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Merlin Software

Software list

As part of the SRIF-3 procurement a variety of software was procured to assist users developing applications on Merlin. In addition, in consultation with the researchers, a number of commercial applications are available and can be found under the /applications directory. 

This page contains information on the latest software releases installed on the system and a brief summary of the application. These fall under 4 main categories:

1. Compilers

2. Math Libraries

3. Software Development Tools - application debuggers and profilers

4. Research Applications/Packages.

A complete glossary of applications can be found here


1. Compilers

Compiler Version Location
Intel9.1 & 10.0module load intel/compilers (/opt/intel/ )
Portland Group7.2.5 (default) / 8.0.1module load pgi/compilers
Pathscale EKO3.2module load pathscale/compilers
NAG Compiler module load nag/compilers
GNU compilers4.2.4module load gnu/compilers


2. Math Libraries

Library Version Location
atlas module load libs/atlas
Intel CMKL9.1module load intel/mkl (/opt/intel/mkl)
FFTW/FFTW32.1.5 / 3.1.2 
NAG Fortran?module load libs/NAG-fortran
HDF51.8.1module load libs/hdf5
netCDF3.6.2module load libs/netcdf


3. Software Development Tools

Application Version Brief Description


Allinea OPT


 OPT profiles the performance of parallel and scalar applications, allowing users to find the bottlenecks in programme performance quickly and easily
Allinea DDT DDT helps developers fix bugs in code (serial and parallel) - with a powerful and easy to use GUI.
Intel VTune Performance analysis tool which assists with code optimization. The GUI enables various kinds of code profiling including time based profile, event based profile etc.
Intel Trace Analyzer7.2Provides information to help understand and optimise application performance by quickly locating performance bottlenecks with MPI communication.
Intel Thread Checker?  
Acumen slowspotter (single user license)  
Open Speedshop  


4.Research Applications / Packages

Application Version Brief Description
Blast2.2.18NCBI Blast - finds regions of similarity between biological sequences.
LS-DYNA LS-DYNA is an advanced general purpose multiphysics simulation software package.
Mantlevis Mantlevis renders images derived from over 100 million data points for simulating mantle dynamics.
Molpro2008.1Molpro is a complete system of ab-initio programs for molecular electronic structure calculations.
siesta2.17.2siesta performs electronic structure calculations and ab-initio molecular dynamic simulations
Amber10Amber provides molecular mechanical force fields for the simulation of biomolecules.
CPMD3.9.2CPMD is a parallelised plane wave  / pseudopotential implementation of Density Functional Theory (DFT).
gromacs3.3.3 / 4.0(to be installed)Gromacs is a versatile package to perform molecular dynamics.
nwchem5.1NWChem provides a quantum mechanical description of the electronic wavefunction / density.
star Galaxy formation code
VASP VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.
TERRA Terra is a tool to understand the dynamics of the Earth's mantle that drives the motions of tectonic plates.
NEMO Nucleus for European Modelling of the Ocean.
Alldmarel Prediction of crystal structures (TBC)
Colombo in-house code
Compass in-house code
Zebedde Zebedde - zeolites by de novo design - is a code that builds molecules from fragments.