Software upgrade coming in May

Posted on Wednesday, March 13, 2019
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.
Update: The software upgrade is now complete. If you have any issues, please let us know.
During this upgrade, we will perform upgrades to all major software on the HPC and Spear. Notable highlights include:
Slurm scheduler will upgrade to v18.08 (notable changes)
python3 will upgrade to v3.7.0 (notable changes) - we will maintain access to older versions via modules.
OpenMPI will upgrade to v4.0.0 (notable changes)
R will upgrade to v3.5.2 (notable changes)
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
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