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scientific_software:softwarelist

List and status of scientific software

OK:Installed and validated/tested. N/T: Installed but not validated/tested. N: Not installed or installed but not working.

Compilers/Programming languages

Number IDSoftware nameModule Name Version Status Notes
1 gcc, gfortran, etc. libs/gcc/system 4.4.7 OK
2 gcc, gfortran, etc. compilers/gcc/4.7.4 4.7.4 OK
3 gcc, gfortran, etc. compilers/gcc/4.8.2 4.8.2 OK
4 gcc, gfortran, etc. compilers/gcc/5.3.0 5.3.0 OK
5 gcc, gfortran, etc. compilers/gcc/6.2.0 6.2.0 OK
6 Intel compiler compilers/intel/2015 2015.3.187 OK Licensed version with debugger
7 java, etc. general/JRE/1.6.0_45 1.6.0_45 OK
8 java, etc. general/JRE/1.7.0_80 1.7.0_80 OK
9 java, etc. general/JRE/1.8.0_65 1.8.0_65 OK
10 perl general/perl/5.12.5 5.12.5 OK
11 perl general/perl/5.22.0 5.22.0 OK
12 perl general/perl/5.21.1_threaded 5.22.1 OK Perl with Threads
13 python general/python/2.7.10 2.7.10 OK
14 python general/python/3.5.1 3.5.1 OK
15 python apps/python/2.7.8/gcc-4.4.7 2.7.8 OK Compiled with gcc-4.4.7

(List not fully updated yet. Check with module av for more.)

Parallelisation Languages

Number IDSoftware nameModule Name Version Status Compiled with Notes
1 OpenMPI libs/openmpi/1.10.0/gcc5.3.0 1.10.0 OK 3
2 OpenMPI libs/openmpi/1.10.0/intel15.0 1.10.0 OK 3
3 OpenMPI libs/openmpi/1.10.2/gcc5.3.0 1.10.2 OK 3
4 OpenMPI libs/openmpi/1.6.5/intel15.0 1.6.5 OK 3
5 OpenMPI libs/openmpi/2.0.0/gcc5.3.0 2.0.0 OK 3
6 OpenMPI libs/openmpi/2.0.0/intel15.0 2.0.0 OK 4
7 OpenMPI libs/openmpi/2.0.1/intel15.0 2.0.1 OK 4
8 OpenMPI mpi/openmpi/1.8.1/gcc-4.4.7 1.8.1 OK 2
9 mpi4py libs/mpi4py/1.3/gcc-4.4.7+python-2.7.8+openmpi-1.8.1/ 1.3 OK 13 Compiled with openmp-1.8.1
Libraries
Number IDSoftware nameModule Name Version Status Compiled with Notes
1 fftw libs/fftw/3.3.4/gcc5.3.0 3.3.4 OK 3
2 fftw libs/fftw2/intel15-double 2.0.0 OK 4 Double precision
3 fftw libs/fftw2/intel15-float 2.0.0 OK 4 Single precision
4 fftw libs/fftw3/intel15-double 3.0.0 OK 4 Double precision
5 fftw libs/fftw4/intel15-float 3.0.0 OK 4 Single precision
6 fftw libs/fftw2_double/2.1.5/gcc-4.4.7 2.1.5 OK 1 Double precision
7 fftw libs/fftw2_double-mpi/2.1.5/gcc-4.4.7+openmpi-1.8.1 2.1.5 OK 4 Double precision
8 fftw libs/fftw2_float/2.1.5/gcc-4.4.7 2.1.5 OK 1 Single precision
9 fftw libs/fftw2_float-mpi/2.1.5/gcc-4.4.7+openmpi-1.8.14 3.0.0 OK 4 Single precision
10 fftw libs/fftw4/intel15-float 3.0.0 OK 4 Single precision

(List not fully updated. Check with module av for more.)

