Cluster list

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|align="center"|simple calculations, student tests, teaching
|align="center"|simple calculations, student tests, teaching
|public
|public
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![[#argon|argon]]
![[#argon|argon]]
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|align="center"|single-processor calculations with lower requirements
|align="center"|single-processor calculations with lower requirements
|public
|public
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![[#krypton|krypton]]
![[#krypton|krypton]]
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|align="center"|single-processor calculations with lower requirements
|align="center"|single-processor calculations with lower requirements
|public
|public
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![[#radon|radon]]
![[#radon|radon]]
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|align="center"|single-processor calculations with average requirements
|align="center"|single-processor calculations with average requirements
|public
|public
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![[#palladium|palladium]]
![[#palladium|palladium]]
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|align="center"|older cluster for memory and/or disk space demanding calculations
|align="center"|older cluster for memory and/or disk space demanding calculations
|public
|public
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![[#iridium|iridium]]
![[#iridium|iridium]]
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|align="center"|general use
|align="center"|general use
|restricted
|restricted
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|Petr Nachtigall<br>Ota Bludsky
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|-
![[#helium|helium]]
![[#helium|helium]]
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|align="center"|parallel molecular dynamics calculations
|align="center"|parallel molecular dynamics calculations
|restricted
|restricted
 +
|Pavel Jungwirth
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|-
![[#francium|francium]]
![[#francium|francium]]
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|align="center"|parallel molecular dynamics calculations with infiniband
|align="center"|parallel molecular dynamics calculations with infiniband
|restricted
|restricted
 +
|Pavel Jungwirth
|-
|-
![[#lithium|lithium]]
![[#lithium|lithium]]
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|align="center"|highly demanding parallel and/or single-processor calculations with large memory and disk space requirements
|align="center"|highly demanding parallel and/or single-processor calculations with large memory and disk space requirements
|restricted
|restricted
 +
|Pavel Hobza
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|-
![[#uranium|uranium]]
![[#uranium|uranium]]
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|align="center"|general use
|align="center"|general use
|public
|public
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![[#barium|barium]]
![[#barium|barium]]
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|align="center"|mostly parallel molecular dynamics calculations
|align="center"|mostly parallel molecular dynamics calculations
|restricted
|restricted
 +
|Pavel Hobza
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|-
![[#thallium|thallium]]
![[#thallium|thallium]]
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|align="center"|general use
|align="center"|general use
|restricted
|restricted
 +
|Pavel Hobza
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|-
![[#neon|neon]]
![[#neon|neon]]
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|align="center"|parallel molecular dynamics calculations with infiniband
|align="center"|parallel molecular dynamics calculations with infiniband
|restricted
|restricted
 +
|Pavel Hobza
|-
|-
![[#erbium|erbium]]
![[#erbium|erbium]]
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|align="center"|general use, parallel calculations
|align="center"|general use, parallel calculations
|restricted
|restricted
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|Martin Kabelac
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Revision as of 13:52, 16 October 2009

Contents

Overview

Description

Depending on the hardware equipment and the age of a cluster there is always a set of typical applications that fit the cluster capabilities. The idea is to run any calculation on a cluster that just fits the job requirements; running it on less capable cluster would slow down the calculation or prevent running it at all, starting a low-demanding job on highly equippped cluster would waste the resources and prevent running jobs that require such equipment.

Cluster survey

Name Year of construction Memory size [GB] / core Disk (scratch) size [GB] Usage Access Owner*
cobalt (?) 2003 1 120 simple calculations, student tests, teaching public
argon 2005 2 160 single-processor calculations with lower requirements public
krypton 2005 1 - 2 160 single-processor calculations with lower requirements public
radon 2005 2 - 4 320 single-processor calculations with average requirements public
palladium 2004 - 2005 3 - 6 240 - 600 older cluster for memory and/or disk space demanding calculations public
iridium 2006 - 2008 2 320 - 1000 general use restricted Petr Nachtigall
Ota Bludsky
helium 2006 - 2008 2 250 - 320 parallel molecular dynamics calculations restricted Pavel Jungwirth
francium 2007 4 640 parallel molecular dynamics calculations with infiniband restricted Pavel Jungwirth
lithium 2006 - 2008 4 - 16 1600 - 6000 highly demanding parallel and/or single-processor calculations with large memory and disk space requirements restricted Pavel Hobza
uranium 2008 2 1500 general use public
barium 2007 - 2009 1 - 2 320 - 1500 mostly parallel molecular dynamics calculations restricted Pavel Hobza
thallium 2007 - 2008 1 - 2 1500 general use restricted Pavel Hobza
neon 2009 0.5 900 parallel molecular dynamics calculations with infiniband restricted Pavel Hobza
erbium 2009 2 - 4 900 - 1800 general use, parallel calculations restricted Martin Kabelac


Clusters

The following text provides detailed information about clusters and nodes. Tables show resources available for calculations, which are usually smaller than total resources mentioned in the general overview above; some of the total node memory (RAM) must always remain reserved for operating system tasks.

cobalt

  • Total nodes: 40
  • Total cores: 40
  • Parallel calculations: no
  • Queuing system: DQS


