LCC

Laboratory of Computational Chemistry

MUNI CEITEC SCI NCBR

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High quality research in the field of computational chemistry, chemoinformatics and bioinformatics cannot be performed without powerful computational resources. LCC members have access to several NCBR computational resources, which range from middle-sized clusters to big SMP (symmetric multi-processing) supercomputers. These clusters are suitable for various types of computational jobs ranging from high-throughput virtual screening, through molecular dynamics simulations to advanced quantum chemical calculations. Some clusters are part of national supercomputing center MetaCentrum VO and benefits from value-added services such as high-capacity storage and backup. All clusters run on Linux operating systems and they are managed via Infinity system. Infinity is developed at LCC with main focus on the simplification of the management of computational jobs and scientific software.

LCC members have also access to stereoscopic projection facilities. The stereoscopic (3D) visualization is necessary for the deeper understanding of complicated processes occurring especially in biomolecular systems, where traditional visualization techniques reach their limits. The 3D visualization can be used by LCC members for result analysis as well as the presentation of processed data.

Computational clusters

LCC members can fully or partially access following NCBR computational clusters: wolf, perian, orca, and sokar. They have also access to entire MetaCentrum VO infrastructure as they are members of academic institution.

wolf

wolf image

Wolf is a small computational cluster formed from about twenty PC computers located in the computer room 1.18/A4 UKB. This room is used for special lectures or courses requiring computers. The cluster provides nearly the same environment as other clusters. Thus it is also used for training skills of students required for proper utilization of Linux operating system, scientific software, batch systems, and other stuff related to supercomputing.

Detailed cluster description together with other useful information is available on-line on the cluster web pages.

perian

perian image

Perian is a computational cluster, which is intended for molecular dynamics simulations of large biomolecular systems and/or quantum chemical calculations of middle systems. It is the part of MetaCentrum VO infrastructure. LCC members can access the cluster via prioritized queues: ncbr_medium and ncbr_long.

Cluster properties:

NodesCores/NodeCPURAMDiskTorque property
108Intel Xeon X5365, 3.0 GHz8 GB200 GBper1
108Intel Xeon E5420, 2.5 GHz8 GB200 GBper2
208Intel Xeon E5620, 2.4 GHz24 GB1 TBper3
1612Intel Xeon E5645, 2.4 GHz48 GB2 TBper4
Total:512 cores

orca

orca image

Orca is a computational cluster, which is intended for prioritized quantum chemical calculations of middle systems. It is the part of MetaCentrum VO infrastructure. Selected members of LCC group can access the cluster via prioritized queue: orca. Other LCC members can utilize this cluster via queues: preemptible and/or backfill.

Cluster properties:

NodesCores/NodeCPURAMDiskTorque property
184AMD Opteron 2218, 2.6 GHz8 GB200 GBorca
Total:72 cores

sokar

orca image

Sokar is a computational cluster, which is intended for quantum chemical calculations of big systems and/or high level quantum chemical calculations. The cluster is accessible to selected members of LCC group.

Cluster properties:

NodesCores/NodeCPURAMDiskTorque property
18Intel Xeon E5530, 2.4 GHz24 GB11 TBmaster
324AMD Opteron 8431, 2.4 GHz96 GB1 TBnode
464AMD Opteron 6274, 2.2 GHz256 GB6 TBnode
Total:336 cores

Stereoscopic projections

Computer room 1.18/A4 UKB

Two computational nodes of cluster WOLF have extension for a stereoscopic visualization. The node wolf01 can be used to project stereo images/video to a screen. The screen is visible for about to twenty watchers (currently limited by the number of available stereo glasses). The node wolf23 has interface for a single 3D NVidia Vision glasses. Thus this node is useful for individual projections and data analysis.

Seminar room 2.12/A4 UKB

The wolf cluster has a special node, which is located in the seminar room 2.12. The name of this node is wolfsr. It has the same configuration as the wolf01 node described above. The node can be used to project stereo images/video to a screen. The screen is visible for about to twenty watchers (currently limited by the number of available stereo glasses).