qsub

NAME

SYNOPSIS

DESCRIPTION

Options on the qsub command allow the specification of attributes which affect the behavior of the job.

The qsub command will pass certain environment variables in the AT&T System Variable_List attribute of the job. These variables will be available to the job. The value for the following variables will be taken from the environment of the qsub command: HOME, LANG, LOGNAME, PATH, MAIL, SHELL, and TZ. These values will be assigned to a new name which is the current name prefixed with the string "PBS_O_". For example, the job will have access to an environment variable named PBS_O_HOME which have the value of the variable HOME in the qsub command environment.

In addition to the above, the following environment variables will be available to the batch job.

PBS_O_HOST

the name of the host upon which the qsub command is running.

PBS_O_QUEUE

the name of the original queue to which the job was submitted.

PBS_O_WORKDIR

the absolute path of the current working directory of the qsub command.

PBS_ENVIRONMENT

set to PBS_BATCH to indicate the job is a batch job, or to PBS_INTERACTIVE to indicate the job is a PBS interactive job, see -I option.

PBS_JOBID

the job identifier assigned to the job by the batch system.

PBS_JOBNAME

the job name supplied by the user.

PBS_NODEFILE

the name of the file contain the list of nodes assigned to the job (for parallel and cluster systems).

PBS_QUEUE

the name of the queue from which the job is executed.

OPTIONS

-a date_time

Declares the time after which the job is eligible for execution.

The date_time argument is in the form: [[[[CC]YY]MM]DD]hhmm[.SS]

Where CC is the first two digits of the year (the century), YY is the second two digits of the year, MM is the two digits for the month, DD is the day of the month, hh is the hour, mm is the minute, and the optional SS is the seconds.

If the month, MM , is not specified, it will default to the current month if the specified day DD , is in the future. Otherwise, the month will be set to next month. Likewise, if the day, DD , is not specified, it will default to today if the time hhmm is in the future. Otherwise, the day will be set to tomorrow. For example, if you sumit a job at 11:15am with a time of -a 1110 , the job will be eligable to run at 11:10am tomorrow.

-A account_string

Defines the account string associated with the job. The account_string is an undefined string of characters and is interpreted by the server which executes the job. See section 2.7.1 of the PBS ERS.

-c interval

Defines the interval at which the job will be checkpointed. If the job executes upon a host which does not support checkpoint, this option will be ignored.

The interval argument is specified as:

n

No checkpointing is to be performed.

s

Checkpointing is to be performed only when the server executing the job is shutdown.

c

Checkpointing is to be performed at the default minimum time for the server executing the job.

c=minutes

Checkpointing is to be performed at an interval of minutes which is the integer number of minutes of CPU time used by the job. This value must be greater than zero.

-C directive_prefix

Defines the prefix that declares a directive to the qsub command within the script file. See the paragraph on script directives in the Extended Description section.

If the -C option is presented with a directive_prefix argument that is the null string, qsub will not scan the script file for directives.

-e path

Defines the path to be used for the standard error stream of the batch job. The path argument is of the form:
    [hostname:]path_name
where hostname is the name of a host to which the file will be returned and path_name is the path name on that host in the syntax recognized by POSIX. The argument will be interpreted as follows:

path_name

Where path_name is not an absolute path name, then the qsub command will expand the path name relative to the current working directory of the command. The command will supply the name of the host upon which it is executing for the hostname component.

hostname:path_name

Where path_name is not an absolute path name, then the qsub command will not expand the path name relative to the current working directory of the command. On delivery of the standard error, the path name will be expanded relative to the user's home directory on the hostname system.

path_name

Where path_name specifies an absolute path name, then the qsub will supply the name of the host on which it is executing for the hostname

hostname:path_name

Where path_name specifies an absolute path name, the path will be used as specified.

If the -e option is not specified, the default file name for the standard error stream will be used. The default name has the following form:
    job_name.esequence_number
where job_name is the name of the job, see -N option, and sequence_number is the job number assigned when the job is submitted.

-h

Specifies that a user hold be applied to the job at submission time.

-I

Declares that the job is to be run "interactively". The job will be queued and scheduled as any PBS batch job, but when executed, the standard input, output, and error streams of the job are connected through qsub to the terminal session in which qsub is running. See the "Extended Description" paragraph for addition information of interactive jobs.

-j join

Declares if the standard error stream of the job will be merged with the standard output stream of the job.

An option argument value of oe directs that the two streams will be merged, intermixed, as standard output. An option argument value of eo directs that the two streams will be merged, intermixed, as standard error.

If the join argument is n or the option is not specified, the two streams will be two separate files.

