Cheaha GettingStarted deprecated - Revision history

Tanthony@uab.edu: Tanthony@uab.edu moved page Cheaha GettingStarted to Cheaha GettingStarted deprecated: Deprecated and moved 10/10/2016. original Link: https://docs.uabgrid.uab.edu/wiki/Cheaha_GettingStarted

2016-10-11T12:51:24Z

Tanthony@uab.edu moved page Cheaha GettingStarted to Cheaha GettingStarted deprecated: Deprecated and moved 10/10/2016. original Link: https://docs.uabgrid.uab.edu/wiki/Cheaha_GettingStarted

← Older revision	Revision as of 12:51, 11 October 2016
(No difference)

Mhanby@uab.edu: /* Windows */

2016-02-16T16:49:32Z

Windows

@@ Line 48: / Line 48: @@
 * Installs without requiring Windows Administrator rights
 =====PuTTY=====
 [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY] is a free suite of SSH and telnet tools written and maintained by [http://www.pobox.com/~anakin/ Simon Tatham]. PuTTY supports SSH, secure FTP (SFTP), and X forwarding (XTERM) among other tools.

Mhanby@uab.edu: /* Windows */ Added MobaXterm to the Windows client list

2016-02-16T16:44:20Z

Windows: Added MobaXterm to the Windows client list

← Older revision		Revision as of 16:44, 16 February 2016
Line 40:		Line 40:
	====Windows====		====Windows====
	There are many SSH clients available for Windows, some commercial and some that are free (GPL). This section will cover two clients that are commonly found on UAB Windows systems.		There are many SSH clients available for Windows, some commercial and some that are free (GPL). This section will cover two clients that are commonly found on UAB Windows systems.
			=====MobaXterm=====
			[http://mobaxterm.mobatek.net/ MobaXterm] is a free (also available for a price in a Profession version) suite of SSH tools. Of the Windows clients we've used, MobaXterm is the easiest to use and feature complete. [http://mobaxterm.mobatek.net/features.html Features] include (but not limited to):
			* SSH client (in a handy web browser like tabbed interface)
			* Embedded Cygwin (which allows Windows users to run many Linux commands like grep, rsync, sed)
			* Remote file system browser (graphical SFTP)
			* X11 forwarding for remotely displaying graphical content from Cheaha
			* Installs without requiring Windows Administrator rights

	=====PuTTY=====		=====PuTTY=====
	[http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY] is a free suite of SSH and telnet tools written and maintained by [http://www.pobox.com/~anakin/ Simon Tatham]. PuTTY supports SSH, secure FTP (SFTP), and X forwarding (XTERM) among other tools.		[http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY] is a free suite of SSH and telnet tools written and maintained by [http://www.pobox.com/~anakin/ Simon Tatham]. PuTTY supports SSH, secure FTP (SFTP), and X forwarding (XTERM) among other tools.
Line 59:		Line 67:
	\|-		\|-
	\|'''Saved Sessions'''		\|'''Saved Sessions'''
	\|cheaha		\|cheaha.uabgrid.uab.edu
	\|-		\|-
	\|}		\|}

Jpr@uab.edu: /* Environment Modules */ Add work around for -V and module invocation from job scripts

2015-07-09T23:13:29Z

Environment Modules: Add work around for -V and module invocation from job scripts

← Older revision		Revision as of 23:13, 9 July 2015
Line 461:		Line 461:
	-------------------------------------------------------------------		-------------------------------------------------------------------
	</pre>		</pre>

			=== Error Using Modules from a Job Script ===

			If you are using modules and the command your job executes runs fine from the command line but fails when you run it from the job, you may be having an issue with the script initialization. If you see this error in your job error output file
			<pre>
			-bash: module: line 1: syntax error: unexpected end of file
			-bash: error importing function definition for `BASH_FUNC_module'
			</pre>
			Add the command `unset module` before calling your module files. The -V job argument will cause a conflict with the module function used in your script.

	== Sample Job Scripts ==		== Sample Job Scripts ==

Mhanby@uab.edu: /* Gromacs */

2015-04-07T02:28:56Z

Gromacs

← Older revision		Revision as of 02:28, 7 April 2015
Line 732:		Line 732:
	#$ -V		#$ -V
	#		#

			# Change directory to the job working directory if not already there
			cd ${USER_SCRATCH}/jobs/gromacs

	# Single precision		# Single precision
	MDRUN=mdrun_mpi		MDRUN=mdrun_mpi
Line 738:		Line 742:
	# slots requests		# slots requests
	export MYFILE=production-Npt-323K_${NSLOTS}CPU		export MYFILE=production-Npt-323K_${NSLOTS}CPU

	~~cd ${USER_SCRATCH}/jobs/gromacs~~

	mpirun -np $NSLOTS $MDRUN -v -np $NSLOTS -s $MYFILE -o $MYFILE -c $MYFILE -x $MYFILE -e $MYFILE -g ${MYFILE}.log		mpirun -np $NSLOTS $MDRUN -v -np $NSLOTS -s $MYFILE -o $MYFILE -c $MYFILE -x $MYFILE -e $MYFILE -g ${MYFILE}.log

