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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queuedefs(4)						     Kernel Interfaces Manual						      queuedefs(4)

NAME
queuedefs - Queue description file for at, batch, and cron commands DESCRIPTION
The queuedefs file describes the characteristics of the queues managed by cron or specifies other characteristics for cron. Each noncom- ment line in this file describes either one queue or a cron characteristic. Each uncommented line should be in one of the following for- mats. q.[njobj][nicen][nwaitw] max_jobs=mjobs log=lcode The fields in these lines are as follows: The name of the queue. Defined queues are as follows: The default queue for jobs started by at The default queue for jobs started by batch The default queue for jobs run from a crontab file Queues d to z are also available for local use. The maximum number of jobs that can be run simultaneously in the queue; if more than njob jobs are ready to run, only the first njob jobs will be run. The others will be initiated as currently running jobs ter- minate. The nice(1) value to give to all jobs in the queue that are not run with a user ID of superuser. The number of seconds to wait before rescheduling a job that was deferred because more than njob jobs were running in that queue, or because the system-wide limit of jobs executing (max_jobs) has been reached. The maximum number of active jobs from all queues that may run at any one time. The default is 25 jobs. Logging level of messages sent to a log file. The default is 4. Defined levels are as follows: level-code level 0 None 1 Low 2 Medium 3 High 4 Full Lines beginning with # are comments, and are ignored. EXAMPLES
The following file specifies that the b queue, for batch jobs, can have up to 50 jobs running simultaneously; that those jobs will be run with a nice value of 20. If a job cannot be run because too many other jobs are running, cron will wait 60 seconds before trying again to run it. All other queues can have up to 100 jobs running simultaneously; they will be run with a nice value of 2. If a job cannot be run because too many other jobs are running cron will wait 60 seconds before trying again to run it. b.50j20n60w The following file specifies that a total of 25 active jobs will be allowed by cron over all the queues at any one time, and cron will log all messages to the log file. The last two lines are comments that are ignored. max_jobs=25 log=4 # This is a comment # And so is this FILES
Main cron directory The default location for the queue description file. RELATED INFORMATION
Commands: at(1), cron(8), crontab(1), nice(1) delim off queuedefs(4)