-k keep

Defines which (if either) of standard output or standard error will be retained on the execution host. If set for a stream, this option overrides the path name for that stream. If not set, neither stream is retained on the execution host.

The argument is either the single letter "e" or "o", or the letters "e" and "o" combined in either order. Or the argument is the letter n.

e

The standard error stream is to retained on the execution host. The stream will be placed in the home directory of the user under whose user id the job executed. The file name will be the default file name given by: job_name.esequence where job_name is the name specified for the job, and sequence is the sequence number component of the job identifier.

o

The standard output stream is to retained on the execution host. The stream will be placed in the home directory of the user under whose user id the job executed. The file name will be the default file name given by: job_name.osequence where job_name is the name specified for the job, and sequence is the sequence number component of the job identifier.

eo

Both the standard output and standard error streams will be retained.

oe

Both the standard output and standard error streams will be retained.

n

Neither stream is retained.

-l resource_list

Defines the resources that are required by the job and establishes a limit to the amount of resource that can be consumed. If not set for a generally available resource, such as CPU time, the limit is infinite. The resource_list argument is of the form:
    resource_name[=[value]][,resource_name[=[value]],...]

-m mail_options

Defines the set of conditions under which the execution server will send a mail message about the job. The mail_options argument is a string which consists of either the single character "n", or one or more of the characters "a", "b", and "e".

If the character "n" is specified, no mail will be sent.

For the letters "a", "b", and "e":

a

mail is sent when the job is aborted by the batch system.

b

mail is sent when the job begins execution.

e

mail is sent when the job terminates.

If the -m option is not specified, mail will be sent if the job is aborted.

-M user_list

Declares the list of users to whom mail is sent by the execution server when it sends mail about the job.

The user_list argument is of the form:
    user[@host][,user[@host],...]
If unset, the list defaults to the submitting user at the qsub host, i.e. the job owner.

-N name

Declares a name for the job. The name specified may be up to and including 15 characters in length. It must consist of printable, non white space characters with the first character alphabetic.

If the -N option is not specified, the job name will be the base name of the job script file specified on the command line. If no script file name was specified and the script was read from the standard input, then the job name will be set to STDIN .

-o path

Defines the path to be used for the standard output stream of the batch job. The path argument is of the form:
    [hostname:]path_name
where hostname is the name of a host to which the file will be returned and path_name is the path name on that host in the syntax recognized by POSIX. The argument will be interpreted as follows:

path_name

Where path_name is not an absolute path name, then the qsub command will expand the path name relative to the current working directory of the command. The command will supply the name of the host upon which it is executing for the hostname component.

hostname:path_name

Where path_name is not an absolute path name, then the qsub command will not expand the path name relative to the current working directory of the command. On delivery of the standard output, the path name will be expanded relative to the user's home directory on the hostname system.

path_name

Where path_name specifies an absolute path name, then the qsub will supply the name of the host on which it is executing for the hostname

hostname:path_name

Where path_name specifies an absolute path name, the path will be used as specified.

If the -o option is not specified, the default file name for the standard output stream will be used. The default name has the following form:
    job_name.osequence_number
where job_name is the name of the job, see -N option, and sequence_number is the job number assigned when the job is submitted.

-p priority

Defines the priority of the job. The priority argument must be a integer between -1024 and +1023 inclusive. The default is no priority which is equivalent to a priority of zero.

-q destination

Defines the destination of the job. The destination names a queue, a server, or a queue at a server.

The qsub command will submit the script to the server defined by the destination argument. If the destination is a routing queue, the job may be routed by the server to a new destination.

If the -q option is not specified, the qsub command will submit the script to the default server. See PBS_DEFAULT under the Environment Variables section on this man page and the PBS ERS section 2.7.4, "Default Server".

If the -q option is specified, it is in one of the following three forms:
    queue
    @server
    queue@server

If the destination argument names a queue and does not name a server, the job will be submitted to the named queue at the default server.

If the destination argument names a server and does not name a queue, the job will be submitted to the default queue at the named server.

If the destination argument names both a queue and a server, the job will be submitted to the named queue at the named server.

-r y|n

Declares whether the job is rerunable. See the qrerun command. The option argument is a single character, either y or n .

If the argument is "y", the job is rerunable. If the argument is "n", the job is not rerunable. The default value is 'y', rerunable.

-S path_list

Declares the shell that interprets the job script.

The option argument path_list is in the form:
    path[@host][,path[@host],...]
Only one path may be specified for any host named. Only one path may be specified without the corresponding host name. The path selected will be the one with the host name that matched the name of the execution host. If no matching host is found, then the path specified without a host will be selected, if present.

If the -S option is not specified, the option argument is the null string, or no entry from the path_list is selected, the execution will use the user's login shell on the execution host.

