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qsub(1B) | PBS | qsub(1B) |
NAME¶
qsub - submit pbs jobSYNOPSIS¶
qsub [-a date_time] [-A account_string] [-b secs] [-c checkpoint_options] [-C directive_prefix] [-d path] [-D path] [-e path] [-f] [-h] [-I] [-j join] [-k keep] [-l resource_list] [-m mail_options] [-M user_list] [-N name] [-o path] [-p priority] [-P proxy_username[:group]] [-q destination] [-r c] [-S path_list] [-t num_jobs] [-T prologue/epilogue script_name] [-u user_list] [-v variable_list] [-V] [-w] path [-W additional_attributes] [-x] [-X] [-z] [script]DESCRIPTION¶
To create a job is to submit an executable script to a batch server. The batch server will be the default server unless the option is specified. See discussion of PBS_DEFAULT under Environment Variables below. Typically, the script is a shell script which will be executed by a command shell such as sh or csh. 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 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_SERVER
- the hostname of the pbs_server which qsub submits the job to.
- 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_ARRAYID
- each member of a job array is assigned a unique identifier (see -t)
- PBS_ENVIRONMENT
- set to to indicate the job is a batch job, or to 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 argument is in the form:
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, is not specified, it will default to the current month if the
specified day is in the future. Otherwise, the month will be set to next
month. Likewise, if the day, is not specified, it will default to today if the
time is in the future. Otherwise, the day will be set to tomorrow. For
example, if you submit a job at 11:15am with a time of the job will be
eligible to run at 11:10am tomorrow.
- -A account_string
- Defines the account string associated with the job. The 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.
- -b seconds
- Defines the maximum number of seconds qsub will block attempting to contact pbs_server. If pbs_server is down, or for a variety of communication failures, qsub will continually retry connecting to pbs_server for job submission. This value overrides the CLIENTRETRY parameter in torque.cfg. This is a non-portable TORQUE extension. Portability-minded users can use the PBS_CLIENTRETRY environmental variable. A negative value is interpreted as infinity. The default is 0.
- -c checkpoint_options
- Defines the options that will apply to the job. If the job executes upon a host which does not support checkpoint, these options will be ignored.
- Valid checkpoint options are:
- none
- No checkpointing is to be performed.
- enabled
- Specify that checkpointing is allowed but must be explicitly invoked by either the qhold or qchkpt commands.
- shutdown
- Specify that checkpointing is to be done on a job at pbs_mom shutdown.
- periodic
- Specify that periodic checkpointing is enabled. The default interval is 10 minutes and can be changed by the $checkpoint_interval option in the mom config file or by specifying an interval when the job is submitted
- interval=minutes
- Checkpointing is to be performed at an interval of which is the integer number of minutes of wall time used by the job. This value must be greater than zero.
- depth=number
- Specify a number (depth) of checkpoint images to be kept in the checkpoint directory.
- dir=path
- Specify a checkpoint directory (default is /var/spool/torque/checkpoint).
- -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 option is presented with a argument that is the null string, qsub will not scan the script file for directives.
- -d path
- Defines the working directory path to be used for the job. If the option is not specified, the default working directory is the home directory. This option sets the environment variable PBS_O_INITDIR.
- -D path
- Defines the root directory to be used for the job. This option sets the environment variable PBS_O_ROOTDIR.
- -e path
- Defines the path to be used for the standard error stream
of the batch job. The argument is of the form:
- 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 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:path_name
- Where path_name specifies an absolute path name, the path will be used as specified.
- hostname:
- Where hostname specifies the name of the host that the file should be returned to. The path will be the default file name.
- If the option is not specified or the path_name is
not specified or is specified and is a directory, the default file name
for the standard error stream will be used. The default name has the
following form:
- -f
- Specifies that the job is fault tolerant. The attribute will be set to true, which indicates that the job can survive the loss of a mom other than the "mother superior" mom (the first node in the exec hosts )
- -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. Interactive jobs are forced to not rerunable. 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 directs that the two streams will be merged, intermixed, as standard output. An option argument value of directs that the two streams will be merged, intermixed, as standard error.
- If the argument is 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 argument is of the form:
- -m mail_options
- Defines the set of conditions under which the execution server will send a mail message about the job. The 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 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 argument is of the form:
- -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 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
- -o path
- Defines the path to be used for the standard output stream
of the batch job. The argument is of the form:
- 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 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:path_name
- Where path_name specifies an absolute path name, the path will be used as specified.
- hostname:
- Where hostname specifies the name of the host that the file should be returned to. The path will be the default file name.
- If the option is not specified or the path_name is
not specified or is specified and is a directory, the default file name
for the standard output stream will be used. The default name has the
following form:
- -p priority
- Defines the priority of the job. The argument must be a integer between -1024 and +1023 inclusive. The default is no priority which is equivalent to a priority of zero.
- -P proxy_user[:group]
- Proxy user for whom the job should be submitted. This option is only available for the super user.
