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 2859 mainline packages:

abinit mumps r-car
abyss munge r-caret
accfft muparser r-category
ack muscle r-catools
activeharmony muse r-cdcfluview
adept-utils muster r-cellranger
adios mvapich2 r-cghflasso
adios2 mxml r-checkmate
adlbx mxnet r-checkpoint
adol-c nag r-chemometrics
aegean nalu r-chron
aida nalu-wind r-circlize
albany namd r-class
albert nano r-classint
alglib nanoflann r-cli
allinea-forge nanopb r-clipr
allinea-reports nasm r-cluster
allpaths-lg nauty r-clusterprofiler
alquimia ncbi-magicblast r-cner
alsa-lib ncbi-rmblastn r-coda
amg ncbi-toolkit r-codetools
amg2013 nccl r-coin
amp nccmp r-colorspace
ampliconnoise ncdu r-complexheatmap
amrex ncftp r-corpcor
amrvis ncl r-corrplot
andi nco r-covr
angsd ncurses r-cowplot
ant ncview r-crayon
antlr ndiff r-crosstalk
ants nek5000 r-ctc
ape nekbone r-cubature
aperture-photometry nekcem r-cubist
apex nektar r-curl
apple-libunwind neovim r-data-table
applewmproto nest r-dbi
appres netcdf r-dbplyr
apr netcdf-cxx r-delayedarray
apr-util netcdf-cxx4 r-deldir
aragorn netcdf-fortran r-dendextend
archer netgauge r-deoptim
argobots netgen r-deoptimr
argp-standalone netlib-lapack r-deseq
argtable netlib-scalapack r-deseq2
arlecore netlib-xblas r-desolve
armadillo nettle r-devtools
arpack-ng neuron r-diagrammer
arrow nextflow r-dicekriging
ascent nfft r-dichromat
asciidoc nghttp2 r-diffusionmap
aspa nginx r-digest
aspcud ngmlr r-diptest
aspect ninja r-dirichletmultinomial
aspell ninja-fortran r-dismo
aspell6-de nlohmann-json r-dnacopy
aspell6-en nlopt r-do-db
aspell6-es nmap r-domc
aspera-cli nnvm r-doparallel
assimp node-js r-dorng
astra notmuch r-dose
astral npb r-downloader
astyle npm r-dplyr
at-spi2-atk npth r-dt
at-spi2-core nspr r-dtw
atk numactl r-dygraphs
atlas numdiff r-e1071
atom-dft nut r-edger
atompaw nwchem r-ellipse
atop ocaml r-ensembldb
augustus occa r-ergm
autoconf oce r-evaluate
autodock-vina oclint r-expm
autogen oclock r-factoextra
automaded octave r-factominer
automake octave-optim r-fastcluster
axel octave-splines r-fastmatch
axl octave-struct r-ff
bamdst octopus r-fftwtools
bamtools of-adios-write r-fgsea
bamutil of-precice r-filehash
barrnap omega-h r-findpython
bash ompss r-fit-models
bash-completion ompt-openmp r-flashclust
bats oniguruma r-flexclust
bazel ont-albacore r-flexmix
bbcp opa-psm2 r-fnn
bbmap opam r-forcats
bc opari2 r-foreach
bcftools openbabel r-forecast
bcl2fastq2 openblas r-foreign
bdftopcf opencoarrays r-formatr
bdw-gc opencv r-formula
bear openexr r-fpc
beast1 openfast r-fracdiff
beast2 openfoam-com r-futile-logger
bedops openfoam-org r-futile-options
bedtools2 openfst r-gbm
beforelight opengl r-gcrma
benchmark openglu r-gdata
berkeley-db openjpeg r-gdsfmt
bertini openmc r-geiger
bib2xhtml openmpi r-genefilter
bigreqsproto opennurbs r-genelendatabase
binutils openpmd-api r-geneplotter
bioawk openscenegraph r-genie3
biopieces openslide r-genomeinfodb
bismark openspeedshop r-genomeinfodbdata
bison openspeedshop-utils r-genomicalignments
bitmap openssh r-genomicfeatures
blasr openssl r-genomicranges
blasr-libcpp opium r-geomorph
blast-plus optional-lite r-geoquery
blat opus r-geosphere
blaze orfm r-getopt
blis orthofinder r-getoptlong
bliss orthomcl r-ggally
blitz osu-micro-benchmarks r-ggbio
bmake otf r-ggdendro
bml otf2 r-ggjoy
bohrium p4est r-ggmap
bolt p7zip r-ggplot2
bookleaf-cpp pacbio-daligner r-ggpubr
boost pacbio-damasker r-ggrepel
boostmplcartesianproduct pacbio-dazz-db r-ggridges
bowtie pacbio-dextractor r-ggsci