-u user_list

Defines the user name under which the job is to run on the execution system.

The user_list argument is of the form:
    user[@host][,user[@host],...]
Only one user name may be given per specified host. Only one of the user specifications may be supplied without the corresponding host specification. That user name will used for execution on any host not named in the argument list. If unset, the user list defaults to the user who is running qsub.

-v variable_list

Expands the list of environment variables that are exported to the job.

In addition to the variables described in the "Description" section above, variable_list names environment variables from the qsub command environment which are made available to the job when it executes. The variable_list is a comma separated list of strings of the form variable or variable=value . These variables and their values are passed to the job.

-V

Declares that all environment variables in the qsub command's environment are to be exported to the batch job.

-W additional_attributes

The -W option allows for the specification of additional job attributes. The general syntax of the -W is in the form:
    -W attr_name=attr_value[,attr_name=attr_value...]
Note if white space occurs anywhere within the option argument string or the equal sign, "=", occurs within an attribute_value string, then the string must be enclosed with either single or double quote marks.

PBS currently supports the following attributes within the -W option.

depend=dependency_list
Defines the dependency between this and other jobs. The dependency_list is in the form:
type[:argument[:argument...][,type:argument...] .
The argument is either a numeric count or a PBS job id according to type . If argument is a count, it must be greater than 0. If it is a job id and not fully specified in the form seq_number.server.name , it will be expanded according to the default server rules which apply to job IDs on most commands. If argument is null (the preceeding colon need not be specified), the dependency of the cooresponding type is cleared (unset).

synccount:count

This job is the first in a set of jobs to be executed at the same time. Count is the number of additional jobs in the set.

syncwith:jobid

This job is an additional member of a set of jobs to be executed at the same time. In the above and following dependency types, jobid is the job identifier of the first job in the set.

after:jobid[:jobid...]

This job may be scheduled for execution at any point after jobs jobid have started execution.

afterok:jobid[:jobid...]

This job may be scheduled for execution only after jobs jobid have terminated with no errors. See the csh warning under "Extended Description".

afternotok:jobid[:jobid...]

This job may be scheduled for execution only after jobs jobid have terminated with errors. See the csh warning under "Extended Description".

afterany:jobid[:jobid...]

This job may be scheduled for execution after jobs jobid have terminated, with or without errors.

on:count

This job may be scheduled for execution after count dependencies on other jobs have been satisfied. This form is used in conjunction with one of the before forms, see below.

before:jobid[:jobid...]

When this job has begun execution, then jobs jobid... may begin.

beforeok:jobid[:jobid...]

If this job terminates execution without errors, then jobs jobid... may begin. See the csh warning under "Extended Description".

beforenotok:jobid[:jobid...]

If this job terminates execution with errors, then jobs jobid... may begin. See the csh warning under "Extended Description".

beforeany:jobid[:jobid...]

When this job terminates execution, jobs jobid... may begin.

If any of the before forms are used, the jobs referenced by jobid must have been submitted with a dependency type of on.

If any of the before forms are used, the jobs referenced by jobid must have the same owner as the job being submitted. Otherwise, the dependency is ignored.

Error processing of the existence, state, or condition of the job on which the newly submitted job is a deferred service, i.e. the check is performed after the job is queued. If an error is detected, the new job will be deleted by the server. Mail will be sent to the job submitter stating the error.

Dependency examples:
qsub -W depend=afterok:123.big.iron.com /tmp/script
qsub -W depend=before:234.hunk1.com:235.hunk1.com /tmp/script

group_list=g_list
Defines the group name under which the job is to run on the execution system. The g_list argument is of the form:
group[@host][,group[@host],...]
Only one group name may be given per specified host. Only one of the group specifications may be supplied without the corresponding host specification. That group name will used for execution on any host not named in the argument list. If not set, the AT&T System group_list defaults to the primary group of the user under which the job will be run.

interactive=true
If the interactive attribute is specified, the job is an interactive job. The -I option is a alternative method of specifying this attribute.

stagein=file_list
stageout=file_list
Specifies which files are staged (copied) in before job start or staged out after the job completes execution. On completion of the job, all staged-in and staged-out files are removed from the execution system. The file_list is in the form
local_file@hostname:remote_file[,...]
regardless of the direction of the copy. The name local_file is the name of the file on the system where the job executed. It may be an absolute path or relative to the home directory of the user. The name remote_file is the destination name on the host specified by hostname . The name may be absolute or relative to the user's home directory on the destination host. The use of wildcards in the file name is not recommended. The file names map to a remote copy program (rcp) call on the execution system in the follow manner:
For stagein: rcp hostname:remote_file local_file
For stageout: rcp local_file hostname:remote_file

-z

Directs that the qsub command is not to write the job identifier assigned to the job to the command's standard output.

