Package ListΒΆ

This is a list of things you can install using Spack. It is automatically generated based on the packages in the latest Spack release.

Spack currently has 2736 mainline packages:

abinit nasm r-circlize
abyss nauty r-class
accfft ncbi-rmblastn r-classint
ack nccl r-cli
activeharmony nccmp r-clipr
adept-utils ncdu r-cluster
adios ncftp r-clusterprofiler
adios2 ncl r-cner
adlbx nco r-coda
adol-c ncurses r-codetools
aegean ncview r-coin
albany ndiff r-colorspace
albert nek5000 r-complexheatmap
alglib nekbone r-corpcor
allinea-forge nekcem r-corrplot
allinea-reports nektar r-covr
allpaths-lg neovim r-cowplot
alquimia netcdf r-crayon
alsa-lib netcdf-cxx r-crosstalk
amg netcdf-cxx4 r-cubature
amg2013 netcdf-fortran r-cubist
amp netgauge r-curl
ampliconnoise netgen r-data-table
amrex netlib-lapack r-dbi
andi netlib-scalapack r-dbplyr
angsd netlib-xblas r-delayedarray
ant nettle r-deldir
antlr neuron r-dendextend
ants nextflow r-deoptim
ape nfft r-deoptimr
apex nghttp2 r-deseq
applewmproto nginx r-deseq2
appres ngmlr r-desolve
apr ninja r-devtools
apr-util ninja-fortran r-diagrammer
aragorn nlohmann-json r-dicekriging
archer nlopt r-dichromat
argp-standalone nmap r-diffusionmap
argtable nnvm r-digest
arlecore node-js r-diptest
armadillo notmuch r-dirichletmultinomial
arpack-ng npb r-dismo
ascent npm r-dnacopy
asciidoc npth r-do-db
aspa nspr r-domc
aspcud numactl r-doparallel
aspect numdiff r-dorng
aspell nut r-dose
aspell6-de nwchem r-downloader
aspell6-en ocaml r-dplyr
aspell6-es occa r-dt
assimp oce r-dtw
astra oclint r-dygraphs
astral oclock r-e1071
astyle octave r-edger
atk octave-optim r-ellipse
atlas octave-splines r-ensembldb
atom-dft octave-struct r-ergm
atompaw octopus r-evaluate
atop of-adios-write r-expm
augustus omega-h r-factoextra
autoconf ompss r-factominer
autodock-vina ompt-openmp r-fastmatch
autogen oniguruma r-ff
automaded ont-albacore r-fftwtools
automake opa-psm2 r-fgsea
axel opam r-filehash
bamtools opari2 r-fit-models
bamutil openbabel r-flashclust
barrnap openblas r-flexclust
bash opencoarrays r-flexmix
bash-completion opencv r-fnn
bats openexr r-forcats
bazel openfast r-foreach
bbcp openfoam-com r-forecast
bbmap openfoam-org r-foreign
bc openfst r-formatr
bcftools opengl r-formula
bcl2fastq2 openglu r-fpc
bdftopcf openjpeg r-fracdiff
bdw-gc openmc r-futile-logger
bear openmpi r-futile-options
beast1 opennurbs r-gbm
beast2 openpmd-api r-gcrma
bedops openscenegraph r-gdata
bedtools2 openslide r-gdsfmt
beforelight openspeedshop r-geiger
benchmark openspeedshop-utils r-genefilter
berkeley-db openssh r-geneplotter
bertini openssl r-genie3
bib2xhtml opium r-genomeinfodb
bigreqsproto opus r-genomeinfodbdata
binutils orfm r-genomicalignments
bioawk orthofinder r-genomicfeatures
biopieces orthomcl r-genomicranges
bismark osu-micro-benchmarks r-geomorph
bison otf r-geoquery
bitmap otf2 r-geosphere
blasr-libcpp p4est r-getopt
blast-plus p7zip r-getoptlong
blat pacbio-daligner r-ggally
blaze pacbio-damasker r-ggbio
bliss pacbio-dazz-db r-ggdendro
blitz pacbio-dextractor r-ggjoy
bmake pagit r-ggmap
bml pagmo r-ggplot2
bohrium paml r-ggpubr
bookleaf-cpp panda r-ggrepel
boost pandaseq r-ggridges
boostmplcartesianproduct pango r-ggsci
bowtie papi r-ggvis
bowtie2 papyrus r-gistr
boxlib paradiseo r-git2r
bpp-core parallel r-glmnet
bpp-phyl parallel-netcdf r-globaloptions
bpp-seq paraver r-glue
bpp-suite paraview r-gmodels
bracken parmetis r-gmp
braker parmgridgen r-go-db
branson parsimonator r-googlevis
breakdancer parsplice r-gosemsim
breseq partitionfinder r-gostats
brigand patch r-gplots
bsseeker2 patchelf r-graph
bucky pathfinder r-gridbase
bumpversion pax-utils r-gridextra
busco pbbam r-gseabase
butter pbmpi r-gss
bwa pcma r-gsubfn
byobu pcre r-gtable
bzip2 pcre2 r-gtools
c-blosc pdf2svg r-gtrellis
c-lime pdftk r-gviz
caffe pdsh r-haven
cairo pdt r-hexbin
caliper pegtl r-highr
callpath pennant r-hmisc
camellia percept r-hms
candle-benchmarks perl r-htmltable
cantera perl-algorithm-diff r-htmltools
canu perl-app-cmd r-htmlwidgets
cap3 perl-array-utils r-httpuv
cares perl-b-hooks-endofscope r-httr
cask perl-bio-perl r-hwriter
casper perl-bit-vector r-hypergraph
catalyst perl-cairo r-ica
catch perl-capture-tiny r-igraph
cbench perl-carp-clan r-illuminaio
cblas perl-class-data-inheritable r-impute
cbtf perl-class-inspector r-influencer
cbtf-argonavis perl-class-load r-inline
cbtf-argonavis-gui perl-class-load-xs r-interactivedisplaybase
cbtf-krell perl-contextual-return r-ipred
cbtf-lanl perl-cpan-meta-check r-iranges
ccache perl-data-optlist r-irdisplay
cctools perl-data-stag r-irkernel
cdbfasta perl-dbd-mysql r-irlba
cdd perl-dbfile r-iso
cddlib perl-dbi r-iterators
cdhit perl-devel-cycle r-janitor
cdo perl-devel-globaldestruction r-jaspar2018
ceed perl-devel-overloadinfo r-jomo
cereal perl-devel-stacktrace r-jpeg
cfitsio perl-digest-md5 r-jsonlite
cgal perl-dist-checkconflicts r-kegg-db
cgm perl-encode-locale r-kegggraph
cgns perl-eval-closure r-keggrest
charliecloud perl-exception-class r-kernlab
charm perl-exporter-tiny r-kernsmooth
check perl-extutils-depends r-kknn
chlorop perl-extutils-makemaker r-knitr
chombo perl-extutils-pkgconfig r-labeling
cistem perl-file-copy-recursive r-lambda-r
cityhash perl-file-listing r-laplacesdemon
clamr perl-file-pushd r-lars
clapack perl-file-sharedir-install r-lattice
cleaveland4 perl-file-slurp-tiny r-latticeextra
cleverleaf perl-file-slurper r-lava
clfft perl-file-which r-lazyeval
clhep perl-font-ttf r-leaflet
clingo perl-gd r-leaps
cloc perl-gd-graph r-learnbayes
cloog perl-gd-text r-lhs
cloverleaf perl-graph r-limma
cloverleaf3d perl-graph-readwrite r-lme4
clustalo perl-html-parser r-lmtest
clustalw perl-html-tagset r-locfit
cmake perl-http-cookies r-log4r
cmocka perl-http-daemon r-lpsolve
cmor perl-http-date r-lsei
cnmem perl-http-message r-lubridate
cnpy perl-http-negotiate r-magic
cntk perl-inline r-magrittr
cntk1bitsgd perl-inline-c r-makecdfenv
codar-cheetah perl-intervaltree r-maldiquant
coevp perl-io-html r-mapproj
cohmm perl-io-sessiondata r-maps
coinhsl perl-io-socket-ssl r-maptools
colm perl-io-string r-markdown
colordiff perl-json r-mass
comd perl-libwww-perl r-matr
compiz perl-list-moreutils r-matrix
compositeproto perl-log-log4perl r-matrixmodels
conduit perl-lwp r-matrixstats
constype perl-lwp-mediatypes r-mclust
converge perl-lwp-protocol-https r-mcmcglmm
coreutils perl-math-cdf r-mco
corset perl-math-matrixreal r-mda
cosmomc perl-module-build r-memoise
cosp2 perl-module-implementation r-mergemaid
cp2k perl-module-runtime r-methodss3
cppad perl-module-runtime-conflicts r-mgcv
cppcheck perl-moose r-mgraster
cpprestsdk perl-mozilla-ca r-mice
cppunit perl-mro-compat r-mime
cppzmq perl-namespace-clean r-minfi
cpu-features perl-net-http r-minqa
cpuinfo perl-net-scp-expect r-misc3d
cram perl-net-ssleay r-mitml
cryptopp perl-package-deprecationmanager r-mixtools
cscope perl-package-stash r-mlbench
csdp perl-package-stash-xs r-mlinterfaces
ctffind perl-padwalker r-mlr
cub perl-parallel-forkmanager r-mlrmbo
cube perl-params-util r-mmwrweek
cuda perl-parse-recdescent r-mnormt
cuda-memtest perl-pdf-api2 r-modelmetrics
cudnn perl-pegex r-modelr
cufflinks perl-perlio-gzip r-modeltools
cups perl-perlio-utf8-strict r-mpm
curl perl-soap-lite r-msnbase
cvs perl-star-fusion r-multcomp
czmq perl-statistics-descriptive r-multtest
dakota perl-statistics-pca r-munsell
daligner perl-sub-exporter r-mvtnorm
damageproto perl-sub-exporter-progressive r-mzid
damselfly perl-sub-identify r-mzr
darshan-runtime perl-sub-install r-nanotime
darshan-util perl-sub-name r-ncbit
dash perl-sub-uplevel r-ncdf4
datamash perl-svg r-network
dataspaces perl-swissknife r-networkd3
davix perl-task-weaken r-nlme
dbus perl-term-readkey r-nloptr
dealii perl-test-cleannamespaces r-nmf
dealii-parameter-gui perl-test-deep r-nnet
deconseq-standalone perl-test-differences r-nnls
dejagnu perl-test-exception r-nor1mix
delly2 perl-test-fatal r-np
denovogear perl-test-memory-cycle r-numderiv
dia perl-test-most r-oligoclasses
dialign-tx perl-test-needs r-oo
diamond perl-test-requires r-openssl
diffsplice perl-test-requiresinternet r-org-hs-eg-db
direnv perl-test-warn r-organismdbi
discovar perl-test-warnings r-packrat
discovardenovo perl-text-csv r-pacman
dislin perl-text-diff r-pamr
dlpack perl-text-simpletable r-pan
dmlc-core perl-text-soundex r-parallelmap
dmxproto perl-text-unidecode r-paramhelpers
docbook-xml perl-time-hires r-party
docbook-xsl perl-time-piece r-partykit
dos2unix perl-try-tiny r-pathview
double-conversion perl-uri r-pbapply
doxygen perl-uri-escape r-pbdzmq
dri2proto perl-version r-pbkrtest
dri3proto perl-want r-pcamethods
dsdp perl-www-robotrules r-pcapp
dsrc perl-xml-libxml r-permute
dtcmp perl-xml-parser r-pfam-db
dyninst perl-xml-parser-lite r-phangorn
ea-utils perl-xml-simple r-phantompeakqualtools
easybuild perl-yaml-libyaml r-phyloseq
ebms petsc r-picante
eccodes pexsi r-pkgconfig
eclipse-gcj-parser pfft r-pkgmaker
ecp-proxy-apps pflotran r-plogr
ed pfunit r-plot3d
editres pgdspider r-plotly
eigen pgi r-plotrix
elasticsearch phantompeakqualtools r-pls
elemental phast r-plyr
elfutils phasta r-pmcmr
elk phist r-png
elpa phylip r-powerlaw
emacs picard r-prabclus
emboss pidx r-praise
encodings pigz r-preprocesscore
environment-modules pilon r-prettyunits
eospac pindel r-proc
es piranha r-prodlim
esmf pism r-progress
essl pixman r-protgenerics
ethminer pkg-config r-proto
etsf-io pkgconf r-proxy
everytrace planck-likelihood r-pryr
everytrace-example plasma r-psych
evieext platypus r-ptw
exabayes plink r-purrr
examinimd plplot r-quadprog
exampm plumed r-quantmod
exasp2 pmgr-collective r-quantreg
exmcutils pmix r-quantro
exodusii pnfft r-qvalue
exonerate pngwriter r-r6
expat pnmpi r-randomforest
expect poamsa r-ranger
express pocl r-rappdirs
extrae polymake r-raster
exuberant-ctags poppler r-rbgl
f90cache poppler-data r-rbokeh
fabtests porta r-rcolorbrewer
falcon portage r-rcpp
farmhash postgresql r-rcpparmadillo
fast-gbs ppl r-rcppblaze
fastjar prank r-rcppcctz
fastmath presentproto r-rcppcnpy
fastme preseq r-rcppeigen
fastphase price r-rcppprogress
fastq-screen primer3 r-rcurl
fastqc prinseq-lite r-rda
fastqvalidator printproto r-readr
fasttree prng r-readxl
fastx-toolkit probconsrna r-registry
fenics prodigal r-rematch
fermi proj r-reordercluster
fermikit protobuf r-reportingtools
fermisciencetools proxymngr r-repr
ferret pruners-ninja r-reprex
ffmpeg ps-lite r-reshape
fftw psi4 r-reshape2
fimpute pslib r-rex
findutils psm r-rgdal
fio psmc r-rgenoud
fish pstreams r-rgeos
fixesproto pugixml r-rgl
flac pumi r-rgooglemaps
flang pv r-rgraphviz
flann pvm r-rhdf5
flash py-3to2 r-rhtslib
flecsale py-4suite-xml r-rinside
flecsi py-abipy r-rjags
flex py-adios r-rjava
flint py-affine r-rjson
flit py-alabaster r-rjsonio
fltk py-apache-libcloud r-rlang
flux py-apipkg r-rmarkdown
fluxbox py-appdirs r-rminer
fmt py-appnope r-rmpfr
foam-extend py-apscheduler r-rmpi
folly py-argcomplete r-rmysql
font-adobe-100dpi py-argparse r-rngtools
font-adobe-75dpi py-ase r-robustbase
font-adobe-utopia-100dpi py-asn1crypto r-rocr
font-adobe-utopia-75dpi py-astroid r-rodbc
font-adobe-utopia-type1 py-astropy r-roxygen2
font-alias py-attrs r-rpart
font-arabic-misc py-autopep8 r-rpart-plot
font-bh-100dpi py-avro r-rpostgresql
font-bh-75dpi py-avro-json-serializer r-rprojroot
font-bh-lucidatypewriter-100dpi py-babel r-rsamtools
font-bh-lucidatypewriter-75dpi py-backports-abc r-rsnns
font-bh-ttf py-backports-functools-lru-cache r-rsolnp
font-bh-type1 py-backports-shutil-get-terminal-size r-rsqlite
font-bitstream-100dpi py-backports-ssl-match-hostname r-rstan
font-bitstream-75dpi py-basemap r-rstudioapi
font-bitstream-speedo py-bcbio-gff r-rtracklayer
font-bitstream-type1 py-beautifulsoup4 r-rtsne
font-cronyx-cyrillic py-binwalk r-rvcheck
font-cursor-misc py-biom-format r-rvest
font-daewoo-misc py-biopython r-rzmq
font-dec-misc py-bitarray r-s4vectors
font-ibm-type1 py-bitstring r-samr
font-isas-misc py-bleach r-sandwich
font-jis-misc py-blessings r-scales
font-micro-misc py-bokeh r-scatterplot3d
font-misc-cyrillic py-boltons r-sdmtools
font-misc-ethiopic py-bottleneck r-segmented
font-misc-meltho py-breakseq2 r-selectr
font-misc-misc py-brian r-seqinr
font-mutt-misc py-brian2 r-seqlogo
font-schumacher-misc py-bsddb3 r-seurat
font-screen-cyrillic py-bx-python r-sf
font-sony-misc py-cartopy r-sfsmisc
font-sun-misc py-cclib r-shape
font-util py-cdat-lite r-shiny
font-winitzki-cyrillic py-cdo r-shinydashboard
font-xfree86-type1 py-certifi r-shortread
fontcacheproto py-cffi r-siggenes
fontconfig py-chardet r-simpleaffy
fontsproto py-checkm-genome r-smoof
fonttosfnt py-click r-sn
fp16 py-cligj r-snow
fpc py-cloudpickle r-snowfall
fr-hit py-cnvkit r-snprelate
freebayes py-cogent r-som
freeglut py-colorama r-somaticsignatures
freetype py-colormath r-sourcetools
fseq py-configparser r-sp
fsl py-counter r-sparsem
fslsfonts py-coverage r-spatial
fstobdf py-cpuinfo r-spdep
ftgl py-crispresso r-speedglm
funhpc py-crossmap r-spem
fyba py-cryptography r-splitstackshape
gapbs py-csvkit r-sqldf
gapcloser py-current r-squash
gapfiller py-cutadapt r-stanheaders
gasnet py-cvxopt r-statmod
gatk py-cycler r-statnet-common
gaussian py-cython r-stringi
gawk py-dask r-stringr
gblocks py-dateutil r-strucchange
gcc py-dbf r-subplex
gccmakedep py-decorator r-summarizedexperiment
gccxml py-deeptools r-survey
gconf py-dendropy r-survival
gcta py-dev r-sva
gdal py-dill r-tarifx
gdb py-discover r-tclust
gdbm py-dlcpar r-tensora
gdk-pixbuf py-docopt r-testit
gdl py-docutils r-testthat
geant4 py-doxypy r-tfbstools
gearshifft py-doxypypy r-tfmpvalue
gemmlowp py-dryscrape r-th-data
genemark-et py-dxchange r-threejs
genomefinisher py-dxfile r-tibble
genometools py-easybuild-easyblocks r-tidycensus
geopm py-easybuild-easyconfigs r-tidyr
geos py-easybuild-framework r-tidyselect
gettext py-edffile r-tidyverse
gflags py-editdistance r-tiff
ghost py-elasticsearch r-tigris
ghostscript py-elephant r-timedate
ghostscript-fonts py-emcee r-tmixclust
giflib py-entrypoints r-topgo
git py-enum34 r-trimcluster
git-imerge py-epydoc r-truncnorm
git-lfs py-espresso r-trust
gl2ps py-espressopp r-tseries
glew py-et-xmlfile r-tsne
glfmultiples py-eventlet r-ttr
glib py-execnet r-udunits2
glimmer py-fastaindex r-units
glm py-fasteners r-utf8
global py-faststructure r-utils
globalarrays py-fiscalyear r-uuid
globus-toolkit py-flake8 r-variantannotation
glog py-flask r-varselrf
gloo py-flask-compress r-vcd
glpk py-flask-socketio r-vegan
glproto py-flexx r-vgam
glvis py-fparser r-vipor
gmake py-funcsigs r-viridis
gmap-gsnap py-functools32 r-viridislite
gmime py-future r-visnetwork
gmp py-futures r-vsn
gmsh py-gdbgui r-whisker
gnat py-genders r-withr
gnu-prolog py-genshi r-xde
gnupg py-gevent r-xgboost
gnuplot py-git-review r-xlconnect
gnutls py-git2 r-xlconnectjars
go py-gnuplot r-xlsx
go-bootstrap py-goatools r-xlsxjars
gobject-introspection py-gpaw r-xmapbridge
googletest py-greenlet r-xml
gotcha py-griddataformats r-xml2
gource py-guidata r-xtable
gperf py-guiqwt r-xts
gperftools py-h5py r-xvector
gplates py-html2text r-yaml
grackle py-html5lib r-yapsa
gradle py-htseq r-yaqcaffy
grandr py-httpbin r-yarn
graph500 py-hypothesis r-zlibbioc
graphicsmagick py-idna r-zoo
graphlib py-igraph racon
graphmap py-illumina-utils raft
graphviz py-imagesize ragel
grib-api py-iminuit raja
groff py-importlib randfold
gromacs py-ipaddress random123
gsl py-ipdb randrproto
gslib py-ipykernel rapidjson
gtkorvo-atl py-ipython ravel
gtkorvo-cercs-env py-ipython-genutils raxml
gtkorvo-dill py-ipywidgets ray
gtkorvo-enet py-isort rdma-core
gtkplus py-itsdangerous rdp-classifier
gts py-jdcal re2c
guidance py-jedi readfq
guile py-jinja2 readline
gurobi py-joblib recordproto
h5hut py-jpype redundans
h5part py-jsonschema relion
h5utils py-junit-xml rempi
h5z-zfp py-jupyter-client rename
hacckernels py-jupyter-console rendercheck
hadoop py-jupyter-core renderproto
hapcut2 py-jupyter-notebook repeatmasker
hapdip py-keras resourceproto
haploview py-kiwisolver revbayes
harfbuzz py-latexcodec rgb
harminv py-lazy rhash
hdf py-lazy-object-proxy rlwrap
hdf5 py-lazyarray rmlab
hdf5-blosc py-libconf rna-seqc
help2man py-libensemble rngstreams
hepmc py-line-profiler rockstar
heppdt py-linecache2 root
hic-pro py-lit rose
highfive py-llvmlite rr
highwayhash py-lmfit rsbench
hiop py-localcider rsem
hisat2 py-locket rstart
hisea py-lockfile rsync
hmmer py-logilab-common rtags
hoomd-blue py-lrudict rtax
hpccg py-lxml ruby
hpctoolkit py-lzstring ruby-gnuplot
hpctoolkit-externals py-macholib ruby-narray
hpgmg py-machotools ruby-ronn
hpl py-macs2 ruby-rubyinline
hpx py-maestrowf ruby-svn2git
hpx5 py-mako ruby-terminal-table
hsakmt py-mappy rust
hstr py-markdown rust-bindgen
htop py-markupsafe sabre
htslib py-matplotlib sailfish
httpie py-mccabe salmon
hub py-mdanalysis sambamba
hunspell py-meep samblaster
hwloc py-memory-profiler samrai
hybpiper py-methylcode samtools
hydra py-mg-rast-tools sandbox
hydrogen py-misopy sas
hypre py-mistune satsuma2
i3 py-mock savanna
ibmisc py-moltemplate saws
iceauth py-mongo sbt
icedtea py-monotonic scala
icet py-monty scalasca
ico py-more-itertools scalpel
icu4c py-mpi4py scan-for-matches
id3lib py-mpmath scons
idba py-multiprocess scorec-core
igraph py-multiqc scorep
igv py-mx scotch
igvtools py-mxnet scr
ilmbase py-myhdl screen
image-magick py-mysqldb1 scripts
imake py-natsort scrnsaverproto
imp py-nbconvert sctk
impute2 py-nbformat sdl2
infernal py-neo sdl2-image
inputproto py-nestle sed
intel py-netcdf4 seqan
intel-daal py-netifaces seqprep
intel-gpu-tools py-networkx seqtk
intel-ipp py-nose serf
intel-mkl py-nosexcover sessreg
intel-mkl-dnn py-numba setxkbmap
intel-mpi py-numexpr sga
intel-parallel-studio py-numexpr3 shapeit
intel-tbb py-numpy shared-mime-info
intel-xed py-numpydoc shiny-server
intltool py-olefile shocklibs
ior py-ont-fast5-api shoremap
iozone py-openpmd-validator shortbred
ipopt py-openpyxl shortstack
isaac py-openslide-python showfont
isaac-server py-ordereddict sickle
isl py-oset siesta
itstool py-owslib signalp
itsx py-packaging signify
jags py-palettable silo
jansson py-pandas simplemoc
jasper py-paramiko simul
jbigkit py-partd simulationio
jchronoss py-pathlib2 singularity
jdk py-pathos sleef
jellyfish py-pathspec slepc
jemalloc py-patsy slurm
jmol py-pbr smalt
jq py-perf smproxy
json-c py-performance snakemake
json-cwx py-periodictable snap
json-glib py-petsc4py snap-berkeley
jsoncpp py-pexpect snap-korf
judy py-phonopy snappy
julia py-pickleshare snbone
k8 py-pil sniffles
kahip py-pillow snpeff
kaiju py-pip snphylo
kaks-calculator py-pipits snptest
kaldi py-pkgconfig soap2
kallisto py-plotly soapdenovo-trans
kbproto py-pluggy soapdenovo2
kdiff3 py-ply soapindel
kealib py-pmw soapsnp
kentutils py-poster sofa-c
kmergenie py-pox somatic-sniper
kokkos py-ppft sortmerna
kraken py-prettytable sosflow
krb5 py-proj sowing
krims py-projectq sox
kripke py-prompt-toolkit spades
kvasir-mpl py-protobuf spark
laghos py-psutil sparsehash
lammps py-psyclone sparta
last py-ptyprocess spdlog
latte py-pudb spectrum-mpi
launchmon py-py speex
lazyten py-py2bit spglib
lbann py-py2cairo sph2pipe
lbxproxy py-py2neo spherepack
lcals py-py4j spindle
lcms py-pyani spot
ldc py-pyasn1 sqlite
ldc-bootstrap py-pybedtools sqlitebrowser
legion py-pybigwig squid
leveldb py-pybind11 sra-toolkit
lftp py-pybtex sspace-longread
libaec py-pybtex-docutils sspace-standard
libaio py-pychecker sst-dumpi
libapplewm py-pycodestyle sst-macro
libarchive py-pycparser stacks
libassuan py-pycrypto staden-io-lib
libatomic-ops py-pycurl star
libbeagle py-pydatalog star-ccm-plus
libbsd py-pydispatcher startup-notification
libbson py-pydot stat
libcanberra py-pyelftools stc
libcap py-pyepsg stow
libceed py-pyfaidx strace
libcerf py-pyfasta stream
libcheck py-pyfftw strelka
libcint py-pyflakes stress
libcircle py-pygdbmi stringtie
libconfig py-pygments structure
libcroco py-pygobject sublime-text
libctl py-pygpu subread
libdivsufsort py-pygtk subversion
libdmx py-pylint suite-sparse
libdrm py-pymatgen sumaclust
libdwarf py-pyminifier sundials
libedit py-pymol superlu
libelf py-pympler superlu-dist
libemos py-pynn superlu-mt
libepoxy py-pypar supernova
libev py-pyparsing sw4lite
libevent py-pypeflow swap-assembler
libevpath py-pyprof2html swarm
libfabric py-pyqt swfft
libffi py-pyrad swiftsim
libffs py-pysam swig
libfontenc py-pyscaf symengine
libfs py-pyserial sympol
libgcrypt py-pyshp sz
libgd py-pyside tabix
libgeotiff py-pysocks talloc
libgit2 py-pysqlite tantan
libgpg-error py-pytables tar
libgpuarray py-pytest targetp
libgridxc py-pytest-cov task
libgtextutils py-pytest-flake8 taskd
libharu py-pytest-httpbin tasmanian
libhio py-pytest-mock tassel
libice py-pytest-runner tau
libiconv py-pytest-xdist tcl
libint py-python-daemon tcl-tcllib
libjpeg py-python-engineio tcl-tclxml
libjpeg-turbo py-python-gitlab tclap
libksba py-python-levenshtein tcoffee
liblbxutil py-python-socketio tcptrace
liblockfile py-pythonqwt tcsh
libmatheval py-pytz tealeaf
libmaxminddb py-pyutilib tetgen
libmesh py-pyvcf tethex
libmng py-pywavelets texinfo
libmongoc py-pyyaml texlive
libmonitor py-qtawesome the-platinum-searcher
libnbc py-qtconsole the-silver-searcher
libnl py-qtpy thrift
libogg py-quantities thrust
liboldx py-quast tig
libpcap py-radical-utils tinyxml
libpciaccess py-ranger tinyxml2
libpfm4 py-rasterio tioga
libpipeline py-readme-renderer tk
libpng py-regex tmalign
libpsl py-reportlab tmhmm
libpthread-stubs py-requests tmux
libquo py-requests-toolbelt tmuxinator
librom py-restview tophat
libshm py-rope tppred
libsigsegv py-rpy2 transabyss
libsm py-rsa transdecoder
libsodium py-rseqc transposome
libspatialindex py-rtree transset
libsplash py-saga-python trapproto
libssh py-scandir tree
libssh2 py-scientificpython trf
libsvm py-scikit-image triangle
libszip py-scikit-learn trilinos
libtermkey py-scipy trimgalore
libtiff py-seaborn trimmomatic
libtool py-setuptools trinity
libunistring py-setuptools-git trnascan-se
libunwind py-setuptools-scm turbine
libuuid py-sfepy turbomole
libuv py-sh tut
libvorbis py-shapely twm
libvterm py-shiboken tycho2
libwebsockets py-simplegeneric typhon
libwindowswm py-simplejson typhonio
libx11 py-singledispatch uberftp
libxau py-sip ucx
libxaw py-six udunits2
libxaw3d py-slepc4py ufo-core
libxc py-slurm-pipeline ufo-filters
libxcb py-sncosmo umpire
libxcomposite py-snowballstemmer unblur
libxcursor py-snuggs uncrustify
libxdamage py-spectra unibilium
libxdmcp py-spefile unison
libxevie py-spglib units
libxext py-sphinx unixodbc
libxfixes py-sphinx-bootstrap-theme unuran
libxfont py-sphinx-rtd-theme unzip
libxfont2 py-sphinxcontrib-bibtex usearch
libxfontcache py-sphinxcontrib-programoutput util-linux
libxft py-sphinxcontrib-websupport util-macros
libxi py-spyder uuid
libxinerama py-spykeutils valgrind
libxkbcommon py-sqlalchemy vampirtrace
libxkbfile py-statsmodels vardictjava
libxkbui py-stevedore varscan
libxml2 py-storm vc
libxmu py-subprocess32 vcftools
libxp py-symengine vcsh
libxpm py-symfit vdt
libxpresent py-sympy vecgeom
libxprintapputil py-tabulate veclibfort
libxprintutil py-tappy vegas2
libxrandr py-terminado velvet
libxrender py-testinfra verilator
libxres py-tetoolkit videoproto
libxscrnsaver py-theano viennarna
libxshmfence py-tifffile viewres
libxslt py-toml vim
libxsmm py-tomopy virtualgl
libxstream py-toolz visit
libxt py-tornado vizglow
libxtrap py-tqdm vmatch
libxtst py-traceback2 voropp
libxv py-traitlets votca-csg
libxvmc py-tuiview votca-ctp
libxxf86dga py-twisted votca-tools
libxxf86misc py-typing votca-xtp
libxxf86vm py-tzlocal vpfft
libyogrt py-udunits vpic
libzip py-umi-tools vsearch
likwid py-unittest2 vt
linkphase3 py-unittest2py3k vtk
linux-headers py-urllib3 vtkh
listres py-urwid vtkm
llvm py-vcversioner wannier90
llvm-openmp-ompt py-virtualenv wcslib
lmdb py-virtualenv-clone wget
lmod py-virtualenvwrapper wgsim
lndir py-vmd-python windowswmproto
log4cplus py-vsc-base wireshark
log4cxx py-vsc-install wt
loki py-wcsaxes wx
lordec py-wcwidth wxpropgrid
lrslib py-webkit-server x11perf
lrzip py-weblogo xapian-core
lsof py-werkzeug xauth
ltrace py-wheel xbacklight
lua py-widgetsnbextension xbiff
lua-bitlib py-wrapt xbitmaps
lua-jit py-xarray xbraid
lua-lpeg py-xattr xcalc
lua-luafilesystem py-xlrd xcb-demo
lua-luaposix py-xlsxwriter xcb-proto
lua-mpack py-xmlrunner xcb-util
luit py-xopen xcb-util-cursor
lulesh py-xpyb xcb-util-errors
lumpy-sv py-xvfbwrapper xcb-util-image
lwgrp py-yamlreader xcb-util-keysyms
lwm2 py-yapf xcb-util-renderutil
lz4 py-yt xcb-util-wm
lzma py-zmq xcb-util-xrm
lzo py-zope-event xclip
m4 py-zope-interface xclipboard
macsio python xclock
mad-numdiff qbank xcmiscproto
mafft qbox xcmsdb
magics qhull xcompmgr
magma qmcpack xconsole
makedepend qmd-progress xcursor-themes
mallocmc qrupdate xcursorgen
man-db qt xdbedizzy
manta qt-creator xditview
maq qtgraph xdm
mariadb qthreads xdpyinfo
masa quantum-espresso xdriinfo
masurca quinoa xedit
matio qwt xerces-c
matlab r xev
maven r-a4 xextproto
maverick r-a4base xeyes
mawk r-a4classif xf86bigfontproto
mbedtls r-a4core xf86dga
mc r-a4preproc xf86dgaproto
mcl r-a4reporting xf86driproto
mdtest r-abadata xf86miscproto
meep r-abaenrichment xf86rushproto
mefit r-abind xf86vidmodeproto
megahit r-absseq xfd
memaxes r-acde xfindproxy
meme r-acepack xfontsel
memkind r-acgh xfs
meraculous r-acme xfsinfo
mercurial r-ada xfwp
mesa r-adabag xgamma
mesa-glu r-ade4 xgc
meshkit r-adegenet xhost
meson r-adsplit xineramaproto
mesquite r-affxparser xinit
metabat r-affy xinput
metaphysicl r-affycomp xios
metasv r-affycompatible xkbcomp
metis r-affycontam xkbdata
mfem r-affycoretools xkbevd
microbiomeutil r-affydata xkbprint
minced r-affyexpress xkbutils
mindthegap r-affyilm xkeyboard-config
miniaero r-affyio xkill
miniamr r-affypdnn xload
miniasm r-affyplm xlogo
miniconda2 r-affyqcreport xlsatoms
miniconda3 r-affyrnadegradation xlsclients
minife r-agdex xlsfonts
minighost r-agilp xmag
minigmg r-agimicrorna xman
minimap2 r-aims xmessage
minimd r-aldex2 xmh
miniqmc r-allelicimbalance xmlf90
minisign r-alpine xmlto
minismac2d r-als xmodmap
minitri r-alsace xmore
minixyce r-altcdfenvs xorg-cf-files
mira r-ampliqueso xorg-docs
mirdeep2 r-analysispageserver xorg-gtest
mitofates r-anaquin xorg-server
mitos r-aneufinder xorg-sgml-doctools
mkfontdir r-aneufinderdata xphelloworld
mkfontscale r-annaffy xplor-nih
mlhka r-annotate xplsprinters
moab r-annotationdbi xpr
modern-wheel r-annotationfilter xprehashprinterlist
molcas r-annotationforge xprop
mono r-annotationhub xproto
mosh r-ape xproxymanagementprotocol
mothur r-assertthat xqilla
motif r-backports xrandr
motioncor2 r-bamsignals xrdb
mozjs r-base64 xrefresh
mpark-variant r-base64enc xrootd
mpc r-bbmisc xrx
mpe2 r-beanplot xsbench
mpest r-bh xscope
mpfr r-bindr xsdk
mpibash r-bindrcpp xsdktrilinos
mpiblast r-biobase xset
mpich r-biocgenerics xsetmode
mpifileutils r-biocinstaller xsetpointer
mpilander r-biocparallel xsetroot
mpileaks r-biocstyle xsimd
mpip r-biom-utils xsm
mpir r-biomart xstdcmap
mpix-launch-swift r-biomformat xtensor
mrbayes r-biostrings xtensor-python
mrnet r-biovizbase xterm
mrtrix3 r-bit xtl
mscgen r-bit64 xtrans
msgpack-c r-bitops xtrap
mshadow r-blob xts
multitail r-bookdown xvidtune
multiverso r-boot xvinfo
mummer r-brew xwd
mumps r-broom xwininfo
munge r-bsgenome xwud
muparser r-bumphunter xz
muscle r-c50 yajl
muse r-callr yambo
muster r-car yaml-cpp
mvapich2 r-caret yasm
mxml r-category yorick
mxnet r-catools z3
nag r-cdcfluview zeromq
nalu r-cellranger zfp
nalu-wind r-cghflasso zip
namd r-checkmate zlib
nano r-checkpoint zoltan
nanoflann r-chemometrics zsh
nanopb r-chron zstd

