Cluster 1: Difference between revisions

From DISI
Jump to navigation Jump to search
(sdrt)
 
(8 intermediate revisions by the same user not shown)
Line 1: Line 1:
Our cluster at the [[University of Toronto]] St George Campus in the Faculty of Pharmacy is described on this page. We also have [[Cluster 0]] and [[Cluster 2]] at [[UCSF]] in San Francisco.  
This cluster is defunct. Please use [[Cluster 2]].


= Status =
= Status =
Cluster 1 is being wound down.  '''Please plan to move your files to [[Cluster 2]] in May 2014.'''   
Cluster 1 is being wound down.  '''Please plan to move your files to [[Cluster 2]] asap.'''   


{{TOCright}}
{{TOCright}}
Line 18: Line 18:
  /nfs/home/<userid>/
  /nfs/home/<userid>/


We expect you to run docking calculations in /project/. 1TB default. Not backed up.
We expect you to run docking calculations in work. 1TB default. Not backed up.
  /nfs/work/<userid>/
  /nfs/work/<userid>/


If you have large amounts of data you want kept, e.g. from the synchrotron, you may request repository space to keep it.  Backed up. Size by agreement.
If you have large amounts of data you want kept, e.g. from the synchrotron, you may request repository space to keep it.  Backed up. Size by agreement. Please compress your image files!
  /nfs/store/<userid>/
  /nfs/store/<userid>/


Line 40: Line 40:


== routine access to cluster ==
== routine access to cluster ==
* sgehead. includes [[csd]] license. [[pgf license]]
* sgehead. includes [[csd]] license.


== pipeline pilot license ==
== pipeline pilot license ==
Line 69: Line 69:
* fawlty
* fawlty
* towers
* towers
== Name reuse pool  ==
*  vertigo
* sundance
* spotless
* lostark
* airplane
* brian
* terminator
* psycho
* strangelove


== Cloud machines  (hypervisor) ==
== Cloud machines  (hypervisor) ==
Line 87: Line 76:
* Strangelove
* Strangelove
* Rocky
* Rocky
== Unknown/unassigned function ==
* blues
* goldmember
* darkness


== 389 Server ==
== 389 Server ==
* spinaltap
* spinaltap


= Physical Machines =  
= Physical Machines =
NB this section needs updating!
 
 
== Rack 1 ==  
== Rack 1 ==  
Currently in Donnelly 630.  Totals: 426 cores for cluster. 128 cores for infrastructure. 60 TB RAID-10 formatted.  (130 TB raw)
Currently in Pharmacy 848.  Totals: 448 cores for cluster. 128 cores for infrastructure. 60 TB RAID-10 formatted.  (130 TB raw)


* 3x ( Dell PowerEdge C6145. =  2 x ( 256 GB / 64 cores / 6 TB raw disk ))  64 x 2 x 3 = 384 cores.
* 3x ( Dell PowerEdge C6145. =  2 x ( 256 GB / 64 cores / 6 TB raw disk ))  64 x 2 x 3 = 384 cores.
* HP disk head node, (25 TB raw disk systems ) x 4.   
* HP disk head node, (25 TB raw disk systems ) x 4.   
* Dell disk head node x 1, Dell SAS 2TB x 8??.
* Dell disk head node x 1, Dell SAS 2TB x 8??.
* DL165 x 48x4 = 32 cores.
* DL165 x 38x3 = 24 cores.
* Dell Switch: switch-1-1.
* Dell Switch: switch-1-1.
* UPS
* UPS


== Rack 2 ==
== Rack 2 ==
Currently in Pharmacy 8xx. Planned June 2013
Currently in Pharmacy 848.
 
* Dell PowerEdge C6145  
* Dell PowerEdge C6145  
* Dell Switch: switch-2-1.
* Dell Switch: switch-2-1.
* 42 tape robot backup system
* dedicated computer for backup
== Rack 3 ==
Currently in Pharmacy 8xx. Planned June 2013
* Dell PowerEdge C6145
* Dell Switch: switch-3-1.
* legacy nodes
== Rack 4 ==
Currently in Pharmacy 8xx. Planned June 2013
* will be: Dell PowerEdge 6145
* Dell Switch: switch-4-1.
* legacy nodes
== Rack 5 ==
Currently in Pharmacy 8xx. Planned June 2013
* will be: Dell PowerEdge 6145
* Dell Switch: switch-5-1.
* legacy nodes


== Wet Lab ==
== Wet Lab ==
Donnelly 940. Planned June 2013.
Donnelly 940.  
 
