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 user[:group]] [-q destination] [-r c] [-S path_list] [-t array_request] [-u user_list] [-v variable_list] [-V ] [-W additional_attributes] [-X] [-z] [script]
To create a job is to submit an executable script to a batch server. The batch server will be the default server unless the -q 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.
The qsub command will pass certain environment variables in the 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.
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.
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:
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.
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".
If the character "n" is specified, no normal mail is sent. Mail for job cancels and other events outside of normal job processing are still sent.
For the letters "a", "b", and "e":
If the -m option is not specified, mail will be sent if the job is aborted.
The user_list argument is of the form:
If unset, the list defaults to the submitting user at the qsub host, i.e. the job owner.
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.
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:
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:
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.
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:
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.
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.
The option argument path_list is in the form:
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 users login shell on the execution host.
The array_request 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.
An optional slot limit can be specified to limit the amount of jobs that can run concurrently in the job array. The default value is unlimited. The slot limit must be the last thing specified in the array_request and is delimited from the array by a percent sign (%).
qsub script.sh -t 0-299%5
The user_list argument is of the form:
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.
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.
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.
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 preceding colon need not be specified), the dependency of the corresponding type is cleared (unset). These are the valid dependencies:
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.
Array dependencies make a job depend on an array or part of an array. If no count is given, then the entire array is assumed. Array dependency examples are here.
If any of the before forms are used, the jobs referenced by arrayid must have been submitted with a dependency type of on. If any of the before forms are used, the jobs referenced by arrayid must have the same owner as the job being submitted. Otherwise, the dependency is ignored.
Error processing of the existence, state, or condition of he 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.
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 group_list defaults to the primary group of the user under which the job will be run.
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 users 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:
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.
The qsub command accepts a script 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 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.
The qsub command reads the script for the job from standard input if the script operand is missing or is the single character "-".
The script 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.
Unless the -z option is set, the job identifier assigned to the job will be written to standard output if the job is successfully created.
The qsub command will write a diagnostic message to standard error for each error occurrence.
The values of some or all of the variables in the qsub commands 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.
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.
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.
If the -C option is found in a directive in the script file, it will be ignored.
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:
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
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:
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.
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)
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