Virtual Machines - Revision history

imported>Lmperry at 22:27, 3 December 2014

2014-12-03T22:27:03Z

← Older revision		Revision as of 22:27, 3 December 2014
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	The CNI has received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.		The CNI has received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.

	''NOTE: CNI is switching to LXC - Please visit the [[LXC]] page to learn more about getting started with [[LXC]].		'''NOTE: CNI is switching to LXC - Please visit the [[LXC]] page to learn more about getting started with [[LXC]].'''

	== VM accounts ==		== VM accounts ==

imported>Lmperry at 22:26, 3 December 2014

2014-12-03T22:26:45Z

← Older revision		Revision as of 22:26, 3 December 2014
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	The CNI has received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.		The CNI has received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.

			''NOTE: CNI is switching to LXC - Please visit the [[LXC]] page to learn more about getting started with [[LXC]].

	== VM accounts ==		== VM accounts ==

imported>Lmperry: /* Data access */

2014-05-27T23:40:32Z

Data access

← Older revision		Revision as of 23:40, 27 May 2014
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	== Data access ==		== Data access ==
	Users can access their data from NIMS using NIMSfs. ~~* MORE ON THAT SOON *~~		Users can access their data from NIMS using NIMSfs. All your NIMS data are available in /nimsfs. This means you don't need to download anything. Once you log in to your VM there should be a link to /nimsfs on your desktop.

			Note that NIMSfs is a read-only filesystem, so you can't save anything there.

	All analysis should be done and results saved to the scratch folder located at /scratch (a link can be found on each user's desktop.)		All analysis should be done and results saved to the scratch folder located at /scratch (a link can be found on each user's desktop.)

imported>Lmperry: /* Data access */

2014-05-27T18:33:15Z

Data access

← Older revision		Revision as of 18:33, 27 May 2014
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	Users can access their data from NIMS using NIMSfs. * MORE ON THAT SOON *		Users can access their data from NIMS using NIMSfs. * MORE ON THAT SOON *

	All analysis should be done and results saved to the scratch folder located at /scratch (a link can be found on each user's desktop.		All analysis should be done and results saved to the scratch folder located at /scratch (a link can be found on each user's desktop.)

	== Software ==		== Software ==

imported>Lmperry at 18:32, 27 May 2014

2014-05-27T18:32:45Z

← Older revision		Revision as of 18:32, 27 May 2014
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	The CNI has received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.		The CNI has received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.

	== ~~Hardware~~ ==		== VM accounts ==
	~~The machine which hosts the Virtual Machines boasts 768 GB of RAM and multiple Intel(R) Xeon(R) CPU E5-4650 processors~~. ~~Each~~ VM ~~will~~ be ~~configured~~ to ~~match specific needs for processing~~.		VM accounts are created based upon scanning group membership. If you would like an account or a VM setup for your group, please contact us.

			== Data access ==
			Users can access their data from NIMS using NIMSfs. * MORE ON THAT SOON *

			All analysis should be done and results saved to the scratch folder located at /scratch (a link can be found on each user's desktop.

	== Software ==		== Software ==
	~~Information about~~ installed ~~software here~~.		Each VM has the following software pre-installed <em>(from NeuroDebian wherever possible):</em>
			* Freesurfer (v5.3.0)
			* fsl mrtix afni octave ants itksnap ipython1x python-numpy python-scipy python-nipype python-nibabel python-dipy python-nitime python-nipy mricron mriconvert gifti-bin dicomnifti nifti2dicom qnifti2dicom

	~~== VM accounts ==~~		If specific software is required please contact us.
	~~Information about getting access to a vm here~~.

	== ~~Data access~~ ==		== Hardware ==
	~~Information about how users~~ will ~~access their data here~~.		The machine which hosts the Virtual Machines boasts 768 GB of RAM and 4X Intel(R) Xeon(R) CPU E5-4650 processors. Each VM will be configured to match specific needs for processing.

	== X-Window sessions ==		== X-Window sessions ==

imported>Lmperry: /* Hardware */

2014-05-27T18:22:18Z

Hardware

← Older revision		Revision as of 18:22, 27 May 2014
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	== Hardware ==		== Hardware ==
	~~Information about~~ the ~~server's hardware here~~.		The machine which hosts the Virtual Machines boasts 768 GB of RAM and multiple Intel(R) Xeon(R) CPU E5-4650 processors. Each VM will be configured to match specific needs for processing.