OPERANDS

If the script operand is not provided or the operand is the single character "-", the qsub command reads the script from standard input. When the script is being read from Standard Input, qsub will copy the file to a temporary file. This temporary file is passed to the library interface routine pbs_submit. The temporary file is removed by qsub after pbs_submit returns or upon the receipt of a signal which would cause qsub to terminate.  

STANDARD INPUT

INPUT FILES

When the job is created, a copy of the script file is made and that copy cannot be modified.  

STANDARD OUTPUT

STANDARD ERROR

ENVIRONMENT VARIABLES

The environment variable PBS_DEFAULT defines the name of the default server. Typically, it corresponds to the system name of the host on which the server is running. If PBS_DEFAULT is not set, the default is defined by an administrator established file.

The environment variable PBS_DPREFIX determines the prefix string which identifies directives in the script.  

EXTENDED DESCRIPTION

Script Processing:

A job script may consist of PBS directives, comments and executable statements. A PBS directive provides a way of specifying job attributes in addition to the command line options. For example:

:
#PBS -N Job_name
#PBS -l walltime=10:30,mem=320kb
#PBS -m be
#
step1 arg1 arg2
step2 arg3 arg4

The qsub command scans the lines of the script file for directives. An initial line in the script that begins with the characters "#!" or the character ":" will be ignored and scanning will start with the next line. Scanning will continue until the first executable line, that is a line that is not blank, not a directive line, nor a line whose first non white space character is "#". If directives occur on subsequent lines, they will be ignored.

A line in the script file will be processed as a directive to qsub if and only if the string of characters starting with the first non white space character on the line and of the same length as the directive prefix matches the directive prefix.

The remainder of the directive line consists of the options to qsub in the same syntax as they appear on the command line. The option character is to be preceded with the "-" character.

If an option is present in both a directive and on the command line, that option and its argument, if any, will be ignored in the directive. The command line takes precedence.

If an option is present in a directive and not on the command line, that option and its argument, if any, will be processed as if it had occurred on the command line.

The directive prefix string will be determined in order of preference from:

The value of the -C option argument if the option is specified on the command line.

The value of the environment variable PBS_DPREFIX if it is defined.

The four character string #PBS .

User Authorization:

When the user submits a job from a system other than the one on which the PBS Server is running, the name under which the job is to be executed is selected according to the rules listed under the -u option. The user submitting the job must be authorized to run the job under the execution user name. This authorization is provided if

(1)

The host on which qsub is run is trusted by the execution host (see /etc/hosts.equiv),

(2)

The execution user has an .rhosts file naming the submitting user on the submitting host.

C-Shell .logout File:

The following warning applies for users of the c-shell, csh. If the job is executed under the csh and a .logout file exists in the home directory in which the job executes, the exit status of the job is that of the .logout script, not the job script. This may impact any inter-job dependencies. To preserve the job exit status, either remove the .logout file or place the following line as the first line in the .logout file
   set EXITVAL = $status
and the following line as the last executable line in .logout
   exit $EXITVAL

Interactive Jobs:

If the -I option is specified on the command line or in a script directive, or if the "interactive" job attribute declared true via the -W option, -W interactive=true , either on the command line or in a script directive, the job is an interactive job. The script will be processed for directives, but will not be included with the job. When the job begins execution, all input to the job is from the terminal session in which qsub is running.

When an interactive job is submitted, the qsub command will not terminate when the job is submitted. Qsub will remain running until the job terminates, is aborted, or the user interrupts qsub with an SIGINT (the control-C key). If qsub is interrupted prior to job start, it will query if the user wishes to exit. If the user response "yes", qsub exits and the job is aborted.

One the interactive job has started execution, input to and output from the job pass through qsub. Keyboard generated interrupts are passed to the job. Lines entered that begin with the tilde ('~') character and contain special sequences are escaped by qsub. The recognized escape sequences are:

~.

Qsub terminates execution. The batch job is also terminated.

~susp

Suspend the qsub program if running under the C shell. "susp" is the suspend character, usually CNTL-Z.

~asusp

Suspend the input half of qsub (terminal to job), but allow output to continue to be displayed. Only works under the C shell. "asusp" is the auxiliary suspend character, usually CNTL-Y.

EXIT STATUS

If the qsub command fails, the command exits with a value greater than zero.  

SEE ALSO

Index

NAME

SYNOPSIS

DESCRIPTION

OPTIONS

OPERANDS

STANDARD INPUT

INPUT FILES

STANDARD OUTPUT

STANDARD ERROR

ENVIRONMENT VARIABLES

EXTENDED DESCRIPTION

EXIT STATUS

SEE ALSO