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Tag: Intel oneAPI MKL

[Computed on Discoverer] Calculation and visualization of protein conformations generation in implicit solvent

[Computed on Discoverer] Calculation and visualization of protein conformations generation in implicit solvent

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We have numerous results we would like to share with you. One instance is the computation that demonstrates the conformation changes that make the protein to fold and unfold. The proper analysis of those changes help to measure the free energy of different processes related to the protein chain transformations. Our protein model representation depicts the side chains of each residue by utilizing a coarse grain force field, as illustrated in the video slides. By doing this, we significantly reduce…

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[Computed on Discoverer] Computation and visualization of ensemble averages

[Computed on Discoverer] Computation and visualization of ensemble averages

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The molecular dynamics simulations provide great details at the nanoscale level for relatively big systems (up to several million atoms). Very often the material environment of certain functional groups, selected atoms, clusters of atoms, and other low to high-level structural elements, is numerically evaluated employing radial distribution functions (RDF). That method is powerful, well studied, and largely implemented for analysis. But it cannot provide a visual spatial estimate for the investigated environment. If you have a molecule surrounded by ions,…

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ABINIT 9.8.2 on Discoverer HPC

ABINIT 9.8.2 on Discoverer HPC

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ABINIT is a powerful package for calculating a variety of optical, mechanical, vibrational, and other observable properties of materials. It is written in Fortran 95 and supports distributed parallelization model based on MPI library. This post is about how ABINIT 9.8.2 code can be compiled for high productivity on Discoverer HPC. The compilation of ABINIT code relies on the presence of a number of external auxiliary libraries, which have to be installed on the build host in advance. Most important…

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Create high productive CP2K 2022.1 build that works on AMD Zen2 microarchitecture

Create high productive CP2K 2022.1 build that works on AMD Zen2 microarchitecture

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CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. While it can be successfully compiled by using Intel oneAPI, Intel oneAPI MKL, and Intel MPI, the produced executables cannot run simulations of large systems on AMD Zen2 CPU. For instance, the SCF minimization fails by sending “Segmentation fault” message to the standard error. The debugging results point to a problem with handling…

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Which FFTW3 build to use on Discoverer

Which FFTW3 build to use on Discoverer

FFTW3 is an important library package that provides large number of HPC applications with a collection of external subroutines for computing the discrete Fourier transform (DFT) in one or more dimensions. In HPC environment it is a common case to have several different builds of FFTW3 available to support the variety of installed MPI libraries, threads libraries, and common models for application code building, linking, and executing. But in spite how many such builds are presented locally, the most compatible…

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