Mhanby@uab.edu: /* Gromacs */

2015-04-07T01:58:40Z

Gromacs

← Older revision		Revision as of 01:58, 7 April 2015
Line 724:		Line 724:
	#		#
	# Use OpenMPI parallel environment and 4 slots		# Use OpenMPI parallel environment and 4 slots
	#$ -pe openmpi 4		#$ -pe openmpi* 4
	#		#
	# Load the appropriate module(s)		# Load the appropriate module(s)
Line 739:		Line 739:
	export MYFILE=production-Npt-323K_${NSLOTS}CPU		export MYFILE=production-Npt-323K_${NSLOTS}CPU

	cd ~/jobs/gromacs		cd ${USER_SCRATCH}/jobs/gromacs

	mpirun -np $NSLOTS $MDRUN -v -np $NSLOTS -s $MYFILE -o $MYFILE -c $MYFILE -x $MYFILE -e $MYFILE -g ${MYFILE}.log		mpirun -np $NSLOTS $MDRUN -v -np $NSLOTS -s $MYFILE -o $MYFILE -c $MYFILE -x $MYFILE -e $MYFILE -g ${MYFILE}.log

Mhanby@uab.edu at 19:36, 6 March 2015

2015-03-06T19:36:25Z

← Older revision		Revision as of 19:36, 6 March 2015
Line 81:		Line 81:
	\|-		\|-
	\|'''User name'''		\|'''User name'''
	\|~~BLAZERID~~ (insert your blazerid here)		\|blazerid (insert your blazerid here)
	\|-		\|-
	\|'''Port'''		\|'''Port'''

Mhanby@uab.edu: /* Mac OS X */

2015-03-06T19:32:53Z

Mac OS X

← Older revision		Revision as of 19:32, 6 March 2015
Line 35:		Line 35:
	Mac OS X is a Unix operating system (BSD) and has a built in ssh client.		Mac OS X is a Unix operating system (BSD) and has a built in ssh client.
	# Start a terminal (click Finder, type Terminal and double click on Terminal under the Applications category)		# Start a terminal (click Finder, type Terminal and double click on Terminal under the Applications category)
	# At the prompt, enter the following command to connect to Cheaha ('''Replace ~~BLAZERID~~ with your Cheaha userid''')		# At the prompt, enter the following command to connect to Cheaha ('''Replace blazerid with your Cheaha userid''')
	ssh '''~~BLAZERID~~'''@cheaha.uabgrid.uab.edu		ssh '''blazerid'''@cheaha.uabgrid.uab.edu

	====Windows====		====Windows====

Mhanby@uab.edu: /* Linux */

2015-03-06T19:32:06Z

Linux

← Older revision		Revision as of 19:32, 6 March 2015
Line 29:		Line 29:
	Linux systems, regardless of the flavor (RedHat, SuSE, Ubuntu, etc...), should already have an SSH client on the system as part of the default install.		Linux systems, regardless of the flavor (RedHat, SuSE, Ubuntu, etc...), should already have an SSH client on the system as part of the default install.
	# Start a terminal (on RedHat click Applications -> Accessories -> Terminal, on Ubuntu Ctrl+Alt+T)		# Start a terminal (on RedHat click Applications -> Accessories -> Terminal, on Ubuntu Ctrl+Alt+T)
	# At the prompt, enter the following command to connect to Cheaha ('''Replace ~~BLAZERID~~ with your Cheaha userid''')		# At the prompt, enter the following command to connect to Cheaha ('''Replace blazerid with your Cheaha userid''')
	ssh '''~~BLAZERID~~'''@cheaha.uabgrid.uab.edu		ssh '''blazerid'''@cheaha.uabgrid.uab.edu

	====Mac OS X====		====Mac OS X====

Jpr@uab.edu: Changed the Access heading to more explicitly identify account requests

2015-01-29T15:37:23Z

Changed the Access heading to more explicitly identify account requests

← Older revision		Revision as of 15:37, 29 January 2015
Line 1:		Line 1:
	Cheaha is a cluster computing environment for UAB researchers.Information about the history and future plans for Cheaha is available on the [[cheaha]] page.		Cheaha is a cluster computing environment for UAB researchers.Information about the history and future plans for Cheaha is available on the [[cheaha]] page.

	== Access ==		== Access (Cluster Account Request) ==

	To request an account on [[Cheaha]], please [mailto:support@vo.uabgrid.uab.edu submit an authorization request to the IT Research Computing staff]. Please include some background information about the work you plan on doing on the cluster and the group you work with, ie. your lab or affiliation.		To request an account on [[Cheaha]], please [mailto:support@vo.uabgrid.uab.edu submit an authorization request to the IT Research Computing staff]. Please include some background information about the work you plan on doing on the cluster and the group you work with, ie. your lab or affiliation.