qsub-torque (1) - Linux Manuals
qsub-torque: submit pbs job
NAME
qsub - submit pbs job
SYNOPSIS
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 node exclusive] [-N name] [-o path] [-p priority] [-P proxy_username[:group]] [-q destination] [-r c] [-S path_list] [-t array_request] [-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.
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:
where is the name of a host to which the file will be returned and 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 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.
- Where path_name specifies an absolute path name, the path will be used as specified. hostname:
where job_name is the name of the job, see option, and sequence_number is the job number assigned when the job is submitted.
-
- 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
-
- 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 unset, the list defaults to the submitting user at the qsub host, i.e. the job owner.
where is the name of a host to which the file will be returned and is the path name on that host in the syntax recognized by POSIX. The argument will be interpreted as follows:
-
- path_name
where job_name is the name of the job, see option, and sequence_number is the job number assigned when the job is submitted.
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.
Specifies to use the script prologue.prescript
Only one user name may be given per specified host. Only one of the specifications may be supplied without the corresponding 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.
Note if white space occurs anywhere within the option argument string or the equal sign, "=", occurs within an string, then the string must be enclosed with either single or double quote marks.
Defines the dependency between this and other jobs. The is in the form:
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 it will be expanded according to the default server rules which apply to job IDs on most commands. If argument is null (the preceding colon need not be specified), the dependency of the corresponding 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.
- Array Dependencies
- It is now possible to have a job depend on an array. These dependencies are in the form depend=arraydep:arrayid[num]. If [num] is not present, then the dependencies applies to the entire array. If [num] is present, then num means the number of jobs that must meet the condition for the dependency to be satisfied.
- afterstartarray:arrayid[count]
- This job may be scheduled for execution only after jobs in arrayid have started execution.
- afterokarray:arrayid[count]
- This job may be scheduled for execution only after jobs in arrayid have terminated with no errors.
- afternotok:arrayid[count]
- This job may be scheduled for execution only after jobs in arrayid have terminated with errors.
- afteranyarray:arrayid[count]
- This job may be scheduled for execution after jobs in array id have terminated, with or without errors.
- beforestartarray:arrayid[count]
- This job may be scheduled for execution only before jobs in arrayid have started execution.
- beforeokarray:arrayid[count]
- This job may be scheduled for execution only before jobs in arrayid have terminated with no errors.
- beforenotok:arrayid[count]
- This job may be scheduled for execution only before jobs in arrayid have terminated with errors.
- beforeanyarray:arrayid[count]
- This job may be scheduled for execution before jobs in array id have terminated, with or without errors.
- 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:
Defines the group name under which the job is to run on the execution system. The argument is of the form:
Only one group name may be given per specified host. Only one of the specifications may be supplied without the corresponding specification. That group name will used for execution on any host not named in the argument list. If not set, the
If the interactive attribute is specified, the job is an interactive job. The -I option is a alternative method of specifying this attribute.
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
regardless of the direction of the copy. The name 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 is the destination name on the host specified by 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
Data staging examples:
If TORQUE has been compiled with wordexp support, then variables can be used in the specified paths. Currently only $PBS_JOBID, $HOME, and $TMPDIR are supported for stagein.
Sets umask used to create stdout and stderr spool files in pbs_mom spool directory. Values starting with 0 are treated as octal values, otherwise the value is treated as a decimal umask value.
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 whitespaceQSUBSLEEP 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:
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 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
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
and the following line as the last executable line in .logout
Interactive Jobs:
If the option is specified on the command line or in a script directive, or if the "interactive" job attribute declared true via the -W option, 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.
Once 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
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)