Applications

Number IDSoftware nameModule Name (general/) Version Status Compiled with Notes
1 CP2K¹ cp2k/3.0.0/gcc5.3.0 3.0.0 OK PSMP, SSMP version
2 CP2K¹ cp2k/3.0.0/intel15.0 3.0.0 OK POPT version
2 CPMD cpmd/4.1 4.1 OK -
3 Gaussian gaussian/09C 0.9C OK -
4 Gaussian gaussian/09E 0.9E OK -
5 Gromacs² gromacs/double/4.6.7 4.6.7 OK -
6 Gromacs² gromacs/double/4.6.7plumed 4.6.7 OK Plumed 2.2.3
7 Gromacs² gromacs/double/5.1.3 5.1.3 OK -
8 Gromacs² gromacs/double/5.1.3cuda 5.1.3 N/T -
9 Gromacs² gromacs/double/5.1.4plumed 5.1.4 OK Plumed 2.2.4
10 Gromacs² gromacs/double/5.1.4drude 5.1.4 OK Drude
11 Gromacs² gromacs/single/4.6.7 4.6.7 OK -
12 Gromacs² gromacs/single/4.6.7plumed 4.6.7 OK Plumed 2.2.3
13 Gromacs² gromacs/single/5.1.3 5.1.3 OK -
14 Gromacs² gromacs/single/5.1.4plumed 5.1.4 OK Plumed 2.2.4
15 Gromacs² gromacs/single/5.1.4drude 5.1.4 OK Drude
16 IMP IMP/2.6.2 2.6.2 OK -
17 LAMMPS lammps/Jul16/intel15.0 Jul16 OK -
18 LAMMPS lammps/Jul16/intel15.0plumed Jul16 OK -
19 Mathematica mathematica/10.0 10.0 OK -
20 Matlab matlab/2015b 2015b OK -
21 NAMD NAMD/2.9plumed 2.9 OK Plumed 2.2.3
22 NAMD NAMD/2.9plumedcuda 2.19 N/T Plumed 2.2.3
23 NAMD NAMD/2.10 2.10 OK -
24 NAMD NAMD/2.10cuda 2.10 N/T -
25 NAMD NAMD/2.11 2.11 OK -
26 Octopus octopus/6.0 6.0 OK -
27 Orca orca/3.0.3 3.0.3 OK -
28 Orca quantum-espresso/5.4.0 5.4.0 OK -
29 Orca quantum-espresso/6.0 6.0 OK -
30 R R/3.2.1 3.2.1 OK -
31 R R/3.3.0 3.3.0 OK -
32 Siesta siesta/4.0/intel15.0 4.0 OK -

Applications with private license

Number IDSoftware nameModule Name (private-licenced/) Version Status Compiled with Notes
1 Amber amber/12/cuda-intel15.0 12 N/T -
2 Amber amber/12/intel15.0 12 N/T -
3 Autofit³ autofit 15 OK -
4 GAMS gams/24.3.1 24.3.1 N/T -
5 Lumerical FDTD lumerical/fdtd8.7.3 8.7.3 OK -
6 Lumerical FDTD lumerical/fdtd8.17 8.17 OK -
7 VASP vasp/5.4.1/intel15.0 5.4.1 OK -
8 VASP vasp/5.4.1/intel15.0lo 5.4.1 OK Low optimization

¹Cp2k

For jobs using a single node(<20 cores) use the SSMP(threads) version. For jobs using many nodes use PSMP(MPI with threads in each node) or POPT(MPI) version.

²Gromacs

In your script put this two lines:

NPROC=$( ($NSLOTS / 20) )

export OMP_NUM_THREADS=20

and use in mpirun -np $NPROC etc.

³Autofit

  • Use it with interactive session e.g. qrsh -pe smp 20, or check how here:interactive_jobs;
  • Copy the script files to your home directory from the $AUTOFIT directory;
  • Run: python prog_A_v15c_linux.py and use the number of cores you requested in the session;
scientific_software/softwarelist.txt · Last modified: 2017/04/25 11:00 by admin