Clusters of Department of Theoretical Chemistry

A: Major Equipment - Computational clusters

1) Cluster fock.jh-inst.cas.cz (960 CPU cores)

  • 29 computational nodes + 1 head node
  • Each node with 2x CPU Intel Xeon Gold 6226R @ 2.9 GHz (32 cores), 384 GB RAM, 3 TB SSD disk space
  • Connectivity provided by two 1Gb/s ethernet networks (management and data)
  • 24 kVA power backup solution
  • OS Debian GNU/Linux with SoGE queueing system

2) Cluster kohn.jh-inst.cas.cz (616 CPU cores)

  • 54 computational nodes + 1 head node
  • 20 nodes with 2x CPU Intel Xeon E5-2667 v3 @ 3.2 GHz (16 cores), 128 GB RAM and 34 nodes with 2x CPU Intel Xeon X5687 @ 3.6 GHz (8 cores), 48 GB RAM,  4 TB disc space
  • Connectivity provided by 3 networks: 2x 1Gb/s ethernet (management and data), 1x 40 Gb/s InfiniBand for HPC parallel environment
  • 20 kVA power backup solution
  • OS Debian GNU/Linux with SoGE queueing system

3) Cluster gpu.jh-inst.cas.cz (612 CPU cores)

  • 28 computational nodes + 1 head node
  • Each node with 2x CPU Intel Xeon, several generations and architectures starting with X5675 @ 3.07 GHz (12 cores) and ending with Gold 6226R @ 2.9 GHz (32 cores), up to 750 GB RAM, 2-4 TB disc space per node
  • 12 nodes are equipped with GPU computational card Nvidia Tesla
  • 1 node equipped with Intel Xeon Phi computational card
  • Connectivity provided by two networks: 2x 1Gb/s ethernet (management and data)
  • 16 kVA power backup solution
  • OS Debian GNU/Linux with SGE queueing system


B: Available Methods

1) Computational clusters are equipped with the following free and commercial software

  • Compiler Intel, GNU
  • Libraries: Intel MPI, Intel MKL, OpenMPI, OFED, FFTW, Global Arrays
  • Quantum chemistry programs: CP2K, CRYSTAL, DALTON, GAMESS(US), Gaussian, Molpro, Molcas, Molden, NWChem, ORCA, TmoleX, Turbomole, VASP, VMD

2) Locally developed or locally extended/modified methods (most of them still under development)

  • Discrete Momentum Representation (DMR) method for vibrationally inelastic collisions of electrons with polyatomic molecules - fully developed in the department
  • Two-electron R-matrix method for description of large Rydberg molecules - fully developed in the department
  • Hilbert-space Multireference CC methods including LPNO versions
  • Density matrix renormalization group (DMRG) method for strongly correlated systems
  • DMRG-based externally corrected CC methods including LPNO version
  • Molecular dynamics with non-adiabatic and spin-orbit couplings implemented in Newton-X

Department of Theoretical Chemistry