I am attempting to submit alot of jobs to this CONDOR program, in which it utilizes alot of computers and puts a single job onto each. Anyways, im trying to use the same program (autodock) to analyze different input files (dpf files), where each input file has a different name but same file... (0 Replies)
Dear all,
I'm a new guy doing some quntum calculation with gaussian on my rocks clusters. Recently, my cluster upgraded to rocks 5.3, but something strange happened. Everything goes correct except a serious problem. when I summit my gaussian job with script to sge queue, the job does run,... (0 Replies)
Hey all
Im looking to reduce the number of cpus available on a certain node in our cluster available for jobs using SGE.
i.e. we have one node that has 24 cpus available for jobs on SGE, i would like to reduce that to 16. Thanks (1 Reply)
Hello Unix.com
I want to know how can I extract from a large email list only the users.
1@a.com
2@b.com
3@c.com
I want to extract only 1, 2, 3.
Thanks in advance.
Galford D. Weller (2 Replies)
Hi,
I was trying to run a program that calls 8 processors (with max. RAM of 2 GB per processor). I want to run this program on my cluster that runs SGE. The cluster has 2 nodes, and each node has 62 cores, and 248GB/node. Currently, I use the scripts below, but the program (softx below) crashes... (0 Replies)
Hi,
I'm trying to edit my working bash script to an SGE script in order to submit it as a job to the cluster.
Currently I have:
#!/bin/bash
# Perform fastqc on files in a specified directory.
for ((j=1; j <=17; j++))
do
directory=/data4/una/batch"$j"/
... (0 Replies)
Hello,
I'm working on a SGE cluster and trying to echo the variables passed to the qsub command.
My script is as follows
#!/bin/bash
#$ -V
#$ -cwd
#$ -pe make 10
if ; then
echo "Variable is not set"
else
echo "Variable says: $StatedUserName"
fi
and I run the... (1 Reply)
Discussion started by: nans
1 Replies
LEARN ABOUT DEBIAN
cd-hit-para
CD-HIT-PARA.PL(1) User Commands CD-HIT-PARA.PL(1)NAME
cd-hit-para.pl - divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs
SYNOPSIS
cd-hit-para.pl options
DESCRIPTION
This script divide a big clustering job into pieces and submit jobs to remote computers over a network to make it parallel. After
all the jobs finished, the script merge the clustering results as if you just run a single cd-hit or cd-hit-est.
You can also use it to divide big jobs on a single computer if your computer does not have enough RAM (with -L option).
Requirements:
1 When run this script over a network, the directory where you
run the scripts and the input files must be available on all the remote hosts with identical path.
2 If you choose "ssh" to submit jobs, you have to have
passwordless ssh to any remote host, see ssh manual to know how to set up passwordless ssh.
3 I suggest to use queuing system instead of ssh,
I currently support PBS and SGE
4 cd-hit cd-hit-2d cd-hit-est cd-hit-est-2d
cd-hit-div cd-hit-div.pl must be in same directory where this script is in.
Options
-i input filename in fasta format, required
-o output filename, required
--P program, "cd-hit" or "cd-hit-est", default "cd-hit"
--B filename of list of hosts,
requred unless -Q or -L option is supplied
--L number of cpus on local computer, default 0
when you are not running it over a cluster, you can use this option to divide a big clustering jobs into small pieces, I suggest you
just use "--L 1" unless you have enough RAM for each cpu
--S Number of segments to split input DB into, default 64
--Q number of jobs to submit to queue queuing system, default 0
by default, the program use ssh mode to submit remote jobs
--T type of queuing system, "PBS", "SGE" are supported, default PBS
--R restart file, used after a crash of run
-h print this help
More cd-hit/cd-hit-est options can be speicified in command line
Questions, bugs, contact Weizhong Li at liwz@sdsc.edu
cd-hit-para.pl 4.6-2012-04-25 April 2012 CD-HIT-PARA.PL(1)