abinit

Homepage:
Spack package:
Versions:
8.8.2, 8.6.3, 8.2.2, 8.0.8b
Build Dependencies:
libxc, netcdf-fortran, lapack, fftw, mpi, blas, hdf5, scalapack
Link Dependencies:
libxc, netcdf-fortran, lapack, fftw, mpi, blas, hdf5, scalapack
Description:
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time- Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.

abyss

Homepage:
Spack package:
Versions:
2.0.2, 1.5.2
Build Dependencies:
boost, automake, mpi, sparsehash, sqlite, libtool, autoconf
Link Dependencies:
boost, libtool, sqlite, mpi, sparsehash
Description:
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.

accfft

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cuda, cmake, parallel-netcdf, fftw
Link Dependencies:
cuda, parallel-netcdf, fftw
Description:
AccFFT extends existing FFT libraries for CUDA-enabled Graphics Processing Units (GPUs) to distributed memory clusters

ack

Homepage:
Spack package:
Versions:
2.22, 2.18, 2.16, 2.14
Build Dependencies:
perl
Link Dependencies:
perl
Description:
ack 2.14 is a tool like grep, optimized for programmers. Designed for programmers with large heterogeneous trees of source code, ack is written purely in portable Perl 5 and takes advantage of the power of Perl's regular expressions.

activeharmony

Homepage:
Spack package:
Versions:
4.5
Description:
Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application).

adept-utils

Homepage:
Spack package:
Versions:
1.0.1, 1.0
Build Dependencies:
boost, cmake, mpi
Link Dependencies:
boost, mpi
Description:
Utility libraries for LLNL performance tools.

adios

Homepage:
Spack package:
Versions:
develop, 1.13.1, 1.13.0, 1.12.0, 1.11.1, 1.11.0, 1.10.0, 1.9.0
Build Dependencies:
m4, lz4, automake, mpi, sz, zfp, bzip2, zlib, dataspaces, szip, autoconf, hdf5, c-blosc, python, libevpath, libtool, netcdf
Link Dependencies:
zfp, hdf5, sz, lz4, bzip2, zlib, dataspaces, szip, mpi, c-blosc, libevpath, netcdf
Description:
The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.

adios2

Homepage:
Spack package:
Versions:
develop, 2.1.0, 2.0.0
Build Dependencies:
zeromq, bzip2, adios, mpi, hdf5, py-mpi4py, python, py-numpy, zfp, cmake
Link Dependencies:
zeromq, bzip2, adios, mpi, hdf5, python, zfp
Run Dependencies:
python, py-numpy, py-mpi4py
Description:
Next generation of ADIOS developed in the Exascale Computing Program

adlbx

Homepage:
Spack package:
Versions:
0.8.0
Build Dependencies:
mpi, exmcutils
Link Dependencies:
mpi, exmcutils
Description:
ADLB/X: Master-worker library + work stealing and data dependencies

adol-c

Homepage:
Spack package:
Versions:
develop, 2.6.3, 2.6.2, 2.6.1
Build Dependencies:
boost, automake, libtool, autoconf, m4
Link Dependencies:
boost
Description:
A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.

aegean

Homepage:
Spack package:
Versions:
0.15.2
Build Dependencies:
genometools
Link Dependencies:
genometools
Description:
The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome Annotations. The toolkit includes a variety of analysis programs as well as a C library whose API provides access to AEGeAn's core functions and data structures.

albany

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, trilinos, mpi
Link Dependencies:
trilinos, mpi
Description:
Albany is an implicit, unstructured grid, finite element code for the solution and analysis of multiphysics problems. The Albany repository on the GitHub site contains hundreds of regression tests and examples that demonstrate the code's capabilities on a wide variety of problems including fluid mechanics, solid mechanics (elasticity and plasticity), ice-sheet flow, quantum device modeling, and many other applications.

albert

Homepage:
Spack package:
Versions:
4.0a_opt4
Build Dependencies:
readline
Link Dependencies:
readline
Description:
Albert is an interactive program to assist the specialist in the study of nonassociative algebra.

alglib

Homepage:
Spack package:
Versions:
3.11.0
Description:
ALGLIB is a cross-platform numerical analysis and data processing library.

allinea-forge

Homepage:
Spack package:
Versions:
6.0.4
Description:
Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and Fortran applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.

allinea-reports

Homepage:
Spack package:
Versions:
6.0.4
Description:
Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site

allpaths-lg

Homepage:
Spack package:
Versions:
52488
Description:
ALLPATHS-LG is our original short read assembler and it works on both small and large (mammalian size) genomes.

alquimia

Homepage:
Spack package:
Versions:
develop, xsdk-0.3.0, xsdk-0.2.0
Build Dependencies:
pflotran, petsc, cmake, mpi, hdf5
Link Dependencies:
pflotran, petsc, mpi, hdf5
Description:
Alquimia is an interface that exposes the capabilities of mature geochemistry codes such as CrunchFlow and PFLOTRAN

alsa-lib

Homepage:
Spack package:
Versions:
1.1.4.1
Description:
The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib contains the user space library that developers compile ALSA applications against.

amg

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
AMG is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. The driver provided with AMG builds linear systems for various 3-dimensional problems.

amg2013

Homepage:
Spack package:
Versions:
master
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
AMG2013 is a parallel algebraic multigrid solver for linear systems arising from problems on unstructured grids. It has been derived directly from the BoomerAMG solver in the hypre library, a large linear solver library that is being developed in the Center for Applied Scientific Computing (CASC) at LLNL.

amp

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
boost, silo, petsc, trilinos, hdf5, blas, mpi, lapack, cmake, zlib
Link Dependencies:
boost, silo, petsc, trilinos, hdf5, blas, mpi, lapack, zlib
Description:
The Advanced Multi-Physics (AMP) package is an open source parallel object-oriented computational framework that is designed with single and multi-domain multi-physics applications in mind. AMP can be used to build powerful and flexible multi-physics simulation algorithms from lightweight operator, solver, linear algebra, material database, discretization, and meshing components. The AMP design is meant to enable existing investments in application codes to be leveraged without having to adopt dramatically different data structures while developing new computational science applications. Application components are represented as discrete mathematical operators that only require a minimal interface and through operator composition the incremental development of complex parallel applications is enabled. AMP is meant to allow application domain scientists, computer scientists and mathematicians to simulate, collaborate, and conduct research on various aspects of massively parallel simulation algorithms.

ampliconnoise

Homepage:
Spack package:
Versions:
1.29
Build Dependencies:
gsl, mpi
Link Dependencies:
gsl, mpi
Description:
AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.

amrex

Homepage:
Spack package:
Versions:
develop, 17.06, master
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
AMReX is the successor to BoxLib. It is a Block-Structured AMR Framework.

andi

Homepage:
Spack package:
Versions:
0.10
Build Dependencies:
m4, libdivsufsort, autoconf, automake, gsl, libtool
Link Dependencies:
libdivsufsort, gsl
Description:
andi is used for for estimating the evolutionary distance between closely related genomes.

angsd

Homepage:
Spack package:
Versions:
0.921, 0.919
Build Dependencies:
htslib
Link Dependencies:
htslib
Description:
Angsd is a program for analysing NGS data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.

ant

Homepage:
Spack package:
Versions:
1.9.9, 1.9.8, 1.9.7, 1.9.6
Build Dependencies:
java
Link Dependencies:
java
Description:
Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other

antlr

Homepage:
Spack package:
Versions:
2.7.7
Build Dependencies:
python, java
Link Dependencies:
python
Run Dependencies:
java
Description:
ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. It's widely used to build languages, tools, and frameworks. From a grammar, ANTLR generates a parser that can build and walk parse trees.

ants

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake
Description:
ANTs extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute.

ape

Homepage:
Spack package:
Versions:
2.2.1
Build Dependencies:
gsl, libxc
Link Dependencies:
gsl, libxc
Description:
A tool for generating atomic pseudopotentials within a Density- Functional Theory framework

apex

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
boost, binutils, cmake, ompt-openmp, activeharmony
Link Dependencies:
boost, binutils, activeharmony, ompt-openmp
Description:

applewmproto

Homepage:
Spack package:
Versions:
1.4.2
Build Dependencies:
pkgconfig, util-macros
Description:
Apple Rootless Window Management Extension. This extension defines a protcol that allows X window managers to better interact with the Mac OS X Aqua user interface when running X11 in a rootless mode.

appres

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libx11, libxt, util-macros, xproto, pkgconfig
Link Dependencies:
libx11, libxt
Description:
The appres program prints the resources seen by an application (or subhierarchy of an application) with the specified class and instance names. It can be used to determine which resources a particular program will load.

apr

Homepage:
Spack package:
Versions:
1.6.2, 1.5.2
Description:
Apache portable runtime.

apr-util

Homepage:
Spack package:
Versions:
1.6.0, 1.5.4
Build Dependencies:
expat, openssl, postgresql, gdbm, libiconv, sqlite, unixodbc, apr
Link Dependencies:
expat, openssl, postgresql, gdbm, libiconv, sqlite, unixodbc, apr
Description:
Apache Portable Runtime Utility

aragorn

Homepage:
Spack package:
Versions:
1.2.38
Description:
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

archer

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
cmake, llvm-openmp-ompt, llvm, ninja
Link Dependencies:
llvm-openmp-ompt, llvm
Description:
ARCHER, a data race detection tool for large OpenMP applications.

argp-standalone

Homepage:
Spack package:
Versions:
1.3
Description:
Standalone version of the argp interface from glibc for parsing unix- style arguments.

argtable

Homepage:
Spack package:
Versions:
2-13
Description:
Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.

arlecore

Homepage:
Spack package:
Versions:
3.5.2.2
Build Dependencies:
r
Run Dependencies:
r
Description:
An Integrated Software for Population Genetics Data Analysis

armadillo

Homepage:
Spack package:
Versions:
8.100.1, 7.950.1, 7.900.1, 7.500.0, 7.200.2, 7.200.1
Build Dependencies:
superlu, arpack-ng, hdf5, blas, lapack, cmake
Link Dependencies:
blas, lapack, superlu, arpack-ng, hdf5
Description:
Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use.

arpack-ng

Homepage:
Spack package:
Versions:
develop, 3.6.0, 3.5.0, 3.4.0, 3.3.0
Build Dependencies:
automake, mpi, blas, autoconf, lapack, cmake, libtool
Link Dependencies:
blas, lapack, mpi
Description:
ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Important Features: * Reverse Communication Interface. * Single and Double Precision Real Arithmetic Versions for Symmetric, Non-symmetric, Standard or Generalized Problems. * Single and Double Precision Complex Arithmetic Versions for Standard or Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. * Example driver routines that may be used as templates to implement numerous Shift-Invert strategies for all problem types, data types and precision. This project is a joint project between Debian, Octave and Scilab in order to provide a common and maintained version of arpack. Indeed, no single release has been published by Rice university for the last few years and since many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifications, arpack-ng aims to tackle this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere.

ascent

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
adios, py-mpi4py, mpi, python, py-numpy, py-sphinx, cmake, conduit, vtkh
Link Dependencies:
adios, py-mpi4py, mpi, python, cmake, conduit, vtkh
Run Dependencies:
py-numpy
Description:
Ascent is an open source many-core capable lightweight in situ visualization and analysis infrastructure for multi-physics HPC simulations.

asciidoc

Homepage:
Spack package:
Versions:
8.6.9
Build Dependencies:
docbook-xsl, libxslt, libxml2, docbook-xml
Link Dependencies:
docbook-xsl, libxslt, libxml2, docbook-xml
Description:
A presentable text document format for writing articles, UNIX man pages and other small to medium sized documents.

aspa

Homepage:
Spack package:
Versions:
master
Build Dependencies:
blas, lapack, mpi, hdf5
Link Dependencies:
blas, lapack, mpi, hdf5
Description:
A fundamental premise in ExMatEx is that scale-bridging performed in heterogeneous MPMD materials science simulations will place important demands upon the exascale ecosystem that need to be identified and quantified.

aspcud

Homepage:
Spack package:
Versions:
1.9.4
Build Dependencies:
boost, re2c, cmake, clingo
Link Dependencies:
clingo
Description:
Aspcud: Package dependency solver Aspcud is a solver for package dependencies. A package universe and a request to install, remove, or upgrade packages have to be encoded in the CUDF format. Such a CUDF document can then be passed to aspcud along with an optimization criteria to obtain a solution to the given package problem.

aspect

Homepage:
Spack package:
Versions:
develop, 2.0.0
Build Dependencies:
cmake, dealii, dealii-parameter-gui
Link Dependencies:
dealii, dealii-parameter-gui
Description:
Parallel, extendible finite element code to simulate convection in the Earth's mantle and elsewhere.

aspell

Homepage:
Spack package:
Versions:
0.60.6.1
Description:
GNU Aspell is a Free and Open Source spell checker designed to eventually replace Ispell.

aspell6-de

Homepage:
Spack package:
Versions:
6-de-20030222-1
Build Dependencies:
aspell
Link Dependencies:
aspell
Description:
German (de) dictionary for aspell.

aspell6-en

Homepage:
Spack package:
Versions:
2017.01.22-0
Build Dependencies:
aspell
Link Dependencies:
aspell
Description:
English (en) dictionary for aspell.

aspell6-es

Homepage:
Spack package:
Versions:
1.11-2
Build Dependencies:
aspell
Link Dependencies:
aspell
Description:
Spanish (es) dictionary for aspell.

assimp

Homepage:
Spack package:
Versions:
4.0.1
Build Dependencies:
boost, cmake
Link Dependencies:
boost
Description:
Open Asset Import Library (Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner.

astra

Homepage:
Spack package:
Versions:
2016-11-30
Description:
A Space Charge Tracking Algorithm.

astral

Homepage:
Spack package:
Versions:
4.10.7
Build Dependencies:
zip, java
Run Dependencies:
java
Description:
ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees.

astyle

Homepage:
Spack package:
Versions:
3.1, 3.0.1, 2.06, 2.05.1, 2.04
Description:
A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.

atk

Homepage:
Spack package:
Versions:
2.20.0, 2.14.0
Build Dependencies:
pkgconfig, glib, gobject-introspection
Link Dependencies:
glib, gobject-introspection
Description:
ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.

atlas

Homepage:
Spack package:
Versions:
3.11.39, 3.11.34, 3.10.3, 3.10.2
Description:
Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines in the LAPACK library.

atom-dft

Homepage:
Spack package:
Versions:
4.2.6
Build Dependencies:
xmlf90, libgridxc
Link Dependencies:
xmlf90, libgridxc
Description:
ATOM is a program for DFT calculations in atoms and pseudopotential generation.

