Software upgrade coming in May

In May, we will perform our annual software upgrade. Approximately 500 packages will be upgraded to newer versions. We will be perform the upgrade sometime during the break between semesters; specific dates to be announced in early April.  We expect the upgrade to take approximately one week.

During this upgrade, we will perform upgrades to all major software on the HPC and Spear.  Notable highlights include:

The full list:

abinit    8.10.1
abyss    2.1.5
adobe-source-code-pro-fonts    2.030.1.050
apr    1.6.5
armadillo    9.200.6
arpack    3.5.0
assimp    3.3.1
atsas    2.8.4
automake    1.16.1
bbftp-client    3.2.1
bbreceiver    20161020
bcftools    1.9
bcl2fastq2    2.20.0.422
beagle    2.1
beast    1.10.4
best    2.3.1
blat    34
boost    1.66.0
boost-intel    1.66.0
bowtie    1.0.1
bwa    0.7.17
cairo    1.14.8
cdo    1.9.6
ceph    12.2.11
ceres-solver    1.13.0
CGAL-4.9    0.2.beta1
cgnslib    3.3.1
charmm    41
clang    6.0.0
clang    7.0.1
clustalw    2.1
clustalx    2.1
cmake    3.13.3
cpuset-1.5.7    43.4
ctags    5.8
cudnn    7.0.5
cufflinks    2.1.1
Cython    0.29.3
daq    2.0.6
dcraw    9.28.0
debootstrap    1.0.109
distribution-gpg-keys    1.28
dpkg    1.18.25
dyninst    9.3.1
eigen3    3.3.7
elpa    2017.05.003
elph    1.0.1
fasta    36.3.8e
fastqc    0.11.7
ffmpeg    3.1.7
fftw2    2.1.5
fftw2-intel    2.1.5
fftw2-pgi    2.1.5
fftw    3.3.8
fftw-intel    3.3.8
fftw-pgi    3.3.8
fonttools    3.8.0
freefem++    3.62
freexl    1.0.5
ga    5.6.5
GaIn    1.0
ga-intel    5.6.5
gcc821    8.2.1
gd    2.2.5
gdal    2.2.4
git-2.21.0    0.1.rc1
glimmer    3.02b
globus-cli    1.10.0
gmm    5.2
gperftools    2.7
grads    2.0.2
GraphicsMagick    1.3.31
grib_api    1.27.0
gromacs    2019
gromacs-intel    2019
gromacs-pgi    2019
gtkglext    1.2.0
gts_gerris-0.7.6    48.1
gulp    5.1
h5py    2.8.0
hdf    4.2.13
hdf5    1.10.4
hdf5-intel    1.10.4
hdf5-pgi    1.10.4
hdf-intel    4.2.13
hdf-pgi    4.2.13
hdfview    3.0.0
hmmer    3.1b2
hpc-modules    2.14
HTSeq    0.6.1
htslib    1.9
hwloc    2.0.3
hypre    2.15.1
hypre-intel    2.15.1
iipsrv-1.0.0    6.0
intel-pgi-fakedeps    2
ipython    3.2.1
jags    4.2.0
json    3.5.0
julia    1.1.0
koji    1.16.1
lame    3.100
lammps    20181212
lammps-intel    20181212
lapack    3.8.0
last    963
lastfmlib    0.4.0
leptonica    1.77.0
libbitmask    2.0
libctl    3.2.2
libebml    1.3.6
libgeotiff    1.4.0
libgit2    0.27.8
libharu    2.3.0
libiconv    1.15
libmatheval    1.1.11
libmatroska    1.4.9
libmemcached    1.0.18
libmfx    1.25
libpfm    4.10.1