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
c01 - c40 40 c01_a - c40_a Intel Pentium 4 2.80GHz 1 800 MB 120 GB


argon

  • Total nodes: 44
  • Total cores: 44
  • Parallel calculations: no
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
a01 - a44 44 aq Intel Pentium 4 3.40 GHz 1 1.8 GB 160 GB


krypton

  • Total nodes: 44
  • Total cores: 44
  • Parallel calculations: no
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
k01 - k16 16 kq2 Intel Pentium 4 3.40 GHz 1 1.8 GB 160 GB
k17 - k44 28 kq1 Intel Pentium 4 3.40 GHz 1 0.8 GB 160 GB


radon

  • Total nodes: 46
  • Total cores: 46
  • Parallel calculations: no
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
r01 - r24 24 rq4 AMD Athlon 64 3500+ 1 3.6 GB 320 GB
r25 - r46 22 rq2 AMD Athlon 64 3500+ 1 1.6 GB 320 GB


palladium

  • Total nodes: 24
  • Total cores: 48
  • Parallel calculations: yes, within a single node (in pqXp queues, max 2 processor per job)
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
p01 - p04 4 pqos AMD Opteron 244 2 2.6 GB 240 GB
p05 - p14 10 pqop AMD Opteron 244 2 2.6 GB 240 GB
p15 - p18 4 pqns AMD Opteron 250 2 5.6 GB 600 GB
p19 - p24 6 pqnp AMD Opteron 250 2 5.6 GB 600 GB


iridium

  • Total nodes: 50
  • Total cores: 120
  • Parallel calculations: yes, special setup
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
i01 - i34 34 <unknown> Intel Core2 6600 2.40GHz 2 1.6 GB 320 GB
i35 - i40 6 <unknown> Intel Core2 Duo E6750 2.66GHz 2 1.6 GB 320 GB
i41 - i42 2 <unknown> Intel Core2 Quad Q6600 2.40GHz 4 1.8 GB 1000 GB
i43 - i50 8 <unknown> Intel Core2 Quad Q9550 2.83GHz 4 1.8 GB 1000 GB


helium

  • Total nodes: 16
  • Total cores: 64
  • Parallel calculations: yes, accross nodes, MPI
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
h01 - h06 6 hq AMD Opteron Dual Core 275 4 1.8 GB 320 GB
h07 - h16 10 hq AMD Opteron Dual Core 2216 4 1.8 GB 250 GB


francium

  • Total nodes: 24
  • Total cores: 96
  • Parallel calculations: yes, accross nodes, MPI, infiniband
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
f01 - f24 24 fq AMD Opteron Dual Core 2214 4 3.8 GB 640 GB


lithium

  • Total nodes: 16
  • Total cores: 82
  • Parallel calculations: yes, within a single node, MPI
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
l01 - l04 4 lq-4-8 AMD Opteron Dual Core 285 4 7.8 GB 3000 GB
l05 - l08 4 lq-2-16 AMD Opteron 256 2 15.4 GB 3000 GB
l09 1 lq-2-16 AMD Opteron 854 2 15.4 GB 1600 GB
l10 - l16 7 lq-8-4 Intel Xeon E5430 2.66GHz 8 3.8 GB 6000 GB


uranium

  • Total nodes: 24
  • Total cores: 192
  • Parallel calculations: yes, within a single node, MPI
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
u01 - u14 14 columbusq Intel Xeon E5430 2.66GHz 8 1.8 GB 1500 GB
u15 - u24 10 uq Intel Xeon E5430 2.66GHz 8 1.8 GB 1500 GB


barium

  • Total nodes: 24
  • Total cores: 172
  • Parallel calculations: yes, within a single node, MPI
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
b01 - b02 2 bq-4-1 Intel Core2 Quad 2.40GHz 4 0.8 GB 320 GB
b03 - b05 3 bq-4-2 Intel Core2 Quad 2.40GHz 4 1.8 GB 320 GB
b06 - b14 9 bq-8-1 Intel Xeon E5345 2.33GHz 8 0.8 GB 1320 GB
b15 - b19 5 bq-8-1 Intel Xeon E5430 2.66GHz 8 0.8 GB 1500 GB
b20 - b24 5 bq-8-1-f Intel Xeon E5430 2.66GHz 8 0.8 GB 1500 GB


thallium

  • Total nodes: 19
  • Total cores: 124
  • Parallel calculations: yes, accross multiple nodes, MPI
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
t01 - t07 7 tq-4-2 Intel Core2 Quad 2.40GHz 4 1.8 GB 1500 GB
t08 - t14 7 tq-8-1 Intel Xeon E5345 2.33GHz 8 0.8 GB 1500 GB
t15 - t19 5 tq-4-2 Intel Xeon E5430 2.66GHz 8 0.8 GB 1500 GB


neon

  • Total nodes: 24
  • Total cores: 192
  • Parallel calculations: yes, accross nodes, MPI, infiniband
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
n01 - n24 24 nq Intel Xeon E5430 2.66GHz 8 0.4 GB 900 GB


erbium

  • Total nodes: 7
  • Total cores: 26
  • Parallel calculations: yes, within a single node, MPI
  • Queuing system: SGE


Nodes # of nodes Queue CPU Cores/node Available RAM/core Scratch/node
e01 1 eq-2-2 AMD Opteron 250 2 1.8 GB 900 GB
e02 - e03 2 eq-4-2 Intel Core2 Extreme X9650 3.00GHz 4 1.8 GB 900 GB
e04 1 eq-4-2 Intel Core2 Quad Q6600 2.40GHz 4 1.8 GB 900 GB
e05 - e07 3 eq-4-4 Intel Core2 Quad Q9650 3.00GHz 4 3.8 GB 1800 GB


Totals

Total # of nodes Total # of cores Total RAM Total disk space
407 1298 (2.7 TB) (278 TB)
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