bowtie2 pagit r-ggvis
boxlib pagmo r-gistr
bpp-core paml r-git2r
bpp-phyl panda r-glimma
bpp-seq pandaseq r-glmnet
bpp-suite pango r-globaloptions
bracken pangomm r-glue
braker papi r-gmodels
branson papyrus r-gmp
breakdancer paradiseo r-go-db
breseq parallel r-googlevis
brigand parallel-netcdf r-goplot
bsseeker2 paraver r-gosemsim
bucky paraview r-goseq
bumpversion parmetis r-gostats
busco parmgridgen r-gplots
butter parquet r-graph
bwa parsimonator r-gridbase
bwtool parsplice r-gridextra
byobu partitionfinder r-gseabase
bzip2 patch r-gss
c-blosc patchelf r-gsubfn
c-lime pathfinder r-gtable
caffe pax-utils r-gtools
cairo pbbam r-gtrellis
cairomm pbmpi r-gviz
caliper pcma r-haven
callpath pcre r-hexbin
camellia pcre2 r-highr
candle-benchmarks pdf2svg r-hmisc
cantera pdftk r-hms
canu pdsh r-htmltable
cap3 pdt r-htmltools
cares pegtl r-htmlwidgets
cask pennant r-httpuv
casper percept r-httr
catalyst perl r-hwriter
catch perl-algorithm-diff r-hypergraph
cbench perl-app-cmd r-ica
cblas perl-array-utils r-igraph
cbtf perl-b-hooks-endofscope r-illuminaio
cbtf-argonavis perl-bio-perl r-impute
cbtf-argonavis-gui perl-bit-vector r-influencer
cbtf-krell perl-cairo r-inline
cbtf-lanl perl-capture-tiny r-interactivedisplaybase
ccache perl-carp-clan r-ipred
cctools perl-class-data-inheritable r-iranges
cdbfasta perl-class-inspector r-irdisplay
cdd perl-class-load r-irkernel
cddlib perl-class-load-xs r-irlba
cdhit perl-compress-raw-bzip2 r-iso
cdo perl-compress-raw-zlib r-iterators
ceed perl-contextual-return r-janitor
cereal perl-cpan-meta-check r-jaspar2018
ceres-solver perl-data-optlist r-jomo
cfitsio perl-data-stag r-jpeg
cgal perl-dbd-mysql r-jsonlite
cgm perl-dbfile r-kegg-db
cgns perl-dbi r-kegggraph
channelflow perl-devel-cycle r-keggrest
charliecloud perl-devel-globaldestruction r-kernlab
charmpp perl-devel-overloadinfo r-kernsmooth
chatterbug perl-devel-stacktrace r-kknn
check perl-digest-md5 r-knitr
chlorop perl-dist-checkconflicts r-ks
chombo perl-encode-locale r-labeling
cistem perl-eval-closure r-lambda-r
cityhash perl-exception-class r-laplacesdemon
clamr perl-exporter-tiny r-lars
clapack perl-extutils-depends r-lattice
cleaveland4 perl-extutils-makemaker r-latticeextra
cleverleaf perl-extutils-pkgconfig r-lava
clfft perl-file-copy-recursive r-lazyeval
clhep perl-file-listing r-leaflet
clingo perl-file-pushd r-leaps
cloc perl-file-sharedir-install r-learnbayes
cloog perl-file-slurp-tiny r-lhs
cloverleaf perl-file-slurper r-limma
cloverleaf3d perl-file-which r-lme4
clustalo perl-font-ttf r-lmtest
clustalw perl-gd r-locfit
cmake perl-gd-graph r-log4r
cmocka perl-gd-text r-lpsolve
cmor perl-gdgraph-histogram r-lsei
cnmem perl-graph r-lubridate
cnpy perl-graph-readwrite r-magic
cntk perl-html-parser r-magrittr
cntk1bitsgd perl-html-tagset r-makecdfenv
codar-cheetah perl-http-cookies r-maldiquant
codes perl-http-daemon r-mapproj
coevp perl-http-date r-maps
cohmm perl-http-message r-maptools
coinhsl perl-http-negotiate r-markdown
colm perl-inline r-mass
colordiff perl-inline-c r-matr
comd perl-intervaltree r-matrix
commons-lang perl-io-compress r-matrixmodels
commons-lang3 perl-io-html r-matrixstats
commons-logging perl-io-sessiondata r-mclust
compiz perl-io-socket-ssl r-mcmcglmm
compositeproto perl-io-string r-mco
conduit perl-json r-mda
constype perl-libwww-perl r-memoise
converge perl-list-moreutils r-mergemaid
coreutils perl-log-log4perl r-methodss3
corset perl-lwp r-mgcv
cosmomc perl-lwp-mediatypes r-mgraster
cosp2 perl-lwp-protocol-https r-mice
cp2k perl-math-cdf r-mime