* 4 instrument workstations
* 4 instrument workstations
* 3 linux desktops HP Z430
* 1 linux desktop HP Z420
* 1 windows7 desktop HP Z400
* 1 windows7 desktop HP Z400
* 1 color printer
* 1 color printer
Line 149: Line 106:


== Dry Lab ==
== Dry Lab ==
Donnelly 650. Planned June 2013.
Donnelly 650.  
* 6 linux desktops. HP Z430
* 8 linux desktops. HP Z420
* 1 windows7 desktop HP Z400
* 6 Mac lab laptops
* 1 switch: switch-d-1
 
== Other Offices and locations ==
* BKS office
* JJI office
* desk space in OICR


[[About our cluster]]
[[About our cluster]]
[[Category:Cluster]]
[[Category:Cluster]]
[[Category:Internal]]
[[Category:Internal]]
[[Category:YYZ]]

Latest revision as of 05:29, 3 June 2015

This cluster is defunct. Please use Cluster 2.

Status

Cluster 1 is being wound down. Please plan to move your files to Cluster 2 asap.

Toronto - our cluster

Obtaining credentials

For command line access to our cluster, please contact Teague, Therese or John for credentials. For your main email address, you may well use your gmail account or other public account for most purposes.

Disk usage conventions

We differentiate dockers from everyone else. If you are a full time member of the group, your disk space allocation will be like this:

Your home directory is for important or small files. 500 GB default. Backed up.

/nfs/home/<userid>/

We expect you to run docking calculations in work. 1TB default. Not backed up.

/nfs/work/<userid>/

If you have large amounts of data you want kept, e.g. from the synchrotron, you may request repository space to keep it. Backed up. Size by agreement. Please compress your image files!

/nfs/store/<userid>/

If you generate private databases, you may request /db/ space. Backup by arrangement. Size by agreement.

/nfs/db/<userid>/

If you have software you want to share, you may request /software/ space. backed up. 500 GB.

/nfs/software/<userid>/

Getting set up with lab software

svn co dockenv
cp $SOFT/labenv.csh ~/.csh 

OR

cp $SOFT/labenv.sh ~/.bashrc

for bash users.

Roles and Functions of Computers

routine access to cluster

  • sgehead. includes csd license.

pipeline pilot license

  • ppilot

Sysadmin

static web server

  • runaway (vm on rocky)
  • includes wiki, www
  • NB was contact at some point, kinda liked that name for a webserver
  • includes drupal
  • includes wordpress

postgres server

  • production: taxi
  • intern: raiders

dynamic web server (ZINC, etc)

  • oz

SEA server

  • fawlty
  • mysql server is on msqlserver aka inception
  • fingerprint server is on fingerprint aka darkcrystal

NFS Disk servers

  • fawlty
  • towers

Cloud machines (hypervisor)

  • Django
  • Pulp
  • Raiders
  • Strangelove
  • Rocky

389 Server

  • spinaltap

Physical Machines

Rack 1

Currently in Pharmacy 848. Totals: 448 cores for cluster. 128 cores for infrastructure. 60 TB RAID-10 formatted. (130 TB raw)

  • 3x ( Dell PowerEdge C6145. = 2 x ( 256 GB / 64 cores / 6 TB raw disk )) 64 x 2 x 3 = 384 cores.
  • HP disk head node, (25 TB raw disk systems ) x 4.
  • Dell disk head node x 1, Dell SAS 2TB x 8??.
  • DL165 x 3. 8x3 = 24 cores.
  • Dell Switch: switch-1-1.
  • UPS

Rack 2

Currently in Pharmacy 848.

  • Dell PowerEdge C6145
  • Dell Switch: switch-2-1.

Wet Lab

Donnelly 940.

  • 4 instrument workstations
  • 1 linux desktop HP Z420
  • 1 windows7 desktop HP Z400
  • 1 color printer
  • 3 Mac lab laptops
  • 1 switch: switch-w-1

Dry Lab

Donnelly 650.

  • 8 linux desktops. HP Z420

About our cluster