Unix Batch command, and running jobs in queues.


 
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Old 10-21-2009
Unix Batch command, and running jobs in queues.

Hello all, I have a quick question. I work in a computational science laboratory, and we recently got a few mac pros to do molecular optimizations on. However, on our normal supercomputers, there are queue systems, mainly PBS.

Anyway, the macs obviously don't have PBS, but I've read about the "batch" and "at" commands in unix.

What I want to do is create a batch file, with multiple commands in it (basically multiple job submit commands), and I want the first one to run immediately, and the second one to run as soon as the first one finishes.

I know that there are different queues used with this command. Accessed by the "-q x" where x is the queue you want. So technically I want to have two different queues cause I want two different jobs to run at the same time.

So I've made a batch file containing four lines that submit four different jobs, like so...

g09 model1.txt &
g09 model2.txt &
g09 model3.txt &
g09 model4.txt &
CTRL-d

However, when I submit it, I don't see anything running when I use the top command, like I do when I just submit the job without using batch. The command I used to submit the batch file was.

batch -q b -f batch1.txt

And I'm in the folder that "batch1.txt" is in. What am I doing wrong?

Thanks in advance...
 
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QMOD(1) 						   Sun Grid Engine User Commands						   QMOD(1)

NAME
qmod - modify a Sun Grid Engine queue and running job SYNTAX
qmod [ options ] [ wc_job_range_list | wc_queue_list ] DESCRIPTION
Qmod enables users classified as owners (see queue_conf(5) for details) of a workstation to modify the state of Sun Grid Engine queues for his/her machine as well as the state of his/her own jobs. A manager/operator or root can execute qmod for any queue and job in a cluster but only from administrative hosts. Find additional information concerning wc_queue_list and wc_job_list in sge_types(1). OPTIONS
-c Note: Deprecated, may be removed in future release. Please use the -cj or -cq switch instead. Clears the error state of the specified jobs(s)/queue(s). -cj Clears the error state of the specified jobs(s). -cq Clears the error state of the specified queue(s). -d Disables the queue(s), i.e. no further jobs are dispatched to disabled queues while jobs already executing in these queues are allowed to finish. -e Enables the queue(s). -f Force the modification action for the queue despite the apparent current state of the queue. For example if a queue appears to be suspended but the job execution seems to be continuing the manager/operator can force a suspend operation which will send a SIGSTOP to the jobs. In any case, the queue or job status will be set even if the sge_execd(8) controlling the queues/jobs cannot be reached. Requires manager/operator privileges. -help Prints a listing of all options. -r Note: Deprecated, may be removed in future release. Please use the -rj or -rq switch instead. If applied to queues, reschedules all jobs currently running in this queue. If applied to running jobs, reschedules the jobs. Requires root or manager privileges. In order for a job to be rescheduled, it or the queue in which it is executing must have the rerun flag activated. (See -r option in the qsub(1) man page and the rerun option in the queue_conf(5) man page for more informa- tion.) Additional restrictions apply for parallel and checkpointing jobs. (See the reschedule_unknown description in the sge_conf(5) man page for details). -rj If applied to running jobs, reschedules the jobs. Requires root or manager privileges. -rq If applied to queues, reschedules all jobs currently running in this queue. Requires root or manager privileges. -s Note: Deprecated, may be removed in future release. Please use the -sj or -sq switch instead. If applied to queues, suspends the queues and any jobs which might be active. If applied to running jobs, suspends the jobs. -sj If applied to running jobs, suspends the jobs. If a job is both suspended explicitly and via suspension of its queue, a following unsuspend of the queue will not release the suspension state on the job. -sq If applied to queues, suspends the queues and any jobs which might be active. -us Note: Deprecated, may be removed in future release. Please use the -usj or -usq switch instead. If applied to queues, unsuspends the queues and any jobs which might be active. If applied to jobs, unsuspends the jobs. -usj If applied to jobs, unsuspends the jobs. If a job is both suspended explicitly and via suspension of its queue, a following unsus- pend of the queue will not release the suspension state on the job. -usq If applied to queues, unsuspends the queues and any jobs which might be active. ENVIRONMENTAL VARIABLES
SGE_ROOT Specifies the location of the Sun Grid Engine standard configuration files. SGE_CELL If set, specifies the default Sun Grid Engine cell. To address a Sun Grid Engine cell qmod uses (in the order of prece- dence): The name of the cell specified in the environment variable SGE_CELL, if it is set. 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 infor- mation 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. FILES
<sge_root>/<cell>/common/act_qmaster Sun Grid Engine master host file SEE ALSO
sge_intro(1), sge_ckpt(1), qstat(1), queue_conf(5), sge_execd(8), sge_types(1). COPYRIGHT
See sge_intro(1) for a full statement of rights and permissions. SGE 6.2u5 $Date$ QMOD(1)