Install operating system - Revision history

Frodo: /* NFS and Public DNS */

2014-09-22T18:32:25Z

NFS and Public DNS

← Older revision		Revision as of 18:32, 22 September 2014
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	== NFS and Public DNS ==		== NFS and Public DNS ==
	We use EXT4 over NFS. We tend to hang several enclosures off a head node. Do not mix equipment from different vendors. We recommend SAS, which has finally come down in price, and RAID6 formatting. We currently use enclosures that host 12 disks of 4TB each.		We use EXT4 over NFS. We tend to hang several enclosures off a head node. Do not mix equipment from different vendors. We recommend SAS, which has finally come down in price, and RAID6 formatting. We currently use enclosures that host 12 disks of 4TB each.
	Disk planning. Suggest /nfs/home on a fast dedicated machine. Suggest /nfs/work for large work area. Suggest /nfs/store for online archive.
			== Disk planning ==

			Suggest /nfs/home on a fast dedicated machine. Suggest /nfs/work for large work area. Suggest /nfs/store for online archive.
	Depending on your local environment, you may need to coordinate the use of public IP names and addresses with your ISP or department.		Depending on your local environment, you may need to coordinate the use of public IP names and addresses with your ISP or department.

Frodo at 15:04, 17 April 2014

2014-04-17T15:04:15Z

← Older revision		Revision as of 15:04, 17 April 2014
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	Foreman is the provisioning server, available from http://theforeman.org/. We recommend using the latest [[Centos]], currently 6.5.		Foreman is the provisioning server, available from http://theforeman.org/. We recommend using the latest [[Centos]], currently 6.5.
	Here is how to set one up: [[Foreman]]		Here is how to set one up: [[Foreman]]

			== Rack Organization Planning ==
			This becomes more important as your cluster grows. Put the managed switch in the middle for shorter cable lengths. Buy power and ethernet cables of several short lengths, 1.5', 3'. Use an addressable PDU if you can afford it. Put disks, generally heavier, at the bottom, cpu machines at the top. Label machines front and back with public and private IP address and names. Give every enclosure a name so you can refer to it.

	== DHCP and Cluster DNS ==		== DHCP and Cluster DNS ==
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	== NFS and Public DNS ==		== NFS and Public DNS ==
	We use ~~XFS~~ over NFS. We tend to hang several enclosures off a head node. We recommend SAS, which has finally come down in price, and RAID6 formatting. We ~~tend to~~ use enclosures that host 12 disks of 4TB each.		We use EXT4 over NFS. We tend to hang several enclosures off a head node. Do not mix equipment from different vendors. We recommend SAS, which has finally come down in price, and RAID6 formatting. We currently use enclosures that host 12 disks of 4TB each.
	* Public DNS		Disk planning. Suggest /nfs/home on a fast dedicated machine. Suggest /nfs/work for large work area. Suggest /nfs/store for online archive.
	* Set up NFS Servers
	~~Setup NAS with 389 and cluster~~
	~~Create~~/~~export NFS mounts~~
	Depending on your local environment, you may need to coordinate the use of public IP names and addresses with your ISP or department.		Depending on your local environment, you may need to coordinate the use of public IP names and addresses with your ISP or department.

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	* Configure SGE hosts/groups		* Configure SGE hosts/groups

	~~== Provision nodes ==~~		== Set up License server(s) ==
	~~We can provide guidance, based on our experience.~~

	== Set up License server ==
	Will be used for PGF and Epik in the middleware step.		Will be used for PGF and Epik in the middleware step.

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	== Portal and Security ==		== Portal and Security ==
	We recommend setting up a portal and blocking all inbound access to all other computers. Use two portals at distinct geographical locations for added robustness.		We recommend setting up a portal and blocking all inbound access to all other computers. Use two portals at distinct geographical locations for added robustness. We recommend not using

	== Add a new node to the cluster ==		== Add a new node to the cluster ==

Frodo: /* Foreman */

2014-04-17T14:53:22Z

Foreman

← Older revision		Revision as of 14:53, 17 April 2014
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	== Foreman ==		== Foreman ==
	Foreman is the provisioning server. We recommend using [[Centos]] 6.3.		Foreman is the provisioning server, available from http://theforeman.org/. We recommend using the latest [[Centos]], currently 6.5.
	Here is how to set one up: [[Foreman]]		Here is how to set one up: [[Foreman]]

Frodo: /* Hypervisor */

2014-04-17T14:52:15Z

Hypervisor

← Older revision		Revision as of 14:52, 17 April 2014
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	== Hypervisor ==		== Hypervisor ==
	We use ~~(xxx)~~, ~~but any should do~~, including virtualbox, vmware~~, among many others~~. [[Hypervisor]]		We use libvirt, http://libvirt.org. Others also work well, including virtualbox, vmware. [[Hypervisor]]

	== Foreman ==		== Foreman ==

Frodo: /* Document */

2014-03-20T11:51:43Z

Document

← Older revision		Revision as of 11:51, 20 March 2014
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	== Document ==		== Document ==
	Document the system configuration, licenses, access codes.		[http://wiki.bkslab.org Document]] the system configuration, licenses, access codes. We encourage you to set up your own wiki, wordpress or other site for this purpose, but this is of course optional.

	Return to [[So you want to set up a lab]].		Return to [[So you want to set up a lab]].

