10-19-2011
7 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
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)
Discussion started by: olifu02
0 Replies
2. UNIX for Dummies Questions & Answers
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)
Discussion started by: liuzhencc
0 Replies
3. UNIX and Linux Applications
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)
Discussion started by: olifu02
1 Replies
4. UNIX for Dummies Questions & Answers
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)
Discussion started by: galford
2 Replies
5. UNIX for Beginners Questions & Answers
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)
Discussion started by: pc2001
0 Replies
6. Shell Programming and Scripting
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"$j"/
... (0 Replies)
Discussion started by: una1992
0 Replies
7. Shell Programming and Scripting
Hello,
I'm working on a SGE cluster and trying to echo the variables passed to the qsub command.
My script is as follows
#!/bin/bash
#$ -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)