Provided by: gridengine-client_8.1.9+dfsg-10build1_amd64 
NAME
qsub, qsh, qlogin, qrsh, qalter, qresub - submit jobs to Grid Engine
SYNTAX
qsub [options] [command [command_args] | -- [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 | -u * [-- [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 option of qsh.
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 queuing system. It
does not open an xterm(1) window on the X display, but uses the current terminal for user
I/O. It establishes a telnet(1)-like connection with the remote host, using the
configured mechanisms described in remote_startup(5). Qlogin is invoked exactly like qsh
and its jobs can only run on INTERACTIVE queues. Qlogin jobs can only be used if the
sge_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. With a command, it establishes a rsh(1)-like
connection with the remote host. If no command is given to qrsh, an rlogin(1)-like session
is established. It uses the configured mechanisms described in remote_startup(5). 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 sge_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 user's 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). An option specified with qalter
completely replaces any parameters previously specified for the job by that option, e.g.
if the job has a resource requirement corresponding to -l h_rt=3600,h_vmem=2G, then after
a qalter -l h_rt=7200, the resource requirement is simply h_rt=7200; it is not currently
possible to override one or more values.
Some submit options, such as the job script, cannot be changed with qalter. If parameters
are set with qalter, the output from qstat -j acquires an additional field, version, which
is incremented each time.
If a server JSV is defined, modifications are forbidden unless they are explicitly allowed
by the sge_conf(5) parameter jsv_allowed_mod. (See also jsv(1).)
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 and with a cleared hold state. The only modification to the
copied jobs supported by qresub is assignment of a new 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.
See sge_shepherd(8) for the significance of exit codes returned by the submitted job.
For qsub, qsh, qrsh, and qlogin the administrator and the user may define default request
files (see sge_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
$SGE_ROOT/$SGE_CELL/common/sge_request. User private default request files are processed
under the locations $HOME/.sge_request and $cwd/.sge_request. The working directory local
default request file has the highest precedence, then the home directory 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 request 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 is of the form [[CC]YY]MMDDhhmm[.SS]; for the details, please see
date_time in sge_types(5).
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).)
-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.
-ar ar_id
Available for qsub, qalter, qrsh, qsh, or qlogin only.
Assigns the submitted job to be a part of an existing Advance Reservation with id
ar_id. The complete list of existing Advance Reservations can be obtained using
the qrstat(1) command.
Note that the -ar option implicitly adds 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).)
-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 account_name definition in
sge_types(5). In the absence of this parameter Grid Engine will place the default
account string "sge" 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).)
-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 argument 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
it is executed.
If the argument of -b is 'n' then command needs to be a script, and it will be
handled as such. 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 scripts.
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 the 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 a 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.
-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. (The binding
facility depends on the platform, and on Grid Engine being compiled with
appropriate support.)
To make Grid Engine 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 only 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. In presence of SMT or CMT it may contain more than the
number of cores selected, 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 (e.g. "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 sge_pe(5). In addition, SGE_BINDING is set as for env binding.
set (the default if nothing else is specified) means that the binding strategy is
applied by Grid Engine. Each shepherd (on the master host, or those connected to
with qrsh -inherit) is bound to the relevant cores. The binding is inherited by
the task that is started, so that processes or threads it spawns are bound to those
cores, but it is up to the task to make any more specific bindings of its sub-tasks
within the set of bound cores it inherits. How Grid Engine does this depends on
the underlying hardware architecture of the execution host where the submitted job
will be started. In addition, SGE_BINDING is set as for env binding.
Binding will be done to restrict the job to run exclusively on the selected cores,
if possible on the platform; otherwise bound processes may still be able to use
other cores. The operating system will probably allow other unbound processes to
use these cores. Note that if all cores on a node are specified to be bound by one
job, that is probably equivalent to no binding, with the task free to use all the
cores.
