From Molecular Modeling Wiki

Contents 1 Overview 1.1 Description 1.2 Cluster survey 2 Clusters 2.1 cobalt 2.2 argon 2.3 krypton 2.4 radon 2.5 palladium 2.6 iridium 2.7 helium 2.8 francium 2.9 lithium 2.10 uranium 2.11 barium 2.12 thallium 3 Totals

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

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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

Name	Year of construction	Memory size [GB] / core	Disk (scratch) size [GB]	Usage	Access
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
helium	2006 - 2008	2	250 - 320	parallel molecular dynamics calculations	restricted
francium	2007	4	640	parallel molecular dynamics calculations with infiniband	restricted
lithium	2006 - 2008	4 - 16	1600 - 6000	highly demanding parallel and/or single-processor calculations with large memory and disk space requirements	restricted
uranium	2008	2	1500	general use	public
barium	2007 - 2008	1 - 2	320 - 1500	mostly parallel molecular dynamics calculations	restricted
thallium	2007 - 2008	1 - 2	1500	general use	restricted
neon	2009	0.5	900	mostly parallel molecular dynamics calculations	restricted

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: 14
• Total cores: 10
• 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: 19
• Total cores: 132
• 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

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

Totals

Total # of nodes	Total # of cores	Total RAM	Total disk space
366	1032	2.5 TB	240 TB