atompaw

Homepage:
Spack package:
Versions:
4.0.0.13, 3.1.0.3
Build Dependencies:
blas, lapack, libxc
Link Dependencies:
blas, lapack, libxc
Description:
A Projector Augmented Wave (PAW) code for generating atom-centered functions. Official website: http://pwpaw.wfu.edu User's guide: ~/doc/atompaw-usersguide.pdf

atop

Homepage:
Spack package:
Versions:
2.2-3
Build Dependencies:
ncurses, zlib
Link Dependencies:
ncurses, zlib
Description:
Atop is an ASCII full-screen performance monitor for Linux

augustus

Homepage:
Spack package:
Versions:
3.3, 3.2.3
Build Dependencies:
boost, gsl, bamtools, zlib
Link Dependencies:
boost, gsl, bamtools, zlib
Description:
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

autoconf

Homepage:
Spack package:
Versions:
2.69, 2.62, 2.59, 2.13
Build Dependencies:
m4, perl
Run Dependencies:
m4, perl
Description:
Autoconf -- system configuration part of autotools

autodock-vina

Homepage:
Spack package:
Versions:
1_1_2
Build Dependencies:
boost
Link Dependencies:
boost
Description:
AutoDock Vina is an open-source program for doing molecular docking

autogen

Homepage:
Spack package:
Versions:
5.18.12
Build Dependencies:
pkgconfig, guile, libxml2
Link Dependencies:
guile, libxml2
Description:
AutoGen is a tool designed to simplify the creation and maintenance of programs that contain large amounts of repetitious text. It is especially valuable in programs that have several blocks of text that must be kept synchronized.

automaded

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
boost, callpath, cmake, mpi
Link Dependencies:
boost, callpath, mpi
Description:
AutomaDeD (Automata-based Debugging for Dissimilar parallel tasks) is a tool for automatic diagnosis of performance and correctness problems in MPI applications. It creates control-flow models of each MPI process and, when a failure occurs, these models are leveraged to find the origin of problems automatically. MPI calls are intercepted (using wrappers) to create the models. When an MPI application hangs, AutomaDeD creates a progress-dependence graph that helps finding the process (or group of processes) that caused the hang.

automake

Homepage:
Spack package:
Versions:
1.16.1, 1.15.1, 1.15, 1.14.1, 1.11.6
Build Dependencies:
autoconf, perl
Run Dependencies:
perl
Description:
Automake -- make file builder part of autotools

axel

Homepage:
Spack package:
Versions:
2.16.1
Build Dependencies:
gettext, m4, openssl, autoconf, automake, pkgconf, libtool
Link Dependencies:
gettext, openssl
Description:
Axel is a light command line download accelerator for Linux and Unix

bamtools

Homepage:
Spack package:
Versions:
2.5.1, 2.5.0, 2.4.1, 2.4.0, 2.3.0, 2.2.3
Build Dependencies:
cmake
Link Dependencies:
zlib
Description:
C++ API & command-line toolkit for working with BAM data.

bamutil

Homepage:
Spack package:
Versions:
1.0.13
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

barrnap

Homepage:
Spack package:
Versions:
0.8
Run Dependencies:
hmmer
Description:
Barrnap predicts the location of ribosomal RNA genes in genomes.

bash

Homepage:
Spack package:
Versions:
4.4.12, 4.4, 4.3
Build Dependencies:
ncurses, readline
Link Dependencies:
ncurses, readline
Description:
The GNU Project's Bourne Again SHell.

bash-completion

Homepage:
Spack package:
Versions:
develop, 2.7, 2.3
Build Dependencies:
automake, autoconf, libtool
Run Dependencies:
bash
Description:
Programmable completion functions for bash.

bats

Homepage:
Spack package:
Versions:
0.4.0
Description:
Bats is a TAP-compliant testing framework for Bash.

bazel

Homepage:
Spack package:
Versions:
0.13.0, 0.12.0, 0.11.1, 0.11.0, 0.10.1, 0.10.0, 0.9.0, 0.4.5, 0.4.4, 0.3.1, 0.3.0, 0.2.3, 0.2.2b, 0.2.2
Build Dependencies:
zip, java
Link Dependencies:
zip, java
Run Dependencies:
java
Description:
Bazel is Google's own build tool

bbcp

Homepage:
Spack package:
Versions:
git
Build Dependencies:
openssl, zlib
Link Dependencies:
openssl, zlib
Description:
Securely and quickly copy data from source to target

bbmap

Homepage:
Spack package:
Versions:
37.36
Build Dependencies:
java
Link Dependencies:
java
Description:
Short read aligner for DNA and RNA-seq data.

bc

Homepage:
Spack package:
Versions:
1.07
Build Dependencies:
texinfo, ed
Description:
bc is an arbitrary precision numeric processing language. Syntax is similar to C, but differs in many substantial areas. It supports interactive execution of statements.

bcftools

Homepage:
Spack package:
Versions:
1.8, 1.7, 1.6, 1.4, 1.3.1, 1.2
Build Dependencies:
libzip, htslib
Link Dependencies:
libzip, htslib
Description:
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF- compressed.

bcl2fastq2

Homepage:
Spack package:
Versions:
2.20.0.422, 2.19.1.403, 2.18.0.12, 2.17.1.14
Build Dependencies:
boost, libgcrypt, cmake, libxslt, libxml2, zlib
Link Dependencies:
boost, libgcrypt, cmake, libxslt, libxml2, zlib
Description:
The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files.

bdftopcf

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
pkgconfig, libxfont, util-macros, fontsproto, xproto
Link Dependencies:
libxfont
Description:
bdftopcf is a font compiler for the X server and font server. Fonts in Portable Compiled Format can be read by any architecture, although the file is structured to allow one particular architecture to read them directly without reformatting. This allows fast reading on the appropriate machine, but the files are still portable (but read more slowly) on other machines.

bdw-gc

Homepage:
Spack package:
Versions:
7.6.0, 7.4.4
Build Dependencies:
libatomic-ops
Link Dependencies:
libatomic-ops
Description:
The Boehm-Demers-Weiser conservative garbage collector is a garbage collecting replacement for C malloc or C++ new.

bear

Homepage:
Spack package:
Versions:
2.2.0, 2.0.4
Build Dependencies:
python, cmake
Link Dependencies:
python
Description:
Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems.

beast1

Homepage:
Spack package:
Versions:
1.8.4
Run Dependencies:
java
Description:
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.

beast2

Homepage:
Spack package:
Versions:
2.4.6
Build Dependencies:
java
Link Dependencies:
java
Description:
BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time- measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

bedops

Homepage:
Spack package:
Versions:
2.4.35, 2.4.34, 2.4.30
Description:
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

bedtools2

Homepage:
Spack package:
Versions:
2.27.1, 2.27.0, 2.26.0, 2.25.0, 2.23.0
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.

beforelight

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libx11, libxt, libxscrnsaver, util-macros, pkgconfig
Link Dependencies:
libx11, libxt, libxscrnsaver
Description:
The beforelight program is a sample implementation of a screen saver for X servers supporting the MIT-SCREEN-SAVER extension. It is only recommended for use as a code sample, as it does not include features such as screen locking or configurability.

benchmark

Homepage:
Spack package:
Versions:
develop, 1.4.0, 1.3.0, 1.2.0, 1.1.0, 1.0.0
Build Dependencies:
cmake
Description:
A microbenchmark support library

berkeley-db

Homepage:
Spack package:
Versions:
6.2.32, 6.1.29, 6.0.35, 5.3.28
Description:
Oracle Berkeley DB

bertini

Homepage:
Spack package:
Versions:
1.5
Build Dependencies:
gmp, flex, mpfr, bison, mpi
Link Dependencies:
gmp, mpfr, mpi
Description:
Bertini is a general-purpose solver, written in C, that was created for research about polynomial continuation. It solves for the numerical solution of systems of polynomial equations using homotopy continuation.

bib2xhtml

Homepage:
Spack package:
Versions:
3.0-15-gf506
Description:
bib2xhtml is a program that converts BibTeX files into HTML.

bigreqsproto

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
pkgconfig, util-macros
Description:
Big Requests Extension. This extension defines a protocol to enable the use of requests that exceed 262140 bytes in length.

binutils

Homepage:
Spack package:
Versions:
2.29.1, 2.28, 2.27, 2.26, 2.25, 2.24, 2.23.2, 2.20.1
Build Dependencies:
gettext, m4, flex, bison, zlib
Link Dependencies:
gettext, zlib
Description:
GNU binutils, which contain the linker, assembler, objdump and others

bioawk

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
bison, zlib
Link Dependencies:
zlib
Description:
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.

bismark

Homepage:
Spack package:
Versions:
0.19.0, 0.18.2
Run Dependencies:
perl, bowtie2, samtools
Description:
A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bison

Homepage:
Spack package:
Versions:
3.0.4, 2.7
Build Dependencies:
m4
Run Dependencies:
m4
Description:
Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

bitmap

Homepage:
Spack package:
Versions:
1.0.8
Build Dependencies:
libx11, libxaw, xbitmaps, util-macros, libxt, libxmu, pkgconfig, xproto
Link Dependencies:
libx11, libxaw, libxmu, libxt
Description:
bitmap, bmtoa, atobm - X bitmap (XBM) editor and converter utilities.

blasr-libcpp

Homepage:
Spack package:
Versions:
5.3.1
Build Dependencies:
python, pbbam, hdf5
Link Dependencies:
pbbam, hdf5
Description:
Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences.

blast-plus

Homepage:
Spack package:
Versions:
2.6.0, 2.2.30
Build Dependencies:
libpng, bzip2, openssl, jpeg, python, gnutls, zlib, perl, lzo, pcre, freetype
Link Dependencies:
libpng, bzip2, openssl, jpeg, python, gnutls, zlib, perl, lzo, pcre, freetype
Description:
Basic Local Alignment Search Tool.

blat

Homepage:
Spack package:
Versions:
35
Build Dependencies:
libpng
Link Dependencies:
libpng
Description:
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.

blaze

Homepage:
Spack package:
Versions:
3.2, 3.1, 3.0, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2.0, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0
Description:
Blaze is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain- specific language with HPC-grade performance, making it one of the most intuitive and fastest C++ math libraries available.

bliss

Homepage:
Spack package:
Versions:
0.73
Build Dependencies:
gmp, libtool
Link Dependencies:
gmp
Description:
bliss: A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs

blitz

Homepage:
Spack package:
Versions:
1.0.1, 1.0.0
Description:
N-dimensional arrays for C++

bmake

Homepage:
Spack package:
Versions:
20180512, 20171207
Description:
Portable version of NetBSD make(1).

bml

Homepage:
Spack package:
Versions:
develop, 1.2.3, 1.2.2, 1.1.0
Build Dependencies:
blas, lapack, cmake, mpi
Link Dependencies:
blas, lapack, mpi
Description:
The basic matrix library (bml) is a collection of various matrix data formats (in dense and sparse) and their associated algorithms for basic matrix operations.

bohrium

Homepage:
Spack package:
Versions:
develop, 0.9.0
Build Dependencies:
cuda, py-numpy, blas, cmake, opencv, zlib, boost, netlib-lapack, py-cython, python, opencl, swig
Link Dependencies:
cuda, boost, opencl, netlib-lapack, python, blas, opencv, zlib
Run Dependencies:
py-numpy
Test Dependencies:
python, py-numpy
Description:
Library for automatic acceleration of array operations

bookleaf-cpp

Homepage:
Spack package:
Versions:
2.0.1, 2.0
Build Dependencies:
silo, typhon, yaml-cpp, mpi, caliper, cmake, parmetis
Link Dependencies:
silo, typhon, yaml-cpp, mpi, caliper, parmetis
Description:
BookLeaf is a 2D unstructured hydrodynamics mini-app.

boost

Homepage:
Spack package:
Versions:
develop, 1.67.0, 1.66.0, 1.65.1, 1.65.0, 1.64.0, 1.63.0, 1.62.0, 1.61.0, 1.60.0, 1.59.0, 1.58.0, 1.57.0, 1.56.0, 1.55.0, 1.54.0, 1.53.0, 1.52.0, 1.51.0, 1.50.0, 1.49.0, 1.48.0, 1.47.0, 1.46.1, 1.46.0, 1.45.0, 1.44.0, 1.43.0, 1.42.0, 1.41.0, 1.40.0, 1.39.0, 1.38.0, 1.37.0, 1.36.0, 1.35.0, 1.34.1, 1.34.0
Build Dependencies:
bzip2, py-numpy, mpi, python, icu4c, zlib
Link Dependencies:
python, bzip2, icu4c, mpi, zlib
Run Dependencies:
py-numpy
Description:
Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

boostmplcartesianproduct

Homepage:
Spack package:
Versions:
20161205
Description:
Cartesian_product is an extension to the Boost.MPL library and as such requires a version of the Boost libraries on your system.

bowtie

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
tbb
Link Dependencies:
tbb
Description:
Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

bowtie2

Homepage:
Spack package:
Versions:
2.3.4.1, 2.3.1, 2.3.0, 2.2.5
Build Dependencies:
tbb, readline, zlib
Link Dependencies:
tbb, readline, zlib
Run Dependencies:
python, perl
Description:
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

boxlib

Homepage:
Spack package:
Versions:
16.12.2
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
BoxLib, a software framework for massively parallel block-structured adaptive mesh refinement (AMR) codes.

bpp-core

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake
Description:
Bio++ core library.

bpp-phyl

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
bpp-seq, cmake, bpp-core
Link Dependencies:
bpp-seq, bpp-core
Description:
Bio++ phylogeny library.

bpp-seq

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake, bpp-core
Link Dependencies:
bpp-core
Description:
Bio++ seq library.

bpp-suite

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
texinfo, cmake, bpp-seq, bpp-phyl, bpp-core
Link Dependencies:
bpp-seq, bpp-phyl, bpp-core
Description:
BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.

bracken

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
python, perl-parallel-forkmanager, perl-exporter-tiny, perl-list-moreutils, perl
Link Dependencies:
python, perl-parallel-forkmanager, perl-exporter-tiny, perl-list-moreutils, perl
Description:
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

braker

Homepage:
Spack package:
Versions:
1.11
Build Dependencies:
perl, genemark-et, augustus, bamtools, samtools
Link Dependencies:
genemark-et, augustus, bamtools, samtools
Run Dependencies:
perl
Description:
BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS

branson

Homepage:
Spack package:
Versions:
develop, 1.01
Build Dependencies:
boost, cmake, mpi, parmetis, metis
Link Dependencies:
boost, mpi, parmetis, metis
Description:
Branson's purpose is to study different algorithms for parallel Monte Carlo transport. Currently it contains particle passing and mesh passing methods for domain decomposition.

breakdancer

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
BreakDancer-1.3.6, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs..

breseq

Homepage:
Spack package:
Versions:
0.31.1
Build Dependencies:
m4, autoconf, automake, libtool
Run Dependencies:
bedtools2, r
Description:
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes.

brigand

Homepage:
Spack package:
Versions:
1.3.0, 1.2.0, 1.1.0, 1.0.0, master
Description:
Brigand Meta-programming library

bsseeker2

Homepage:
Spack package:
Versions:
2.1.2
Build Dependencies:
python, py-pysam
Run Dependencies:
python, py-pysam
Description:
A versatile aligning pipeline for bisulfite sequencing data.

bucky

Homepage:
Spack package:
Versions:
1.4.4
Description:
BUCKy is a free program to combine molecular data from multiple loci. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis.

bumpversion

Homepage:
Spack package:
Versions:
0.5.3, 0.5.0
Build Dependencies:
python, py-setuptools
Link Dependencies:
python
Run Dependencies:
python
Description:
Version-bump your software with a single command.

busco

Homepage:
Spack package:
Versions:
3.0.1, 2.0.1
Build Dependencies:
python, hmmer, blast-plus, augustus
Link Dependencies:
python, hmmer, blast-plus, augustus
Run Dependencies:
python
Description:
Assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

butter

Homepage:
Spack package:
Versions:
0.3.3
Build Dependencies:
perl, bowtie, samtools
Link Dependencies:
bowtie, samtools
Run Dependencies:
perl
Description:
butter: Bowtie UTilizing iTerative placEment of Repetitive small rnas. A wrapper for bowtie to produce small RNA-seq alignments where multimapped small RNAs tend to be placed near regions of confidently high density.

bwa

Homepage:
Spack package:
Versions:
0.7.17, 0.7.16a, 0.7.15, 0.7.13, 0.7.12
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

byobu

Homepage:
Spack package:
Versions:
5.123
Build Dependencies:
tmux
Run Dependencies:
tmux
Description:
Byobu: Text-based window manager and terminal multiplexer.

bzip2

Homepage:
Spack package:
Versions:
1.0.6
Description:
bzip2 is a freely available, patent free high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

c-blosc

Homepage:
Spack package:
Versions:
1.12.1, 1.11.1, 1.9.2, 1.9.1, 1.9.0, 1.8.1, 1.8.0
Build Dependencies:
zstd, lz4, cmake, snappy, zlib
Link Dependencies:
zstd, lz4, snappy, zlib
Description:
Blosc, an extremely fast, multi-threaded, meta-compressor library

c-lime

Homepage:
Spack package:
Versions:
2-3-9
Description:
LIME (which can stand for Lattice QCD Interchange Message Encapsulation or more generally, Large Internet Message Encapsulation) is a simple packaging scheme for combining records containing ASCII and/or binary data.

caffe

Homepage:
Spack package:
Versions:
1.0, rc5, rc4, rc3, rc2
Build Dependencies:
cuda, leveldb, py-numpy, gflags, glog, blas, cmake, opencv, lmdb, matlab, boost, protobuf, hdf5, python
Link Dependencies:
cuda, leveldb, gflags, glog, blas, opencv, lmdb, matlab, boost, protobuf, hdf5, python
Run Dependencies:
py-numpy
Description:
Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors.

cairo

Homepage:
Spack package:
Versions:
1.14.12, 1.14.8, 1.14.0
Build Dependencies:
libx11, libpng, libxext, libxcb, pixman, glib, python, fontconfig, libxrender, pkgconfig, freetype
Link Dependencies:
libx11, libpng, libxext, libxcb, pixman, glib, fontconfig, libxrender, freetype
Description:
Cairo is a 2D graphics library with support for multiple output devices.

caliper

Homepage:
Spack package:
Versions:
1.6.0, master
Build Dependencies:
papi, libpfm4, libunwind, mpi, sosflow, python, dyninst, cmake
Link Dependencies:
libpfm4, libunwind, mpi, sosflow, papi, dyninst
Description:
Caliper is a program instrumentation and performance measurement framework. It provides data collection mechanisms and a source-code annotation API for a variety of performance engineering use cases, e.g., performance profiling, tracing, monitoring, and auto-tuning.

callpath

Homepage:
Spack package:
Versions:
1.0.4, 1.0.2, 1.0.1
Build Dependencies:
libdwarf, dyninst, cmake, adept-utils, mpi
Link Dependencies:
libdwarf, dyninst, adept-utils, mpi, elf
Description:
Library for representing callpaths consistently in distributed-memory performance tools.

camellia

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, hdf5, moab, trilinos, mpi
Link Dependencies:
hdf5, moab, trilinos, mpi
Description:
Camellia: user-friendly MPI-parallel adaptive finite element package, with support for DPG and other hybrid methods, built atop Trilinos.

candle-benchmarks

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
py-tqdm, py-theano, py-scikit-learn, py-mpi4py, python, py-requests, py-h5py, py-keras, py-matplotlib, py-mdanalysis, opencv
Link Dependencies:
python, opencv
Run Dependencies:
py-tqdm, py-theano, py-scikit-learn, py-mpi4py, py-requests, py-h5py, py-keras, py-matplotlib, py-mdanalysis
Description:
ECP-CANDLE Benchmarks

cantera

Homepage:
Spack package:
Versions:
2.3.0, 2.2.1
Build Dependencies:
googletest, py-numpy, blas, py-cython, matlab, boost, sundials, scons, py-scipy, fmt, python, lapack, eigen, py-3to2
Link Dependencies:
boost, googletest, eigen, fmt, python, blas, lapack, sundials, matlab
Run Dependencies:
py-numpy, py-scipy, py-3to2
Description:
Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes.

canu

Homepage:
Spack package:
Versions:
1.5
Run Dependencies:
gnuplot, jdk, perl
Description:
A single molecule sequence assembler for genomes large and small.

cap3

Homepage:
Spack package:
Versions:
2015-02-11
Description:
CAP3 is DNA Sequence Assembly Program

cares

Homepage:
Spack package:
Versions:
develop, 1.13.0
Build Dependencies:
cmake
Description:
c-ares: A C library for asynchronous DNS requests

cask

Homepage:
Spack package:
Versions:
0.8.1, 0.7.4
Build Dependencies:
emacs
Run Dependencies:
emacs
Description:
Cask is a project management tool for Emacs Lisp to automate the package development cycle; development, dependencies, testing, building, packaging and more.

casper

Homepage:
Spack package:
Versions:
0.8.2
Build Dependencies:
boost, jellyfish
Link Dependencies:
boost, jellyfish
Description:
CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness. Using this sophisticated merging method, we could get elongated reads from the forward and reverse reads.

catalyst

Homepage:
Spack package:
Versions:
5.4.1, 5.4.0, 5.3.0, 5.2.0, 5.1.2, 5.0.1, 4.4.0
Build Dependencies:
libx11, mesa, mpi, python, libxt, cmake, git
Link Dependencies:
libx11, mesa, mpi, python, libxt, git
Description:
Catalyst is an in situ use case library, with an adaptable application programming interface (API), that orchestrates the alliance between simulation and analysis and/or visualization tasks.

catch

Homepage:
Spack package:
Versions:
2.2.1, 2.1.0, 2.0.1, 1.12.1, 1.12.0, 1.11.0, 1.10.0, 1.9.7, 1.9.6, 1.9.5, 1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.8.1, 1.8.0, 1.7.2, 1.7.1, 1.7.0, 1.6.1, 1.6.0, 1.5.9, 1.5.0, 1.4.0, 1.3.5, 1.3.0
Build Dependencies:
cmake
Description:
Catch tests

cbench

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
blas, lapack, mpi, fftw
Link Dependencies:
blas, lapack, mpi, fftw
Description:
Cbench is intended as a relatively straightforward toolbox of tests, benchmarks, applications, utilities, and framework to hold them together with the goal to facilitate scalable testing, benchmarking, and analysis of a Linux parallel compute cluster.

cblas

Homepage:
Spack package:
Versions:
2015-06-06
Build Dependencies:
blas
Link Dependencies:
blas
Description:
The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations.

cbtf

Homepage:
Spack package:
Versions:
develop, 1.9.1.1, 1.9.1.0
Build Dependencies:
boost, mrnet, cmake, xerces-c, libxml2
Link Dependencies:
boost, mrnet, xerces-c, libxml2
Description:
CBTF project contains the base code for CBTF that supports creating components, component networks and the support to connect these components and component networks into sequential and distributed network tools.

cbtf-argonavis

Homepage:
Spack package:
Versions:
develop, 1.9.1.1, 1.9.1.0
Build Dependencies:
boost, libmonitor, cuda, papi, mrnet, cmake, cbtf-krell, cbtf
Link Dependencies:
boost, libmonitor, cuda, elf, papi, mrnet, cbtf-krell, cbtf
Description:
CBTF Argo Navis project contains the CUDA collector and supporting libraries that was done as a result of a DOE SBIR grant.

cbtf-argonavis-gui

Homepage:
Spack package:
Versions:
develop, 1.3.0.0
Build Dependencies:
cuda, xerces-c, mrnet, cmake, cbtf-krell, qtgraph, boost, graphviz, openspeedshop-utils, qt, cbtf-argonavis, cbtf
Link Dependencies:
cuda, boost, openspeedshop-utils, xerces-c, graphviz, cbtf-argonavis, cbtf, mrnet, qtgraph, cbtf-krell, qt
Description:
CBTF Argo Navis GUI project contains the GUI that views OpenSpeedShop performance information by loading in the Sqlite database files.

cbtf-krell

Homepage:
Spack package:
Versions:
develop, 1.9.1.1, 1.9.1.0
Build Dependencies:
mpich2, binutils, xerces-c, openmpi, papi, gotcha, mrnet, cmake, boost, libmonitor, mpich, mpt, libunwind, mvapich, dyninst, llvm-openmp-ompt, cbtf, mvapich2
Link Dependencies:
mpich2, binutils, xerces-c, openmpi, papi, mrnet, gotcha, boost, libmonitor, mpich, mpt, libunwind, mvapich, dyninst, llvm-openmp-ompt, cbtf, mvapich2
Description:
CBTF Krell project contains the Krell Institute contributions to the CBTF project. These contributions include many performance data collectors and support libraries as well as some example tools that drive the data collection at HPC levels of scale.

cbtf-lanl

Homepage:
Spack package:
Versions:
develop, 1.9.1.1, 1.9.1.0
Build Dependencies:
mrnet, cmake, xerces-c, cbtf, cbtf-krell
Link Dependencies:
mrnet, xerces-c, cbtf, cbtf-krell
Description:
CBTF LANL project contains a memory tool and data center type system command monitoring tool.

ccache

Homepage:
Spack package:
Versions:
3.3.4, 3.3.3, 3.3.2, 3.3.1, 3.3, 3.2.9
Build Dependencies:
gperf, libxslt, zlib
Link Dependencies:
gperf, libxslt, zlib
Description:
ccache is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again.

cctools

Homepage:
Spack package:
Versions:
6.1.1
Build Dependencies:
openssl, readline, perl, python, swig, zlib
Link Dependencies:
openssl, readline, swig, zlib
Run Dependencies:
python, perl
Description:
The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.