- -q destination
- Defines the destination of the job. The names a queue, a server, or a queue at a server.
- The qsub command will submit the script to the server defined by the argument. If the destination is a routing queue, the job may be routed by the server to a new destination.
- If the 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 option is specified, it is in one of the following
three forms:
- If the 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 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 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 or
- 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 is in the form:
- If the option is not specified, the option argument is the null string, or no entry from the is selected, the execution will use the user's login shell on the execution host.
- -t array_request
- Specifies the task ids of a job array. Single task arrays are allowed.
- The argument is an integer id or a range of integers. Multiple ids or id ranges can be combined in a comma delimted list. Examples : -t 1-100 or -t 1,10,50-100
- -T script_name
- Allows for per job prologue and epilogue scripts. The full script name will be prologue.[name] or epilogue.[name]. For the job submission, only request the name of the prologue or epilogue script.
- Example:
- -u user_list
- Defines the user name under which the job is to run on the execution system.
- The argument is of the form:
- -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, names environment variables from the qsub command environment which are made available to the job when it executes. The is a comma separated list of strings of the form or 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 path
- Defines the working directory path to be used for the job. If the option is not specified, the default working directory is the current directory. This option sets the environment variable PBS_O_WORKDIR.
- -W additional_attributes
- The -W option allows for the specification of additional
job attributes. The general syntax of the -W is in the form:
- PBS currently supports the following attributes within the -W option.
- 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.
- -x
- When running an interactive job, the -x flag makes it so that the script won't be parsed for PBS directives, but instead will be a command that is launched once the interactive job has started. The job will terminate at the completion of this command.
- -X
- Enables X11 forwarding. The DISPLAY environment variable must be set.
- -z
- Directs that the qsub command is not to write the job
identifier assigned to the job to the command's standard output.
OPERANDS¶
The qsub command accepts a operand that is the path to the script of the job. If the path is relative, it will be expanded relative to the working directory of the qsub command. If the 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¶
The qsub command reads the script for the job from standard input if the operand is missing or is the single character "-".INPUT FILES¶
The file is read by the qsub command. Qsub acts upon any directives found in the script. When the job is created, a copy of the script file is made and that copy cannot be modified.STANDARD OUTPUT¶
Unless the option is set, the job identifier assigned to the job will be written to standard output if the job is successfully created.STANDARD ERROR¶
The qsub command will write a diagnostic message to standard error for each error occurrence.ENVIRONMENT VARIABLES¶
The values of some or all of the variables in the qsub command's environment are exported with the job, see the -v and -V options. 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. The environment variable PBS_CLIENTRETRY defines the maximum number of seconds qsub will block. See the -b option above. Despite the name, currently qsub is the only client that supports this option.TORQUE.CFG¶
The torque.cfg file, located in PBS_SERVER_HOME (/var/spool/torque by default) controls the behavior of the qsub command. This file contains a list of parameters and values separated by whitespace QSUBSLEEP takes an integer operand which specifies time to sleep when running qsub command. Used to prevent users from overwhelming the scheduler. SUBMITFILTER specifies the path to the submit filter used to pre-process job submission. The default path is $(libexecdir)/qsub_filter, which falls back to /usr/local/sbin/torque_submitfilter for backwards compatibility. This torque.cfg parameter overrides this default. SERVERHOST specifies the value for the PBS_SERVER environment variable QSUBHOST specifies the hostname for the jobs QSUB_O_HOST variable QSUBSENDUID specifies a uid to use for the jobs PBS_O_UID variable XAUTHPATH specifies the path to xauth CLIENTRETRY specifies the integer seconds between retry attempts to communicate with pbs_server VALIDATEGROUP set this parameter to force qsub to verify the submitter's group id DEFAULTCKPT specifies the default value for the jobs checkpoint attribute. The user overrides this with the -c qsub option. VALIDATEPATH set this parameter to force qsub to validate local existence of a "-d" working directory RERUNNABLEBYDEFAULT this parameter specifies if a job is rerunnable by default. The default is true, setting this to false causes the rerunnable attribute value to be false unless the users specifies otherwise with the -r option FAULT_TOLERANT_BY_DEFAULT this parameter specifies if a job is fault tolerant by default. The default value for the fault_tolerant job attribute is false, setting this parameter to true causes the default value of the attribute to be true. The user can specify their preference with the -f qsub option. For example: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:- (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.
- ~.
- 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¶
Upon successful processing, the qsub exit status will be a value of zero. If the qsub command fails, the command exits with a value greater than zero.SEE ALSO¶
qalter(1B), qdel(1B), qhold(1B), qmove(1B), qmsg(1B), qrerun(1B), qrls(1B), qselect(1B), qsig(1B), qstat(1B), pbs_connect(3B), pbs_job_attributes(7B), pbs_queue_attributes(7B), pbs_resources_irix5(7B), pbs_resources_sp2(7B), pbs_resources_sunos4(7B), pbs_resources_unicos8(7B), pbs_server_attributes(7B), and pbs_server(8B)Local |