	== Software ==		== Software ==

imported>Lmperry at 22:56, 12 November 2013

2013-11-12T22:56:32Z

← Older revision		Revision as of 22:56, 12 November 2013
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	The CNI has received ~~generous~~ funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.		The CNI has received funding from [http://biox.stanford.edu/biox/neuro.html BIO-X Neuroventures] for a high-powered compute server which will be used to provide computational resources to CNI users.

	== Hardware ==		== Hardware ==

imported>Lmperry: /* X-Window sessions */

2013-11-12T22:44:07Z

X-Window sessions

← Older revision		Revision as of 22:44, 12 November 2013
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	== X-Window sessions ==		== X-Window sessions ==
	We have configured the CNIVMs to use FreeNX. FreeNX is a system that allows a user to access the desktop of their CNIVM from another machine over the Internet. You can use this to login graphically to your CNIVM desktop from a remote location. Users that want access to a desktop session on their CNIVM should follow directions below to install the OpenNX client, which works hand-in-hand with FreeNX.		We have configured the CNIVMs to use FreeNX. FreeNX is a system that allows a user to access the desktop of their CNIVM from another machine over the Internet. You can use this to login graphically to your CNIVM desktop from a remote location. Users that want access to a desktop session on their CNIVM should follow directions below to install and configure the OpenNX client, which works hand-in-hand with FreeNX.

	===OpenNX Client===		===OpenNX Client===

imported>Lmperry: /* Session Management */

2013-11-12T22:34:56Z

Session Management

← Older revision		Revision as of 22:34, 12 November 2013
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	====Session Management====		====Session Management====
	Depending on your workflow you might want to return to a session if some work is still ongoing. OpenNX allows you to resume your session if you disconnect from it, or if it was unexpectedly terminated. Of course, you can also end your session once you are done working on a project. <br>		Depending on your workflow you might want to return to a session if some work is still ongoing. OpenNX allows you to resume your session if you disconnect from it, or if it was unexpectedly terminated. Of course, you can also end your session once you are done working on a project. <br>
	~~'''~~Ending a session~~'''~~		=====Ending a session=====
	: There are a couple of ways to end a session		: There are a couple of ways to end a session
	:# ''Clicking Close'': Click the close button for the x-window > You will then be prompted with the window in figure 1 below. From here you can select to either "Disconnect" or "End" your session. Clicking "End" will close the session and stop all your running jobs and close all your windows. The next time you login you will have a "fresh" working state.		:# ''Clicking Close'': Click the close button for the x-window > You will then be prompted with the window in figure 1 below. From here you can select to either "Disconnect" or "End" your session. Clicking "End" will close the session and stop all your running jobs and close all your windows. The next time you login you will have a "fresh" working state.
	:# ''Shutdown": From within the lubuntu desktop Choose > Shutdown and click yes when prompted to shutdown the computer >> This will not actually shutdown the computer, just your session.		:# ''Shutdown": From within the lubuntu desktop Choose > Shutdown and click yes when prompted to shutdown the computer >> This will not actually shutdown the computer, just your session.

	~~'''~~Disconnecting and ~~Resuming~~ a session~~'''~~		=====Disconnecting and resuming a session=====
	:If you would like to continue working on your session at a later time, then you want to simply disconnect from it and reconnect later. Follow the steps below.		:If you would like to continue working on your session at a later time, then you want to simply disconnect from it and reconnect later. Follow the steps below.
	:#Click the close button for the x-window ''OR'' close your X Window (xming or Xquartx)		:#Click the close button for the x-window ''OR'' close your X Window (xming or Xquartx)

imported>Lmperry: /* Session Management */

2013-11-12T22:33:59Z

Session Management

← Older revision		Revision as of 22:33, 12 November 2013
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	====Session Management====		====Session Management====
	Depending on your workflow you might want to return to a session if some work is still ongoing. OpenNX allows you to resume your session if you disconnect from it, or if it was unexpectedly terminated. Of course, you can also end your session once you are done working on a project.		Depending on your workflow you might want to return to a session if some work is still ongoing. OpenNX allows you to resume your session if you disconnect from it, or if it was unexpectedly terminated. Of course, you can also end your session once you are done working on a project. <br>
	'''Ending a session'''		'''Ending a session'''
	: There are a couple of ways to end a session		: There are a couple of ways to end a session