cdbfasta

Homepage:
Spack package:
Versions:
2017-03-16
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Fast indexing and retrieval of fasta records from flat file databases

cdd

Homepage:
Spack package:
Versions:
0.61a
Build Dependencies:
libtool
Description:
The program cdd+ (cdd, respectively) is a C++ (ANSI C) implementation of the Double Description Method [MRTT53] for generating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron given by a system of linear inequalities

cddlib

Homepage:
Spack package:
Versions:
0.94h
Build Dependencies:
gmp, libtool
Link Dependencies:
gmp
Description:
The C-library cddlib is a C implementation of the Double Description Method of Motzkin et al. for generating all vertices (i.e. extreme points) and extreme rays of a general convex polyhedron in R^d given by a system of linear inequalities

cdhit

Homepage:
Spack package:
Versions:
4.6.8
Build Dependencies:
perl
Run Dependencies:
perl
Description:
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

cdo

Homepage:
Spack package:
Versions:
1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.7.2
Build Dependencies:
fftw, libuuid, curl, udunits2, grib-api, szip, proj, hdf5, magics, libxml2, netcdf, eccodes
Link Dependencies:
fftw, libuuid, curl, udunits2, grib-api, szip, proj, hdf5, magics, libxml2, netcdf, eccodes
Description:
CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

ceed

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
gslib, nek5000, petsc, magma, mfem, hpgmg, libceed, hypre, nekbone, pumi, nekcem, laghos, occa, suite-sparse
Link Dependencies:
gslib, nek5000, petsc, magma, mfem, hpgmg, libceed, hypre, nekbone, pumi, nekcem, laghos, occa, suite-sparse
Description:
Ceed is a collection of benchmarks, miniapps, software libraries and APIs for efficient high-order finite element and spectral element discretizations for exascale applications developed in the Department of Energy (DOE) and partially supported by the Exascale Computing Project (ECP). This is a Spack bundle package that installs the CEED software components.

cereal

Homepage:
Spack package:
Versions:
1.2.2, 1.2.1, 1.2.0, 1.1.2, 1.1.1, 1.1.0, 1.0.0, 0.9.1
Build Dependencies:
cmake
Description:
cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.

cfitsio

Homepage:
Spack package:
Versions:
3.420, 3.410, 3.370
Build Dependencies:
bzip2
Link Dependencies:
bzip2
Description:
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

cgal

Homepage:
Spack package:
Versions:
4.12, 4.11, 4.9.1, 4.9, 4.7, 4.6.3
Build Dependencies:
boost, gmp, mpfr, cmake, qt, zlib
Link Dependencies:
boost, gmp, mpfr, qt, zlib
Description:
The Computational Geometry Algorithms Library (CGAL) is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics.

cgm

Homepage:
Spack package:
Versions:
16.0, 13.1.1, 13.1.0, 13.1
Build Dependencies:
oce, mpi
Link Dependencies:
oce, mpi
Description:
The Common Geometry Module, Argonne (CGMA) is a code library which provides geometry functionality used for mesh generation and other applications.

cgns

Homepage:
Spack package:
Versions:
3.3.1, 3.3.0
Build Dependencies:
cmake, hdf5, mpi
Link Dependencies:
hdf5, mpi
Description:
The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.

charliecloud

Homepage:
Spack package:
Versions:
0.2.4
Description:
Lightweight user-defined software stacks for HPC.

charm

Homepage:
Spack package:
Versions:
develop, 6.8.2, 6.8.1, 6.8.0, 6.7.1, 6.7.0, 6.6.1, 6.6.0, 6.5.1
Build Dependencies:
papi, cuda, automake, mpi, autoconf
Link Dependencies:
papi, cuda, automake, mpi, autoconf
Description:
Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers.

check

Homepage:
Spack package:
Versions:
0.10.0
Description:
Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format.

chlorop

Homepage:
Spack package:
Versions:
1.1
Run Dependencies:
awk
Description:
Chlorop predicts the presence of chloroplast transit peptides in protein sequences and the location of potential cTP cleavage sites. You will need to obtain the tarball by visiting the URL and completing the form. You can then either run spack install with the tarball in the directory, or add it to a mirror. You will need to set the CHLOROTMP environment variable to the full path of the directory you want chlorop to use as a temporary directory.

chombo

Homepage:
Spack package:
Versions:
develop, 3.2
Build Dependencies:
gmake, blas, lapack, mpi, hdf5
Link Dependencies:
blas, lapack, mpi, hdf5
Description:
The Chombo package provides a set of tools for implementing finite difference and finite-volume methods for the solution of partial differential equations on block-structured adaptively refined logically rectangular (i.e. Cartesian) grids.

cistem

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
wx, fftw
Link Dependencies:
wx, fftw
Description:
cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

cityhash

Homepage:
Spack package:
Versions:
2013-07-31, master
Description:
CityHash, a family of hash functions for strings.

clamr

Homepage:
Spack package:
Versions:
master
Build Dependencies:
mpe, cmake, mpi
Link Dependencies:
mpe, cmake, mpi
Description:
The CLAMR code is a cell-based adaptive mesh refinement (AMR) mini-app developed as a testbed for hybrid algorithm development using MPI and OpenCL GPU code.

clapack

Homepage:
Spack package:
Versions:
3.2.1
Build Dependencies:
atlas
Link Dependencies:
atlas
Description:
CLAPACK is a f2c'ed version of LAPACK. The CLAPACK library was built using a Fortran to C conversion utility called f2c. The entire Fortran 77 LAPACK library is run through f2c to obtain C code, and then modified to improve readability. CLAPACK's goal is to provide LAPACK for someone who does not have access to a Fortran compiler.

cleaveland4

Homepage:
Spack package:
Versions:
4.4
Build Dependencies:
r, samtools, viennarna, perl, perl-math-cdf, bowtie
Link Dependencies:
viennarna, bowtie, samtools
Run Dependencies:
perl-math-cdf, r, perl
Description:
CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA targets

cleverleaf

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
boost, cmake, samrai, hdf5
Link Dependencies:
boost, samrai, hdf5
Description:
CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with Adaptive Mesh Refinement using the SAMRAI toolkit from Lawrence Livermore National Laboratory. The primary goal of CleverLeaf is to evaluate the application of AMR to the Lagrangian-Eulerian hydrodynamics scheme used by CloverLeaf.

clfft

Homepage:
Spack package:
Versions:
2.12.2
Build Dependencies:
boost, cmake, opencl
Link Dependencies:
boost, opencl
Description:
a software library containing FFT functions written in OpenCL

clhep

Homepage:
Spack package:
Versions:
2.4.0.1, 2.4.0.0, 2.3.4.5, 2.3.4.4, 2.3.4.3, 2.3.4.2, 2.3.4.1, 2.3.4.0, 2.3.3.2, 2.3.3.1, 2.3.3.0, 2.3.2.2, 2.3.2.1, 2.3.1.1, 2.3.1.0, 2.3.0.0, 2.2.0.8, 2.2.0.5, 2.2.0.4
Build Dependencies:
cmake
Description:
CLHEP is a C++ Class Library for High Energy Physics.

clingo

Homepage:
Spack package:
Versions:
5.2.2
Build Dependencies:
python, doxygen, cmake
Link Dependencies:
python
Description:
Clingo: A grounder and solver for logic programs Clingo is part of the Potassco project for Answer Set Programming (ASP). ASP offers a simple and powerful modeling language to describe combinatorial problems as logic programs. The clingo system then takes such a logic program and computes answer sets representing solutions to the given problem.

cloc

Homepage:
Spack package:
Versions:
1.74
Build Dependencies:
perl
Link Dependencies:
perl
Description:
Count, or compute differences of, physical lines of source code in the given files (may be archives such as compressed tarballs or zip files) and/or recursively below the given directories.

cloog

Homepage:
Spack package:
Versions:
0.18.1, 0.18.0, 0.17.0
Build Dependencies:
gmp, isl
Link Dependencies:
gmp, isl
Description:
CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra.

cloverleaf

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
cuda, mpi
Link Dependencies:
cuda, mpi
Description:
Proxy Application. CloverLeaf is a miniapp that solves the compressible Euler equations on a Cartesian grid, using an explicit, second-order accurate method.

cloverleaf3d

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. CloverLeaf3D is 3D version of the CloverLeaf mini- app. CloverLeaf is a mini-app that solves the compressible Euler equations on a Cartesian grid, using an explicit, second-order accurate method.

clustalo

Homepage:
Spack package:
Versions:
1.2.4
Build Dependencies:
argtable
Link Dependencies:
argtable
Description:
Clustal Omega: the last alignment program you'll ever need.

clustalw

Homepage:
Spack package:
Versions:
2.1
Description:
Multiple alignment of nucleic acid and protein sequences.

cmake

Homepage:
Spack package:
Versions:
3.11.3, 3.11.2, 3.11.1, 3.11.0, 3.10.2, 3.10.1, 3.10.0, 3.9.4, 3.9.0, 3.8.2, 3.8.1, 3.8.0, 3.7.2, 3.7.1, 3.6.1, 3.6.0, 3.5.2, 3.5.1, 3.5.0, 3.4.3, 3.4.0, 3.3.1, 3.1.0, 3.0.2, 2.8.10.2
Build Dependencies:
expat, ncurses, py-sphinx, libarchive, curl, zlib, rhash, python, bzip2, openssl, qt, libuv, xz
Link Dependencies:
rhash, expat, bzip2, ncurses, curl, openssl, libarchive, libuv, xz, qt, zlib
Description:
A cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

cmocka

Homepage:
Spack package:
Versions:
1.1.1, 1.1.0, 1.0.1
Build Dependencies:
cmake
Description:
Unit-testing framework in pure C

cmor

Homepage:
Spack package:
Versions:
3.3.0, 3.2.0, 3.1.2
Build Dependencies:
udunits2, py-numpy, hdf5, python, uuid, netcdf
Link Dependencies:
python, udunits2, uuid, netcdf, hdf5
Run Dependencies:
py-numpy
Description:
Climate Model Output Rewriter is used to produce CF-compliant netCDF files. The structure of the files created by the library and the metadata they contain fulfill the requirements of many of the climate community's standard model experiments.

cnmem

Homepage:
Spack package:
Versions:
git
Build Dependencies:
cmake
Description:
CNMem mempool for CUDA devices

cnpy

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake
Description:
cnpy: library to read/write .npy and .npz files in C/C++.

cntk

Homepage:
Spack package:
Versions:
2.0, master
Build Dependencies:
cuda, cub, cntk1bitsgd, multiverso, kaldi, cudnn, opencv, boost, openblas, libzip, protobuf, mpi, nccl
Link Dependencies:
cuda, cub, cntk1bitsgd, multiverso, kaldi, cudnn, opencv, boost, openblas, libzip, protobuf, mpi, nccl
Description:
The Microsoft Cognitive Toolkit is a unified deep-learning toolkit that describes neural networks as a series of computational steps via a directed graph.

cntk1bitsgd

Homepage:
Spack package:
Versions:
master, c8b77d
Description:
CNTK1bitSGD is the header-only 1-bit stochastic gradient descent (1bit- SGD) library for the Computational Network Toolkit (CNTK).

codar-cheetah

Homepage:
Spack package:
Versions:
develop, 0.1
Build Dependencies:
python, savanna
Link Dependencies:
savanna
Run Dependencies:
python
Description:
CODAR Cheetah: The CODAR Experiment Harness for Exascale science applications.

coevp

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
silo, flann, lapack, mpi
Link Dependencies:
silo, flann, lapack, mpi
Description:
CoEVP is a scale-bridging proxy application for embedded viscoplasticity applications. It is created and maintained by The Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. Due to the size and complexity of the studied models, as well as restrictions on distribution, the currently available LULESH proxy application provides the coarse-scale model implementation and the ASPA proxy application provides the adaptive sampling support.

cohmm

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
gnuplot
Link Dependencies:
gnuplot
Description:
An anticipated important use-case for next-generation supercomputing is multiscale modeling, in which continuum equations for large-scale material deformation are augmented with high-fidelity, fine-scale simulations that provide constitutive data on demand.

coinhsl

Homepage:
Spack package:
Versions:
2014.01.17, 2014.01.10
Build Dependencies:
blas
Link Dependencies:
blas
Description:
CoinHSL is a collection of linear algebra libraries (KB22, MA27, MA28, MA54, MA57, MA64, MA77, MA86, MA97, MC19, MC34, MC64, MC68, MC69, MC78, MC80, OF01, ZB01, ZB11) bundled for use with IPOPT and other applications that use these HSL routines. Note: CoinHSL is licensed software. You will need to request a license from Research Councils UK and download a .tar.gz archive of CoinHSL yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

colm

Homepage:
Spack package:
Versions:
0.12.0
Description:
Colm Programming Language Colm is a programming language designed for the analysis and transformation of computer languages. Colm is influenced primarily by TXL. It is in the family of program transformation languages.

colordiff

Homepage:
Spack package:
Versions:
1.0.18
Build Dependencies:
perl
Link Dependencies:
perl
Description:
Colorful diff utility.

comd

Homepage:
Spack package:
Versions:
develop, 1.1
Build Dependencies:
graphviz, mpi
Link Dependencies:
graphviz, mpi
Description:
CoMD is a reference implementation of classical molecular dynamics algorithms and workloads as used in materials science. It is created and maintained by The Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement it as needed to test performance of new architectures, programming models, etc. New versions of CoMD will be released to incorporate the lessons learned from the co-design process.

compiz

Homepage:
Spack package:
Versions:
0.7.8
Build Dependencies:
libxrandr, libxfixes, libxcb, libpng, libsm, glib, gconf, libxml2, libice, libxinerama, libxrender, libxcomposite, libxslt, libxdamage
Link Dependencies:
libxrandr, libxfixes, libxcb, libpng, libsm, glib, gconf, libxml2, libice, libxinerama, libxrender, libxcomposite, libxslt, libxdamage
Description:
compiz - OpenGL window and compositing manager. Compiz is an OpenGL compositing manager that use GLX_EXT_texture_from_pixmap for binding redirected top-level windows to texture objects. It has a flexible plug- in system and it is designed to run well on most graphics hardware.

compositeproto

Homepage:
Spack package:
Versions:
0.4.2
Build Dependencies:
pkgconfig, util-macros
Description:
Composite Extension. This package contains header files and documentation for the composite extension. Library and server implementations are separate.

conduit

Homepage:
Spack package:
Versions:
0.3.1, 0.3.0, 0.2.1, 0.2.0, master
Build Dependencies:
silo, py-numpy, mpi, hdf5, python, doxygen, py-sphinx, cmake
Link Dependencies:
silo, mpi, hdf5, python, doxygen, cmake
Run Dependencies:
py-numpy
Description:
Conduit is an open source project from Lawrence Livermore National Laboratory that provides an intuitive model for describing hierarchical scientific data in C++, C, Fortran, and Python. It is used for data coupling between packages in-core, serialization, and I/O tasks.

constype

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
pkgconfig, util-macros
Description:
constype prints on the standard output the Sun code for the type of display that the specified device is. It was originally written for SunOS, but has been ported to other SPARC OS'es and to Solaris on both SPARC & x86.

converge

Homepage:
Spack package:
Versions:
2.4.10, 2.3.23, 2.2.0, 2.1.0, 2.0.0
Build Dependencies:
mpi, openmpi
Link Dependencies:
mpi, openmpi
Description:
CONVERGE is a revolutionary computational fluid dynamics (CFD) program that eliminates the grid generation bottleneck from the simulation process. CONVERGE was developed by engine simulation experts and is straightforward to use for both engine and non-engine simulations. Unlike many CFD programs, CONVERGE automatically generates a perfectly orthogonal, structured grid at runtime based on simple, user-defined grid control parameters. This grid generation method completely eliminates the need to manually generate a grid. In addition, CONVERGE offers many other features to expedite the setup process and to ensure that your simulations are as computationally efficient as possible.

coreutils

Homepage:
Spack package:
Versions:
8.26, 8.23
Description:
The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

corset

Homepage:
Spack package:
Versions:
1.06
Description:
Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts.

cosmomc

Homepage:
Spack package:
Versions:
2016.11, 2016.06
Build Dependencies:
planck-likelihood, py-numpy, py-scipy, mpi, python, py-matplotlib, py-pandas, py-six
Link Dependencies:
planck-likelihood, python, mpi
Run Dependencies:
py-numpy, py-scipy, python, py-matplotlib, py-pandas, py-six
Description:
CosmoMC is a Fortran 2008 Markov-Chain Monte-Carlo (MCMC) engine for exploring cosmological parameter space, together with Fortran and python code for analysing Monte-Carlo samples and importance sampling (plus a suite of scripts for building grids of runs, plotting and presenting results).

cosp2

Homepage:
Spack package:
Versions:
master
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. CoSP2 represents a sparse linear algebra parallel algorithm for calculating the density matrix in electronic tructure theory. The algorithm is based on a recursive second-order Fermi- Operator expansion method (SP2) and is tailored for density functional based tight-binding calculations of non-metallic systems.

cp2k

Homepage:
Spack package:
Versions:
5.1, 4.1, 3.0
Build Dependencies:
libint, wannier90, plumed, mpi, fftw, blas, elpa, pexsi, libxc, python, lapack, libxsmm, scalapack
Link Dependencies:
libint, wannier90, plumed, mpi, fftw, blas, elpa, pexsi, libxc, lapack, libxsmm, scalapack
Description:
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems

cppad

Homepage:
Spack package:
Versions:
develop, 20170114
Build Dependencies:
cmake
Description:
A Package for Differentiation of C++ Algorithms.

cppcheck

Homepage:
Spack package:
Versions:
1.81, 1.78, 1.72, 1.68
Run Dependencies:
py-pygments
Description:
A tool for static C/C++ code analysis.

cpprestsdk

Homepage:
Spack package:
Versions:
2.9.1
Build Dependencies:
boost, cmake
Link Dependencies:
boost
Description:
The C++ REST SDK is a Microsoft project for cloud-based client-server communication in native code using a modern asynchronous C++ API design. This project aims to help C++ developers connect to and interact with services.

cppunit

Homepage:
Spack package:
Versions:
1.13.2
Description:
Obsolete Unit testing framework for C++

cppzmq

Homepage:
Spack package:
Versions:
develop, 4.2.2
Build Dependencies:
zeromq, cmake
Link Dependencies:
zeromq
Description:
C++ binding for 0MQ

cpu-features

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake
Description:
A cross platform C99 library to get cpu features at runtime.

cpuinfo

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake
Description:
cpuinfo is a library to detect essential for performance optimization information about host CPU.

cram

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, cmake, mpi
Link Dependencies:
python, mpi
Description:
Cram runs many small MPI jobs inside one large MPI job.

cryptopp

Homepage:
Spack package:
Versions:
7.0.0, 5.6.3, 5.6.2, 5.6.1
Build Dependencies:
gmake
Description:
Crypto++ is an open-source C++ library of cryptographic schemes. The library supports a number of different cryptography algorithms, including authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2), public-key encryption (RSA, DSA), and a few obsolete/historical encryption algorithms (MD5, Panama).

cscope

Homepage:
Spack package:
Versions:
15.8b
Build Dependencies:
pkgconfig, flex, ncurses, bison
Link Dependencies:
ncurses
Description:
Cscope is a developer's tool for browsing source code.

csdp

Homepage:
Spack package:
Versions:
6.1.1
Build Dependencies:
atlas
Link Dependencies:
atlas
Description:
CSDP is a library of routines that implements a predictor corrector variant of the semidefinite programming algorithm of Helmberg, Rendl, Vanderbei, and Wolkowicz

ctffind

Homepage:
Spack package:
Versions:
4.1.8
Build Dependencies:
wx, fftw
Link Dependencies:
wx, fftw
Description:
Fast and accurate defocus estimation from electron micrographs.

cub

Homepage:
Spack package:
Versions:
1.7.1, 1.6.4, 1.4.1
Description:
CUB is a C++ header library of cooperative threadblock primitives and other utilities for CUDA kernel programming.

cube

Homepage:
Spack package:
Versions:
4.4, 4.3.5, 4.3.4, 4.3.3, 4.2.3
Build Dependencies:
qt, zlib
Link Dependencies:
qt, zlib
Description:
Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performance space consisting of the dimensions: - performance metric - call path - system resource

cuda

Homepage:
Spack package:
Versions:
9.2.88, 9.1.85, 9.0.176, 8.0.61, 8.0.44, 7.5.18, 6.5.14
Description:
CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). Note: This package does not currently install the drivers necessary to run CUDA. These will need to be installed manually. See: https://docs.nvidia.com/cuda/ for details.

cuda-memtest

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cuda, cmake
Link Dependencies:
cuda
Description:
Maintained and updated fork of cuda_memtest. original homepage: http://sourceforge.net/projects/cudagpumemtest . This software tests GPU memory for hardware errors and soft errors using CUDA or OpenCL.

cudnn

Homepage:
Spack package:
Versions:
6.0, 5.1
Build Dependencies:
cuda
Link Dependencies:
cuda
Description:
NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks

cups

Homepage:
Spack package:
Versions:
2.2.3
Build Dependencies:
gnutls
Link Dependencies:
gnutls
Description:
CUPS is the standards-based, open source printing system developed by Apple Inc. for macOS and other UNIX-like operating systems. CUPS uses the Internet Printing Protocol (IPP) to support printing to local and network printers. This provides the core CUPS libraries, not a complete CUPS install.

curl

Homepage:
Spack package:
Versions:
7.60.0, 7.59.0, 7.56.0, 7.54.0, 7.53.1, 7.52.1, 7.50.3, 7.50.2, 7.50.1, 7.49.1, 7.47.1, 7.46.0, 7.45.0, 7.44.0, 7.43.0, 7.42.1
Build Dependencies:
zlib, libssh, openssl, libssh2, nghttp2
Link Dependencies:
zlib, libssh, openssl, libssh2, nghttp2
Description:
cURL is an open source command line tool and library for transferring data with URL syntax

cvs

Homepage:
Spack package:
Versions:
1.12.13
Description:
CVS a very traditional source control system

czmq

Homepage:
Spack package:
Versions:
4.0.2, 3.0.2
Build Dependencies:
pkgconfig, zeromq, autoconf, automake, libtool
Link Dependencies:
zeromq
Description:
A C interface to the ZMQ library

dakota

Homepage:
Spack package:
Versions:
6.3
Build Dependencies:
boost, mpi, python, blas, lapack, cmake
Link Dependencies:
boost, python, lapack, mpi, blas
Description:
The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems analysis methods. Dakota contains algorithms for: - optimization with gradient and non gradient-based methods; - uncertainty quantification with sampling, reliability, stochastic - expansion, and epistemic methods; - parameter estimation with nonlinear least squares methods; - sensitivity/variance analysis with design of experiments and - parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty.

daligner

Homepage:
Spack package:
Versions:
1.0
Description:
Daligner: The Dazzler "Overlap" Module.

damageproto

Homepage:
Spack package:
Versions:
1.2.1
Build Dependencies:
pkgconfig, util-macros
Description:
X Damage Extension. This package contains header files and documentation for the X Damage extension. Library and server implementations are separate.

damselfly

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake
Description:
Damselfly is a model-based parallel network simulator.

darshan-runtime

Homepage:
Spack package:
Versions:
3.1.6, 3.1.0, 3.0.0
Build Dependencies:
mpi, zlib
Link Dependencies:
mpi, zlib
Description:
Darshan (runtime) is a scalable HPC I/O characterization tool designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. DarshanRuntime package should be installed on systems where you intend to instrument MPI applications.

darshan-util

Homepage:
Spack package:
Versions:
3.1.6, 3.1.0, 3.0.0
Build Dependencies:
bzip2, zlib
Link Dependencies:
bzip2, zlib
Run Dependencies:
bzip2
Description:
Darshan (util) is collection of tools for parsing and summarizing log files produced by Darshan (runtime) instrumentation. This package is typically installed on systems (front-end) where you intend to analyze log files produced by Darshan (runtime).

dash

Homepage:
Spack package:
Versions:
0.5.9.1
Build Dependencies:
autoconf, libtool, automake, m4
Link Dependencies:
libedit
Description:
The Debian Almquist Shell.

datamash

Homepage:
Spack package:
Versions:
1.3, 1.1.0, 1.0.7, 1.0.6, 1.0.5
Description:
GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files.

dataspaces

Homepage:
Spack package:
Versions:
develop, 1.6.2
Build Dependencies:
m4, autoconf, automake, mpi, libtool
Link Dependencies:
mpi
Description:
an extreme scale data management framework.

davix

Homepage:
Spack package:
Versions:
0.6.7
Build Dependencies:
pkgconfig, openssl, cmake, libxml2, libuuid
Link Dependencies:
openssl, libxml2, libuuid
Description:
High-performance file management over WebDAV/HTTP.

dbus

Homepage:
Spack package:
Versions:
1.11.2, 1.9.0, 1.8.8, 1.8.6, 1.8.4, 1.8.2
Build Dependencies:
expat
Link Dependencies:
expat
Description:
D-Bus is a message bus system, a simple way for applications to talk to one another. D-Bus supplies both a system daemon (for events such new hardware device printer queue ) and a per-user-login-session daemon (for general IPC needs among user applications). Also, the message bus is built on top of a general one-to-one message passing framework, which can be used by any two applications to communicate directly (without going through the message bus daemon).

dealii

Homepage:
Spack package:
Versions:
develop, 9.0.0, 8.5.1, 8.5.0, 8.4.2, 8.4.1, 8.4.0, 8.3.0, 8.2.1, 8.1.0
Build Dependencies:
trilinos, python, tbb, blas, cmake, gsl, boost, sundials, bzip2, suite-sparse, slepc, doxygen, nanoflann, lapack, scalapack, cuda, petsc, oce, gmsh, netcdf-cxx, metis, zlib, graphviz, assimp, mpi, adol-c, muparser, hdf5, p4est, netcdf, arpack-ng
Link Dependencies:
trilinos, python, tbb, blas, cmake, gsl, boost, sundials, bzip2, suite-sparse, slepc, doxygen, nanoflann, lapack, scalapack, cuda, petsc, oce, netcdf-cxx, metis, zlib, graphviz, assimp, mpi, adol-c, muparser, hdf5, p4est, netcdf, arpack-ng
Run Dependencies:
gmsh
Description:
C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs.

