Cluster list
From Molecular Modeling Wiki
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/manager* |
|---|---|---|---|---|---|---|
| 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 | 2 | 900 | parallel molecular dynamics calculations with infiniband | restricted | Pavel Hobza |
| erbium | 2009 | 2 - 4 | 900 - 1800 | general use, parallel calculations | restricted | Martin Kabelac |
| sodium | 2009 | 1.5 | 450 | general use, parallel calculations | restricted | Pavel Jungwirth |
| vanad | 2010 | 3 | 450 | general use, parallel calculations | restricted | Ota Bludsky |
| zinc | 2010 | 3 | 1800 | general use, parallel calculations | restricted | Pavel Hobza |
*Please contact this person when requiring an account on a restricted-access cluster.
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.
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: 28
- Total cores: 204
- 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-8-2 | Intel Xeon E5345 2.33GHz | 8 | 1.8 GB | 1320 GB |
| b15 - b19 | 5 | bq-8-2 | Intel Xeon E5430 2.66GHz | 8 | 1.8 GB | 1500 GB |
| b20 - b24 | 5 | bq-8-2-f | Intel Xeon E5430 2.66GHz | 8 | 1.8 GB | 1500 GB |
| b25 - b28 | 4 | bq-8-1 | Intel Xeon E5520 2.27GHz | 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 | 1.8 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 |
sodium
- 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 |
|---|---|---|---|---|---|---|
| s01 - s24 | 24 | sq | Intel Xeon E5530 2.40GHz | 8 | 1.3 GB | 450 GB |
vanad
- Total nodes: 6
- Total cores: 40
- Parallel calculations: yes, within a single node, MPI
- Queuing system: SGE
| Nodes | # of nodes | Queue | CPU | Cores/node | Available RAM/core | Scratch/node |
|---|---|---|---|---|---|---|
| v01 - v04 | 4 | sq | Intel Xeon E5620 2.40GHz | 8 | 2.8 GB | 450 GB |
| v05 - v06 | 2 | sq | Intel Xeon E5620 2.40GHz | 4 | 2.8 GB | 450 GB |
zinc
- Total nodes: 36
- Total cores: 288
- Parallel calculations: yes, within a single node, MPI
- Queuing system: SGE
| Nodes | # of nodes | Queue | CPU | Cores/node | Available RAM/core | Scratch/node |
|---|---|---|---|---|---|---|
| z01 - z36 | 36 | zq | Intel Xeon E5620 2.40GHz | 8 | 2.8 GB | 1800 GB |
Closed
The following clusters have been decomposed and annihilated.
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 |
Totals
The total numbers only include counts from working clusters.
| Total # of nodes | Total # of cores | Total RAM | Total disk space |
|---|---|---|---|
| 441 | 1562 | (3.6 TB) | (300 TB) |
