Cheaha Quick Start - Revision history

Jelaiw@uab.edu: /* Hello Cheaha! */

2017-05-10T14:33:37Z

Hello Cheaha!

← Older revision		Revision as of 14:33, 10 May 2017
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	== Hello Cheaha! ==		== Hello Cheaha! ==
	A shared cluster environment like Cheaha uses a job scheduler to run tasks on the cluster to provide optimal resource sharing among users. Cheaha uses a job scheduling system ~~call~~ Slurm to schedule and manage jobs. A user needs to tell Slurm about resource requirements (e.g. CPU, memory) so that it can schedule jobs effectively. These resource requirements along with actual application code can be specified in a single file commonly referred as 'Job Script/File'. Following is a simple job script that prints job number and hostname.		A shared cluster environment like Cheaha uses a job scheduler to run tasks on the cluster to provide optimal resource sharing among users. Cheaha uses a job scheduling system called Slurm to schedule and manage jobs. A user needs to tell Slurm about resource requirements (e.g. CPU, memory) so that it can schedule jobs effectively. These resource requirements along with actual application code can be specified in a single file commonly referred as 'Job Script/File'. Following is a simple job script that prints job number and hostname.

	<pre>		<pre>

Jpr@uab.edu: Update support links with {{CheahaSupportRequest}} transclusion

2017-03-28T22:40:56Z

Update support links with {{CheahaSupportRequest}} transclusion

← Older revision		Revision as of 22:40, 28 March 2017
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	Cheaha is a shared cluster computing environment for UAB researchers. Cheaha offers total 110 TFLOPS compute power, 4.7 PB high-performance storage and 20 TB memory. See [[Cheaha2_GettingStarted#Hardware \|Hardware]] for more details on compute platform, but first let's get started with an example and see how easy it is to use.		Cheaha is a shared cluster computing environment for UAB researchers. Cheaha offers total 110 TFLOPS compute power, 4.7 PB high-performance storage and 20 TB memory. See [[Cheaha2_GettingStarted#Hardware \|Hardware]] for more details on compute platform, but first let's get started with an example and see how easy it is to use.

	If you have any questions about Cheaha usage then please contact Research Computing team ~~at support@vo.uabgrid.uab.edu~~ .		If you have any questions about Cheaha usage then please contact Research Computing team {{CheahaSupportRequest}}.

	== Logging In ==		== Logging In ==
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	== Support ==		== Support ==
	If you have any questions about our documentation or need any help with Cheaha then please ~~contact us at [mailto:support@vo.uabgrid.uab.edu support@vo.uabgrid.uab.edu]~~ . Cheaha is maintained by [[About_Research_Computing\|UAB IT's Research Computing team]].		If you have any questions about our documentation or need any help with Cheaha then please {{CheahaSupportRequest}}.

			Cheaha is maintained by [[About_Research_Computing\|UAB IT's Research Computing team]].

Tanthony@uab.edu: /* Logging In */

2016-10-28T16:51:18Z

Logging In

← Older revision		Revision as of 16:51, 28 October 2016
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	== Logging In ==		== Logging In ==
	More [[~~Cheaha2_GettingStarted~~#Login\|detailed login instructions]] are also available.		More [[Cheaha_GettingStarted#Login\|detailed login instructions]] are also available.

	Most users will authenticate to Cheaha using their BlazerID and associated password using an SSH (Secure Shell) client. The basic syntax is as follows:		Most users will authenticate to Cheaha using their BlazerID and associated password using an SSH (Secure Shell) client. The basic syntax is as follows:

Mhanby@uab.edu at 23:12, 21 October 2016

2016-10-21T23:12:58Z

← Older revision		Revision as of 23:12, 21 October 2016
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	#SBATCH --output=res.txt		#SBATCH --output=res.txt
	#SBATCH --ntasks=1		#SBATCH --ntasks=1
			#SBATCH --partition=express
	#SBATCH --time=10:00		#SBATCH --time=10:00
	#SBATCH --mem-per-cpu=100		#SBATCH --mem-per-cpu=100
	#SBATCH --mail-type=FAIL		#SBATCH --mail-type=FAIL
	#SBATCH --mail-user=~~$USER@uab.edu~~		#SBATCH --mail-user=YOUR_EMAIL_ADDRESS

