfully.
25 It was not possible to register a new job according to the
configured max_u_jobs or max_jobs limit. Additional information
may be found in sge_conf(5)
>0 Error occurred.
EXAMPLES
The following is the simplest form of a Grid Engine script file.
=====================================================
#!/bin/csh
a.out
=====================================================
The next example is a more complex Grid Engine script.
=====================================================
#!/bin/csh
# Which account to be charged cpu time
#$ -A santa_claus
# date-time to run, format [[CC]yy]MMDDhhmm[.SS]
#$ -a 12241200
# to run I want 6 or more parallel processes
# under the PE pvm. the processes require
# 128M of memory
#$ -pe pvm 6- -l mem=128
# If I run on dec_x put stderr in /tmp/foo, if I
# run on sun_y, put stderr in /usr/me/foo
#$ -e dec_x:/tmp/foo,sun_y:/usr/me/foo
# Send mail to these users
#$ -M santa@nothpole,claus@northpole
# Mail at beginning/end/on suspension
#$ -m bes
# Export these environmental variables
#$ -v PVM_ROOT,FOOBAR=BAR
# The job is located in the current
# working directory.
#$ -cwd
a.out
==========================================================
FILES
$REQUEST.oJID[.TASKID] STDOUT of job #JID
$REQUEST.eJID[.TASKID] STDERR of job
$REQUEST.poJID[.TASKID] STDOUT of par. env. of job
$REQUEST.peJID[.TASKID] STDERR of par. env. of job
$cwd/.ge_aliases cwd path aliases
$cwd/.ge_request cwd default request
$HOME/.ge_aliases user path aliases
$HOME/.ge_request user default request
<ge_root>/<cell>/common/ge_aliases
cluster path aliases
<ge_root>/<cell>/common/ge_request
cluster default request
<ge_root>/<cell>/common/act_qmaster
Grid Engine master host file
SEE ALSO
ge_intro(1), qconf(1), qdel(1), qhold(1), qmod(1), qrls(1), qstat(1),
accounting(5), ge_aliases(5), ge_conf(5), ge_request(5), ge_pe(5),
complex(5).
COPYRIGHT
If configured correspondingly, qrsh and qlogin contain portions of the
rsh, rshd, telnet and telnetd code copyrighted by The Regents of the
University of California. Therefore, the following note applies with
respect to qrsh and qlogin: This product includes software developed by
the University of California, Berkeley and its contributors.
See ge_intro(1) as well as the information provided in
<ge_root>/3rd_party/qrsh and <ge_root>/3rd_party/qlogin for a statement
of further rights and permissions.