cppad perl-math-cephes r-minfi
cppcheck perl-math-matrixreal r-minqa
cppgsl perl-module-build r-misc3d
cpprestsdk perl-module-implementation r-mitml
cppunit perl-module-runtime r-mixtools
cppzmq perl-module-runtime-conflicts r-mlbench
cpu-features perl-moose r-mlinterfaces
cpuinfo perl-mozilla-ca r-mlr
cram perl-mro-compat r-mlrmbo
cryptopp perl-namespace-clean r-mmwrweek
cscope perl-net-http r-mnormt
csdp perl-net-scp-expect r-modelmetrics
ctffind perl-net-ssleay r-modelr
cub perl-package-deprecationmanager r-modeltools
cube perl-package-stash r-mpm
cubelib perl-package-stash-xs r-msnbase
cubew perl-padwalker r-multcomp
cuda perl-parallel-forkmanager r-multicool
cuda-memtest perl-params-util r-multtest
cudnn perl-parse-recdescent r-munsell
cufflinks perl-pdf-api2 r-mvtnorm
cups perl-pegex r-mzid
curl perl-perl6-slurp r-mzr
cvs perl-perlio-gzip r-nanotime
czmq perl-perlio-utf8-strict r-ncbit
dakota perl-soap-lite r-ncdf4
daligner perl-star-fusion r-network
damageproto perl-statistics-descriptive r-networkd3
damselfly perl-statistics-pca r-nlme
darshan-runtime perl-sub-exporter r-nloptr
darshan-util perl-sub-exporter-progressive r-nmf
dash perl-sub-identify r-nnet
datamash perl-sub-install r-nnls
dataspaces perl-sub-name r-nor1mix
davix perl-sub-uplevel r-np
dbus perl-svg r-numderiv
dealii perl-swissknife r-oligoclasses
dealii-parameter-gui perl-task-weaken r-oo
deconseq-standalone perl-term-readkey r-openssl
dejagnu perl-test-cleannamespaces r-org-hs-eg-db
delly2 perl-test-deep r-organismdbi
denovogear perl-test-differences r-packrat
dia perl-test-exception r-pacman
dialign-tx perl-test-fatal r-pamr
diamond perl-test-memory-cycle r-pan
diffsplice perl-test-most r-parallelmap
direnv perl-test-needs r-paramhelpers
discovar perl-test-requires r-party
discovardenovo perl-test-requiresinternet r-partykit
dislin perl-test-warn r-pathview
dlpack perl-test-warnings r-pbapply
dmd perl-text-csv r-pbdzmq
dmlc-core perl-text-diff r-pbkrtest
dmtcp perl-text-simpletable r-pcamethods
dmxproto perl-text-soundex r-pcapp
docbook-xml perl-text-unidecode r-permute
docbook-xsl perl-time-hires r-pfam-db
dos2unix perl-time-piece r-phangorn
dotnet-core-sdk perl-try-tiny r-phantompeakqualtools
double-conversion perl-uri r-phyloseq
doxygen perl-uri-escape r-picante
dri2proto perl-version r-pkgconfig
dri3proto perl-want r-pkgmaker
dsdp perl-www-robotrules r-plogr
dsrc perl-xml-libxml r-plot3d
dtcmp perl-xml-parser r-plotly
dyninst perl-xml-parser-lite r-plotrix
ea-utils perl-xml-simple r-pls
easybuild perl-yaml-libyaml r-plyr
ebms petsc r-pmcmr
eccodes pexsi r-png
eclipse-gcj-parser pfft r-powerlaw
ecp-proxy-apps pflotran r-prabclus
ed pfunit r-praise
editres pgdspider r-preprocesscore
eigen pgi r-prettyunits
elasticsearch pgmath r-proc
elemental phantompeakqualtools r-prodlim
elfutils phast r-progress
elk phasta r-protgenerics
elpa phist r-proto
emacs phylip r-proxy
emboss picard r-pryr
encodings pidx r-psych
environment-modules pigz r-ptw
eospac pilon r-purrr
er pindel r-quadprog
es piranha r-quantmod
esmf pism r-quantreg
essl pixman r-quantro
ethminer pkg-config r-qvalue
etsf-io pkgconf r-r6
everytrace planck-likelihood r-randomforest
everytrace-example plasma r-ranger
evieext platypus r-rappdirs
exabayes plink r-raster
examinimd plplot r-rbgl
exampm plumed r-rbokeh
exasp2 pmgr-collective r-rcolorbrewer
exmcutils pmix r-rcpp
exodusii pnfft r-rcpparmadillo
exonerate pngwriter r-rcppblaze
expat pnmpi r-rcppcctz
expect poamsa r-rcppcnpy
express pocl r-rcppeigen
extrae polymake r-rcppprogress