	srun hostname		srun hostname

Mhanby@uab.edu: Modified all relevant occurrences of SLURM to Slurm

2016-10-20T20:03:09Z

Modified all relevant occurrences of SLURM to Slurm

← Older revision		Revision as of 20:03, 20 October 2016
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	== Hello Cheaha! ==		== Hello Cheaha! ==
	A shared cluster environment like Cheaha uses a job scheduler to run tasks on the cluster to provide optimal resource sharing among users. Cheaha uses a job scheduling system call ~~SLURM~~ to schedule and manage jobs. A user needs to tell ~~SLURM~~ about resource requirements (e.g. CPU, memory) so that it can schedule jobs effectively. These resource requirements along with actual application code can be specified in a single file commonly referred as 'Job Script/File'. Following is a simple job script that prints job number and hostname.		A shared cluster environment like Cheaha uses a job scheduler to run tasks on the cluster to provide optimal resource sharing among users. Cheaha uses a job scheduling system call Slurm to schedule and manage jobs. A user needs to tell Slurm about resource requirements (e.g. CPU, memory) so that it can schedule jobs effectively. These resource requirements along with actual application code can be specified in a single file commonly referred as 'Job Script/File'. Following is a simple job script that prints job number and hostname.

	<pre>		<pre>
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	</pre>		</pre>

	Lines starting with '#SBATCH' have a special meaning in the ~~SLURM~~ world. ~~SLURM~~ specific configuration options are specified after the '#SBATCH' characters. Above configuration options are useful for most job scripts and for additional configuration options refer to ~~SLURM~~ commands manual. A job script is submitted to the cluster using ~~SLURM~~ specific commands. There are many commands available, but following three commands are the most common:		Lines starting with '#SBATCH' have a special meaning in the Slurm world. Slurm specific configuration options are specified after the '#SBATCH' characters. Above configuration options are useful for most job scripts and for additional configuration options refer to Slurm commands manual. A job script is submitted to the cluster using Slurm specific commands. There are many commands available, but following three commands are the most common:
	* sbatch - to submit job		* sbatch - to submit job
	* scancel - to delete job		* scancel - to delete job
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	</pre>		</pre>

	When the job script is submitted, ~~SLURM~~ queues it up and assigns it a job number (e.g. 52707 in above example). The job number is available inside job script using environment variable $JOB_ID. This variable can be used inside job script to create job related directory structure or file names.		When the job script is submitted, Slurm queues it up and assigns it a job number (e.g. 52707 in above example). The job number is available inside job script using environment variable $JOB_ID. This variable can be used inside job script to create job related directory structure or file names.

	== Software ==		== Software ==
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	== Graphical Interface ==		== Graphical Interface ==
	Some applications use graphical interface to perform certain actions (e.g. submit buttons, file selections etc.). Cheaha supports graphical applications using an interactive X-Windows session with ~~SLURMS~~ sinteractive command. This will allow you to run graphical applications like MATLAB or AFNI on Cheaha. Refer to [[Cheaha2_GettingStarted#Interactive_Resources \| Interactive Resources]] for details on running graphical X-Windows applications.		Some applications use graphical interface to perform certain actions (e.g. submit buttons, file selections etc.). Cheaha supports graphical applications using an interactive X-Windows session with Slurms sinteractive command. This will allow you to run graphical applications like MATLAB or AFNI on Cheaha. Refer to [[Cheaha2_GettingStarted#Interactive_Resources \| Interactive Resources]] for details on running graphical X-Windows applications.

	== Scheduling Policies and partitions ==		== Scheduling Policies and partitions ==
	The primary job scheduler on Cheaha is '''[[~~SLURM~~]]'''.		The primary job scheduler on Cheaha is '''[[Slurm]]'''.

	The following partitions (Queues in SGE context) are currently available on Cheaha via ~~SLURM~~		The following partitions (Queues in SGE context) are currently available on Cheaha via Slurm
	express (default partition): Priority 2 :: Max Runtime 2 hours		express (default partition): Priority 2 :: Max Runtime 2 hours
	short: Priority 2 :: Max Runtime 12 hours		short: Priority 2 :: Max Runtime 12 hours
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	--partition argument (--time=48:00:00 --partition=medium)		--partition argument (--time=48:00:00 --partition=medium)

	Graphical based jobs can be run as an interactive job using the [[~~SLURM~~#Interactive_Session \| sinteractive]] command		Graphical based jobs can be run as an interactive job using the [[Slurm#Interactive_Session \| sinteractive]] command

	== Support ==		== Support ==
	If you have any questions about our documentation or need any help with Cheaha then please contact us at [mailto:support@vo.uabgrid.uab.edu support@vo.uabgrid.uab.edu] . Cheaha is maintained by [[About_Research_Computing\|UAB IT's Research Computing team]].		If you have any questions about our documentation or need any help with Cheaha then please contact us at [mailto:support@vo.uabgrid.uab.edu support@vo.uabgrid.uab.edu] . Cheaha is maintained by [[About_Research_Computing\|UAB IT's Research Computing team]].