dealii-parameter-gui

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, qt
Link Dependencies:
qt
Description:
A qt based graphical user interface for editing deal.II .prm parameter files.

deconseq-standalone

Homepage:
Spack package:
Versions:
0.4.3
Build Dependencies:
perl
Link Dependencies:
perl
Description:
The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets.

dejagnu

Homepage:
Spack package:
Versions:
1.6, 1.4.4
Build Dependencies:
expect, tcl
Link Dependencies:
expect, tcl
Description:
DejaGnu is a framework for testing other programs. Its purpose is to provide a single front end for all tests.

delly2

Homepage:
Spack package:
Versions:
2017-08-03
Build Dependencies:
boost, htslib, bcftools
Link Dependencies:
boost, htslib, bcftools
Description:
Delly2 is an integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short- read massively parallel sequencing data..

denovogear

Homepage:
Spack package:
Versions:
1.1.1, 1.1.0
Build Dependencies:
boost, cmake, htslib, eigen
Description:
DeNovoGear is a software package to detect de novo mutations using next- generation sequencing data. It supports the analysis of many differential experimental designs and uses advanced statistical models to reduce the false positve rate.

dia

Homepage:
Spack package:
Versions:
0.97.3
Build Dependencies:
gtkplus, python, intltool, libxml2, libuuid, libxinerama, libsm, swig, libxslt, freetype, libxrender
Link Dependencies:
gtkplus, python, libxrender, libuuid, libxinerama, libsm, swig, libxslt, freetype, libxml2
Description:
Dia is a program for drawing structured diagrams.

dialign-tx

Homepage:
Spack package:
Versions:
1.0.2
Description:
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

diamond

Homepage:
Spack package:
Versions:
0.9.21, 0.9.20, 0.9.19, 0.9.14, 0.8.38, 0.8.26
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

diffsplice

Homepage:
Spack package:
Versions:
0.1.2beta, 0.1.1
Description:
A novel tool for discovering and quantitating alternative splicing variants present in an RNA-seq dataset, without relying on annotated transcriptome or pre-determined splice pattern.

direnv

Homepage:
Spack package:
Versions:
2.11.3
Build Dependencies:
go
Description:
direnv is an environment switcher for the shell.

discovar

Homepage:
Spack package:
Versions:
52488
Description:
DISCOVAR is a variant caller and small genome assembler.

discovardenovo

Homepage:
Spack package:
Versions:
52488
Build Dependencies:
jemalloc, samtools
Link Dependencies:
jemalloc, samtools
Description:
DISCOVAR de novo is a large (and small) de novo genome assembler. It quickly generates highly accurate and complete assemblies using the same single library data as used by DISCOVAR. It currently doesn't support variant calling, for that, please use DISCOVAR instead.

dislin

Homepage:
Spack package:
Versions:
11.1.linux.i586_64, 11.0.linux.i586_64
Build Dependencies:
mesa, motif
Link Dependencies:
mesa, motif
Description:
DISLIN is a high level and easy to use graphics library for displaying data as curves, bar graphs, pie charts, 3D-colour plots, surfaces, contours and maps.

dlpack

Homepage:
Spack package:
Versions:
master
Description:
DLPack is an RFC for common tensor and operator guidelines in deep learning systems.

dmlc-core

Homepage:
Spack package:
Versions:
20170508, master
Build Dependencies:
cmake
Description:
DMLC-Core is the backbone library to support all DMLC projects, offers the bricks to build efficient and scalable distributed machine learning libraries.

dmxproto

Homepage:
Spack package:
Versions:
2.3.1
Build Dependencies:
pkgconfig, util-macros
Description:
Distributed Multihead X (DMX) Extension. This extension defines a protocol for clients to access a front-end proxy X server that controls multiple back-end X servers making up a large display.

docbook-xml

Homepage:
Spack package:
Versions:
4.5
Description:
Docbook DTD XML files.

docbook-xsl

Homepage:
Spack package:
Versions:
1.79.1
Build Dependencies:
docbook-xml
Link Dependencies:
docbook-xml
Description:
Docbook XSL vocabulary.

dos2unix

Homepage:
Spack package:
Versions:
7.3.4
Description:
DOS/Mac to Unix and vice versa text file format converter.

double-conversion

Homepage:
Spack package:
Versions:
2.0.1, 2.0.0, 1.1.5, 1.1.4, 1.1.3
Build Dependencies:
cmake
Description:
This project (double-conversion) provides binary-decimal and decimal- binary routines for IEEE doubles. The library consists of efficient conversion routines that have been extracted from the V8 JavaScript engine. The code has been refactored and improved so that it can be used more easily in other projects. There is extensive documentation in src/double-conversion.h. Other examples can be found in test/cctest/test-conversions.cc.

doxygen

Homepage:
Spack package:
Versions:
1.8.12, 1.8.11, 1.8.10
Build Dependencies:
flex, cmake, bison
Run Dependencies:
graphviz
Description:
Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..

dri2proto

Homepage:
Spack package:
Versions:
2.8
Build Dependencies:
pkgconfig, util-macros
Description:
Direct Rendering Infrastructure 2 Extension. This extension defines a protocol to securely allow user applications to access the video hardware without requiring data to be passed through the X server.

dri3proto

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
pkgconfig, util-macros
Description:
Direct Rendering Infrastructure 3 Extension. This extension defines a protocol to securely allow user applications to access the video hardware without requiring data to be passed through the X server.

dsdp

Homepage:
Spack package:
Versions:
5.8
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
The DSDP software is a free open source implementation of an interior- point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method. It allows feasible and infeasible starting points and provides approximate certificates of infeasibility when no feasible solution exists.

dsrc

Homepage:
Spack package:
Versions:
2.0.2
Description:
DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format.

dtcmp

Homepage:
Spack package:
Versions:
1.1.0, 1.0.3
Build Dependencies:
lwgrp, mpi
Link Dependencies:
lwgrp, mpi
Description:
The Datatype Comparison Library provides comparison operations and parallel sort algorithms for MPI applications.

dyninst

Homepage:
Spack package:
Versions:
develop, 9.3.2, 9.3.0, 9.2.0, 9.1.0, 8.2.1, 8.1.2, 8.1.1
Build Dependencies:
libdwarf, boost, cmake
Link Dependencies:
libdwarf, boost, elf
Description:
API for dynamic binary instrumentation. Modify programs while they are executing without recompiling, re-linking, or re-executing.

ea-utils

Homepage:
Spack package:
Versions:
1.04.807
Build Dependencies:
subversion, zlib, gsl, bamtools, perl
Link Dependencies:
subversion, gsl, bamtools, zlib
Description:
Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

easybuild

Homepage:
Spack package:
Versions:
3.1.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-easybuild-easyblocks, py-easybuild-easyconfigs, py-easybuild-framework
Description:
EasyBuild is a software build and installation framework for (scientific) software on HPC systems.

ebms

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
This is a miniapp for the Energy Banding Monte Carlo (EBMC) neutron transportation simulation code. It is adapted from a similar miniapp provided by Andrew Siegel, whose algorithm is described in [1], where only one process in a compute node is used, and the compute nodes are divided into memory nodes and tracking nodes. Memory nodes do not participate in particle tracking. Obviously, there is a lot of resource waste in this design.

eccodes

Homepage:
Spack package:
Versions:
2.5.0, 2.2.0
Build Dependencies:
libpng, libaec, py-numpy, openjpeg, python, cmake, netcdf, jasper
Link Dependencies:
libpng, libaec, netcdf, python, openjpeg, jasper
Run Dependencies:
python, py-numpy
Description:
ecCodes is a package developed by ECMWF for processing meteorological data in GRIB (1/2), BUFR (3/4) and GTS header formats.

eclipse-gcj-parser

Homepage:
Spack package:
Versions:
4.8
Description:
GCJ requires the Eclipse Java parser, but does not ship with it. This builds that parser into an executable binary, thereby making GCJ work.

ecp-proxy-apps

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
amg, minitri, minife, nekbone, sw4lite, swfft, comd, macsio, xsbench, miniamr, candle-benchmarks, laghos
Link Dependencies:
amg, minitri, minife, nekbone, sw4lite, swfft, comd, macsio, xsbench, miniamr, candle-benchmarks, laghos
Description:
This is a collection of packages that represents the official suite of DOE/ECP proxy applications. This is a Spack bundle package that installs the ECP proxy application suite.

ed

Homepage:
Spack package:
Versions:
1.4
Description:
GNU ed is a line-oriented text editor. It is used to create, display, modify and otherwise manipulate text files, both interactively and via shell scripts.

editres

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libx11, libxaw, util-macros, libxt, libxmu, pkgconfig
Link Dependencies:
libx11, libxaw, libxmu, libxt
Description:
Dynamic resource editor for X Toolkit applications.

eigen

Homepage:
Spack package:
Versions:
3.3.4, 3.3.3, 3.3.1, 3.2.10, 3.2.9, 3.2.8, 3.2.7
Build Dependencies:
scotch, mpfr, fftw, gmp, suite-sparse, cmake, metis
Link Dependencies:
scotch, mpfr, fftw, gmp, suite-sparse, metis
Description:
Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms.

elasticsearch

Homepage:
Spack package:
Versions:
6.2.4
Run Dependencies:
jdk
Description:
Elasticsearch is a search engine based on Lucene. It provides a distributed, multitenant-capable full-text search engine with an HTTP web interface and schema-free JSON documents.

elemental

Homepage:
Spack package:
Versions:
develop, 0.87.7, 0.87.6
Build Dependencies:
gmp, mpfr, netlib-lapack, scalapack, blas, intel-mkl, cmake, openblas, veclibfort, mpi, essl, python, lapack, mpc, metis
Link Dependencies:
gmp, mpfr, netlib-lapack, blas, intel-mkl, scalapack, openblas, veclibfort, mpi, essl, python, lapack, mpc, metis
Description:
Elemental: Distributed-memory dense and sparse-direct linear algebra and optimization library.

elfutils

Homepage:
Spack package:
Versions:
0.170, 0.168, 0.163
Build Dependencies:
gettext, flex, bison
Link Dependencies:
gettext
Description:
elfutils is a collection of various binary tools such as eu-objdump, eu- readelf, and other utilities that allow you to inspect and manipulate ELF files. Refer to Table 5.Tools Included in elfutils for Red Hat Developer for a complete list of binary tools that are distributed with the Red Hat Developer Toolset version of elfutils.

elk

Homepage:
Spack package:
Versions:
3.3.17
Build Dependencies:
fftw, blas, lapack, mpi, libxc
Link Dependencies:
fftw, blas, lapack, mpi, libxc
Description:
An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features.

elpa

Homepage:
Spack package:
Versions:
2017.05.003, 2017.05.002, 2016.11.001.pre, 2016.05.004, 2016.05.003, 2015.11.001
Build Dependencies:
blas, lapack, mpi, scalapack
Link Dependencies:
blas, lapack, mpi, scalapack
Description:
Eigenvalue solvers for Petaflop-Applications (ELPA)

emacs

Homepage:
Spack package:
Versions:
26.1, 25.3, 25.2, 25.1, 24.5
Build Dependencies:
gtkplus, libpng, libxpm, giflib, libxaw, libtiff, gnutls, pkgconfig, zlib, libx11, pcre, ncurses
Link Dependencies:
gtkplus, libpng, libxpm, giflib, ncurses, libxaw, libtiff, libx11, gnutls, pcre, zlib
Description:
The Emacs programmable text editor.

emboss

Homepage:
Spack package:
Versions:
6.6.0
Build Dependencies:
libgd, libxpm, postgresql
Link Dependencies:
libgd, libxpm, postgresql
Description:
EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community

encodings

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
pkgconfig, util-macros, mkfontscale, font-util
Link Dependencies:
font-util
Description:
X.org encodings font.

environment-modules

Homepage:
Spack package:
Versions:
3.2.10
Build Dependencies:
tcl
Link Dependencies:
tcl
Run Dependencies:
tcl
Description:
The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles.

eospac

Homepage:
Spack package:
Versions:
6.4.0beta.2, 6.4.0beta.1, 6.3.1
Description:
A collection of C routines that can be used to access the Sesame data library.

es

Homepage:
Spack package:
Versions:
0.9.1
Build Dependencies:
readline
Link Dependencies:
readline
Description:
Es is an extensible shell. The language was derived from the Plan 9 shell, rc, and was influenced by functional programming languages, such as Scheme, and the Tcl embeddable programming language. This implementation is derived from Byron Rakitzis's public domain implementation of rc.

esmf

Homepage:
Spack package:
Versions:
7.0.1
Build Dependencies:
netcdf-fortran, xerces-c, mpi, zlib, lapack, parallel-netcdf, netcdf, libxml2
Link Dependencies:
netcdf-fortran, xerces-c, mpi, zlib, lapack, parallel-netcdf, netcdf, libxml2
Test Dependencies:
perl
Description:
The Earth System Modeling Framework (ESMF) is high-performance, flexible software infrastructure for building and coupling weather, climate, and related Earth science applications. The ESMF defines an architecture for composing complex, coupled modeling systems and includes data structures and utilities for developing individual models.

essl

Homepage:
Spack package:
Versions:
6.1, 5.5
Description:
IBM's Engineering and Scientific Subroutine Library (ESSL).

ethminer

Homepage:
Spack package:
Versions:
0.12.0
Build Dependencies:
boost, cuda, json-c, mesa, python, cmake, curl, zlib
Link Dependencies:
boost, cuda, json-c, mesa, python, curl, zlib
Description:
The ethminer is an Ethereum GPU mining worker.

etsf-io

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
netcdf-fortran, hdf5
Link Dependencies:
netcdf-fortran, hdf5
Description:
ETSF_IO is a library implementing the Nanoquanta/ETSF file format specifications. ETSF_IO enables an architecture-independent exchange of crystallographic data, electronic wavefunctions, densities and potentials, as well as spectroscopic data. It is meant to be used by quantum-physical and quantum-chemical applications relying upon Density Functional Theory (DFT).

everytrace

Homepage:
Spack package:
Versions:
develop, 0.2.2
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Get stack trace EVERY time a program exits.

everytrace-example

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, everytrace, openmpi
Link Dependencies:
everytrace, openmpi
Description:
Get stack trace EVERY time a program exits.

evieext

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
pkgconfig, util-macros
Description:
Extended Visual Information Extension (XEVIE). This extension defines a protocol for a client to determine information about core X visuals beyond what the core protocol provides.

exabayes

Homepage:
Spack package:
Versions:
1.5
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.

examinimd

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
kokkos, mpi
Link Dependencies:
kokkos, mpi
Description:
ExaMiniMD is a proxy application and research vehicle for particle codes, in particular Molecular Dynamics (MD). Compared to previous MD proxy apps (MiniMD, COMD), its design is significantly more modular in order to allow independent investigation of different aspects. To achieve that the main components such as force calculation, communication, neighbor list construction and binning are derived classes whose main functionality is accessed via virtual functions. This allows a developer to write a new derived class and drop it into the code without touching much of the rest of the application.

exampm

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake
Description:
Exascale Material Point Method (MPM) Mini-App

exasp2

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
bml, blas, lapack, mpi
Link Dependencies:
bml, blas, lapack, mpi
Description:
ExaSP2 is a reference implementation of typical linear algebra algorithms and workloads for a quantum molecular dynamics (QMD) electronic structure code. The algorithm is based on a recursive second- order Fermi-Operator expansion method (SP2) and is tailored for density functional based tight-binding calculations of material systems. The SP2 algorithm variants are part of the Los Alamos Transferable Tight-binding for Energetics (LATTE) code, based on a matrix expansion of the Fermi operator in a recursive series of generalized matrix-matrix multiplications. It is created and maintained by Co-Design Center for Particle Applications (CoPA). The code is intended to serve as a vehicle for co-design by allowing others to extend and/or reimplement as needed to test performance of new architectures, programming models, etc.

exmcutils

Homepage:
Spack package:
Versions:
0.5.3
Description:
ExM C-Utils: Generic C utility library for ADLB/X and Swift/T

exodusii

Homepage:
Spack package:
Versions:
2016-08-09
Build Dependencies:
mpi, cmake, netcdf, hdf5
Link Dependencies:
mpi, netcdf, hdf5
Description:
Exodus II is a C++/Fortran library developed to store and retrieve data for finite element analyses. It's used for preprocessing (problem definition), postprocessing (results visualization), and data transfer between codes. An Exodus II data file is a random access, machine independent, binary file that is written and read via C, C++, or Fortran API routines.

exonerate

Homepage:
Spack package:
Versions:
2.4.0
Build Dependencies:
pkgconfig, glib
Link Dependencies:
glib
Description:
Pairwise sequence alignment of DNA and proteins

expat

Homepage:
Spack package:
Versions:
2.2.5, 2.2.2, 2.2.0
Build Dependencies:
libbsd
Link Dependencies:
libbsd
Description:
Expat is an XML parser library written in C.

expect

Homepage:
Spack package:
Versions:
5.45
Build Dependencies:
automake, libtool, autoconf, tcl, m4
Link Dependencies:
tcl
Description:
Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.

express

Homepage:
Spack package:
Versions:
2015-11-29
Build Dependencies:
boost, cmake, bamtools, zlib
Link Dependencies:
boost, bamtools, zlib
Description:
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

extrae

Homepage:
Spack package:
Versions:
3.4.1
Build Dependencies:
boost, libdwarf, gettext, libunwind, mpi, binutils, papi, dyninst, libxml2
Link Dependencies:
boost, libdwarf, gettext, dyninst, libunwind, mpi, binutils, papi, elf, libxml2
Description:
Extrae is the package devoted to generate tracefiles which can be analyzed later by Paraver. Extrae is a tool that uses different interposition mechanisms to inject probes into the target application so as to gather information regarding the application performance. The Extrae instrumentation package can instrument the MPI programin model, and the following parallel programming models either alone or in conjunction with MPI : OpenMP, CUDA, OpenCL, pthread, OmpSs

exuberant-ctags

Homepage:
Spack package:
Versions:
5.8
Description:
The canonical ctags generator

f90cache

Homepage:
Spack package:
Versions:
0.99
Description:
f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations.

fabtests

Homepage:
Spack package:
Versions:
1.6.0, 1.5.3
Build Dependencies:
libfabric
Link Dependencies:
libfabric
Description:
Fabtests provides a set of examples that uses libfabric

falcon

Homepage:
Spack package:
Versions:
2017-05-30
Build Dependencies:
python, py-networkx
Link Dependencies:
python
Run Dependencies:
py-pypeflow, py-setuptools, py-networkx, pacbio-dazz-db, python, pacbio-dextractor, pacbio-daligner, pacbio-damasker
Description:
Falcon: a set of tools for fast aligning long reads for consensus and assembly. The Falcon tool kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience.

farmhash

Homepage:
Spack package:
Versions:
92e897
Build Dependencies:
cmake
Description:
FarmHash provides hash functions for strings and other data.

fast-gbs

Homepage:
Spack package:
Versions:
2017-01-25
Run Dependencies:
py-pyvcf, bwa, py-cutadapt, platypus, parallel, python, sabre, samtools
Description:
A bioinformatic pipeline designed to extract a high-quality SNP catalog starting from FASTQ files obtained from sequencing genotyping-by- sequencing (GBS) libraries.

fastjar

Homepage:
Spack package:
Versions:
0.98
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Fastjar is a version of Sun's 'jar' utility, written entirely in C.

fastmath

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
phasta, petsc, trilinos, zoltan, moab, hypre, sundials, pumi, superlu-dist, arpack-ng, mpi, boxlib, mesquite, chombo
Link Dependencies:
phasta, petsc, trilinos, zoltan, moab, hypre, sundials, pumi, superlu-dist, arpack-ng, mpi, boxlib, mesquite, chombo
Description:
FASTMath is a suite of ~15 numerical libraries frequently used together in various SciDAC and CSE applications. The suite includes discretization libraries for structured, AMR and unstructured grids as well as solver libraries for ODE's, Time Integrators, Iterative, Non- Linear, and Direct Solvers.

fastme

Homepage:
Spack package:
Versions:
2.1.5.1
Build Dependencies:
autoconf, libtool, automake, m4
Description:
FastME is a distance based phylogeny reconstruction program that works on distance matrices and, as of v2.0, sequence data.

fastphase

Homepage:
Spack package:
Versions:
2016-03-30
Description:
Software for haplotype reconstruction, and estimating missing genotypes from population data.

fastq-screen

Homepage:
Spack package:
Versions:
0.11.2
Build Dependencies:
bwa, bowtie2, bowtie, samtools
Link Dependencies:
bwa, bowtie2, bowtie, samtools
Run Dependencies:
perl-gd-graph, perl
Description:
FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

fastqc

Homepage:
Spack package:
Versions:
0.11.7, 0.11.5, 0.11.4
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
java
Description:
A quality control tool for high throughput sequence data.

fastqvalidator

Homepage:
Spack package:
Versions:
2017-01-10
Description:
The fastQValidator validates the format of fastq files.

fasttree

Homepage:
Spack package:
Versions:
2.1.10
Description:
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

fastx-toolkit

Homepage:
Spack package:
Versions:
0.0.14
Build Dependencies:
libgtextutils
Link Dependencies:
libgtextutils
Description:
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

fenics

Homepage:
Spack package:
Versions:
2016.1.0, 1.6.0, 1.5.0
Build Dependencies:
scotch, petsc, py-sphinx, slepc, python, mpi, py-six, cmake, trilinos, parmetis, boost, vtk, py-setuptools, py-sympy, qt, hdf5, py-ply, py-numpy, swig, eigen, suite-sparse
Link Dependencies:
scotch, petsc, hdf5, qt, boost, vtk, parmetis, slepc, python, mpi, trilinos, eigen, suite-sparse
Run Dependencies:
py-ply, py-sympy, py-six, swig, py-numpy
Description:
FEniCS is organized as a collection of interoperable components that together form the FEniCS Project. These components include the problem- solving environment DOLFIN, the form compiler FFC, the finite element tabulator FIAT, the just-in-time compiler Instant, the code generation interface UFC, the form language UFL and a range of additional components.

fermi

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
zlib
Link Dependencies:
zlib
Run Dependencies:
perl
Description:
A WGS de novo assembler based on the FMD-index for large genomes.

fermikit

Homepage:
Spack package:
Versions:
2017-11-7
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
De novo assembly based variant calling pipeline for Illumina short reads

fermisciencetools

Homepage:
Spack package:
Versions:
11r5p3
Description:
The Fermi Science Tools consists of the basic tools necessary to analyze Fermi data. This is the binary version for Linux x86_64 with libc-2.17.

ferret

Homepage:
Spack package:
Versions:
6.96
Build Dependencies:
netcdf-fortran, readline, hdf5, netcdf, zlib
Link Dependencies:
netcdf-fortran, readline, hdf5, netcdf, zlib
Description:
Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets.

ffmpeg

Homepage:
Spack package:
Versions:
3.2.4
Build Dependencies:
yasm
Link Dependencies:
yasm
Description:
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.

fftw

Homepage:
Spack package:
Versions:
3.3.7, 3.3.6-pl2, 3.3.5, 3.3.4, 2.1.5
Build Dependencies:
automake, autoconf, mpi, libtool
Link Dependencies:
mpi
Description:
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

fimpute

Homepage:
Spack package:
Versions:
2014-01
Description:
FImpute uses an overlapping sliding window approach to efficiently exploit relationships or haplotype similarities between target and reference individuals.

findutils

Homepage:
Spack package:
Versions:
4.6.0, 4.4.2, 4.4.1, 4.4.0, 4.2.33, 4.2.32, 4.2.31, 4.2.30, 4.2.29, 4.2.28, 4.2.27, 4.2.26, 4.2.25, 4.2.23, 4.2.20, 4.2.18, 4.2.15, 4.1.20, 4.1
Description:
The GNU Find Utilities are the basic directory searching utilities of the GNU operating system.

fio

Homepage:
Spack package:
Versions:
2.19
Build Dependencies:
gtkplus, cairo, py-sphinx
Link Dependencies:
gtkplus, cairo
Description:
Flexible I/O Tester.

fish

Homepage:
Spack package:
Versions:
2.7.1, 2.7.0, 2.2.0
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
fish is a smart and user-friendly command line shell for OS X, Linux, and the rest of the family.

fixesproto

Homepage:
Spack package:
Versions:
5.0
Build Dependencies:
pkgconfig, util-macros
Description:
X Fixes Extension. The extension makes changes to many areas of the protocol to resolve issues raised by application interaction with core protocol mechanisms that cannot be adequately worked around on the client side of the wire.

flac

Homepage:
Spack package:
Versions:
1.3.2, 1.3.1, 1.3.0
Build Dependencies:
libvorbis, id3lib
Link Dependencies:
libvorbis, id3lib
Description:
Encoder/decoder for the Free Lossless Audio Codec

flang

Homepage:
Spack package:
Versions:
develop, 20180319
Build Dependencies:
cmake, llvm
Link Dependencies:
llvm
Description:
Flang is a Fortran compiler targeting LLVM.

flann

Homepage:
Spack package:
Versions:
1.9.1, 1.8.5, 1.8.4, 1.8.1, 1.8.0
Build Dependencies:
cuda, boost, latex, py-numpy, mpi, hdf5, python, cmake, matlab
Link Dependencies:
cuda, boost, latex, hdf5, mpi, python
Run Dependencies:
py-numpy, matlab
Test Dependencies:
gtest, hdf5
Description:
FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces. It contains a collection of algorithms we found to work best for nearest neighbor search and a system for automatically choosing the best algorithm and optimum parameters depending on the dataset. FLANN is written in C++ and contains bindings for the following languages: C, MATLAB and Python.

