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 |
| Intel | 9.1 & 10.0 | module load intel/compilers (/opt/intel/ ) |
| Portland Group | 7.2.5 (default) / 8.0.1 | module load pgi/compilers |
| Pathscale EKO | 3.2 | module load pathscale/compilers |
| NAG Compiler | module load nag/compilers | |
| GNU compilers | 4.2.4 | module load gnu/compilers |
2. Math Libraries
| Library | Version | Location |
| ACML | ? | |
| atlas | module load libs/atlas | |
| Intel CMKL | 9.1 | module load intel/mkl (/opt/intel/mkl) |
| FFTW/FFTW3 | 2.1.5 / 3.1.2 | |
| ScaLAPACK | ? | |
| NAG Fortran | ? | module load libs/NAG-fortran |
| GSL | 1.9 | |
| HDF5 | 1.8.1 | module load libs/hdf5 |
| netCDF | 3.6.2 | module 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 Analyzer | 7.2 | Provides information to help understand and optimise application performance by quickly locating performance bottlenecks with MPI communication. |
| Intel Thread Checker? | ||
| ipm | ||
| Acumen slowspotter (single user license) | ||
| tau | 2.17.2 | |
| Open Speedshop |
4.Research Applications / Packages
| Application | Version | Brief Description |
| Blast | 2.2.18 | NCBI 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. | |
| Molpro | 2008.1 | Molpro is a complete system of ab-initio programs for molecular electronic structure calculations. |
| siesta | 2.17.2 | siesta performs electronic structure calculations and ab-initio molecular dynamic simulations |
| Amber | 10 | Amber provides molecular mechanical force fields for the simulation of biomolecules. |
| CPMD | 3.9.2 | CPMD is a parallelised plane wave / pseudopotential implementation of Density Functional Theory (DFT). |
| gromacs | 3.3.3 / 4.0(to be installed) | Gromacs is a versatile package to perform molecular dynamics. |
| nwchem | 5.1 | NWChem 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. |