libpq    11.0
libspatialite    4.3.0a
libsx    2.05
libunwind    1.3.1
libva    2.4.0
libwebp    1.0.2
libxc    4.3.0
libxcb    1.13
lighttpd    1.4.53
llvm3.9    3.9.1
llvm    6.0.0
llvm    7.0.1
Lmod    7.8.9
lttng-ust    2.10.2
mafft    7.407
mariadb-connector-c    3.0.8
mauve-2.4.0    1HPC
mbedtls    2.16.0
MCT    2.10.0
MCT-intel    2.10.0
MCT-pgi    2.10.0
migrate-n-4    3.6.11
mira    4.0.2
mirage    0.9.5.2
mkvtoolnix    7.4.0
mmtsb    1
mock-core-configs    29.4
molden    5.9
motd    1.1
mpb    1.5
mpi4py    3.0.0
mpiblast    1.6.0
mpifasta    3.4
mpihmmer-0.92    2HPC_OPENMPI
mpimrbayes-new    3.2.1
mrbayes-new    3.2.1
mummer    3.23
mvapich2    2.3
mvapich2_intel    2.3
mvapich2_pgi    2.3
namd    2.13
namd-intel    2.13
nasm    2.13.03
ncbi-vdb    2.9.4
ncbi-vdb    2.9.4
ncl    6.5.0
ncl-intel    6.5.0
ncl-pgi    6.5.0
nco    4.7.8
nco-intel    4.7.8
ncview    2.1.8
nedit    5.7
netcdf    4.6.2
netcdf    4.6.2
netcdf-cxx    4.2
netcdf-cxx-intel    4.2
netcdf-cxx-pgi    4.2
netcdf-fortran    4.4.4
netcdf-fortran-intel    4.4.4
netcdf-fortran-pgi    4.4.4
netcdf-intel    4.6.2
netcdf-pgi    4.6.1
newtonx    1.4.0.2
ngs-sdk    2.9.4
ninja-build    1.9.0
numpy    1.15.1
nwchem    6.8.1
ocaml-sexplib    7.0.5
ocaml-type-conv    3.0.5
octave    4.4.1
ogdi    3.2.1
openblas    0.3.5
opencv    3.2.0
openlibm    0.5.3
openmpi    4.0.0
openmpi_intel    4.0.0
openmpi_pgi    4.0.0
orca    4.0.0.2
parallel-kmeans    1
paraview    5.5.2
parmetis    4.0.3
parmetis-intel    4.0.3
parmetis-pgi    4.0.3
pcre2    10.32
pcsc-perl    1.4.14
pdtoolkit    3.25
perl-Array-Utils    0.5
perl-Set-IntSpan    1.19
pgplot    5.2.2
php    7.3.2RC1
pjproject    2.7.2
pnetcdf    1.8.1
pnetcdf-intel    1.8.1
proj    4.9.3
pygtkglext    1.1.0
pyhdf    0.8.3
python3    3.7.0
python3    3.7.0
python-ase    3.16.2
python-biopython    1.73
python-click    7.0
python-empy    3.3.3
python-packaging    17.1
python-pkgconfig    1.3.1
python-psutil    5.4.3
python-pygments    2.2.0
python-pysocks    1.6.8
python-rpm-generators    7
python-shapely    1.6.4
python-ttfquery-1.0.4    5.8_
python-urllib3    1.24.1
python-virtualenv    16.0.0
python-virtualenv    16.0.0
qt5    5.11.3
qt5-qt3d    5.11.3
qt5-qtbase    5.11.3
qt5-qtcanvas3d    5.11.3
qt5-qtcharts    5.11.3
qt5-qtconfiguration    0.3.1
qt5-qtconnectivity    5.11.3
qt5-qtdatavis3d    5.11.3
qt5-qtdeclarative    5.11.3
qt5-qtdeclarative    5.11.3
qt5-qtimageformats    5.11.3
qt5-qtquickcontrols2    5.11.3
qt5-qtscript    5.11.3
qt5-qtsensors    5.11.3
qt5-qtserialport    5.11.3
qt5-qtsvg    5.11.3