flash

Homepage:
Spack package:
Versions:
1.2.11
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments.

flecsale

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
python, cmake, openssl, flecsi
Link Dependencies:
python, openssl, flecsi
Description:
Flecsale is an ALE code based on FleCSI

flecsi

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, legion
Link Dependencies:
legion
Description:
FleCSI is a compile-time configurable framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. Current support includes multi-dimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces,and dependency closures.

flex

Homepage:
Spack package:
Versions:
2.6.4, 2.6.3, 2.6.1, 2.6.0, 2.5.39
Build Dependencies:
gettext, m4, autoconf, bison, help2man, automake, libtool
Description:
Flex is a tool for generating scanners.

flint

Homepage:
Spack package:
Versions:
develop, 2.5.2, 2.4.5
Build Dependencies:
gmp, autoconf, mpfr
Link Dependencies:
gmp, mpfr
Description:
FLINT (Fast Library for Number Theory).

flit

Homepage:
Spack package:
Versions:
2.0-alpha.1
Run Dependencies:
python, py-toml, py-matplotlib, py-numpy
Description:
Floating-point Litmus Tests (FLiT) is a C++ test infrastructure for detecting variability in floating-point code caused by variations in compiler code generation, hardware and execution environments.

fltk

Homepage:
Spack package:
Versions:
1.3.3
Build Dependencies:
libx11
Link Dependencies:
libx11
Description:
FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. FLTK is designed to be small and modular enough to be statically linked, but works fine as a shared library. FLTK also includes an excellent UI builder called FLUID that can be used to create applications in minutes.

flux

Homepage:
Spack package:
Versions:
0.8.0, master
Build Dependencies:
zeromq, hwloc, libuuid, lua, autoconf, jansson, lua-luaposix, asciidoc, munge, python, automake, py-cffi, czmq, libtool
Link Dependencies:
jansson, zeromq, hwloc, libuuid, python, lua, czmq, munge, lua-luaposix
Run Dependencies:
py-cffi
Description:
A next-generation resource manager (pre-alpha)

fluxbox

Homepage:
Spack package:
Versions:
1.3.7
Build Dependencies:
expat, libx11, libxext, libxrender, pkg-config, freetype
Link Dependencies:
expat, libx11, libxrender, libxext, freetype
Description:
Fluxbox is a windowmanager for X that was based on the Blackbox 0.61.1 code. It is very light on resources and easy to handle but yet full of features to make an easy, and extremely fast, desktop experience.

fmt

Homepage:
Spack package:
Versions:
4.1.0, 4.0.0, 3.0.2, 3.0.1, 3.0.0
Build Dependencies:
cmake
Description:
fmt (formerly cppformat) is an open-source formatting library. It can be used as a safe alternative to printf or as a fast alternative to C++ IOStreams.

foam-extend

Homepage:
Spack package:
Versions:
4.0, 3.2, 3.1, 3.0
Build Dependencies:
scotch, paraview, flex, parmgridgen, mpi, python, zlib, cmake, parmetis, metis
Link Dependencies:
scotch, paraview, mpi, python, zlib, parmetis, metis
Description:
The Extend Project is a fork of the OpenFOAM opensource library for Computational Fluid Dynamics (CFD). This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark.

folly

Homepage:
Spack package:
Versions:
2017.06.05.00, 2016.11.14.00, 2016.11.07.00, 2016.10.31.00, 2016.10.24.00, 2016.10.17.00
Build Dependencies:
boost, m4, autoconf, double-conversion, gflags, glog, pkgconfig, automake, libevent, libtool
Link Dependencies:
boost, libevent, double-conversion, gflags, glog
Description:
Folly (acronymed loosely after Facebook Open Source Library) is a library of C++11 components designed with practicality and efficiency in mind. Folly contains a variety of core library components used extensively at Facebook. In particular, it's often a dependency of Facebook's other open source C++ efforts and place where those projects can share code.

font-adobe-100dpi

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org adobe-100dpi font.

font-adobe-75dpi

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org adobe-75dpi font.

font-adobe-utopia-100dpi

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org adobe-utopia-100dpi font.

font-adobe-utopia-75dpi

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org adobe-utopia-75dpi font.

font-adobe-utopia-type1

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
pkgconfig, mkfontscale, mkfontdir, util-macros, fontconfig, font-util
Description:
X.org adobe-utopia-type1 font.

font-alias

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
pkgconfig, util-macros, font-util
Link Dependencies:
font-util
Description:
X.org alias font.

font-arabic-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org arabic-misc font.

font-bh-100dpi

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org bh-100dpi font.

font-bh-75dpi

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org bh-75dpi font.

font-bh-lucidatypewriter-100dpi

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org bh-lucidatypewriter-100dpi font.

font-bh-lucidatypewriter-75dpi

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org bh-lucidatypewriter-75dpi font.

font-bh-ttf

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org bh-ttf font.

font-bh-type1

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
pkgconfig, mkfontscale, mkfontdir, util-macros, fontconfig, font-util
Link Dependencies:
font-util
Description:
X.org bh-type1 font.

font-bitstream-100dpi

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org bitstream-100dpi font.

font-bitstream-75dpi

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org bitstream-75dpi font.

font-bitstream-speedo

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
pkgconfig, mkfontscale, mkfontdir, util-macros, fontconfig, font-util
Link Dependencies:
font-util
Description:
X.org bitstream-speedo font.

font-bitstream-type1

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
pkgconfig, mkfontscale, mkfontdir, util-macros, fontconfig, font-util
Link Dependencies:
font-util
Description:
X.org bitstream-type1 font.

font-cronyx-cyrillic

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org cronyx-cyrillic font.

font-cursor-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org cursor-misc font.

font-daewoo-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org daewoo-misc font.

font-dec-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org dec-misc font.

font-ibm-type1

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
pkgconfig, mkfontscale, mkfontdir, util-macros, fontconfig, font-util
Link Dependencies:
font-util
Description:
X.org ibm-type1 font.

font-isas-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org isas-misc font.

font-jis-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org jis-misc font.

font-micro-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org micro-misc font.

font-misc-cyrillic

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org misc-cyrillic font.

font-misc-ethiopic

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
pkgconfig, mkfontscale, mkfontdir, util-macros, fontconfig, font-util
Link Dependencies:
font-util
Description:
X.org misc-ethiopic font.

font-misc-meltho

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
pkgconfig, mkfontscale, mkfontdir, util-macros, fontconfig, font-util
Link Dependencies:
font-util
Description:
X.org misc-meltho font.

font-misc-misc

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org misc-misc font.

font-mutt-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org mutt-misc font.

font-schumacher-misc

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org schumacher-misc font.

font-screen-cyrillic

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org screen-cyrillic font.

font-sony-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org sony-misc font.

font-sun-misc

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org sun-misc font.

font-util

Homepage:
Spack package:
Versions:
1.3.1
Build Dependencies:
pkgconfig, util-macros
Description:
X.Org font package creation/installation utilities.

font-winitzki-cyrillic

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
bdftopcf, fontconfig, mkfontdir, util-macros, font-util, pkgconfig
Link Dependencies:
font-util
Description:
X.org winitzki-cyrillic font.

font-xfree86-type1

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
pkgconfig, mkfontscale, mkfontdir, util-macros, fontconfig, font-util
Link Dependencies:
font-util
Description:
X.org xfree86-type1 font.

fontcacheproto

Homepage:
Spack package:
Versions:
0.1.3
Description:
X.org FontcacheProto protocol headers.

fontconfig

Homepage:
Spack package:
Versions:
2.12.3, 2.12.1, 2.11.1
Build Dependencies:
pkgconfig, gperf, font-util, freetype, libxml2
Link Dependencies:
font-util, freetype, libxml2
Description:
Fontconfig is a library for configuring/customizing font access

fontsproto

Homepage:
Spack package:
Versions:
2.1.3
Build Dependencies:
pkgconfig, util-macros
Description:
X Fonts Extension.

fonttosfnt

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
pkgconfig, util-macros, libfontenc, freetype, xproto
Link Dependencies:
libfontenc, freetype
Description:
Wrap a bitmap font in a sfnt (TrueType) wrapper.

fp16

Homepage:
Spack package:
Versions:
master
Description:
FP16 is a header-only library for conversion to/from half-precision floating point formats

fpc

Homepage:
Spack package:
Versions:
3.0.2
Description:
Free Pascal is a 32, 64 and 16 bit professional Pascal compiler.

fr-hit

Homepage:
Spack package:
Versions:
0.7.1-2013-02-20
Build Dependencies:
python, perl
Link Dependencies:
python, perl
Description:
An efficient algorithm for fragment recruitment for next generation sequences against microbial reference genomes.

freebayes

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
Bayesian haplotype-based genetic polymorphism discovery and genotyping.

freeglut

Homepage:
Spack package:
Versions:
3.0.0
Build Dependencies:
libx11, libxrandr, xrandr, libxi, gl, glu, inputproto, cmake
Link Dependencies:
libx11, libxrandr, xrandr, libxi, gl, glu, inputproto
Description:
FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library

freetype

Homepage:
Spack package:
Versions:
2.7.1, 2.7, 2.5.3
Build Dependencies:
pkgconfig, libpng, bzip2
Link Dependencies:
libpng, bzip2
Description:
FreeType is a freely available software library to render fonts. It is written in C, designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images) of most vector and bitmap font formats.

fseq

Homepage:
Spack package:
Versions:
1.84
Build Dependencies:
java
Run Dependencies:
java
Description:
F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags

fsl

Homepage:
Spack package:
Versions:
5.0.10
Build Dependencies:
expat, libx11, sqlite, libpng, python, mesa-glu, boost, zlib
Link Dependencies:
expat, libx11, sqlite, libpng, mesa-glu, boost, zlib
Run Dependencies:
python
Description:
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Note: A manual download is required for FSL. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

fslsfonts

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
pkgconfig, util-macros, xproto, libfs
Link Dependencies:
libfs
Description:
fslsfonts produces a list of fonts served by an X font server.

fstobdf

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies:
libx11, pkgconfig, util-macros, xproto, libfs
Link Dependencies:
libx11, libfs
Description:
The fstobdf program reads a font from a font server and prints a BDF file on the standard output that may be used to recreate the font. This is useful in testing servers, debugging font metrics, and reproducing lost BDF files.

ftgl

Homepage:
Spack package:
Versions:
2.1.2
Build Dependencies:
m4, automake, gl, glu, pkgconfig, autoconf, freetype, libtool
Link Dependencies:
freetype, gl, glu
Description:
Library to use arbitrary fonts in OpenGL applications.

funhpc

Homepage:
Spack package:
Versions:
develop, 1.3.0, 1.2.0, 1.1.1, 1.1.0, 1.0.0, 0.1.1, 0.1.0
Build Dependencies:
googletest, hwloc, mpi, jemalloc, cmake, qthreads, cereal
Link Dependencies:
googletest, hwloc, mpi, jemalloc, qthreads, cereal
Description:
FunHPC: Functional HPC Programming

fyba

Homepage:
Spack package:
Versions:
4.1.1
Build Dependencies:
autoconf, libtool, automake, m4
Description:
OpenFYBA is the source code release of the FYBA library, distributed by the National Mapping Authority of Norway (Statens kartverk) to read and write files in the National geodata standard format SOSI.

gapbs

Homepage:
Spack package:
Versions:
1.0
Description:
The GAP Benchmark Suite is intended to help graph processing research by standardizing evaluations. Fewer differences between graph processing evaluations will make it easier to compare different research efforts and quantify improvements. The benchmark not only specifies graph kernels, input graphs, and evaluation methodologies, but it also provides an optimized baseline implementation (this repo). These baseline implementations are representative of state-of-the-art performance, and thus new contributions should outperform them to demonstrate an improvement.

gapcloser

Homepage:
Spack package:
Versions:
1.12-r6
Description:
The GapCloser is designed to close the gaps emerging during the scaffolding process

gapfiller

Homepage:
Spack package:
Versions:
1.10
Build Dependencies:
perl
Run Dependencies:
perl
Description:
GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds. Note: A manual download is required for GapFiller. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html

gasnet

Homepage:
Spack package:
Versions:
1.30.0, 1.28.2, 1.28.0, 1.24.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages and libraries such as UPC, Co-Array Fortran, SHMEM, Cray Chapel, and Titanium.

gatk

Homepage:
Spack package:
Versions:
4.0.4.0, 3.8-0
Run Dependencies:
python, java, r
Description:
Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data

gaussian

Homepage:
Spack package:
Versions:
09
Description:
Gaussian is a computer program for computational chemistry

gawk

Homepage:
Spack package:
Versions:
4.1.4
Build Dependencies:
gettext, readline, mpfr, libsigsegv, gmp
Link Dependencies:
gettext, readline, mpfr, libsigsegv, gmp
Description:
If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. To write a program to do this in a language such as C or Pascal is a time- consuming inconvenience that may take many lines of code. The job is easy with awk, especially the GNU implementation: gawk. The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.

gblocks

Homepage:
Spack package:
Versions:
0.91b
Description:
Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences

gcc

Homepage:
Spack package:
Versions:
8.1.0, 7.3.0, 7.2.0, 7.1.0, 6.4.0, 6.3.0, 6.2.0, 6.1.0, 5.5.0, 5.4.0, 5.3.0, 5.2.0, 5.1.0, 4.9.4, 4.9.3, 4.9.2, 4.9.1, 4.8.5, 4.8.4, 4.7.4, 4.6.4, 4.5.4
Build Dependencies:
gmp, gnat, mpfr, binutils, zip, isl, mpc, zlib
Link Dependencies:
gmp, gnat, mpfr, binutils, isl, mpc, zlib
Test Dependencies:
expect, tcl, guile, dejagnu, autogen
Description:
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.

gccmakedep

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
pkgconfig
Description:
X.org gccmakedep utilities.

gccxml

Homepage:
Spack package:
Versions:
develop, latest
Build Dependencies:
cmake
Description:
gccxml dumps an XML description of C++ source code using an extension of the GCC C++ compiler.

gconf

Homepage:
Spack package:
Versions:
3.2.6
Build Dependencies:
libxml2, glib
Link Dependencies:
libxml2, glib
Description:
GConf is a system for storing application preferences.

gcta

Homepage:
Spack package:
Versions:
1.91.2beta_mac, 1.91.2beta
Description:
GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome- wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. GCTA currently supports the following analyses.

gdal

Homepage:
Spack package:
Versions:
2.3.0, 2.1.2, 2.0.2, 1.11.5
Build Dependencies:
zstd, poppler, giflib, opencl, xerces-c, libpng, pcre, gmake, py-setuptools, libgeotiff, curl, perl, python, unixodbc, xz, zlib, pkg-config, libxml2, geos, jasper, hdf, cryptopp, py-numpy, libiconv, qhull, java, jpeg, fyba, proj, libtool, expat, libtiff, kealib, openssl, sqlite, json-c, openjpeg, cfitsio, armadillo, hdf5, postgresql, netcdf
Link Dependencies:
zstd, poppler, libgeotiff, unixodbc, xerces-c, libpng, pcre, curl, giflib, openjpeg, perl, python, opencl, xz, libxml2, geos, jasper, hdf, postgresql, libiconv, qhull, jpeg, fyba, proj, zlib, expat, libtiff, kealib, openssl, sqlite, json-c, hdf5, cfitsio, armadillo, cryptopp, netcdf
Run Dependencies:
python, java, py-numpy, perl
Description:
GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing.

gdb

Homepage:
Spack package:
Versions:
8.1, 8.0.1, 8.0, 7.12.1, 7.11, 7.10.1, 7.10, 7.9.1, 7.9, 7.8.2
Build Dependencies:
python, texinfo, xz
Link Dependencies:
python, xz
Description:
GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes -- or what another program was doing at the moment it crashed.

gdbm

Homepage:
Spack package:
Versions:
1.14.1, 1.13, 1.12, 1.11, 1.10, 1.9.1, 1.9
Build Dependencies:
readline
Link Dependencies:
readline
Description:
GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database.

gdk-pixbuf

Homepage:
Spack package:
Versions:
2.31.2
Build Dependencies:
gettext, libpng, jpeg, libtiff, glib, pkgconfig, gobject-introspection
Link Dependencies:
gettext, libpng, glib, libtiff, jpeg, gobject-introspection
Description:
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

gdl

Homepage:
Spack package:
Versions:
0.9.8
Build Dependencies:
wx, hdf, py-numpy, hdf5, fftw, jpeg, graphicsmagick, plplot, cmake, gsl, proj, libx11, python, eigen, libice, libxinerama, readline, libxxf86vm, libsm, netcdf, pslib
Link Dependencies:
hdf, readline, libice, fftw, jpeg, graphicsmagick, plplot, wx, gsl, proj, libx11, python, eigen, hdf5, libxinerama, libxxf86vm, libsm, netcdf, pslib
Run Dependencies:
python, py-numpy
Description:
A free and open-source IDL/PV-WAVE compiler. GNU Data Language (GDL) is a free/libre/open source incremental compiler compatible with IDL and to some extent with PV-WAVE.

geant4

Homepage:
Spack package:
Versions:
10.04, 10.03.p03, 10.02.p03, 10.02.p02, 10.02.p01, 10.01.p03
Build Dependencies:
expat, mesa, xerces-c, zlib, clhep, libx11, libxmu, cmake, vecgeom, qt, motif
Link Dependencies:
expat, mesa, xerces-c, zlib, clhep, libx11, libxmu, vecgeom, qt, motif
Description:
Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

gearshifft

Homepage:
Spack package:
Versions:
0.2.1-lw
Build Dependencies:
boost, cuda, clfft, opencl, fftw, cmake
Link Dependencies:
boost, cuda, clfft, opencl, fftw
Description:
Benchmark Suite for Heterogenuous FFT Implementations

gemmlowp

Homepage:
Spack package:
Versions:
a6f29d9ac
Description:
Google low-precision matrix multiplication library

genemark-et

Homepage:
Spack package:
Versions:
4.33
Build Dependencies:
perl
Run Dependencies:
perl
Description:
Gene Prediction in Bacteria, archaea, Metagenomes and Metatranscriptomes.

genomefinisher

Homepage:
Spack package:
Versions:
1.4
Run Dependencies:
java
Description:
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references.

genometools

Homepage:
Spack package:
Versions:
1.5.9
Build Dependencies:
cairo, pango, perl
Link Dependencies:
cairo, pango
Run Dependencies:
perl
Description:
genometools is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.

geopm

Homepage:
Spack package:
Versions:
develop, 0.5.0, 0.4.0, 0.3.0, master
Build Dependencies:
m4, automake, ruby-ronn, mpi, doxygen, numactl, autoconf, hwloc, json-c, libtool
Link Dependencies:
numactl, hwloc, json-c, mpi
Run Dependencies:
py-natsort, py-matplotlib, py-numpy, py-pandas
Description:
GEOPM is an extensible power management framework targeting HPC. The GEOPM package provides libgeopm, libgeopmpolicy and applications geopmctl and geopmpolicy, as well as tools for postprocessing. GEOPM is designed to be extended for new control algorithms and new hardware power management features via its plugin infrastructure. Note: GEOPM interfaces with hardware using Model Specific Registers (MSRs). For propper usage make sure MSRs are made available directly or via the msr- safe kernel module by your administrator.

geos

Homepage:
Spack package:
Versions:
3.6.2, 3.6.1, 3.6.0, 3.5.1, 3.5.0, 3.4.3, 3.4.2, 3.4.1, 3.4.0, 3.3.9, 3.3.8, 3.3.7, 3.3.6, 3.3.5, 3.3.4, 3.3.3
Build Dependencies:
python, swig, ruby
Link Dependencies:
python, ruby
Description:
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

gettext

Homepage:
Spack package:
Versions:
0.19.8.1, 0.19.7
Build Dependencies:
bzip2, ncurses, tar, xz, libxml2, libunistring
Link Dependencies:
bzip2, ncurses, tar, xz, libxml2, libunistring
Description:
GNU internationalization (i18n) and localization (l10n) library.

gflags

Homepage:
Spack package:
Versions:
2.1.2
Build Dependencies:
cmake
Description:
The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. Online documentation available at: https://gflags.github.io/gflags/

ghost

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cuda, scotch, hwloc, zoltan, mpi, blas, cmake
Link Dependencies:
cuda, scotch, hwloc, zoltan, mpi, blas, cmake
Description:
GHOST: a General, Hybrid and Optimized Sparse Toolkit. This library provides highly optimized building blocks for implementing sparse iterative eigenvalue and linear solvers multi- and manycore clusters and on heterogenous CPU/GPU machines. For an iterative solver library using these kernels, see the phist package.

ghostscript

Homepage:
Spack package:
Versions:
9.21, 9.18
Build Dependencies:
libtiff, libxext, libpng, lcms, zlib, jpeg, pkgconfig, freetype
Link Dependencies:
libtiff, libxext, jpeg, lcms, libpng, freetype, zlib
Description:
An interpreter for the PostScript language and for PDF.

ghostscript-fonts

Homepage:
Spack package:
Versions:
8.11
Description:
Ghostscript Fonts

giflib

Homepage:
Spack package:
Versions:
5.1.4
Description:
The GIFLIB project maintains the giflib service library, which has been pulling images out of GIFs since 1989.

git

Homepage:
Spack package:
Versions:
2.17.1, 2.17.0, 2.15.1, 2.14.1, 2.13.0, 2.12.2, 2.12.1, 2.12.0, 2.11.1, 2.11.0, 2.9.3, 2.9.2, 2.9.1, 2.9.0, 2.8.4, 2.8.3, 2.8.2, 2.8.1, 2.8.0, 2.7.3, 2.7.1
Build Dependencies:
gettext, m4, tk, automake, libiconv, curl, libtool, expat, pcre, openssl, autoconf, perl, zlib
Link Dependencies:
gettext, expat, openssl, tk, libiconv, perl, pcre, curl, zlib
Description:
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

git-imerge

Homepage:
Spack package:
Versions:
1.1.0, 1.0.0
Build Dependencies:
python, py-argparse, git
Link Dependencies:
python, py-argparse, git
Description:
git-imerge: Incremental merge & rebase for git Perform a merge between two branches incrementally. If conflicts are encountered, figure out exactly which pairs of commits conflict, and present the user with one pairwise conflict at a time for resolution. git-imerge has two primary design goals: * Reduce the pain of resolving merge conflicts to its unavoidable minimum, by finding and presenting the smallest possible conflicts: those between the changes introduced by one commit from each branch. * Allow a merge to be saved, tested, interrupted, published, and collaborated on while it is in progress.

git-lfs

Homepage:
Spack package:
Versions:
2.3.0, 2.2.1, 2.0.2, 1.4.1, 1.3.1
Build Dependencies:
go
Run Dependencies:
git
Description:
Git LFS is a system for managing and versioning large files in association with a Git repository. Instead of storing the large files within the Git repository as blobs, Git LFS stores special "pointer files" in the repository, while storing the actual file contents on a Git LFS server.

gl2ps

Homepage:
Spack package:
Versions:
1.3.9
Build Dependencies:
libpng, libxau, libxcb, libsm, libxmu, cmake, libxdmcp, zlib, expat, libxi, libice, libxt, libxext, libdrm, libxxf86vm, libxdamage, libxfixes
Link Dependencies:
libpng, libxau, libxcb, libsm, libxmu, libxdmcp, zlib, expat, libxi, libice, libxt, libxext, libdrm, libxxf86vm, libxdamage, libxfixes
Description:
GL2PS is a C library providing high quality vector output for any OpenGL application.

glew

Homepage:
Spack package:
Versions:
2.0.0
Build Dependencies:
cmake, gl
Link Dependencies:
gl
Description:
The OpenGL Extension Wrangler Library.

glfmultiples

Homepage:
Spack package:
Versions:
2010-06-16
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
glfMultiples is a GLF-based variant caller for next-generation sequencing data. It takes a set of GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output.

glib

Homepage:
Spack package:
Versions:
2.56.0, 2.55.1, 2.53.1, 2.49.7, 2.49.4, 2.48.1, 2.42.1
Build Dependencies:
gettext, pkgconfig, util-linux, perl, python, libffi, pcre, zlib
Link Dependencies:
gettext, pcre, libffi, util-linux, zlib
Run Dependencies:
python, perl
Description:
GLib provides the core application building blocks for libraries and applications written in C. The GLib package contains a low-level libraries useful for providing data structure handling for C, portability wrappers and interfaces for such runtime functionality as an event loop, threads, dynamic loading and an object system.

glimmer

Homepage:
Spack package:
Versions:
3.02b
Description:
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

glm

Homepage:
Spack package:
Versions:
0.9.7.1
Build Dependencies:
cmake
Description:
OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specification

global

Homepage:
Spack package:
Versions:
6.5
Build Dependencies:
ncurses, exuberant-ctags
Link Dependencies:
ncurses
Run Dependencies:
exuberant-ctags
Description:
The Gnu Global tagging system

globalarrays

Homepage:
Spack package:
Versions:
5.7, 5.6.5, 5.6.4, 5.6.3, 5.6.2, 5.6.1, 5.6
Build Dependencies:
blas, lapack, mpi, scalapack
Link Dependencies:
blas, lapack, mpi, scalapack
Description:
Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency.

globus-toolkit

Homepage:
Spack package:
Versions:
6.0.1506371041, 6.0.1493989444
Build Dependencies:
openssl
Link Dependencies:
openssl
Description:
The Globus Toolkit is an open source software toolkit used for building grids

glog

Homepage:
Spack package:
Versions:
0.3.5, 0.3.4, 0.3.3
Build Dependencies:
cmake, gflags
Link Dependencies:
cmake, gflags
Description:
C++ implementation of the Google logging module.