The loadcheck tool in the utilbin directory can be used to check the host's
capabilities. You can also use -sep in combination with -cb of qconf(5) to find
whether Grid Engine is able to recognize the hardware topology. hwloc-ps(1) can be
used to check the bindings in force on a host.
Possible values for binding_strategy are as follows:
linear:[number[:socket,core]]
striding:number:n[:socket,core]
explicit:socket,core[:socket,core]...
For the binding strategies "linear" and "striding" there is an optional socket and
core pair attached. These denote the mandatory starting point for the first core to
bind on. Logical socket and core numbers are used, per hwloc(7).
linear means that Grid Engine tries to bind the job on number successive cores. If
socket and core are 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 socket and core are specified, then Grid Engine tries to find empty
cores with this starting point. If the binding request cannot be satisfied, then
binding is not done on the host concerned. number may be omitted or specified as
slots. In that case it will be taken as the number of slots assigned to the job on
a per-host basis, on the assumption that one slot per core is used. That allows
binding to work when parallel jobs run across nodes with variable slot counts per
node. Multiple processing units (hardware threads) per core are currently not
taken into account in this, but systems running such parallel jobs will typically
have only a single thread per core. -binding linear is a reasonable overall
default for sge_request(5) in many cases.
striding means that Grid Engine tries to find cores with a certain offset. It will
select number of empty cores with an offset of n-1 cores in between. Start point
for the search algorithm is socket 0 core 0. As soon as number cores are found they
will be used to do the job binding. If there are not enough empty cores, or if the
correct offset cannot be achieved, then no binding will be done on the host
concerned.
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.
Note that a binding like "pe linear:number..." is only useful if the job has
exclusive access to its multiple compute nodes, they all have the same topology,
and the PE has a fixed allocation rule (allocation_rule n). (The $pe_hostfile
content is created on the job's master host, with the same <socket,core>
specification for each.) This method can't be used for job isolation. Similarly,
set requires a fixed allocation per host for distributed parallel jobs.
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 passed 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_socketid, binding_exp_coreid.
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
binding_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 specified. (See
-jsv option below or find more information concerning JSV in jsv1(.))
-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;
r Reschedule when execution host goes into the "unknown" state;
interval
Checkpoint in the specified interval (a time_specifier per sge_types(5)).
The minimum CPU interval is defined in the queue configuration (see queue_conf(5)
for details). If interval is specified, the maximum of that and the queue's
minimum CPU interval is used (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).)
-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.
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).)
-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 sge_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).)
-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.
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).)
-display display_specifier
Available for qsh and qrsh with a command.
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.
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).)
-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.
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).)
-e [[hostname]:]path...
Available for qsub and qalter only, but currently silently ignored by qsh, qrsh,
and qlogin.
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 relative to the current working
directory (if the -cwd switch - see above - is also specified) or to the home
directory. 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; note the lack of an Grid Engine_
prefix in this context:
$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
The tilde sign "~" can be used as an alternative to $HOME, as in csh(1), bash(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).)
-hard 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 normally considered as absolutely essential for the job to commence.
However, 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.
If this option or a corresponding value in qmon is specified then the corresponding
-q and -l resource requirements will be passed to defined JSV instances as
parameter with the names q_hard and l_hard. Find for information in the sections
describing -q and -l. (See -jsv option below or find more information concerning
JSV in jsv(1).)
-h | -h {u|s|o|n|U|O|S}...
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 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 a hold is provided by the qhold(1) facility.
If the job is an 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 submission finishes. (See
-jsv option below or find more information concerning JSV in jsv(1).)
-help Prints a listing of all options.
-hold_jid wc_job_list
Available for qsub, qrsh, and qalter only. See sge_types(5). For the definition of
wc_job_list.
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 patterns, 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. To
remove a job dependency list with qalter, use a null wc_job_list, i.e. use
qalter -hold_jid '' ...
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).)
-hold_jid_ad wc_job_list
Available for qsub, qrsh, and qalter only. See sge_types(5) for the definition of
wc_job_list.