qt5-qttools    5.11.3
qt5-qtwebchannel    5.11.3
qt5-qtwebsockets    5.11.3
qt5-qtx11extras    5.11.3
qt5-qtxmlpatterns    5.11.3
qtwebkit    2.3.4
quantum-espresso    6.3
R2spec    4.2.1
R-3.5.2    3.5.2
R-3.5.2-abind    1.4_5
R-3.5.2-acepack    1.4.1
R-3.5.2-ade4    1.7_13
R-3.5.2-affy    1.60.0
R-3.5.2-affyio    1.52.0
R-3.5.2-ald    1.2
R-3.5.2-annaffy    1.54.0
R-3.5.2-annotate    1.60.0
R-3.5.2-AnnotationDbi    1.44.0
R-3.5.2-ape    5.2
R-3.5.2-askpass    1.1
R-3.5.2-assertthat    0.2.0
R-3.5.2-backports    1.1.2
R-3.5.2-bartMachineJARs    1.1
R-3.5.2-base64enc    0.1_3
R-3.5.2-BH    1.69.0_1
R-3.5.2-bindr    0.1.1
R-3.5.2-bindrcpp    0.2.2
R-3.5.2-Biobase    2.42.0
R-3.5.2-BiocGenerics    0.28.0
R-3.5.2-BiocInstaller    1.32.1
R-3.5.2-BiocManager    1.30.4
R-3.5.2-BiocParallel    1.16.6
R-3.5.2-biomaRt    2.38.0
R-3.5.2-Biostrings    2.50.2
R-3.5.2-bit    1.1_14
R-3.5.2-bit64    0.9_7
R-3.5.2-bitops    1.0_6
R-3.5.2-blob    1.1.1
R-3.5.2-brew    1.0_6
R-3.5.2-broom    0.5.1
R-3.5.2-callr    3.1.1
R-3.5.2-carData    3.0_2
R-3.5.2-caret    6.0_81
R-3.5.2-caTools    1.17.1.1
R-3.5.2-cellranger    1.1.0
R-3.5.2-checkmate    1.9.1
R-3.5.2-cli    1.0.1
R-3.5.2-coda    0.19_2
R-3.5.2-colorspace    1.3_2
R-3.5.2-crayon    1.3.4
R-3.5.2-curl    3.3
R-3.5.2-CVST    0.2_2
R-3.5.2-data.table    1.12.0
R-3.5.2-DBI    1.0.0
R-3.5.2-ddalpha    1.3.8
R-3.5.2-DelayedArray    0.8.0
R-3.5.2-DEoptimR    1.0_8
R-3.5.2-desc    1.2.0
R-3.5.2-DESeq    1.34.1
R-3.5.2-DESeq2    1.22.2
R-3.5.2-deSolve    1.21
R-3.5.2-DEXSeq    1.28.1
R-3.5.2-dichromat    2.0_0
R-3.5.2-digest    0.6.18
R-3.5.2-dimRed    0.2.2
R-3.5.2-diversitree    0.9_10
R-3.5.2-doSNOW    1.0.16
R-3.5.2-dplyr    0.8.0.1
R-3.5.2-DRR    0.0.3
R-3.5.2-ellipsis    0.1.0
R-3.5.2-ergm    3.9.4
R-3.5.2-ergm.count    3.3.0
R-3.5.2-evaluate    0.13
R-3.5.2-fansi    0.4.0
R-3.5.2-flare    1.6.0
R-3.5.2-flsa    1.05
R-3.5.2-forcats    0.4.0
R-3.5.2-foreach    1.4.4
R-3.5.2-formatR    1.5
R-3.5.2-Formula    1.2_3
R-3.5.2-futile.logger    1.4.3
R-3.5.2-futile.options    1.0.1
R-3.5.2-gcrma    2.54.0
R-3.5.2-gdata    2.18.0
R-3.5.2-gdata    2.18.0
R-3.5.2-genefilter    1.64.0
R-3.5.2-geneplotter    1.60.0
R-3.5.2-generics    0.0.2
R-3.5.2-GenomeInfoDb    1.18.2
R-3.5.2-GenomeInfoDbData    1.2.0
R-3.5.2-GenomicAlignments    1.18.1
R-3.5.2-GenomicFeatures    1.34.3
R-3.5.2-GenomicRanges    1.34.0
R-3.5.2-geometry    0.4.0
R-3.5.2-ggplot2    3.1.0
R-3.5.2-ghyp    1.5.7
R-3.5.2-glmnet    2.0_16
R-3.5.2-glue    1.3.0
R-3.5.2-GO.db    3.7.0
R-3.5.2-gower    0.1.2
R-3.5.2-gplots    3.0.1.1
R-3.5.2-graph    1.60.0