gloo

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake
Description:
Gloo is a collective communications library.

glpk

Homepage:
Spack package:
Versions:
4.65, 4.61, 4.57
Build Dependencies:
gmp
Link Dependencies:
gmp
Description:
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.

glproto

Homepage:
Spack package:
Versions:
1.4.17
Build Dependencies:
pkgconfig, util-macros
Description:
OpenGL Extension to the X Window System. This extension defines a protocol for the client to send 3D rendering commands to the X server.

glvis

Homepage:
Spack package:
Versions:
develop, 3.4, 3.3, 3.2, 3.1
Build Dependencies:
libx11, libpng, fontconfig, mfem, gl, glu, libtiff, freetype
Link Dependencies:
libx11, libpng, fontconfig, mfem, gl, glu, libtiff, freetype
Description:
GLVis: an OpenGL tool for visualization of FEM meshes and functions

gmake

Homepage:
Spack package:
Versions:
4.2.1, 4.0
Build Dependencies:
gettext, guile
Link Dependencies:
gettext, guile
Description:
GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program's source files.

gmap-gsnap

Homepage:
Spack package:
Versions:
2018-03-25, 2018-02-12, 2017-06-16, 2014-12-28
Description:
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program

gmime

Homepage:
Spack package:
Versions:
2.6.23
Build Dependencies:
libgpg-error, glib
Link Dependencies:
libgpg-error, glib
Description:
GMime is a C/C++ library which may be used for the creation and parsing of messages using the Multipurpose Internet Mail Extension (MIME).

gmp

Homepage:
Spack package:
Versions:
6.1.2, 6.1.1, 6.1.0, 6.0.0a, 6.0.0, 5.1.3, 4.3.2
Build Dependencies:
autoconf, libtool, automake, m4
Description:
GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.

gmsh

Homepage:
Spack package:
Versions:
3.0.6, 3.0.1, 2.16.0, 2.15.0, 2.12.0, 2.11.0
Build Dependencies:
fltk, gmp, petsc, oce, hdf5, blas, cmake, zlib, netgen, tetgen, slepc, mpi, lapack
Link Dependencies:
fltk, gmp, petsc, oce, hdf5, blas, zlib, netgen, tetgen, slepc, mpi, lapack
Description:
Gmsh is a free 3D finite element grid generator with a built-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language.

gnat

Homepage:
Spack package:
Versions:
2016
Description:
The GNAT Ada compiler. Ada is a modern programming language designed for large, long-lived applications - and embedded systems in particular - where reliability and efficiency are essential.

gnu-prolog

Homepage:
Spack package:
Versions:
1.4.4
Description:
A free Prolog compiler with constraint solving over finite domains.

gnupg

Homepage:
Spack package:
Versions:
2.2.3, 2.1.21
Build Dependencies:
npth, libksba, libgpg-error, libgcrypt, libassuan
Link Dependencies:
npth, libksba, libgpg-error, libgcrypt, libassuan
Description:
GnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880

gnuplot

Homepage:
Spack package:
Versions:
5.2.2, 5.2.0, 5.0.7, 5.0.6, 5.0.5, 5.0.1
Build Dependencies:
libgd, libxpm, readline, pango, wx, libiconv, pkgconfig, cairo, libcerf
Link Dependencies:
libgd, libxpm, readline, pango, wx, libiconv, cairo, libcerf
Description:
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986

gnutls

Homepage:
Spack package:
Versions:
3.5.13, 3.5.10, 3.5.9, 3.3.9
Build Dependencies:
gettext, pkgconfig, nettle, zlib
Link Dependencies:
gettext, nettle, zlib
Description:
GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability.

go

Homepage:
Spack package:
Versions:
1.10.3, 1.10.2, 1.10.1, 1.9.5, 1.9.2, 1.9.1, 1.9, 1.8.3, 1.8.1, 1.8, 1.7.5, 1.7.4, 1.6.4
Build Dependencies:
git, go-bootstrap
Link Dependencies:
git
Run Dependencies:
git
Description:
The golang compiler and build environment

go-bootstrap

Homepage:
Spack package:
Versions:
1.4-bootstrap-20171003, 1.4-bootstrap-20170531, 1.4-bootstrap-20161024
Build Dependencies:
git
Link Dependencies:
git
Run Dependencies:
git
Description:
Old C-bootstrapped go to bootstrap real go

gobject-introspection

Homepage:
Spack package:
Versions:
1.49.2, 1.48.0
Build Dependencies:
sed, python, flex, cairo, bison, glib, pkgconfig
Link Dependencies:
python, cairo, glib
Description:
The GObject Introspection is used to describe the program APIs and collect them in a uniform, machine readable format.Cairo is a 2D graphics library with support for multiple output

googletest

Homepage:
Spack package:
Versions:
1.8.0, 1.7.0, 1.6.0
Build Dependencies:
cmake
Description:
Google test framework for C++. Also called gtest.

gotcha

Homepage:
Spack package:
Versions:
develop, 0.0.2, master
Build Dependencies:
cmake
Description:
C software library for shared library function wrapping, enables tools to intercept calls into shared libraries

gource

Homepage:
Spack package:
Versions:
0.44
Build Dependencies:
libpng, sdl2-image, automake, glm, pkgconfig, boost, jpeg, sdl2, libtool, glew, pcre, autoconf, freetype
Link Dependencies:
glew, libpng, sdl2-image, pcre, boost, jpeg, sdl2, freetype
Description:
Software version control visualization.

gperf

Homepage:
Spack package:
Versions:
3.0.4
Description:
GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

gperftools

Homepage:
Spack package:
Versions:
2.4, 2.3
Build Dependencies:
libunwind
Link Dependencies:
libunwind
Description:
Google's fast malloc/free implementation, especially for multi-threaded applications. Contains tcmalloc, heap-checker, heap-profiler, and cpu- profiler.

gplates

Homepage:
Spack package:
Versions:
2.0.0
Build Dependencies:
glew, boost, cgal, qwt, qt, gdal, python, mesa-glu, cmake, proj
Link Dependencies:
glew, boost, cgal, qwt, qt, gdal, python, mesa-glu, proj
Description:
GPlates is desktop software for the interactive visualisation of plate- tectonics. GPlates offers a novel combination of interactive plate- tectonic reconstructions, geographic information system (GIS) functionality and raster data visualisation. GPlates enables both the visualisation and the manipulation of plate-tectonic reconstructions and associated data through geological time.

grackle

Homepage:
Spack package:
Versions:
3.1, 3.0, 2.2, 2.0.1
Build Dependencies:
mpi, hdf5, libtool
Link Dependencies:
mpi, hdf5, libtool
Description:
Grackle is a chemistry and radiative cooling library for astrophysical simulations with interfaces for C, C++, and Fortran codes. It is a generalized and trimmed down version of the chemistry network of the Enzo simulation code

gradle

Homepage:
Spack package:
Versions:
3.4, 3.3, 3.2.1, 3.2, 3.1, 3.0, 2.14.1, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2.1, 2.2, 2.1, 2.0, 1.12, 1.11, 1.10, 1.9, 1.8, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0, 0.9.2, 0.9.1, 0.9, 0.8, 0.7
Build Dependencies:
java
Link Dependencies:
java
Description:
Gradle is an open source build automation system that builds upon the concepts of Apache Ant and Apache Maven and introduces a Groovy-based domain-specific language (DSL) instead of the XML form used by Apache Maven for declaring the project configuration. Gradle uses a directed acyclic graph ("DAG") to determine the order in which tasks can be run.

grandr

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
gtkplus, xrandr, gconf
Link Dependencies:
gtkplus, xrandr, gconf
Description:
RandR user interface using GTK+ libraries.

graph500

Homepage:
Spack package:
Versions:
3.0.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Graph500 reference implementations.

graphicsmagick

Homepage:
Spack package:
Versions:
1.3.29
Build Dependencies:
libpng, ghostscript-fonts, jpeg, libtiff, libsm, bzip2, lcms, libtool, graphviz, ghostscript, libice, xz, zlib, libxml2, jasper
Link Dependencies:
libpng, ghostscript-fonts, jpeg, libtiff, libsm, bzip2, lcms, libtool, graphviz, ghostscript, libice, xz, zlib, libxml2, jasper
Description:
GraphicsMagick is the swiss army knife of image processing. Provides a robust and efficient collection of tools and libraries which support reading, writing, and manipulating an image in over 88 major formats including important formats like DPX, GIF, JPEG, JPEG-2000, PNG, PDF, PNM, and TIFF.

graphlib

Homepage:
Spack package:
Versions:
3.0.0, 2.0.0
Build Dependencies:
cmake
Description:
Library to create, manipulate, and export graphs Graphlib.

graphmap

Homepage:
Spack package:
Versions:
0.3.0
Description:
A highly sensitive and accurate mapper for long, error-prone reads

graphviz

Homepage:
Spack package:
Versions:
2.40.1
Build Dependencies:
libgd, gtkplus, automake, pango, gts, ghostscript, python, zlib, java, libpng, fontconfig, bison, glib, pkg-config, qt, libtool, expat, flex, cairo, autoconf, swig, freetype
Link Dependencies:
libgd, gtkplus, fontconfig, pango, libpng, glib, gts, qt, zlib, expat, ghostscript, cairo, python, java, freetype
Description:
Graph Visualization Software

grib-api

Homepage:
Spack package:
Versions:
1.24.0, 1.21.0, 1.17.0, 1.16.0
Build Dependencies:
libpng, libaec, py-numpy, openjpeg, python, cmake, netcdf, jasper
Link Dependencies:
libpng, libaec, netcdf, python, openjpeg, jasper
Run Dependencies:
python, py-numpy
Description:
The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages.

groff

Homepage:
Spack package:
Versions:
1.22.3
Build Dependencies:
gawk, ghostscript, sed, gmake
Link Dependencies:
ghostscript
Description:
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. Output may be PostScript or PDF, html, or ASCII/UTF8 for display at the terminal.

gromacs

Homepage:
Spack package:
Versions:
develop, 2018.1, 2018, 2016.4, 2016.3, 5.1.4, 5.1.2
Build Dependencies:
cuda, plumed, cmake, mpi, fftw
Link Dependencies:
cuda, plumed, mpi, fftw
Description:
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is released under the GNU Lesser General Public License.

gsl

Homepage:
Spack package:
Versions:
2.4, 2.3, 2.2.1, 2.1, 2.0, 1.16
Description:
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

gslib

Homepage:
Spack package:
Versions:
1.0.2, 1.0.1, 1.0.0
Build Dependencies:
blas, mpi
Link Dependencies:
blas, mpi
Description:
Highly scalable Gather-scatter code with AMG and XXT solvers

gtkorvo-atl

Homepage:
Spack package:
Versions:
develop, 2.1
Build Dependencies:
cmake, gtkorvo-cercs-env
Link Dependencies:
gtkorvo-cercs-env
Description:
Libatl provides a library for the creation and manipulation of lists of name/value pairs using an efficient binary representation.

gtkorvo-cercs-env

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
cmake
Description:
A utility library used by some GTkorvo packages.

gtkorvo-dill

Homepage:
Spack package:
Versions:
develop, 2.1
Build Dependencies:
cmake
Description:
DILL provides instruction-level code generation, register allocation and simple optimizations for generating executable code directly into memory regions for immediate use.

gtkorvo-enet

Homepage:
Spack package:
Versions:
1.3.13
Description:
ENet reliable UDP networking library. This is a downstream branch of lsalzman's ENet. This version has expanded the client ID to handle more clients. The original is at http://github.com/lsalzman/enet.

gtkplus

Homepage:
Spack package:
Versions:
2.24.32, 2.24.31, 2.24.25
Build Dependencies:
gdk-pixbuf, pango, gobject-introspection, pkgconfig, glib, shared-mime-info, atk
Link Dependencies:
gdk-pixbuf, pango, gobject-introspection, glib, shared-mime-info, atk
Description:
The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.

gts

Homepage:
Spack package:
Versions:
121130
Build Dependencies:
glib
Link Dependencies:
glib
Description:
GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. The source code is available free of charge under the Free Software LGPL license. The code is written entirely in C with an object-oriented approach based mostly on the design of GTK+. Careful attention is paid to performance related issues as the initial goal of GTS is to provide a simple and efficient library to scientists dealing with 3D computational surface meshes.

guidance

Homepage:
Spack package:
Versions:
2.02
Build Dependencies:
ruby, perl, prank, muscle, perl-bio-perl, clustalw, mafft
Link Dependencies:
prank, muscle, ruby, clustalw, mafft
Run Dependencies:
perl-bio-perl, perl
Description:
Guidance: Accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

guile

Homepage:
Spack package:
Versions:
2.2.0, 2.0.14, 2.0.11
Build Dependencies:
gettext, gmp, readline, bdw-gc, pkgconfig, libffi, libunistring, libtool
Link Dependencies:
gettext, gmp, readline, bdw-gc, libffi, libunistring, libtool
Description:
Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.

gurobi

Homepage:
Spack package:
Versions:
7.5.2
Description:
The Gurobi Optimizer was designed from the ground up to be the fastest, most powerful solver available for your LP, QP, QCP, and MIP (MILP, MIQP, and MIQCP) problems. Note: Gurobi is licensed software. You will need to create an account on the Gurobi homepage and download Gurobi Optimizer yourself. Spack will search your current directory for the download file. Alternatively, add this file to a mirror so that Spack can find it. For instructions on how to set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html Please set the path to licence file with the following command (for bash) export GRB_LICENSE_FILE=/path/to/gurobi/license/. See section 4 in $GUROBI_HOME/docs/quickstart_linux.pdf for more details.

h5hut

Homepage:
Spack package:
Versions:
1.99.13
Build Dependencies:
mpi, hdf5
Link Dependencies:
mpi, hdf5
Description:
H5hut (HDF5 Utility Toolkit). High-Performance I/O Library for Particle- based Simulations.

h5part

Homepage:
Spack package:
Versions:
1.6.6
Build Dependencies:
mpi, hdf5
Link Dependencies:
mpi, hdf5
Description:
Portable High Performance Parallel Data Interface to HDF5

h5utils

Homepage:
Spack package:
Versions:
1.12.1
Build Dependencies:
libpng, octave, hdf5, libmatheval, hdf
Link Dependencies:
libpng, octave, hdf5, libmatheval, hdf
Description:
h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format.

h5z-zfp

Homepage:
Spack package:
Versions:
develop, 0.8.0, 0.7.0
Build Dependencies:
zfp, hdf5
Link Dependencies:
zfp, hdf5
Description:
A highly flexible floating point and integer compression plugin for the HDF5 library using ZFP compression.

hacckernels

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake
Description:
HACCKernels: A Benchmark for HACC's Particle Force Kernels. The Hardware/Hybrid Accelerated Cosmology Code (HACC), a cosmology N-body- code framework, is designed to run efficiently on diverse computing architectures and to scale to millions of cores and beyond.

hadoop

Homepage:
Spack package:
Versions:
3.1.0, 2.9.0
Run Dependencies:
java
Description:
The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.

hapcut2

Homepage:
Spack package:
Versions:
2017-07-10
Description:
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to 'just work' with excellent speed and accuracy.

hapdip

Homepage:
Spack package:
Versions:
2018.02.20
Run Dependencies:
k8
Description:
The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data.

haploview

Homepage:
Spack package:
Versions:
4.1
Build Dependencies:
java
Run Dependencies:
java
Description:
Haploview is designed to simplify and expedite the process of haplotype analysis.

harfbuzz

Homepage:
Spack package:
Versions:
1.4.6, 0.9.37
Build Dependencies:
cairo, glib, pkgconfig, icu4c, freetype, zlib
Link Dependencies:
zlib, icu4c, cairo, freetype, glib
Description:
The Harfbuzz package contains an OpenType text shaping engine.

harminv

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.

hdf

Homepage:
Spack package:
Versions:
4.2.13, 4.2.12, 4.2.11
Build Dependencies:
flex, szip, jpeg, bison, zlib
Link Dependencies:
szip, jpeg, zlib
Description:
HDF4 (also known as HDF) is a library and multi-object file format for storing and managing data between machines.

hdf5

Homepage:
Spack package:
Versions:
1.10.2, 1.10.1, 1.10.0-patch1, 1.10.0, 1.8.19, 1.8.18, 1.8.17, 1.8.16, 1.8.15, 1.8.14, 1.8.13, 1.8.12, 1.8.10
Build Dependencies:
numactl, szip, mpi, zlib
Link Dependencies:
numactl, szip, mpi, zlib
Description:
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

hdf5-blosc

Homepage:
Spack package:
Versions:
master
Build Dependencies:
c-blosc, hdf5, libtool
Link Dependencies:
hdf5, c-blosc
Description:
Blosc filter for HDF5

help2man

Homepage:
Spack package:
Versions:
1.47.4
Build Dependencies:
gettext
Description:
help2man produces simple manual pages from the '--help' and '--version' output of other commands.

hepmc

Homepage:
Spack package:
Versions:
3.0.0, 2.06.09, 2.06.08, 2.06.07, 2.06.06, 2.06.05
Build Dependencies:
cmake
Description:
The HepMC package is an object oriented, C++ event record for High Energy Physics Monte Carlo generators and simulation.

heppdt

Homepage:
Spack package:
Versions:
3.04.01, 3.04.00, 3.03.02, 3.03.01, 3.03.00, 2.06.01
Description:
The HepPID library contains translation methods for particle ID's to and from various Monte Carlo generators and the PDG standard numbering scheme. We realize that the generators adhere closely to the standard, but there are occasional differences.

hic-pro

Homepage:
Spack package:
Versions:
2.10.0
Build Dependencies:
python, py-bx-python, py-numpy, bowtie2, r, samtools, r-rcolorbrewer, py-scipy, py-pysam, r-ggplot2
Link Dependencies:
python, bowtie2, r, samtools
Run Dependencies:
py-bx-python, py-numpy, py-scipy, r-rcolorbrewer, py-pysam, r-ggplot2
Description:
HiC-Pro is a package designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps

highfive

Homepage:
Spack package:
Versions:
1.5, 1.2, 1.1, 1.0
Build Dependencies:
boost, cmake, hdf5
Link Dependencies:
boost, hdf5
Description:
HighFive - Header only C++ HDF5 interface

highwayhash

Homepage:
Spack package:
Versions:
dfcb97
Description:
Strong (well-distributed and unpredictable) hashes: - Portable implementation of SipHash - HighwayHash, a 5x faster SIMD hash with security claims

hiop

Homepage:
Spack package:
Versions:
0.1
Build Dependencies:
blas, lapack, cmake, mpi
Link Dependencies:
blas, lapack, mpi
Description:
HiOp is an optimization solver for solving certain mathematical optimization problems expressed as nonlinear programming problems. HiOp is a lightweight HPC solver that leverages application's existing data parallelism to parallelize the optimization iterations by using specialized linear algebra kernels.

hisat2

Homepage:
Spack package:
Versions:
2.1.0
Description:
HISAT2 is a fast and sensitive alignment program for mapping next- generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome).

hisea

Homepage:
Spack package:
Versions:
2017.12.26
Build Dependencies:
boost
Link Dependencies:
boost
Description:
HISEA is an efficient all-vs-all long read aligner for SMRT sequencing data. Its algorithm is designed to produce highest alignment sensitivity among others.

hmmer

Homepage:
Spack package:
Versions:
3.1b2, 3.0, 2.4i, 2.3.2, 2.3.1
Build Dependencies:
gsl, mpi
Link Dependencies:
gsl, mpi
Description:
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

hoomd-blue

Homepage:
Spack package:
Versions:
develop, 2.2.2, 2.1.6
Build Dependencies:
cuda, python, py-numpy, mpi, pkgconfig, doxygen, cmake
Link Dependencies:
cuda, python, mpi
Run Dependencies:
py-numpy
Description:
HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. You define particle initial conditions and interactions in a high-level python script. Then tell HOOMD-blue how you want to execute the job and it takes care of the rest. Python job scripts give you unlimited flexibility to create custom initialization routines, control simulation parameters, and perform in situ analysis.

hpccg

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Proxy Application. Intended to be the 'best approximation to an unstructured implicit finite element or finite volume application in 800 lines or fewer.'

hpctoolkit

Homepage:
Spack package:
Versions:
2017.06, master
Build Dependencies:
papi, mpi, hpctoolkit-externals
Link Dependencies:
papi, mpi, hpctoolkit-externals
Description:
HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur.

hpctoolkit-externals

Homepage:
Spack package:
Versions:
2017.06, master
Description:
HPCToolkit performance analysis tool has many prerequisites and HpctoolkitExternals package provides all these prerequisites.

hpgmg

Homepage:
Spack package:
Versions:
develop, 0.3, a0a5510df23b
Build Dependencies:
cuda, python, petsc, mpi
Link Dependencies:
cuda, petsc, mpi
Description:
HPGMG implements full multigrid (FMG) algorithms using finite-volume and finite-element methods. Different algorithmic variants adjust the arithmetic intensity and architectural properties that are tested. These FMG methods converge up to discretization error in one F-cycle, thus may be considered direct solvers. An F-cycle visits the finest level a total of two times, the first coarsening (8x smaller) 4 times, the second coarsening 6 times, etc.

hpl

Homepage:
Spack package:
Versions:
2.2
Build Dependencies:
blas, mpi
Link Dependencies:
blas, mpi
Description:
HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.

hpx

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
boost, cmake, hwloc
Link Dependencies:
boost, hwloc
Description:
C++ runtime system for parallel and distributed applications.

hpx5

Homepage:
Spack package:
Versions:
4.1.0, 4.0.0, 3.1.0, 2.0.0, 1.3.0, 1.2.0, 1.1.0, 1.0.0
Build Dependencies:
m4, opencl, hwloc, mpi, pkgconfig, automake, libtool, metis, jemalloc, autoconf
Link Dependencies:
opencl, hwloc, jemalloc, mpi, metis
Description:
The HPX-5 Runtime System. HPX-5 (High Performance ParalleX) is an open source, portable, performance-oriented runtime developed at CREST (Indiana University). HPX-5 provides a distributed programming model allowing programs to run unmodified on systems from a single SMP to large clusters and supercomputers with thousands of nodes. HPX-5 supports a wide variety of Intel and ARM platforms. It is being used by a broad range of scientific applications enabling scientists to write code that performs and scales better than contemporary runtimes.

hsakmt

Homepage:
Spack package:
Versions:
1.0.0
Description:
hsakmt is a thunk library that provides a userspace interface to amdkfd (AMD's HSA Linux kernel driver). It is the HSA equivalent of libdrm.

hstr

Homepage:
Spack package:
Versions:
1.22
Build Dependencies:
m4, ncurses, readline, automake, libtool, autoconf
Link Dependencies:
ncurses, readline
Description:
hstr(hh) is a shell history suggest box for Bash and Zsh, which enables easy viewing, searching and using your command history.

htop

Homepage:
Spack package:
Versions:
2.0.2
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
htop is an interactive text-mode process viewer for Unix systems.

htslib

Homepage:
Spack package:
Versions:
1.8, 1.7, 1.6, 1.4, 1.3.1, 1.2
Build Dependencies:
m4, bzip2, autoconf, automake, xz, zlib, libtool
Link Dependencies:
m4, bzip2, autoconf, automake, xz, zlib, libtool
Description:
C library for high-throughput sequencing data formats.

httpie

Homepage:
Spack package:
Versions:
0.9.9, 0.9.8
Build Dependencies:
py-pygments, py-setuptools, py-requests, py-pysocks, python, py-argparse
Link Dependencies:
python
Run Dependencies:
py-pygments, py-setuptools, py-requests, py-pysocks, python, py-argparse
Description:
Modern command line HTTP client.

hub

Homepage:
Spack package:
Versions:
2.2.3, 2.2.2, 2.2.1, 2.2.0, 1.12.4, head
Build Dependencies:
go
Link Dependencies:
go
Description:
The github git wrapper

hunspell

Homepage:
Spack package:
Versions:
1.6.0
Build Dependencies:
autoconf, libtool, automake, m4
Description:
The most popular spellchecking library (sez the author...).

hwloc

Homepage:
Spack package:
Versions:
2.0.1, 2.0.0, 1.11.9, 1.11.8, 1.11.7, 1.11.6, 1.11.5, 1.11.4, 1.11.3, 1.11.2, 1.11.1, 1.9
Build Dependencies:
cuda, pkgconfig, libpciaccess, cairo, numactl, libxml2
Link Dependencies:
cuda, numactl, libpciaccess, cairo, libxml2
Description:
The Hardware Locality (hwloc) software project. The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.

hybpiper

Homepage:
Spack package:
Versions:
1.2.0
Build Dependencies:
blast-plus, bwa, spades, parallel, python, py-biopython, samtools, exonerate
Link Dependencies:
bwa, spades, samtools, blast-plus, parallel, exonerate
Run Dependencies:
python, py-biopython
Description:
HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads

hydra

Homepage:
Spack package:
Versions:
3.2
Description:
Hydra is a process management system for starting parallel jobs. Hydra is designed to natively work with existing launcher daemons (such as ssh, rsh, fork), as well as natively integrate with resource management systems (such as slurm, pbs, sge).

hydrogen

Homepage:
Spack package:
Versions:
develop, 0.99
Build Dependencies:
cuda, gmp, mpfr, mpi, mpc, intel-mkl, cmake, cudnn, openblas, veclibfort, netlib-lapack, essl, lapack, scalapack, cub
Link Dependencies:
cuda, gmp, mpfr, mpi, mpc, intel-mkl, cudnn, openblas, veclibfort, netlib-lapack, essl, lapack, scalapack, cub
Description:
Hydrogen: Distributed-memory dense and sparse-direct linear algebra and optimization library. Based on the Elemental library.