exuberant-ctags poppler r-rcurl
f90cache poppler-data r-rda
fabtests porta r-readr
falcon portage r-readxl
farmhash portcullis r-registry
fast-gbs postgresql r-rematch
fast-global-file-status ppl r-reordercluster
fasta prank r-reportingtools
fastjar precice r-repr
fastmath presentproto r-reprex
fastme preseq r-reshape
fastphase price r-reshape2
fastq-screen primer3 r-rex
fastqc prinseq-lite r-rgdal
fastqvalidator printproto r-rgenoud
fasttree prng r-rgeos
fastx-toolkit probconsrna r-rgl
fenics prodigal r-rgooglemaps
fermi proj r-rgraphviz
fermikit protobuf r-rhdf5
fermisciencetools proxymngr r-rhtslib
ferret pruners-ninja r-rinside
ffmpeg ps-lite r-rjags
fftw psi4 r-rjava
fimpute pslib r-rjson
findutils psm r-rjsonio
fio psmc r-rlang
fish pstreams r-rmarkdown
fixesproto pugixml r-rminer
flac pumi r-rmpfr
flang pv r-rmpi
flann pvm r-rmysql
flash pxz r-rngtools
flatbuffers py-3to2 r-robustbase
flecsale py-4suite-xml r-rocr
flecsi py-abipy r-rodbc
flex py-adios r-rots
flint py-affine r-roxygen2
flit py-alabaster r-rpart
fltk py-apache-libcloud r-rpart-plot
flux-core py-apipkg r-rpostgresql
flux-sched py-appdirs r-rprojroot
fluxbox py-appnope r-rsamtools
fmt py-apscheduler r-rsnns
foam-extend py-argcomplete r-rsolnp
folly py-argparse r-rsqlite
font-adobe-100dpi py-ase r-rstan
font-adobe-75dpi py-asn1crypto r-rstudioapi
font-adobe-utopia-100dpi py-astroid r-rtracklayer
font-adobe-utopia-75dpi py-astropy r-rtsne
font-adobe-utopia-type1 py-atomicwrites r-rvcheck
font-alias py-attrs r-rvest
font-arabic-misc py-autopep8 r-rzmq
font-bh-100dpi py-avro r-s4vectors
font-bh-75dpi py-avro-json-serializer r-samr
font-bh-lucidatypewriter-100dpi py-babel r-sandwich
font-bh-lucidatypewriter-75dpi py-backcall r-scales
font-bh-ttf py-backports-abc r-scatterplot3d
font-bh-type1 py-backports-functools-lru-cache r-sdmtools
font-bitstream-100dpi py-backports-shutil-get-terminal-size r-segmented
font-bitstream-75dpi py-backports-ssl-match-hostname r-selectr
font-bitstream-speedo py-basemap r-seqinr
font-bitstream-type1 py-bcbio-gff r-seqlogo
font-cronyx-cyrillic py-beautifulsoup4 r-seurat
font-cursor-misc py-binwalk r-sf
font-daewoo-misc py-biom-format r-sfsmisc
font-dec-misc py-biopython r-shape
font-ibm-type1 py-bitarray r-shiny
font-isas-misc py-bitstring r-shinydashboard
font-jis-misc py-bleach r-shortread
font-micro-misc py-blessings r-siggenes
font-misc-cyrillic py-bokeh r-simpleaffy
font-misc-ethiopic py-boltons r-sm
font-misc-meltho py-bottleneck r-smoof
font-misc-misc py-breakseq2 r-sn
font-mutt-misc py-brian r-snow
font-schumacher-misc py-brian2 r-snowfall
font-screen-cyrillic py-bsddb3 r-snprelate
font-sony-misc py-bx-python r-som
font-sun-misc py-cartopy r-somaticsignatures
font-util py-cclib r-sourcetools
font-winitzki-cyrillic py-cdat-lite r-sp
font-xfree86-type1 py-cdo r-sparsem
fontcacheproto py-certifi r-spatial
fontconfig py-cffi r-spdep
fontsproto py-chardet r-speedglm
fonttosfnt py-checkm-genome r-spem
fp16 py-cheetah r-splitstackshape
fpc py-click r-sqldf
fr-hit py-cligj r-squash
freebayes py-cloudpickle r-stanheaders
freeglut py-cnvkit r-statmod
freetype py-cogent r-statnet-common
fseq py-colorama r-stringi
fsl py-colormath r-stringr
fslsfonts py-configparser r-strucchange
fstobdf py-counter r-subplex
ftgl py-coverage r-summarizedexperiment
funhpc py-cpuinfo r-survey
fyba py-crispresso r-survival
gapbs py-crossmap r-sva
gapcloser py-cryptography r-tarifx
gapfiller py-csvkit r-tclust
gasnet py-current r-tensora
gatk py-cutadapt r-testit
gaussian py-cvxopt r-testthat