R-3.5.2-gridExtra    2.3
R-3.5.2-gsl    1.9_10.3
R-3.5.2-gsubfn    0.7
R-3.5.2-gtable    0.2.0
R-3.5.2-gtools    3.8.1
R-3.5.2-hexbin    1.27.2
R-3.5.2-HiDimDA    0.2_4
R-3.5.2-highr    0.7
R-3.5.2-Hmisc    4.2_0
R-3.5.2-hms    0.4.2
R-3.5.2-htmlTable    1.13.1
R-3.5.2-htmltools    0.3.6
R-3.5.2-htmlwidgets    1.3
R-3.5.2-httpuv    1.4.5.1
R-3.5.2-httr    1.4.0
R-3.5.2-hwriter    1.3.2
R-3.5.2-igraph    1.2.4
R-3.5.2-INLA    18.07.12
R-3.5.2-inline    0.3.15
R-3.5.2-ipred    0.9_8
R-3.5.2-IRanges    2.16.0
R-3.5.2-iterators    1.0.10
R-3.5.2-itertools    0.1_3
R-3.5.2-jsonlite    1.6
R-3.5.2-KEGG.db    3.2.3
R-3.5.2-KEGGgraph    1.42.0
R-3.5.2-kernlab    0.9_27
R-3.5.2-knitr    1.21
R-3.5.2-labeling    0.3
R-3.5.2-lambda.r    1.2.3
R-3.5.2-later    0.8.0
R-3.5.2-latticeExtra    0.6_28
R-3.5.2-lava    1.6.5
R-3.5.2-lavaan    0.6_3
R-3.5.2-lazyeval    0.2.1
R-3.5.2-limma    3.38.3
R-3.5.2-lme4    1.1_20
R-3.5.2-locfit    1.5_9.1
R-3.5.2-loo    2.0.0
R-3.5.2-lpSolve    5.6.13
R-3.5.2-lubridate    1.7.4
R-3.5.2-MADAM    1.2.2
R-3.5.2-made4    1.56.0
R-3.5.2-magic    1.5_9
R-3.5.2-magrittr    1.5
R-3.5.2-manipulate    1.0.1
R-3.5.2-markdown    0.9
R-3.5.2-matrixcalc    1.0_3
R-3.5.2-MatrixModels    0.4_1
R-3.5.2-matrixStats    0.54.0
R-3.5.2-memoise    1.1.0
R-3.5.2-mime    0.6
R-3.5.2-minqa    1.2.4
R-3.5.2-missForest    1.4
R-3.5.2-mnormt    1.5_5
R-3.5.2-ModelMetrics    1.2.2
R-3.5.2-MplusAutomation    0.7_3
R-3.5.2-multtest    2.38.0
R-3.5.2-munsell    0.5.0
R-3.5.2-mvtnorm    1.0_8
R-3.5.2-network    1.13.0.1
R-3.5.2-networkDynamic    0.9.0
R-3.5.2-nleqslv    3.3.2
R-3.5.2-nloptr    1.2.1
R-3.5.2-numDeriv    2016.8_1
R-3.5.2-openintro    1.7.1
R-3.5.2-openssl    1.2.1
R-3.5.2-openxlsx    4.1.0
R-3.5.2-pander    0.6.3
R-3.5.2-pbivnorm    0.6.0
R-3.5.2-PearsonDS    1.1
R-3.5.2-penalizedLDA    1.1
R-3.5.2-pillar    1.3.0
R-3.5.2-pillar    1.3.1
R-3.5.2-pkgbuild    1.0.2
R-3.5.2-pkgconfig    2.0.2
R-3.5.2-plogr    0.2.0
R-3.5.2-plotrix    3.7_4
R-3.5.2-pls    2.7_0
R-3.5.2-plyr    1.8.4
R-3.5.2-praise    1.0.0
R-3.5.2-preprocessCore    1.44.0
R-3.5.2-prettyunits    1.0.2
R-3.5.2-processx    3.2.1
R-3.5.2-prodlim    2018.04.18
R-3.5.2-progress    1.2.0
R-3.5.2-promises    1.0.1
R-3.5.2-proto    1.0.0
R-3.5.2-ps    1.2.0
R-3.5.2-psych    1.8.12
R-3.5.2-purrr    0.3.0
R-3.5.2-qrLMM    1.3
R-3.5.2-quantreg    5.38
R-3.5.2-qvalue    2.14.1
R-3.5.2-R6    2.3.0
R-3.5.2-randomForest    4.6_14
R-3.5.2-randtoolbox    1.17.1
R-3.5.2-RColorBrewer    1.1_2
R-3.5.2-Rcpp    1.0.0
R-3.5.2-RcppArmadillo    0.9.200.7.0
R-3.5.2-RcppEigen    0.3.3.4.0