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 dependent jobs
have a different array stride to referenced jobs, the dependency may be many-to-one
or one-to-many, e.g. if an array is submitted with -t 1:50:2, depending on one
submitted with -t 1:50, then task n of the dependent depends on task n+1 of the
other.
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 patterns, 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 return an 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 a parameter with the name hold_jid_ad. (See
-jsv option below or find more information concerning JSV in jsv(1).)
-i [[hostname]:]path,...
Available for qsub, and qalter only.
Defines or redefines the path used for the standard input stream of the job. The
path is handled as described in the -e option for the standard error stream.
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).)
-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 SGE_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
SGE_QMASTER_PORT with the option "-v SGE_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).)
-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.
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 the long form yes was specified
during submission. (See -jsv option below or find more information concerning JSV
in jsv(1).)
-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) 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.
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).)
-jsv jsv_url
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 command line of a client is
executed 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(5).
-l resource=expression,...
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, and section "MATCHING TYPES" in sge_types(5)
describes the possible forms of the expression for the requested resources.
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 no change is made to requests for resources marked as consumable. However
the modification will only be effective 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).)
-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 option arguments 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
-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. The modification
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 jsv(1).)
-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(5). 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, this hard resource
requirement will be passed to defined JSV instances as a parameter with the name
masterq. (See -jsv option above or find more information concerning JSV in
jsv(1).)
-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. This option
provides the running job a configured time interval to do cleanup operations before
receiving the SIGSTOP or SIGKILL. The amount of time delay is controlled by the
notify parameter in each queue configuration (see queue_conf(5)).
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).)
-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.
Jobs submitted with -now y option, can only run on INTERACTIVE queues. -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(5).
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 name "INTERACTIVE"
or "QLOGIN" respectively 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. With
no command, "QRLOGIN" is used.
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).)
-noshell
Available only for qrsh with a command line.
Do not start the command line given to qrsh in the 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 and qalter only, but currently silently ignored by qsh, qrsh,
and qlogin.
Specify the path used for the standard output stream of the job. 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, or
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).)
-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)).
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 P. (See -jsv option
above or find more information concerning JSV in jsv(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 eligible for being dispatched earlier 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).)
-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 parallel_env in sge_types(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.
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 specification 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).)
-pty y[es]|n[o]
Available for qrsh, qsub and qlogin only, and normally only effective for
interactive jobs with the builtin remote startup method (see remote_startup(5)).
-pty yes starts the job in a pseudo terminal (pty). If no pty is available, the job
start fails. -pty no starts the job without a pty. By default, qrsh without a
command and qlogin start the job in a pty, and qrsh or qsub 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).)
-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(5). 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 then 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).)
-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 is limited to that number of the
highest priority jobs.
By default jobs are submitted with -R n.
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 the long form yes was specified
during submission. (See -jsv option above or find more information concerning JSV
in jsv(1).)
-r y[es]|n[o]
Available for qsub and qalter only.
Specifies whether a job can be rerun or not. If the value of -r is 'yes', the job
will be rerun if it gets 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 default), the job will not be rerun under such circumstances. It will still
be rerun if it finishes with exit code 99 unless FORBID_RESCHEDULE is set in
qmaster_params in sge_conf(5).
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 the long form yes was specified
during submission. (See -jsv option above or find more information concerning JSV
in jsv(1).)
-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, but are available in its spool area.
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).)
-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.
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 the long form yes was
specified during submission. (See -jsv option above or find more information
concerning JSV in jsv(1).)
-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 normally considered as absolutely essential for the job to commence.
However, 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. However,
requests for consumable resources cannot be soft.
If this option or a corresponding value in qmon is specified then the corresponding
-q and -l resource requirements will be passed to defined JSV instances as
parameter with the names q_soft and l_soft. Find for information in the sections
describing -q and -l. (See -jsv option above or find more information concerning
JSV in jsv(1).)
