Available software

Modules

The base operation system is Ubuntu 16.04 LTS. The additional software components are available via module. In order to list all installed software you can use the command:

module avail

/opt/lx/u16.04/Modules/modulefiles:
abinit/8.0.8b-openmpi-1.10.3-intel-2017              2017/02/02 16:39:48
atlas/3.11.38-gcc-os                                 2016/07/03 14:36:55
espresso/5.4.0-openmpi-1.10.3-intel-201              2016/07/17  6:40:00
fftw/3.4.4-gcc-os                                    2016/07/02 18:38:28
gromacs/5.1.2-openmpi-1.10.3-intel-2017              2016/07/16 13:42:49
hdf5/1.10.0-gcc-os                                   2016/07/03 16:26:56
intel/psxe-2017                                      2016/07/16 13:51:22
java/8                                               2016/07/08  6:37:42
munge/0.5.12                             default     2016/07/02 10:06:46
netcdf/4.4.1                                         2016/07/03 17:04:24
netcdf-fortran/4.4.4                                 2016/07/04  5:57:57
openmpi/1.10.3-intel-2017                            2016/07/16 13:46:04
openmpi/1.6.5-gcc-os                                 2016/07/04  5:54:59
openmpi/1.8.8-gcc-os                     default     2016/07/02 11:36:40
openmpi/1.8.8-intel-2017                             2016/07/08  6:24:22
scalapack/2.0.2-openmpi-1.8.8-gcc-os                 2016/07/02 18:41:23
slurm/16.05.0                            default     2016/07/02 10:06:27
wrf/3.6.1-openmpi-1.10.3                 default     2016/07/16 13:44:10
wrf/3.8.1-openmpi-1.8.8-gcc                          2016/07/03 18:26:10

Each module has name and version. For example the module openmpi/1.8.8-gcc-os denotes software package openmpi, version 1.8.8 compiled with the host OS compiler gcc. The version usually can be skipped if you want to load default module, or only one version is installed. Loaded software components for the current session can be listed using the command:

module list

By default only module and slurm modules are loaded. In order to load a particular software package you can use following command:

module load openmpi

or

module load openmpi/1.8.8-gcc-os

Unloading a module can be done with:

module unload openmpi

Loading a module sets a number of global environment variables such as PATH, LD_LIBRARY_PATH, MANPATH and etc. Also some application specific environment variables may be set as well. For example, in case of intel module the environment variable MKL_ROOT is initialized. Unloading the module removes this entries from the environment variables.

Scientific software
  1. Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
  2. Gromacs is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
  3. WRF is a next-generation mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting needs. It features two dynamical cores, a data assimilation system, and a software architecture facilitating parallel computation and system extensibility.
  4. AbInit is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.
Scientific libraries
  1. FFTW
  2. ScaLAPACK
  3. NetCDF
  4. HDF5
  5. ATLAS

Using Intel Parallel XE Cluster Edition 2017 or OpenMPI builds with Intel Compilers

The Intel Compilers and MKL libraries suite are available via intel module. The HPC cluster has one static license installed on computing node cn001. If you would like to build or develop own software code with the Intel Compiler suite you should create an interactive session on cn001. More information on how to set up an interactive session for the use of the Intel compiler is present here.

Visualization software

The front-end and computing nodes have, by default, the following visualisation software installed:

  1. Gnuplot
  2. Octave
  3. Grace

In addition, there is specific visualization software accessible via modules

  1. VMDmodule load vmd
  2. XCrySDenmodule load xcrysden