R-3.5.2-RcppProgress    0.4.1
R-3.5.2-RcppRoll    0.3.0
R-3.5.2-RCurl    1.95_4.11
R-3.5.2-readxl    1.3.0
R-3.5.2-recipes    0.1.4
R-3.5.2-rematch    1.0.1
R-3.5.2-reshape2    1.4.3
R-3.5.2-Rgraphviz    2.26.0
R-3.5.2-rJava    0.9_10
R-3.5.2-rlang    0.3.1
R-3.5.2-rngWELL    0.10_5
R-3.5.2-robustbase    0.93_3
R-3.5.2-rprojroot    1.3_2
R-3.5.2-Rsamtools    1.34.1
R-3.5.2-RSQLite    2.1.1
R-3.5.2-rstudioapi    0.9.0
R-3.5.2-rtracklayer    1.42.1
R-3.5.2-S4Vectors    0.20.1
R-3.5.2-scales    1.0.0
R-3.5.2-scatterplot3d    0.3_41
R-3.5.2-sendmailR    1.2_1
R-3.5.2-sfsmisc    1.1_3
R-3.5.2-shiny    1.2.0
R-3.5.2-sna    2.4
R-3.5.2-snow    0.4_3
R-3.5.2-sourcetools    0.1.7
R-3.5.2-sp    1.3_1
R-3.5.2-SparseM    1.77
R-3.5.2-SPIA    2.34.0
R-3.5.2-SQUAREM    2017.10_1
R-3.5.2-StanHeaders    2.18.0
R-3.5.2-statmod    1.4.30
R-3.5.2-statnet    2018.10
R-3.5.2-statnet.common    4.2.0
R-3.5.2-stringi    1.3.1
R-3.5.2-stringr    1.3.1
R-3.5.2-subplex    1.5_4
R-3.5.2-SummarizedExperiment    1.12.0
R-3.5.2-swirl    2.4.3
R-3.5.2-sys    2.1
R-3.5.2-tergm    3.5.2
R-3.5.2-testthat    2.0.1
R-3.5.2-texreg    1.36.23
R-3.5.2-tibble    1.4.2
R-3.5.2-tibble    2.0.1
R-3.5.2-tidyr    0.8.2
R-3.5.2-tidyselect    0.2.5
R-3.5.2-timeDate    3043.102
R-3.5.2-timereg    1.9.3
R-3.5.2-TruncatedNormal    1.0
R-3.5.2-trust    0.1_7
R-3.5.2-tsna    0.2.0
R-3.5.2-utf8    1.1.4
R-3.5.2-viridis    0.5.1
R-3.5.2-viridisLite    0.3.0
R-3.5.2-vsn    3.50.0
R-3.5.2-webbioc    1.54.0
R-3.5.2-withr    2.1.2
R-3.5.2-xfun    0.5
R-3.5.2-XML    3.98_1.17
R-3.5.2-xtable    1.8_3
R-3.5.2-XVector    0.22.0
R-3.5.2-yaml    2.2.0
R-3.5.2-zip    1.0.0
R-3.5.2-zlibbioc    1.28.0
rhash    1.3.5
rssh    2.3.4
samtools    0.1.19
samtools    1.9
scalapack    2.0.2
scalapack-intel    2.0.2
scalapack-pgi    2.0.2
scipy    1.1.0
scotch    6.0.6
scotch-intel    6.0.6
scotch-pgi    6.0.6
SFML    2.5.1
siesta    4.1_b4
singularity    3.0.3
slurm    18.08.4
slurm    18.08.4
snort    2.9.7.3
source-highlight    3.1.8
sparsehash    2.0.2
squashfs-tools    4.3
STAR    2.5.3a
stress-ng    0.07.29
suitesparse    4.4.6
SuperLU    5.2.1
superlu_dist    4.0
SuperLU-intel    5.2.1
SuperLU-pgi    5.2.1
svgalib    1.9.25
systemtap    3.3
szip    2.1
szip-intel    2.1
szip-pgi    2.1
tcl-tktreectrl    2.4.1
tesseract    3.04.00
tophat    2.1.1
trans-ABySS    1.5.5
tre-0.8.0    23.20140228gitc2f5d13
trimmomatic    0.36
trlan-201009    2.2
utf8proc    2.2.0
vmd    1.9.1
wayland    1.16.0
wgrib    1.8.1.2c
wombat    1
xcb-proto    1.13
xmgrace    5.1.25
xorg-x11-util-macros    1.19.2
yasm    1.3.0