-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 an error message to the
standard error stream 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, 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 task 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 an error message to the standard
error stream 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).)
-S [[hostname]:]pathname,...
Available for qsub, qsh and qalter.
Specifies the interpreting shell for the job. pathname must be an executable file
which interprets command-line options -c and -s as /bin/sh does.
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.
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).)
-t n[-m[:s]]
Available for qsub 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 argument of -t specifies the number of array job tasks and
the index number which will be associated with the tasks in terms of the range's
start (n), default 1, its end (m), and stride (s), default 1. The index numbers
will be exported to the job tasks via the environment variable SGE_TASK_ID. The
arguments n, m, and s will be available through the environment variables
SGE_TASK_FIRST, SGE_TASK_LAST and SGE_TASK_STEPSIZE.
The 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 SGE_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 an 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 $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 names t_min, t_max and
t_step (See -jsv option above or find more information concerning JSV in jsv(1).)
-tc max_running_tasks
Available for qsub and qalter only.
Used in conjunction with array jobs (see -t option) to set a self-imposed limit on
the maximum number of concurrently running tasks per job.
If this option, or a corresponding value in qmon is specified, then this value will
be passed to defined JSV instances as a parameter with the name tc. (See the -jsv
option above or find more information concerning JSV in jsv(1).)
-terse Available for qsub only.
Causes 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).)
-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.
-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, 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.
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 verification. (See -jsv
option above or find more information concerning JSV in jsv(1).)
-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 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 verification. (See -jsv
option above or find more information concerning JSV in jsv(1).)
-w e|w|n|p|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 specifiers e, w, n, p, 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 a dry scheduling run on an empty cluster,
ignoring load values.
Resource requests exceeding the configured maximal thresholds or requests for
unavailable resource attributes are possible causes for jobs to fail `v'
validation.
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 this option, or a corresponding value in qmon, is specified, then this value
will be passed to defined JSV instances as a parameter with the name w. (See the
-jsv option above or find more information concerning JSV in jsv(1).)
-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 sge_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).)
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.
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).)
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.
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 CMDARGnumber where number is a integer between 0 and
CMDARGS - 1. (See -jsv option above or find more information concerning JSV in
jsv(1).)
xterm_args
Available for qsh only.
Arguments to the xterm(1) executable, as defined in the configuration. For
details, refer to sge_conf(5)).
Information concerning xterm_args will be available in JSV context as parameters
with the name CMDARGS and CMDARGnumber. Find more information above in section
command_args. (See -jsv option above or find more information concerning JSV in
jsv(1).)
ENVIRONMENT VARIABLES
SGE_ROOT Specifies the location of the Grid Engine standard configuration files.
SGE_CELL If set, specifies the default Grid Engine cell. To address a Grid Engine
cell qsub, qsh, qlogin or qalter use the name of the cell specified in the
environment variable SGE_CELL if that is set, and otherwise the name of the
default cell, i.e. default.
SGE_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.
SGE_QMASTER_PORT
If set, specifies the tcp port on which sge_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.
QRSH_WRAPPER Wrapper for qrsh commands (see above).
SGE_JSV_TIMEOUT
If the response time of the client JSV is greater than this timeout value,
then the JSV will attempt to be re-started. The default value is 10
seconds, and this value must be greater than 0. If the timeout has been
reached, the JSV will only try to re-start once, if the timeout is reached
again an error will occur.
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 several variables of the form
SGE_O_NAME whose value is taken from NAME in the submission environment. For each, a
variable with the same value is added to the job context, but with a lower-case version of
the name, i.e. xqs_name_sxx_o_home in the job context corresponds to xQS_NAME_Sxx_O_HOME
in the job environment, and HOME in the submission environment as follows. The context
variables are displayed by qstat(1) with the -j option.
SGE_O_HOME, SGE_O_HOST, SGE_O_MAIL, SGE_O_PATH, SGE_O_TZ, SGE_O_SHELL, SGE_O_TERM
As in the description of SGE_O_NAME above, but the SGE clients use a
library call to determine to determine the host name if HOST is not set.