Jpr@uab.edu: Jpr@uab.edu moved page Cheaha2 Quick Start to Cheaha Quick Start: Content for new SLURM and Gen6

2016-10-11T15:09:50Z

Jpr@uab.edu moved page Cheaha2 Quick Start to Cheaha Quick Start: Content for new SLURM and Gen6

← Older revision	Revision as of 15:09, 11 October 2016
(No difference)

Tanthony@uab.edu: /* Scheduling Policies */ Added scheduling policies and partitions

2016-09-30T13:31:40Z

Scheduling Policies: Added scheduling policies and partitions

← Older revision		Revision as of 13:31, 30 September 2016
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	Some applications use graphical interface to perform certain actions (e.g. submit buttons, file selections etc.). Cheaha supports graphical applications using an interactive X-Windows session with SLURMS sinteractive command. This will allow you to run graphical applications like MATLAB or AFNI on Cheaha. Refer to [[Cheaha2_GettingStarted#Interactive_Resources \| Interactive Resources]] for details on running graphical X-Windows applications.		Some applications use graphical interface to perform certain actions (e.g. submit buttons, file selections etc.). Cheaha supports graphical applications using an interactive X-Windows session with SLURMS sinteractive command. This will allow you to run graphical applications like MATLAB or AFNI on Cheaha. Refer to [[Cheaha2_GettingStarted#Interactive_Resources \| Interactive Resources]] for details on running graphical X-Windows applications.

	== Scheduling Policies ==		== Scheduling Policies and partitions ==
			The primary job scheduler on Cheaha is '''[[SLURM]]'''.

			The following partitions (Queues in SGE context) are currently available on Cheaha via SLURM
			express (default partition): Priority 2 :: Max Runtime 2 hours
			short: Priority 2 :: Max Runtime 12 hours
			medium: Priority 4 :: Max Runtime 50 hours
			long: Priority 6 :: Max Runtime 159 hours (6 days 6 hours)
			interactive: Priority 10 :: Max Runtime 2 hours

			In order to run a job in a partition other than "express" you'll need to specifically request it using the
			--partition argument (--time=48:00:00 --partition=medium)

			Graphical based jobs can be run as an interactive job using the [[SLURM#Interactive_Session \| sinteractive]] command

	== Support ==		== Support ==
	If you have any questions about our documentation or need any help with Cheaha then please contact us at [mailto:support@vo.uabgrid.uab.edu support@vo.uabgrid.uab.edu] . Cheaha is maintained by [[About_Research_Computing\|UAB IT's Research Computing team]].		If you have any questions about our documentation or need any help with Cheaha then please contact us at [mailto:support@vo.uabgrid.uab.edu support@vo.uabgrid.uab.edu] . Cheaha is maintained by [[About_Research_Computing\|UAB IT's Research Computing team]].

Tanthony@uab.edu: /* Support */ added email to link

2016-09-30T13:25:11Z

Support: added email to link

← Older revision		Revision as of 13:25, 30 September 2016
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	== Support ==		== Support ==
	If you have any questions about our documentation or need any help with Cheaha then please contact us on support@vo.uabgrid.uab.edu . Cheaha is maintained by [[About_Research_Computing\|UAB IT's Research Computing team]].		If you have any questions about our documentation or need any help with Cheaha then please contact us at [mailto:support@vo.uabgrid.uab.edu support@vo.uabgrid.uab.edu] . Cheaha is maintained by [[About_Research_Computing\|UAB IT's Research Computing team]].

Tanthony@uab.edu: /* Software */ Remove link to Cheaha Software page

2016-09-30T13:21:40Z

Software: Remove link to Cheaha Software page

← Older revision		Revision as of 13:21, 30 September 2016
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	* [[MATLAB]]		* [[MATLAB]]

	These softwares can be included in a job environment using [http://modules.sourceforge.net/ environment modules]. Environment modules make environment variables modification easy and repeatable~~. Please refer to [[Cheaha_Quick_Start_Softwares]] page for more details~~.		These softwares can be included in a job environment using [http://modules.sourceforge.net/ environment modules]. Environment modules make environment variables modification easy and repeatable.

	== Storage ==		== Storage ==

Tanthony@uab.edu: /* Storage */ added link to storage resources

2016-09-30T13:20:03Z

Storage: added link to storage resources

← Older revision		Revision as of 13:20, 30 September 2016
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	== Storage ==		== Storage ==
	~~Need~~ to ~~talk about GPFS here~~		During 2016, as part of the Alabama Innovation Fund grant working in partnership with numerous departments, 6.6PB raw GPFS storage on DDN SFA12KX hardware was added to meet the growing data needs of UAB researchers.

			More Details can be found on the [[Resources#Storage_Resources \|Storage Resources]] page.

	== Graphical Interface ==		== Graphical Interface ==