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Full Discussion: create an input file
Top Forums UNIX for Dummies Questions & Answers create an input file Post 302286289 by stonna on Tuesday 10th of February 2009 05:43:24 PM
Old 02-10-2009
Hi Jim,

I have installed ancestrymap on Orchestra at harvard med school. The documentation for ancestrymap is located here:

http://genepath.med.harvard.edu/%7Ereich/onlineDoc.pdf

Orchestra allows me to use the program with ease, but I am not sure how to input and output data using the program installed on Orchestra (would like to use input from my home directory, run ancestrymap in orchestra using this input, then output analysis to my home directory). I have an account in Orchestra and am using a compute node to process.

Details on Orchestra are here:

High-Performance Computing (HPC)
Orchestra's HPC service provides flexible high performance computing power for computational research at Harvard Medical School in a cost effective and collaborative manner.
Orchestra runs a sophisticated resource and workload management package called Platform LSF. Rather than run computational jobs directly on orchestra, a user submits her jobs to LSF, which schedules and runs those jobs on the compute nodes that make up the cluster.

Thanks for your help!
 

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LEARN ABOUT X11R4

queuedefs

queuedefs(4)							   File Formats 						      queuedefs(4)

NAME

       queuedefs - queue description file for at, batch, and cron

SYNOPSIS

       /etc/cron.d/queuedefs

DESCRIPTION

       The queuedefs file describes the characteristics of the queues managed by cron(1M). Each non-comment line in this file describes one queue.
       The format of the lines are as follows:

	      q.[njobj][nicen][nwaitw]

       The fields in this line are:

       q	The name of the queue. a is the default queue for jobs started by at(1); b is the default queue for jobs  started  by  batch  (see
		at(1)); c is the default queue for jobs run from a crontab(1) file.

       njob	The  maximum  number of jobs that can be run simultaneously in that queue; if more than njob jobs are ready to run, only the first
		njob jobs will be run, and the others will be run as jobs that are currently running terminate.  The default value is  100.

       nice	The nice(1) value to give to all jobs in that queue that are not run with a user ID of super-user.  The default value is 2.

       nwait	The number of seconds to wait before rescheduling a job that was deferred because more than njob jobs were running in  that  job's
		queue, or because the system-wide limit of jobs executing has been reached.  The default value is 60.

       Lines beginning with # are comments, and are ignored.

EXAMPLES

       Example 1: A sample file.

       #
       #
       a.4j1n
       b.2j2n90w

       This  file  specifies that the a queue, for at jobs, can have up to 4 jobs running simultaneously; those jobs will be run with a nice value
       of 1.  As no nwait value was given, if a job cannot be run because too many other jobs are running cron will wait 60 seconds before  trying
       again to run it.

       The  b  queue, for batch(1) jobs, can have up to 2 jobs running simultaneously; those jobs will be run with a nice(1) value of 2.  If a job
       cannot be run because too many other jobs are running, cron(1M) will wait 90 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, and if a job cannot be run because too many other jobs
       are running cron will wait 60 seconds before trying again to run it.

FILES

       /etc/cron.d/queuedefs	       queue description file for  at, batch, and  cron.

SEE ALSO

       at(1), crontab(1), nice(1), cron(1M)

SunOS 5.10							    1 Mar 1994							      queuedefs(4)
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