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