hypre

Homepage:
Spack package:
Versions:
develop, 2.14.0, 2.13.0, 2.12.1, 2.11.2, 2.11.1, 2.10.1, 2.10.0b, xsdk-0.2.0
Build Dependencies:
blas, lapack, mpi
Link Dependencies:
blas, lapack, mpi
Description:
Hypre is a library of high performance preconditioners that features parallel multigrid methods for both structured and unstructured grid problems.

i3

Homepage:
Spack package:
Versions:
4.14.1
Build Dependencies:
m4, libxkbcommon, libev, automake, pango, yajl, startup-notification, xcb-util-wm, libtool, autoconf, cairo, xcb-util-keysyms, xcb-util-cursor, pkg-config, xcb-util-xrm
Link Dependencies:
libxkbcommon, libev, cairo, pango, xcb-util-keysyms, xcb-util-cursor, yajl, xcb-util-wm, startup-notification, xcb-util-xrm
Description:
i3, improved tiling wm. i3 is a tiling window manager, completely written from scratch. The target platforms are GNU/Linux and BSD operating systems, our code is Free and Open Source Software (FOSS) under the BSD license. i3 is primarily targeted at advanced users and developers.

ibmisc

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
googletest, py-numpy, blitz, cmake, proj, boost, udunits2, netcdf-cxx4, py-cython, python, doxygen, eigen, everytrace
Link Dependencies:
boost, udunits2, netcdf-cxx4, python, blitz, eigen, everytrace, proj
Run Dependencies:
py-numpy, py-cython
Description:
Misc. reusable utilities used by IceBin.

iceauth

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
pkgconfig, util-macros, xproto, libice
Link Dependencies:
libice
Description:
The iceauth program is used to edit and display the authorization information used in connecting with ICE. It operates very much like the xauth program for X11 connection authentication records.

icedtea

Homepage:
Spack package:
Versions:
3.4.0
Build Dependencies:
gtkplus, giflib, lcms, gmake, libxcomposite, libxext, libxinerama, jdk, xproto, libxtst, libxau, libpng, wget, alsa-lib, jpeg, pkgconfig, cups, libxdmcp, zlib, libx11, libxi, libxt, libxrender, freetype
Link Dependencies:
gtkplus, libpng, giflib, alsa-lib, jpeg, lcms, cups, libxdmcp, libxcomposite, libx11, freetype, libxext, libxt, libxinerama, libxi, libxrender, zlib, xproto, libxtst, libxau
Description:
The IcedTea project provides a harness to build the source code from http://openjdk.java.net using Free Software build tools and adds a number of key features to the upstream OpenJDK codebase. IcedTea requires an existing IcedTea or OpenJDK install to build.

icet

Homepage:
Spack package:
Versions:
develop, 2.1.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
The Image Composition Engine for Tiles (IceT) is a high-performance sort-last parallel rendering library.

ico

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libx11, pkgconfig, util-macros, xproto
Link Dependencies:
libx11
Description:
ico is a simple animation program that may be used for testing various X11 operations and extensions. It displays a wire-frame rotating polyhedron, with hidden lines removed, or a solid-fill polyhedron with hidden faces removed.

icu4c

Homepage:
Spack package:
Versions:
60.1, 58.2, 57.1
Description:
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU4C is the C/C++ interface.

id3lib

Homepage:
Spack package:
Versions:
3.8.3
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Library for manipulating ID3v1 and ID3v2 tags

idba

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
m4, autoconf, automake, libtool
Description:
IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.

igraph

Homepage:
Spack package:
Versions:
0.7.1
Build Dependencies:
libxml2
Link Dependencies:
libxml2
Description:
igraph is a library for creating and manipulating graphs.

igv

Homepage:
Spack package:
Versions:
2.4.5, 2.3.50
Build Dependencies:
jdk, ant
Run Dependencies:
jdk
Description:
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

igvtools

Homepage:
Spack package:
Versions:
2.3.98
Build Dependencies:
java
Link Dependencies:
java
Description:
IGVTools suite of command-line utilities for preprocessing data files

ilmbase

Homepage:
Spack package:
Versions:
2.2.0, 2.1.0, 2.0.1, 1.0.2, 0.9.0
Description:
OpenEXR ILM Base libraries (high dynamic-range image file format)

image-magick

Homepage:
Spack package:
Versions:
7.0.5-9, 7.0.2-7, 7.0.2-6
Build Dependencies:
libpng, ghostscript, fontconfig, pango, ghostscript-fonts, jpeg, libtiff, freetype, libtool
Link Dependencies:
libpng, ghostscript, fontconfig, pango, ghostscript-fonts, jpeg, libtiff, freetype
Description:
ImageMagick is a software suite to create, edit, compose, or convert bitmap images.

imake

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
pkgconfig, xproto
Description:
The imake build system.

imp

Homepage:
Spack package:
Versions:
2.8.0
Build Dependencies:
boost, hdf5, python, cmake, swig, eigen
Link Dependencies:
boost, python, swig, eigen, hdf5
Description:
IMP, the Integrative Modeling Platform.

impute2

Homepage:
Spack package:
Versions:
2.3.2
Description:
IMPUTE2 is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009.

infernal

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).

inputproto

Homepage:
Spack package:
Versions:
2.3.2
Build Dependencies:
pkgconfig, util-macros
Description:
X Input Extension. This extension defines a protocol to provide additional input devices management such as graphic tablets.

intel

Homepage:
Spack package:
Versions:
18.0.1, 18.0.0, 17.0.4, 17.0.3, 17.0.2, 17.0.1, 17.0.0, 16.0.4, 16.0.3, 16.0.2
Description:
Intel Compilers.

intel-daal

Homepage:
Spack package:
Versions:
2018.2.199, 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 2016.3.210, 2016.2.181
Description:
Intel Data Analytics Acceleration Library.

intel-gpu-tools

Homepage:
Spack package:
Versions:
1.16
Build Dependencies:
pkgconfig, libpciaccess, flex, cairo, bison, glib, util-macros, libdrm, python
Link Dependencies:
libpciaccess, libdrm, cairo, glib
Description:
Intel GPU Tools is a collection of tools for development and testing of the Intel DRM driver. There are many macro-level test suites that get used against the driver, including xtest, rendercheck, piglit, and oglconform, but failures from those can be difficult to track down to kernel changes, and many require complicated build procedures or specific testing environments to get useful results. Therefore, Intel GPU Tools includes low-level tools and tests specifically for development and testing of the Intel DRM Driver.

intel-ipp

Homepage:
Spack package:
Versions:
2018.2.199, 2018.1.163, 2018.0.128, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 9.0.3.210
Description:
Intel Integrated Performance Primitives.

intel-mkl

Homepage:
Spack package:
Versions:
2018.2.199, 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 2017.0.098, 11.3.3.210, 11.3.2.181
Description:
Intel Math Kernel Library.

intel-mkl-dnn

Homepage:
Spack package:
Versions:
0.11, 0.10, 0.9
Build Dependencies:
intel-mkl, cmake
Link Dependencies:
intel-mkl
Description:
Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL- DNN).

intel-mpi

Homepage:
Spack package:
Versions:
2018.2.199, 2018.1.163, 2018.0.128, 2017.4.239, 2017.3.196, 2017.2.174, 2017.1.132, 5.1.3.223
Description:
Intel MPI

intel-parallel-studio

Homepage:
Spack package:
Versions:
professional.2018.1, professional.2018.0, professional.2017.4, professional.2017.3, professional.2017.2, professional.2017.1, professional.2017.0, professional.2016.4, professional.2016.3, professional.2016.2, professional.2015.6, composer.2018.1, composer.2018.0, composer.2017.4, composer.2017.3, composer.2017.2, composer.2017.1, composer.2017.0, composer.2016.4, composer.2016.3, composer.2016.2, composer.2015.6, cluster.2018.1, cluster.2018.0, cluster.2017.5, cluster.2017.4, cluster.2017.3, cluster.2017.2, cluster.2017.1, cluster.2017.0, cluster.2016.4, cluster.2016.3, cluster.2016.2, cluster.2015.6
Description:
Intel Parallel Studio.

intel-tbb

Homepage:
Spack package:
Versions:
2018.4, 2018.3, 2018.2, 2018.1, 2018, 2017.8, 2017.7, 2017.6, 2017.5, 2017.4, 2017.3, 2017.2, 2017.1, 2017, 4.4.6, 4.4.5, 4.4.4, 4.4.3, 4.4.2, 4.4.1, 4.4
Build Dependencies:
cmake
Description:
Widely used C++ template library for task parallelism. Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.

intel-xed

Homepage:
Spack package:
Versions:
2018.02.14
Build Dependencies:
python
Description:
The Intel X86 Encoder Decoder library for encoding and decoding x86 machine instructions (64- and 32-bit). Also includes libxed-ild, a lightweight library for decoding the length of an instruction.

intltool

Homepage:
Spack package:
Versions:
0.51.0
Build Dependencies:
perl-xml-parser, perl
Run Dependencies:
perl-xml-parser, perl
Description:
intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

ior

Homepage:
Spack package:
Versions:
3.0.1
Build Dependencies:
m4, automake, hdf5, mpi, autoconf, parallel-netcdf, libtool
Link Dependencies:
mpi, hdf5, parallel-netcdf
Description:
The IOR software is used for benchmarking parallel file systems using POSIX, MPI-IO, or HDF5 interfaces.

iozone

Homepage:
Spack package:
Versions:
3_465
Description:
IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported to many machines and runs under many operating systems.

ipopt

Homepage:
Spack package:
Versions:
3.12.9, 3.12.8, 3.12.7, 3.12.6, 3.12.5, 3.12.4, 3.12.3, 3.12.2, 3.12.1, 3.12.0
Build Dependencies:
coinhsl, pkgconfig, blas, lapack, mumps, metis
Link Dependencies:
blas, metis, lapack, mumps, coinhsl
Description:
Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.

isaac

Homepage:
Spack package:
Versions:
develop, 1.4.0, 1.3.3, 1.3.2, 1.3.1, 1.3.0, master
Build Dependencies:
cmake
Link Dependencies:
jansson, boost, cuda, mpi, icet, jpeg
Description:
In Situ Animation of Accelerated Computations: Header-Only Library

isaac-server

Homepage:
Spack package:
Versions:
develop, 1.4.0, 1.3.3, 1.3.2, 1.3.1, 1.3.0, master
Build Dependencies:
cmake
Link Dependencies:
jansson, boost, libwebsockets, jpeg
Description:
In Situ Animation of Accelerated Computations: Server

isl

Homepage:
Spack package:
Versions:
0.19, 0.18, 0.14
Build Dependencies:
gmp
Link Dependencies:
gmp
Description:
isl (Integer Set Library) is a thread-safe C library for manipulating sets and relations of integer points bounded by affine constraints.

itstool

Homepage:
Spack package:
Versions:
2.0.2, 2.0.1, 2.0.0, 1.2.0
Description:
ITS Tool allows you to translate your XML documents with PO files, using rules from the W3C Internationalization Tag Set (ITS) to determine what to translate and how to separate it into PO file messages.

itsx

Homepage:
Spack package:
Versions:
1.0.11
Build Dependencies:
hmmer, perl
Link Dependencies:
hmmer
Run Dependencies:
perl
Description:
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing

jags

Homepage:
Spack package:
Versions:
4.3.0, 4.2.0
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS

jansson

Homepage:
Spack package:
Versions:
2.9
Build Dependencies:
cmake
Description:
Jansson is a C library for encoding, decoding and manipulating JSON data.

jasper

Homepage:
Spack package:
Versions:
2.0.14, 1.900.1
Build Dependencies:
cmake, gl, jpeg
Link Dependencies:
gl, jpeg
Description:
Library for manipulating JPEG-2000 images

jbigkit

Homepage:
Spack package:
Versions:
2.1, 1.6
Description:
JBIG-Kit is a software implementation of the JBIG1 data compression standard.

jchronoss

Homepage:
Spack package:
Versions:
1.2, 1.1.1, 1.1, 1.0
Build Dependencies:
libev, cmake, libxml2, libwebsockets, ncurses
Link Dependencies:
libev, ncurses, libxml2, libwebsockets
Description:
JCHRONOSS aims to help HPC application testing process to scale as much as the application does.

jdk

Homepage:
Spack package:
Versions:
8u172-b11, 8u141-b15, 8u131-b11, 8u92-b14, 8u73-b02, 8u66-b17, 7u80-b0
Description:
The Java Development Kit (JDK) released by Oracle Corporation in the form of a binary product aimed at Java developers.

jellyfish

Homepage:
Spack package:
Versions:
2.2.7, 1.1.11
Build Dependencies:
python, perl
Run Dependencies:
python, perl
Description:
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.

jemalloc

Homepage:
Spack package:
Versions:
4.5.0, 4.4.0, 4.3.1, 4.2.1, 4.2.0, 4.1.0, 4.0.4
Description:
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.

jmol

Homepage:
Spack package:
Versions:
14.8.0
Run Dependencies:
java
Description:
Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.

jq

Homepage:
Spack package:
Versions:
1.5
Build Dependencies:
oniguruma, bison
Link Dependencies:
oniguruma
Description:
jq is a lightweight and flexible command-line JSON processor.

json-c

Homepage:
Spack package:
Versions:
0.13.1, 0.12.1, 0.11
Build Dependencies:
autoconf
Description:
A JSON implementation in C.

json-cwx

Homepage:
Spack package:
Versions:
0.12
Build Dependencies:
autoconf, libtool, automake, m4
Description:
JSON-C with Extensions

json-glib

Homepage:
Spack package:
Versions:
1.2.8
Build Dependencies:
glib
Link Dependencies:
glib
Description:
JSON-GLib is a library for reading and parsing JSON using GLib and GObject data types and API.

jsoncpp

Homepage:
Spack package:
Versions:
1.7.3
Build Dependencies:
cmake
Test Dependencies:
python
Description:
JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.

judy

Homepage:
Spack package:
Versions:
1.0.5
Description:
Judy: General-purpose dynamic array, associative array and hash-trie.

julia

Homepage:
Spack package:
Versions:
0.6.2, 0.5.2, 0.5.1, 0.5.0, 0.4.7, 0.4.6, 0.4.5, 0.4.3, release-0.5, release-0.4, master
Build Dependencies:
m4, openssl, binutils, python, cmake, curl, git
Link Dependencies:
binutils, openssl, python, cmake, curl, git
Run Dependencies:
py-matplotlib, hdf5, mpi
Description:
The Julia Language: A fresh approach to technical computing

k8

Homepage:
Spack package:
Versions:
0.2.4
Run Dependencies:
zlib
Description:
K8 is a Javascript shell based on Google's V8 Javascript engine.

kahip

Homepage:
Spack package:
Versions:
develop, 2.00
Build Dependencies:
scons, argtable, mpi
Link Dependencies:
argtable, mpi
Description:
KaHIP - Karlsruhe High Quality Partitioning - is a family of graph partitioning programs. It includes KaFFPa (Karlsruhe Fast Flow Partitioner), which is a multilevel graph partitioning algorithm, in its variants Strong, Eco and Fast, KaFFPaE (KaFFPaEvolutionary) which is a parallel evolutionary algorithm that uses KaFFPa to provide combine and mutation operations, as well as KaBaPE which extends the evolutionary algorithm. Moreover, specialized techniques are included to partition road networks (Buffoon), to output a vertex separator from a given partition or techniques geared towards efficient partitioning of social networks.

kaiju

Homepage:
Spack package:
Versions:
1.6.2
Run Dependencies:
py-htseq, perl-io-compress
Description:
Kaiju is a program for the taxonomic classification of high-throughput sequencing reads.

kaks-calculator

Homepage:
Spack package:
Versions:
2.0
Description:
KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences.

kaldi

Homepage:
Spack package:
Versions:
master, c024e8
Build Dependencies:
cuda, openfst, blas
Link Dependencies:
cuda, openfst, blas
Run Dependencies:
sph2pipe, sctk, speex
Description:
Kaldi is a toolkit for speech recognition written in C++ and licensed under the Apache License v2.0. Kaldi is intended for use by speech recognition researchers.

kallisto

Homepage:
Spack package:
Versions:
0.43.1
Build Dependencies:
mpich, cmake, hdf5, zlib
Link Dependencies:
mpich, hdf5, zlib
Description:
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.

kbproto

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
pkgconfig, util-macros
Description:
X Keyboard Extension. This extension defines a protcol to provide a number of new capabilities and controls for text keyboards.

kdiff3

Homepage:
Spack package:
Versions:
0.9.98
Build Dependencies:
qt
Link Dependencies:
qt
Description:
Compare and merge 2 or 3 files or directories.

kealib

Homepage:
Spack package:
Versions:
develop, 1.4.7
Build Dependencies:
cmake, hdf5
Link Dependencies:
hdf5
Description:
An HDF5 Based Raster File Format. KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software. Development work on this project has been funded by Landcare Research.

kentutils

Homepage:
Spack package:
Versions:
302.1
Build Dependencies:
libpng, openssl, mariadb
Link Dependencies:
libpng, openssl, mariadb
Description:
Jim Kent command line bioinformatic utilities

kmergenie

Homepage:
Spack package:
Versions:
1.7044
Build Dependencies:
python, py-setuptools, r, zlib
Link Dependencies:
zlib
Run Dependencies:
python, py-setuptools, r
Description:
KmerGenie estimates the best k-mer length for genome de novo assembly.

kokkos

Homepage:
Spack package:
Versions:
develop, 2.5.00, 2.04.11, 2.04.04, 2.04.00, 2.03.13, 2.03.05, 2.03.00, 2.02.15, 2.02.07
Build Dependencies:
cuda, hwloc, qthreads
Link Dependencies:
cuda, hwloc, qthreads
Description:
Kokkos implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms.

kraken

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
perl, jellyfish
Link Dependencies:
jellyfish
Run Dependencies:
perl
Description:
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

krb5

Homepage:
Spack package:
Versions:
1.16.1
Build Dependencies:
openssl
Link Dependencies:
openssl
Description:
Network authentication protocol

krims

Homepage:
Spack package:
Versions:
develop, 0.2.1
Build Dependencies:
cmake
Description:
The bucket of Krimskrams every C or C++ project needs

kripke

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Kripke is a simple, scalable, 3D Sn deterministic particle transport proxy/mini app.

kvasir-mpl

Homepage:
Spack package:
Versions:
develop
Description:
Kvasir metaprogramming library

laghos

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
mfem
Link Dependencies:
mfem
Description:
Laghos (LAGrangian High-Order Solver) is a CEED miniapp that solves the time-dependent Euler equations of compressible gas dynamics in a moving Lagrangian frame using unstructured high-order finite element spatial discretization and explicit high-order time-stepping.

lammps

Homepage:
Spack package:
Versions:
develop, 20180316, 20180222, 20170922, 20170901
Build Dependencies:
voropp, lapack, mpi, fftw, python, blas, latte, cmake, hdf5, netcdf
Link Dependencies:
voropp, lapack, mpi, fftw, python, blas, latte, hdf5, netcdf
Description:
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/spack/spack/pull/5342 for a detailed discussion.

last

Homepage:
Spack package:
Versions:
869
Description:
LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads).

latte

Homepage:
Spack package:
Versions:
develop, 1.1.1, 1.0.1
Build Dependencies:
blas, lapack, cmake, mpi, qmd-progress
Link Dependencies:
blas, lapack, mpi, qmd-progress
Description:
Open source density functional tight binding molecular dynamics.

launchmon

Homepage:
Spack package:
Versions:
1.0.2
Build Dependencies:
boost, autoconf, libgcrypt, automake, libtool, libgpg-error, spectrum-mpi
Link Dependencies:
boost, spectrum-mpi, libgpg-error, libgcrypt, elf
Description:
Software infrastructure that enables HPC run-time tools to co-locate tool daemons with a parallel job.

lazyten

Homepage:
Spack package:
Versions:
develop, 0.4.1
Build Dependencies:
krims, arpack-ng, blas, armadillo, lapack, cmake
Link Dependencies:
armadillo, krims, lapack, arpack-ng, blas
Description:
Lightweight linear algebra library based on lazy matrices

lbann

Homepage:
Spack package:
Versions:
develop, 0.93, 0.92, 0.91
Build Dependencies:
cuda, cnpy, hwloc, cub, hydrogen, cmake, cudnn, opencv, protobuf, mpi, elemental, nccl
Link Dependencies:
cuda, cnpy, hwloc, cub, mpi, protobuf, hydrogen, nccl, elemental, cudnn, opencv
Description:
LBANN: Livermore Big Artificial Neural Network Toolkit. A distributed memory, HPC-optimized, model and data parallel training toolkit for deep neural networks.

lbxproxy

Homepage:
Spack package:
Versions:
1.0.3
Build Dependencies:
libx11, pkgconfig, liblbxutil, libxext, xtrans, libice, util-macros, bigreqsproto, xproxymanagementprotocol
Link Dependencies:
libx11, liblbxutil, libxext, libice
Description:
lbxproxy accepts client connections, multiplexes them over a single connection to the X server, and performs various optimizations on the X protocol to make it faster over low bandwidth and/or high latency connections. Note that the X server source from X.Org no longer supports the LBX extension, so this program is only useful in connecting to older X servers.

lcals

Homepage:
Spack package:
Versions:
1.0.2
Description:
LCALS ("Livermore Compiler Analysis Loop Suite") is a collection of loop kernels based, in part, on historical "Livermore Loops" benchmarks (See the 1986 technical report: "The Livermore Fortran Kernels: A Computer Test of the Numerical Performance Range", by Frank H. McMahon, UCRL-53745.). The suite contains facilities to generate timing statistics and reports.

lcms

Homepage:
Spack package:
Versions:
2.9, 2.8, 2.6
Build Dependencies:
libtiff, jpeg, zlib
Link Dependencies:
libtiff, jpeg, zlib
Description:
Little cms is a color management library. Implements fast transforms between ICC profiles. It is focused on speed, and is portable across several platforms (MIT license).

ldc

Homepage:
Spack package:
Versions:
1.3.0
Build Dependencies:
binutils, curl, ldc-bootstrap, libconfig, cmake, libedit, llvm, zlib
Link Dependencies:
binutils, curl, ldc-bootstrap, libconfig, libedit, llvm, zlib
Run Dependencies:
binutils
Description:
The LDC project aims to provide a portable D programming language compiler with modern optimization and code generation capabilities. LDC is fully Open Source; the parts of the code not taken/adapted from other projects are BSD-licensed (see the LICENSE file for details). Consult the D wiki for further information: http://wiki.dlang.org/LDC

ldc-bootstrap

Homepage:
Spack package:
Versions:
0.17.4
Build Dependencies:
binutils, curl, libconfig, cmake, libedit, llvm, zlib
Link Dependencies:
binutils, llvm, libconfig, libedit, curl, zlib
Description:
The LDC project aims to provide a portable D programming language compiler with modern optimization and code generation capabilities. LDC is fully Open Source; the parts of the code not taken/adapted from other projects are BSD-licensed (see the LICENSE file for details). Consult the D wiki for further information: http://wiki.dlang.org/LDC This old version of the compiler is needed to bootstrap newer ones.

legion

Homepage:
Spack package:
Versions:
develop, 18.05.0, 18.02.0, 17.10.0, 17.08.0, 17.02.0
Build Dependencies:
cmake, gasnet
Link Dependencies:
gasnet
Description:
Legion is a data-centric parallel programming system for writing portable high performance programs targeted at distributed heterogeneous architectures. Legion presents abstractions which allow programmers to describe properties of program data (e.g. independence, locality). By making the Legion programming system aware of the structure of program data, it can automate many of the tedious tasks programmers currently face, including correctly extracting task- and data-level parallelism and moving data around complex memory hierarchies. A novel mapping interface provides explicit programmer controlled placement of data in the memory hierarchy and assignment of tasks to processors in a way that is orthogonal to correctness, thereby enabling easy porting and tuning of Legion applications to new architectures.

leveldb

Homepage:
Spack package:
Versions:
1.20, 1.18
Build Dependencies:
snappy
Link Dependencies:
snappy
Description:
LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.

lftp

Homepage:
Spack package:
Versions:
4.8.1, 4.7.7, 4.6.4
Build Dependencies:
expat, ncurses, readline, openssl, libiconv, zlib
Link Dependencies:
expat, ncurses, readline, openssl, libiconv, zlib
Description:
LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).

libaec

Homepage:
Spack package:
Versions:
1.0.2, 1.0.1, 1.0.0
Build Dependencies:
cmake
Description:
Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). It implements Golomb-Rice compression method under the BSD license and includes a free drop-in replacement for the SZIP library.

libaio

Homepage:
Spack package:
Versions:
0.3.110
Description:
This is the linux native Asynchronous I/O interface library.

libapplewm

Homepage:
Spack package:
Versions:
1.4.1
Build Dependencies:
libx11, pkgconfig, libxext, util-macros, applewmproto, xextproto
Link Dependencies:
libx11, libxext
Description:
AppleWM is a simple library designed to interface with the Apple-WM extension. This extension allows X window managers to better interact with the Mac OS X Aqua user interface when running X11 in a rootless mode.

libarchive

Homepage:
Spack package:
Versions:
3.3.2, 3.2.1, 3.1.2, 3.1.1, 3.1.0
Build Dependencies:
expat, lzma, bzip2, openssl, xz, lz4, lzo, nettle, libxml2, zlib
Link Dependencies:
expat, lzma, bzip2, openssl, xz, lz4, lzo,