gawk py-cycler r-tfbstools
gblocks py-cython r-tfmpvalue
gcc py-dask r-th-data
gccmakedep py-dateutil r-threejs
gccxml py-dbf r-tibble
gconf py-decorator r-tidycensus
gcta py-deeptools r-tidyr
gdal py-dendropy r-tidyselect
gdb py-dill r-tidyverse
gdbm py-discover r-tiff
gdk-pixbuf py-dlcpar r-tigris
gdl py-docopt r-timedate
geant4 py-docutils r-tmixclust
gearshifft py-doxypy r-topgo
gemmlowp py-doxypypy r-trimcluster
genemark-et py-dryscrape r-truncnorm
genomefinisher py-dxchange r-trust
genometools py-dxfile r-tseries
geopm py-easybuild-easyblocks r-tsne
geos py-easybuild-easyconfigs r-ttr
gettext py-easybuild-framework r-udunits2
gflags py-edffile r-units
ghost py-editdistance r-utf8
ghostscript py-elasticsearch r-utils
ghostscript-fonts py-elephant r-uuid
giflib py-emcee r-variantannotation
git py-entrypoints r-varselrf
git-imerge py-enum34 r-vcd
git-lfs py-epydoc r-vegan
gl2ps py-espresso r-vgam
glew py-espressopp r-vipor
glfmultiples py-et-xmlfile r-viridis
glib py-eventlet r-viridislite
glibmm py-execnet r-visnetwork
glimmer py-fastaindex r-vsn
glm py-fasteners r-whisker
global py-faststructure r-withr
globalarrays py-filelock r-xde
globus-toolkit py-fiscalyear r-xgboost
glog py-flake8 r-xlconnect
gloo py-flake8-polyfill r-xlconnectjars
glpk py-flask r-xlsx
glproto py-flask-compress r-xlsxjars
glvis py-flask-socketio r-xmapbridge
gmake py-flexx r-xml
gmap-gsnap py-fn r-xml2
gmime py-fparser r-xtable
gmodel py-funcsigs r-xts
gmp py-functools32 r-xvector
gmsh py-future r-yaml
gnat py-futures r-yapsa
gnu-prolog py-gdbgui r-yaqcaffy
gnupg py-genders r-yarn
gnuplot py-genshi r-zlibbioc
gnutls py-gevent r-zoo
go py-git-review racon
go-bootstrap py-git2 raft
gobject-introspection py-gnuplot ragel
googletest py-goatools raja
gotcha py-gpaw randfold
gource py-greenlet random123
gperf py-griddataformats randrproto
gperftools py-guidata range-v3
gplates py-guiqwt rankstr
grackle py-h5py rapidjson
gradle py-html2text ravel
grandr py-html5lib raxml
graph500 py-htseq ray
graphicsmagick py-httpbin rdma-core
graphlib py-hypothesis rdp-classifier
graphmap py-idna re2c
graphviz py-igraph readfq
grass py-illumina-utils readline
grib-api py-imageio recordproto
grnboost py-imagesize redset
groff py-iminuit redundans
gromacs py-importlib relion
gsl py-ipaddress rempi
gslib py-ipdb rename
gtkmm py-ipykernel rendercheck
gtkorvo-atl py-ipython renderproto
gtkorvo-cercs-env py-ipython-genutils repeatmasker
gtkorvo-dill py-ipywidgets resourceproto
gtkorvo-enet py-isort revbayes
gtkplus py-itsdangerous rgb
gts py-jdcal rhash
guidance py-jedi rlwrap
guile py-jinja2 rmats
gurobi py-joblib rmlab
h5hut py-jpype rna-seqc
h5part py-jsonschema rngstreams
h5utils py-junit-xml rockstar
h5z-zfp py-jupyter-client root
hacckernels py-jupyter-console rose
hadoop py-jupyter-core ross
halc py-jupyter-notebook rr
hapcut2 py-keras rsbench
hapdip py-kiwisolver rsem
haploview py-lark-parser rstart
harfbuzz py-latexcodec rsync
harminv py-lazy rtags
hdf py-lazy-object-proxy rtax
hdf5 py-lazy-property ruby
hdf5-blosc py-lazyarray ruby-gnuplot
help2man py-libconf ruby-narray
hepmc py-libensemble ruby-ronn
heppdt py-line-profiler ruby-rubyinline
hic-pro py-linecache2 ruby-svn2git
highfive py-lit ruby-terminal-table
highwayhash py-llvmlite rust
hiop py-lmfit rust-bindgen
hisat2 py-localcider sabre
hisea py-locket sailfish
hmmer py-lockfile salmon
hoomd-blue py-logilab-common sambamba
hpccg py-lrudict samblaster
hpctoolkit py-lxml samrai
hpctoolkit-externals py-lzstring samtools
hpgmg py-macholib sandbox
hpl py-machotools sas