Note that there is no guarantee that these are in any way "correct", e.g.
you should not rely on SGE_O_HOST for any sort of access control or
auditing;
SGE_O_LOGNAME As above, but the corresponding context variable is sge_log_name.
SGE_O_WORKDIR The absolute path of the current working directory of the submitting
client, reflected in the context as sge_o_workdir and typically
corresponding to the CWD environment variable.
Grid Engine sets other variables in the job's environment, as follows.
ARC, SGE_ARCH The Grid Engine architecture name of the node on which the job is running.
The name is compiled-in into the sge_execd(8) binary.
SGE_BINDING Contains the selected operating system internal processor numbers. There
might be more than the number of selected cores in the presence of SMT or
CMT because each core could be represented by multiple processor
identifiers. The processor numbers are space-separated.
SGE_CKPT_ENV Specifies the checkpointing environment (as selected with the -ckpt option)
under which a checkpointing job executes. Only set for checkpointing jobs.
SGE_CKPT_DIR Only set for checkpointing jobs. Contains path ckpt_dir (see checkpoint(5))
of the checkpoint interface.
SGE_CWD_PATH Specifies the current working directory where the job was started.
SGE_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.
SGE_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.
SGE_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 SGE_O_HOST in
prolog/epilog scripts to transfer the input file from the submit to the
execution host.
SGE_JOB_SPOOL_DIR
The directory used by sge_shepherd(8) to store job related data during job
execution. This directory is owned by root or by a Grid Engine
administrative account.
SGE_TASK_ID The index number of the current array job task (see -t option above). This
is a 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).
SGE_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).
SGE_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).
SGE_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) database.
HOSTNAME The hostname of the node on which the job is running.
JOB_ID A unique identifier assigned by the sge_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 the basename of the qsub script/binary filename or 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.
JOB_SCRIPT The path to the job script which is executed. The value can not be
overwritten by the -v or -V option.
LOGNAME The user's login name from the passwd database.
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 sge_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 after a system crash, or
after migration of a non-application-level checkpointing job. It is set to
2 when a job with application-level checkpointing is restarted with a
checkpoint available. Otherwise its value is 0.
SHELL The user's login shell from the passwd database. 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.
TERM The terminal type imported from the submission session (only for
interactive jobs).
TZ The time zone variable imported from sge_execd(8) if set.
USER The user's login name from the passwd database.
An additional variable, SGE_JOBEXIT_STAT, is set to the job exit status in the epilog only
(see also sge_conf(5)).
RESTRICTIONS
Without -pty y, 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 ( $?JOB_NAME) then
echo "Grid Engine spooled job"
exit 0
endif
or in your .profile:
if [ ! -z "$JOB_NAME" ] then
echo "Grid Engine spooled job"
exit 0
fi
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/sh
./a.out
The next example is a more complex Grid Engine script.
#!/bin/sh
# 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
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/.sge_aliases cwd path aliases
$cwd/.sge_request cwd default request
$HOME/.sge_aliases user path aliases
$HOME/.sge_request user default request
<sge_root>/<cell>/common/sge_aliases
cluster path aliases
<sge_root>/<cell>/common/sge_request
cluster default request
<sge_root>/<cell>/common/act_qmaster
Grid Engine master host file
SEE ALSO
sge_intro(1), qconf(1), qdel(1), qhold(1), qmod(1), qrls(1), qstat(1), accounting(5),
sge_aliases(5), sge_conf(5), sge_request(5), sge_pe(5), sge_shepherd(8), complex(5),
sge_types(5).
COPYRIGHT
If configured correspondingly, qrsh and qlogin contains 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 sge_intro(1) as well as the information provided in <sge_root>/3rd_party/qrsh and
<sge_root>/3rd_party/qlogin for a statement of further rights and permissions.