New Software on the HPC

As part of the maintenance upgrade, we have upgraded many software packages on the HPC to newer versions.  Here is the complete list.

Recently updated software on the HPC:

abinit    8.2.2
abyss    2.0.2
apr    1.5.2
arpack    3.1.5
atsas    2.8.0
autoconf    2.69
bbftp-client    3.2.1
bbreceiver    20161020
beagle    2.1
beast    1.8.4
best    2.3.1
bigdft    1.6.0
blat    34
blcr    0.8.6_b4
boost    1.63.0
bowtie    1.2
bowtie2    2.3.2
bwa    0.7.15
cairo    1.14.8
cdo    1.6.9
CGAL   4.9
chapel    1.13.0
charmm    41
CheSS    1.0
clustalw    2.1
clustalx    2.1
cmake    3.7.2
cpuset    1.5.6
cufflinks    2.1.1
Cython    0.25.2
daq    2.0.6
dcraw    9.27.0
deal.II    8.4.1
dyninst    9.3.1
eigen3    3.3.3
elph    1.0.1
fasta    36.3.8e
fastqc    0.11.5
ffmpeg    3.1.7
fftw2    2.1.5
fftw    3.3.5
FIAT    1.6.0.dev0
fonttools    3.8.0
FPLO14.00    49
freefem++    3.53
freexl    1.0.2
futile    1.8
ga    5.5
GaIn    1.0
gdal    2.1.0
gerris    1.3.2
git    2.12.0
glimmer    3.02b
gmm    5.0
grads    2.0.2
grib_api    1.19.0
gromacs    2016.2
gtkglext    1.2.0
gtkglextmm    1.2.0
gts_gerris    0.7.6
gulp    4.4
h5py    2.5.0
hdf    4.2.12
hdf5    1.8.16
hdfview    2.11.0
hmmer    3.1b2
HTSeq    0.6.1
hwloc    1.11.6
hypre    2.11.1
iipsrv-1.0.0    6.0
ImageMagick    6.9.3.0
ipython    3.2.1
iqs-client    1.0
jags    4.2.0
julia    0.5.0
lame    3.99.5
lammps    20160309
lapack    3.6.1
last    833
libbitmask    2.0
libffi    3.1
libgeotiff    1.4.0
libgit2    0.25.1
libglademm24    2.6.7
libmatheval    1.1.11
libmemcached    1.0.18
libpfm    4.8.0
libspatialite    4.3.0a
libsx    2.05
libunwind    1.1
libxc    3.0.0
libxcb    1.12
llvm3.7    3.7.1
Lmod    7.3.20
mafft    7.309
mauve   2.4.0
MCT    2.9.0
migrate-n    3.6.11
mira    4.0.2
mirage    0.9.5.2
mmtsb    1
moltemplate    2.1.2
motd    1.1
mpi4py    2.0.0
mpiblast    1.6.0
mpifasta    3.4
mpihmmer    0.92
mpimrbayes    3.1.2
mpimrbayes-new    3.2.1
mrbayes    3.1.2
mrbayes-new    3.2.1
mummer    3.23
mvapich2    2.2
namd    2.10
nasm    2.12.02
ncl    6.4.0
nco    4.6.5
ncview    2.1.8
nedit    5.6
netcdf    4.4.1.1
netcdf-c    4.3.3.1
netcdf-cxx    4.2
netcdf-fortran    4.4.4
newtonx    1.4.0.2
numpy    1.12.0
nwchem    6.5.26243
ocaml-sexplib    7.0.5
ocaml-type-conv    3.0.5
octave    4.2.1
ogdi-3.2.0    0.26.beta2
openblas    0.2.19
openlibm    0.5.3
openmpi    2.1.0rc3
parallel-kmeans    1
paraview    4.4.0
paraview-openmpi    4.4.0
parmetis    4.0.3
pastix      5.2.2.20
pdtoolkit    3.23
perl-Array-Utils    0.5
perl-IO-Compress-Bzip2    2.015
perl-Set-IntSpan    1.19
pgplot    5.2.2
php       7.1.5
php-pear    1.10.1
php-pecl-apcu    5.1.8
php-pecl-igbinary    2.0.4
php-pecl-memcached    3.0.3
php-pecl-msgpack    2.0.2
pnetcdf    1.8.1
povray    3.7
primme    1.1
proj    4.9.2
psolver    1.8
psutil    5.2.2
pygtkglext    1.1.0
pyhdf    0.8.3
pyOpenSSL    16.2.0
python3    3.5.1
python-ase    3.13.0
python-biopython    1.68
python-pkgconfig    1.2.2
python-polygon2     2.0.4
python-shapely    1.5.16
python-six    1.10.0
python-ttfquery 1.0.4
python-urllib3    1.20
python-visual    5.74
quantum-espresso    5.4.0
R 3.4.0
samtools    0.1.19
scalapack    2.0.2
schroedinger    1.0.11
scipy    0.18.0
scotch    6.0.4
six    1.10.0
slurm    17.02.3
snort    2.9.7.3
source-highlight    3.1.8
sparsehash    2.0.2
sra_sdk    2.3.5
STAR    2.5.3a
suitesparse    4.4.6
SuperLU    5.2.0
svgalib    1.9.25
szip    2.1
tophat    2.1.1
trans-ABySS    1.5.5
tre            0.8.0
trimmomatic    0.36
trlan         201009
utf8proc    2.1.0
vmd    1.9.1
vtk    7.1.1
wgrib    1.8.1.2c
wombat    1
xcb-proto    1.12
xmgrace    5.1.25
xorg-x11-util-macros    1.19.0
yasm    1.3.0