hpx py-macs2 satsuma2
hpx5 py-maestrowf savanna
hsakmt py-mako saws
hstr py-mappy sbt
htop py-markdown scala
htslib py-markupsafe scalasca
httpie py-matplotlib scalpel
hub py-mccabe scan-for-matches
hunspell py-mdanalysis scons
hwloc py-meep scorec-core
hybpiper py-memory-profiler scorep
hydra py-methylcode scotch
hydrogen py-mg-rast-tools scr
hypre py-misopy screen
i3 py-mistune scripts
ibmisc py-mock scrnsaverproto
iceauth py-moltemplate sctk
icedtea py-mongo sdl2
icet py-monotonic sdl2-image
ico py-monty sed
icu4c py-more-itertools seqan
id3lib py-mpi4py seqprep
idba py-mpmath seqtk
igraph py-multiprocess serf
igv py-multiqc sessreg
igvtools py-mx setxkbmap
ilmbase py-mxnet sga
image-magick py-myhdl shapeit
imake py-mysqldb1 shared-mime-info
imp py-natsort shiny-server
impute2 py-nbconvert shocklibs
infernal py-nbformat shoremap
inputproto py-neo shortbred
intel py-nestle shortstack
intel-daal py-netcdf4 showfont
intel-gpu-tools py-netifaces shuffile
intel-ipp py-networkx sickle
intel-mkl py-nose siesta
intel-mkl-dnn py-nosexcover signalp
intel-mpi py-numba signify
intel-parallel-studio py-numexpr silo
intel-tbb py-numexpr3 simplemoc
intel-xed py-numpy simul
intltool py-numpydoc simulationio
ior py-olefile singularity
iozone py-ont-fast5-api skilion-onedrive
iperf2 py-openpmd-validator sleef
iperf3 py-openpyxl slepc
ipopt py-openslide-python slurm
isaac py-opentuner smalt
isaac-server py-ordereddict smproxy
isl py-oset snakemake
itstool py-owslib snap
itsx py-packaging snap-berkeley
jackcess py-palettable snap-korf
jags py-pandas snappy
jansson py-paramiko snbone
jasper py-partd sniffles
jbigkit py-pathlib2 snpeff
jchronoss py-pathos snphylo
jdk py-pathspec snptest
jellyfish py-patsy soap2
jemalloc py-pbr soapdenovo-trans
jmol py-pep8-naming soapdenovo2
jq py-perf soapindel
json-c py-performance soapsnp
json-cwx py-periodictable sofa-c
json-glib py-petsc4py somatic-sniper
jsoncpp py-pexpect sortmerna
judy py-phonopy sosflow
julia py-pickleshare sowing
k8 py-picrust sox
kahip py-pil spades
kaiju py-pillow span-lite
kaks-calculator py-pip spark
kaldi py-pipits sparsehash
kallisto py-pkgconfig sparta
kbproto py-plotly spdlog
kdiff3 py-pluggy spectrum-mpi
kealib py-ply speex
kentutils py-pmw spglib
kibana py-poster sph2pipe
kim-api py-pox spherepack
kmergenie py-ppft spindle
kokkos py-prettytable spot
kraken py-proj sqlite
krb5 py-projectq sqlitebrowser
krims py-prompt-toolkit squid
kripke py-protobuf sra-toolkit
kvasir-mpl py-psutil sspace-longread
kvtree py-psyclone sspace-standard
laghos py-ptyprocess sst-dumpi
lammps py-pudb sst-macro
last py-py stacks
latte py-py2bit staden-io-lib
launchmon py-py2cairo star
lazyten py-py2neo star-ccm-plus
lbann py-py4j startup-notification
lbxproxy py-pyani stat
lcals py-pyasn1 stc
lcms py-pybedtools steps
ldc py-pybigwig stow
ldc-bootstrap py-pybind11 strace
legion py-pybtex stream
leveldb py-pybtex-docutils strelka
lftp py-pychecker stress
libaec py-pycodestyle string-view-lite
libaio py-pycparser stringtie
libapplewm py-pycrypto structure
libarchive py-pycurl sublime-text
libassuan py-pydatalog subread
libatomic-ops py-pydispatcher subversion
libbeagle py-pydot suite-sparse
libbeato py-pyelftools sumaclust
libbsd py-pyepsg sundials
libbson py-pyfaidx superlu
libcanberra py-pyfasta superlu-dist
libcap py-pyfftw superlu-mt
libceed py-pyflakes supernova
libcerf py-pygdbmi sw4lite
libcheck py-pygments swap-assembler
libcint py-pygobject swarm
libcircle py-pygpu swfft
libconfig py-pygtk swiftsim
libcroco py-pylint swig
