Lx6 and Lx7 compute nodes - Revision history

Hjmegens at 16:53, 23 November 2013

2013-11-23T16:53:45Z

← Older revision		Revision as of 18:53, 23 November 2013
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	For directions on using Putty Check this link :		For directions on using Putty Check this link :
	http://www.hacktabs.com/how-to-setup-ssh-tunneling-in-firefox-and-surf-anonymously/		http://www.hacktabs.com/how-to-setup-ssh-tunneling-in-firefox-and-surf-anonymously/

			== See also ==
			* [[B4F_cluster \| B4F cluster]]

			== External links ==

2013-11-23T16:52:23Z

Out of University access

← Older revision		Revision as of 18:52, 23 November 2013
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	There add in the '''SOCKS Host: localhost; port 9999''';		There add in the '''SOCKS Host: localhost; port 9999''';

			For directions on using Putty Check this link :
	''For directions on using Putty Check this link : http://www.hacktabs.com/how-to-setup-ssh-tunneling-in-firefox-and-surf-anonymously/~~'''~~		http://www.hacktabs.com/how-to-setup-ssh-tunneling-in-firefox-and-surf-anonymously/

2013-11-23T16:51:26Z

Access

← Older revision		Revision as of 18:51, 23 November 2013
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	== Access ==		== Access ==
	Accessing''' computer cluster through ssh protocol''':		Accessing''' computer cluster through ssh protocol''':
			<source lang='bash'>
	ssh username@scompXXXX.wurnet.nl		ssh username@scompXXXX.wurnet.nl
			</source>
	For people that needs visualisation (i.e. R graphs) use:		For people that needs visualisation (i.e. R graphs) use:
			<source lang='bash'>
	ssh -X username@scompXXXX.wurnet.nl		ssh -X username@scompXXXX.wurnet.nl
			</source>

	== Basic Bash programming ==		== Basic Bash programming ==

2013-11-23T16:50:43Z

Out of University access

← Older revision		Revision as of 18:50, 23 November 2013
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	'''1) Connect to abgc.asg.wur.nl'''		'''1) Connect to abgc.asg.wur.nl'''
			<source lang='bash'>
	ssh -D 9999 username@abgc.asg.wur.nl		ssh -D 9999 username@abgc.asg.wur.nl
			</source>
	'''2) Change proxy settings in Firefox''' go to '''Edit > Preferences > Advanced > Network'''.		'''2) Change proxy settings in Firefox''' go to '''Edit > Preferences > Advanced > Network'''.

2013-11-23T16:50:10Z

Submitting jobs

← Older revision		Revision as of 18:50, 23 November 2013
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	Example of qsub commands:		Example of qsub commands:
			<source lang='bash'>
	qsub -l h_vmem=10G -q all.q -cwd -S /usr/bin/perl myscript.pl		qsub -l h_vmem=10G -q all.q -cwd -S /usr/bin/perl myscript.pl
	qsub -l h_vmem=10G -q all.q -cwd -b y ~/bin/./asreml		qsub -l h_vmem=10G -q all.q -cwd -b y ~/bin/./asreml
			</source>

	== Installing programs ==		== Installing programs ==

2013-11-23T16:49:33Z

Installing programs

← Older revision		Revision as of 18:49, 23 November 2013
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	<source lang='bash'>		<source lang='bash'>
	export PATH=$PATH:~/bin/		export PATH=$PATH:~/bin/
	</source		</source>
	This will make all executable in ~/bin installed, so the they can be invoked simply by typing their name in the command line.		This will make all executable in ~/bin installed, so the they can be invoked simply by typing their name in the command line.

2013-11-23T16:49:22Z

Installing programs

← Older revision		Revision as of 18:49, 23 November 2013
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	<source lang='bash'>		<source lang='bash'>
	vim ~/.bashrc		vim ~/.bashrc
	</source>		</source>
	Then add the following line in this file:		Then add the following line in this file:
			<source lang='bash'>
	export PATH=$PATH:~/bin/		export PATH=$PATH:~/bin/
			</source
	This will make all executable in ~/bin installed, so the they can be invoked simply by typing their name in the command line.		This will make all executable in ~/bin installed, so the they can be invoked simply by typing their name in the command line.

2013-11-23T16:48:52Z

Installing programs

← Older revision		Revision as of 18:48, 23 November 2013
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	2) If you are going to be the only one to use this program you can install it in your home directory. Create your own ~/bin directory and compile things there. Then copy the executable directly in your ~/bin/. The next step is to add the path of your new bin to your .bashrc To do so do:		2) If you are going to be the only one to use this program you can install it in your home directory. Create your own ~/bin directory and compile things there. Then copy the executable directly in your ~/bin/. The next step is to add the path of your new bin to your .bashrc To do so do:

	<source lang='bash>		<source lang='bash'>
	vim ~/.bashrc		vim ~/.bashrc
	</source>		</source>

2013-11-23T16:48:29Z

Installing programs

← Older revision		Revision as of 18:48, 23 November 2013
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	2) If you are going to be the only one to use this program you can install it in your home directory. Create your own ~/bin directory and compile things there. Then copy the executable directly in your ~/bin/. The next step is to add the path of your new bin to your .bashrc To do so do:		2) If you are going to be the only one to use this program you can install it in your home directory. Create your own ~/bin directory and compile things there. Then copy the executable directly in your ~/bin/. The next step is to add the path of your new bin to your .bashrc To do so do:

			<source lang='bash>
	vim ~/.bashrc		vim ~/.bashrc
			</source>
	Then add the following line in this file:		Then add the following line in this file:

2013-11-22T23:31:30Z

← Older revision		Revision as of 01:31, 23 November 2013
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	== HPC infrastructure==		== HPC infrastructure==
	Schematic of bioinformatics infrastructure at ABGC. ~~All servers are~~ running Red Hat Enterprise Linux (RHEL). Jobs can be [[submit job with qsub \| submitted]] with the Sun Grid Engine (SGE). A user account is needed to work on the machines.		Schematic of bioinformatics infrastructure at ABGC. Lx5 is running Red Hat Enterprise Linux (RHEL) 6. Lx6 and Lx7 are running Ubuntu LTS 12.04. Jobs can be [[submit job with qsub \| submitted]] with the Sun Grid Engine (SGE). A user account is needed to work on the machines.
	[[File:Bioinformatics-infra2.gif\|thumb\|left\|600px]]		[[File:Bioinformatics-infra2.gif\|thumb\|left\|600px]]
	{{-}}		{{-}}