Intrumentation of Department of Computational Chemistry
A: Major Equipment
1) Cluster kohn.jh-inst.cas.cz (336 CPU cores)
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20 computational nodes + 1 head node
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Each node with 2x CPU Intel Xeon E5-2667 v3 3.2 GHz (16 cores), 128 GB RAM, 4TB disc space
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Connectivity provided by 3 networks: 2x 1Gb/s ethernet (management and data), 1x 40 Gb/s InfiniBand for HPC parallel environment
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20 kVA power backup solution
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OS Debian GNU/Linux with SoGE queueing system
2) Cluster bose.jh-inst.cas.cz (280 CPU cores) – now a part of kohn
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21 computational nodes + 1 head node
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Each node with 2x CPU Intel Xeon X5687 3.6 GHz (8 cores), 48 GB RAM, 4TB disc space
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Connectivity provided by 3 networks: 2x 1Gb/s ethernet (management and data), 1x 40 Gb/s InfiniBand for HPC parallel environment
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16 kVA power backup solution
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OS Debian GNU/Linux with SGE queueing system
3) Cluster gpu.jh-inst.cas.cz (374 CPU cores)
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21 computational nodes + 1 head node
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Each node with 2x CPU Intel Xeon, several generations and architectures starting with X5675 3.07 GHz (12 cores per node) and ending with Gold 6136 3.0 GHz (24 cores per node), 8-20 GB RAM per core, 2-4 TB disc space per node
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13 nodes is equipped with GPU computational card Tesla Nvidia
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1 node equipped with Intel Xeon Phi computational card
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Connectivity provided by two networks: 2x 1Gb/s ethernet (management and data)
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16 kVA power backup solution
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OS Debian GNU/Linux with SGE queueing system
4) in-house mesofluidic experimental systems for studying biophysical interfacial phenomena
B: Available Methods
1) Computational clusters are equipped with the following free and commercial software
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Compiler Intel, GNU
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Libraries: Intel MPI, Intel MKL, OpenMPI, OFED, FFTW, Global Arrays
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Quantum chemistry programs: CP2K 2.6, CRYSTAL14, DALTON 2016, GAMESS(US), Gaussian 09, Molpro 2012, Molcas 8.0, Molden 5.4, NWChem 6.6, ORCA 4.1.1, TmoleX 4.1.1, Turbomole 7.1, VASP 5.4, VMD 1.9.2
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Molecular Dynamics programs: GROMACS 2018, plumed 2.3