libctl py-pymatgen symengine
libdivsufsort py-pyminifier sympol
libdmx py-pymol sz
libdrm py-pympler tabix
libdwarf py-pymysql talloc
libedit py-pynn tantan
libelf py-pypar tar
libemos py-pyparsing targetp
libepoxy py-pypeflow task
libev py-pyprof2html taskd
libevent py-pyqi tasmanian
libevpath py-pyqt tassel
libfabric py-pyrad tau
libffi py-pysam tcl
libffs py-pyscaf tcl-itcl
libfontenc py-pyserial tcl-tcllib
libfs py-pyshp tcl-tclxml
libgcrypt py-pyside tclap
libgd py-pysocks tcoffee
libgeotiff py-pysqlite tcptrace
libgit2 py-pytables tcsh
libgpg-error py-pytest tealeaf
libgpuarray py-pytest-cov templight
libgridxc py-pytest-flake8 templight-tools
libgtextutils py-pytest-httpbin tetgen
libharu py-pytest-mock tethex
libhio py-pytest-runner texinfo
libiberty py-pytest-xdist texlive
libice py-python-daemon the-platinum-searcher
libiconv py-python-engineio the-silver-searcher
libint py-python-gitlab thrift
libjpeg py-python-levenshtein thrust
libjpeg-turbo py-python-socketio tig
libksba py-pythonqwt tinyxml
liblbxutil py-pytorch tinyxml2
liblockfile py-pytz tioga
libmatheval py-pyutilib tk
libmaxminddb py-pyvcf tmalign
libmesh py-pywavelets tmhmm
libmng py-pyyaml tmux
libmongoc py-qtawesome tmuxinator
libmonitor py-qtconsole tophat
libnbc py-qtpy tppred
libnl py-quantities transabyss
libnova py-quast transdecoder
libogg py-radical-utils transposome
liboldx py-ranger transset
libpcap py-rasterio trapproto
libpciaccess py-readme-renderer tree
libpfm4 py-regex trf
libpipeline py-reportlab triangle
libpng py-requests trilinos
libpsl py-requests-toolbelt trimgalore
libpthread-stubs py-restview trimmomatic
libquo py-rope trinity
librom py-rpy2 trnascan-se
libshm py-rsa turbine
libsigcpp py-rseqc turbomole
libsigsegv py-rtree tut
libsm py-saga-python twm
libsodium py-scandir tycho2
libspatialindex py-scientificpython typhon
libsplash py-scikit-image typhonio
libssh py-scikit-learn uberftp
libssh2 py-scipy ucx
libsvm py-seaborn udunits2
libszip py-setuptools ufo-core
libtermkey py-setuptools-git ufo-filters
libtiff py-setuptools-scm umpire
libtool py-sfepy unblur
libunistring py-sh uncrustify
libunwind py-shapely unibilium
libuuid py-shiboken unison
libuv py-simplegeneric units
libvorbis py-simplejson unixodbc
libvterm py-singledispatch unuran
libwebsockets py-sip unzip
libwindowswm py-six usearch
libx11 py-slepc4py util-linux
libxau py-slurm-pipeline util-macros
libxaw py-sncosmo uuid
libxaw3d py-snowballstemmer valgrind
libxc py-snuggs vampirtrace
libxcb py-spectra vardictjava
libxcomposite py-spefile varscan
libxcursor py-spglib vc
libxdamage py-sphinx vcftools
libxdmcp py-sphinx-bootstrap-theme vcsh
libxevie py-sphinx-rtd-theme vdt
libxext py-sphinxcontrib-bibtex vecgeom
libxfixes py-sphinxcontrib-programoutput veclibfort
libxfont py-sphinxcontrib-websupport vegas2
libxfont2 py-spyder veloc
libxfontcache py-spykeutils velvet
libxft py-sqlalchemy verilator
libxi py-statsmodels verrou
libxinerama py-stevedore videoproto
libxkbcommon py-storm viennarna
libxkbfile py-subprocess32 viewres
libxkbui py-symengine vim
libxml2 py-symfit virtualgl
libxmu py-sympy visit
libxp py-tabulate vizglow
libxpm py-tappy vmatch
libxpresent py-terminado voropp
libxprintapputil py-testinfra votca-csg
libxprintutil py-tetoolkit votca-ctp
libxrandr py-theano votca-tools
libxrender py-tifffile votca-xtp
libxres py-toml vpfft
libxscrnsaver py-tomopy vpic
libxshmfence py-toolz vsearch
libxslt py-tornado vt
libxsmm py-tqdm vtk
libxstream py-traceback2 vtkh
libxt py-traitlets vtkm
libxtrap py-tuiview wannier90