Frodo at 11:50, 20 March 2014

2014-03-20T11:50:28Z

← Older revision		Revision as of 11:50, 20 March 2014
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	== Set up License server ==		== Set up License server ==
	PGF, Epik~~, what else?~~		Will be used for PGF and Epik in the middleware step.

	== Set up a database server ==		== Set up a database server ==

Frodo: /* NFS and Public DNS */

2014-03-20T11:49:37Z

NFS and Public DNS

← Older revision		Revision as of 11:49, 20 March 2014
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	Create/export NFS mounts		Create/export NFS mounts
	Depending on your local environment, you may need to coordinate the use of public IP names and addresses with your ISP or department.		Depending on your local environment, you may need to coordinate the use of public IP names and addresses with your ISP or department.

	~~'''All of the above can all be be set up on a single machine in your office without any other hardware being present.'''~~
	~~Thus you can defer the physical installation to this point, if you like. If you have more than a few machines, physical installation requires planning.~~

	== Set up queuing system ==		== Set up queuing system ==

Frodo at 20:08, 19 March 2014

2014-03-19T20:08:38Z

← Older revision		Revision as of 20:08, 19 March 2014
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	== Set up License server ==		== Set up License server ==
			PGF, Epik, what else?

	== Set up a database server ==		== Set up a database server ==
			[[Psql]] and [[rdkit]] as well as [[MySQL]]

	~~== Set up other middleware ==~~
	* [[~~Python~~]] ~~- 2.7 series~~

	~~== Set up lab software ==~~
	* get DOCK 3.7 running

	~~== Fileservers~~ and ~~NFS ==~~


	== Portal and Security ==		== Portal and Security ==

Frodo at 20:02, 19 March 2014

2014-03-19T20:02:56Z

← Older revision		Revision as of 20:02, 19 March 2014
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	== Foreman ==		== Foreman ==
	Foreman is the ~~node creation and~~ provisioning server.		Foreman is the provisioning server. We recommend using [[Centos]] 6.3.
	We recommend [[Centos]] 6.3.
	Here is how to set one up: [[Foreman]]		Here is how to set one up: [[Foreman]]

	== ~~Authentication server~~ ==		== DHCP and Cluster DNS ==
	~~We use 389, but other authentication systems will work fine, including kerberos~~.		This requires planning. Please see our [[Cluster IP planning worksheet]]

	* ~~DNS~~		== Set up provisioning services ==
			* Create local repositories
			* Automatic Provision (PXE)

	* ~~[[Python]] - 2~~.~~7 series~~		== Authentication server ==
			Set up authentication (389) server. Other authentication systems, such as kerberos, are fine, but are beyond the scope of this tutorial.
			* create users. If you interoperate with another cluster, you may have to pay attention to name and/or UID collisions.

	== ~~Fileservers~~ and ~~NFS~~ ==		== NFS and Public DNS ==
	We use XFS over NFS. We tend to hang several enclosures off a head node. We recommend SAS, which has finally come down in price, and RAID6 formatting. We tend to use enclosures that host 12 disks of 4TB each.		We use XFS over NFS. We tend to hang several enclosures off a head node. We recommend SAS, which has finally come down in price, and RAID6 formatting. We tend to use enclosures that host 12 disks of 4TB each.
			* Public DNS
			* Set up NFS Servers
			Setup NAS with 389 and cluster
			Create/export NFS mounts
			Depending on your local environment, you may need to coordinate the use of public IP names and addresses with your ISP or department.

	~~== Portal and Security ==~~		'''All of the above can all be be set up on a single machine in your office without any other hardware being present.'''
	~~We recommend setting~~ up a ~~portal and blocking all inbound access~~ to ~~all other computers~~. ~~Use two portals at distinct geographical locations for added robustness~~.		Thus you can defer the physical installation to this point, if you like. If you have more than a few machines, physical installation requires planning.

	* Perimeter security

	== ~~Queuing~~ system ==		== Set up queuing system ==
	We recommend free versions of Sun Grid Engine [[SGE]].		We recommend free versions of Sun Grid Engine [[SGE]].
	See our guidelines to [[get a queuing system working]].		See our guidelines to [[get a queuing system working]].
			* Create SGE master
			* Setup SGE
			* Provision sgehead
			* Configure SGE hosts/groups

			== Provision nodes ==
			We can provide guidance, based on our experience.

			== Set up License server ==

	== Set up a database server ==		== Set up a database server ==


			== Set up other middleware ==
			* [[Python]] - 2.7 series

			== Set up lab software ==
			* get DOCK 3.7 running

			== Fileservers and NFS ==


			== Portal and Security ==
			We recommend setting up a portal and blocking all inbound access to all other computers. Use two portals at distinct geographical locations for added robustness.

	== Add a new node to the cluster ==		== Add a new node to the cluster ==
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	[[Workstation Install]]		[[Workstation Install]]

			== Document ==
			Document the system configuration, licenses, access codes.

	Return to [[So you want to set up a lab]].		Return to [[So you want to set up a lab]].

Frodo: /* Hypervisor */

2014-03-18T16:24:53Z

Hypervisor

← Older revision		Revision as of 16:24, 18 March 2014
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	== Hypervisor ==		== Hypervisor ==
	We use (xxx), but any should do, including virtualbox, vmware, among many others.		We use (xxx), but any should do, including virtualbox, vmware, among many others. [[Hypervisor]]

	[[Hypervisor]]

	== Foreman ==		== Foreman ==