This page describes all software installed on each of the access nodes for the HPC cluster.

Applications and Tools

	Version	General Access node	SCS node	COAPS node	MET node	Taylor group node	Winkler group node	Kostov group node	Torrey Pines node	IMB node	Physics node	Bruschweiler node
Migrate	2.4.3
Fluidity
R (statistical computing)	2.7.0
MOAB	5.3.5
Condor Documentation	1
STATA	10
VMD	1.8.6
NAMD	2.6
Octave	3.0.2
xmgrace	5.1.22
Matlab Distributed Computing Engine	r2008b
Matlab	7.7.0.471 (R2008b)
LS-DYNA	7600-2-1224
GROMACS	3.3.1
Gaussian	rev E01

Libraries

	Version	General Access node	SCS node	COAPS node	MET node	Taylor group node	Winkler group node	Kostov group node	Torrey Pines node	IMB node	Physics node	Bruschweiler node
Arpack Library	96
MPE for MVAPICH2
FFTW	2.1.5
SciPy/NumPy	1.2.1
OpenMPI GNU	1.3.3-1
MPICH v1 GNU	1.1
MPICH v2 GNU	1.0.3
MPICH v2 PGI	1.0.3
OpenMPI PGI	1.2.4
MPICH v1 PGI	0.9.9
NetCDF	4.0-5
HDF 5	5-1.6.4
MPICH v2 Intel	1.0.3
MPICH v1 Intel	1.1
OpenMPI Intel	1.3.3-1
BioPerl	1.5+
Biopython	1.4+

Programming Languages

	Version	General Access node	SCS node	COAPS node	MET node	Taylor group node	Winkler group node	Kostov group node	Torrey Pines node	IMB node	Physics node	Bruschweiler node
Javac	1.5.0_10
Portland Group Compilers	9.0-4
Intel Fortran	11.1-059
Intel C/C++	11.1-059
GNU Fortran	4.1.2
GNU C/C++	4.1.2

Bioinformatics Suite

Important information about this software category

	Version	General Access node	SCS node	COAPS node	MET node	Taylor group node	Winkler group node	Kostov group node	Torrey Pines node	IMB node	Physics node	Bruschweiler node
GCG	11.1.3
EMBOSS	5.0
ReadSeq	1993
BLAST	2.2.+
MPI-BLAST	1.5.0PIO
FastA	3.5
mpiFastA	3.4
ClustalW	2.0
ClustalX	2.0
T-Coffee	5.65
MAFFT	6.24
SeaView	3.0
HMMER	2.3.2
MEME	3.5.7
Glimmer	3.02
Mauve	2.0.0
MUMmer	3.20
PAUP*	4.0b10
RepMaker	1.1
RAxML	7.0.4
mpiRAxML	7.0.4
MrBayes	3.1.2
mpiMrBayes	3.1.2
GARLI	0.951
mpiGARLI	0.942
PHYLIP	3.67
PAML	4