libxtst py-twisted wcslib
libxv py-typing wget
libxvmc py-tzlocal wgsim
libxxf86dga py-udunits windowswmproto
libxxf86misc py-umi-tools wireshark
libxxf86vm py-unittest2 workrave
libyogrt py-unittest2py3k wt
libzip py-urllib3 wx
likwid py-urwid wxpropgrid
linkphase3 py-vcversioner x11perf
linux-headers py-virtualenv xapian-core
listres py-virtualenv-clone xauth
llvm py-virtualenvwrapper xbacklight
llvm-openmp-ompt py-vmd-python xbiff
lmdb py-vsc-base xbitmaps
lmod py-vsc-install xbraid
lndir py-wcsaxes xcalc
log4cplus py-wcwidth xcb-demo
log4cxx py-webkit-server xcb-proto
loki py-weblogo xcb-util
lordec py-werkzeug xcb-util-cursor
lrslib py-wheel xcb-util-errors
lrzip py-widgetsnbextension xcb-util-image
lsof py-wrapt xcb-util-keysyms
ltrace py-xarray xcb-util-renderutil
lua py-xattr xcb-util-wm
lua-bitlib py-xlrd xcb-util-xrm
lua-jit py-xlsxwriter xclip
lua-lpeg py-xmlrunner xclipboard
lua-luafilesystem py-xopen xclock
lua-luaposix py-xpyb xcmiscproto
lua-mpack py-xvfbwrapper xcmsdb
luit py-yamlreader xcompmgr
lulesh py-yapf xconsole
lumpy-sv py-yt xcursor-themes
lwgrp py-zmq xcursorgen
lwm2 py-zope-event xdbedizzy
lz4 py-zope-interface xditview
lzma python xdm
lzo qbank xdpyinfo
m4 qbox xdriinfo
macsio qhull xedit
mad-numdiff qmcpack xerces-c
mafft qmd-progress xev
magics qorts xextproto
magma qrupdate xeyes
makedepend qt xf86bigfontproto
mallocmc qt-creator xf86dga
man-db qtgraph xf86dgaproto
manta qthreads xf86driproto
maq quantum-espresso xf86miscproto
mariadb quinoa xf86rushproto
masa qwt xf86vidmodeproto
masurca r xfd
matio r-a4 xfindproxy
matlab r-a4base xfontsel
maven r-a4classif xfs
maverick r-a4core xfsinfo
mawk r-a4preproc xfwp
mbedtls r-a4reporting xgamma
mc r-abadata xgc
mcl r-abaenrichment xhmm
mdtest r-abind xhost
med r-absseq xineramaproto
meep r-acde xinit
mefit r-acepack xinput
megahit r-acgh xios
memaxes r-acme xkbcomp
meme r-ada xkbdata
memkind r-adabag xkbevd
meraculous r-ade4 xkbprint
mercurial r-adegenet xkbutils
mesa r-adsplit xkeyboard-config
mesa-glu r-aer xkill
meshkit r-affxparser xload
meson r-affy xlogo
mesquite r-affycomp xlsatoms
metabat r-affycompatible xlsclients
metaphysicl r-affycontam xlsfonts
metasv r-affycoretools xmag
metis r-affydata xman
mfem r-affyexpress xmessage
microbiomeutil r-affyilm xmh
minced r-affyio xmlf90
mindthegap r-affypdnn xmlto
miniaero r-affyplm xmodmap
miniamr r-affyqcreport xmore
miniasm r-affyrnadegradation xorg-cf-files
miniconda2 r-agdex xorg-docs
miniconda3 r-agilp xorg-gtest
minife r-agimicrorna xorg-server
minighost r-aims xorg-sgml-doctools
minigmg r-aldex2 xphelloworld
minimap2 r-allelicimbalance xplor-nih
minimd r-alpine xplsprinters
miniqmc r-als xpr
minisign r-alsace xprehashprinterlist
minismac2d r-altcdfenvs xprop
minitri r-amap xproto
minixyce r-ampliqueso xproxymanagementprotocol
minuit r-analysispageserver xqilla
mira r-anaquin xrandr
mirdeep2 r-aneufinder xrdb
mitofates r-aneufinderdata xrefresh
mitos r-annaffy xrootd
mkfontdir r-annotate xrx
mkfontscale r-annotationdbi xsbench
mlhka r-annotationfilter xscope
moab r-annotationforge xsd
modern-wheel r-annotationhub xsdk
mofem-cephas r-ape xsdktrilinos
mofem-fracture-module r-argparse xset
mofem-minimal-surface-equation r-assertthat xsetmode
mofem-users-modules r-backports xsetpointer
molcas r-bamsignals xsetroot
mono r-base64 xsimd
mosh r-base64enc xsm
mothur r-bbmisc xstdcmap
motif r-beanplot xtensor
motioncor2 r-bh xtensor-python
mount-point-attributes r-biasedurn xterm
mozjs r-bindr xtl
mpark-variant r-bindrcpp xtrans
mpc r-biobase xtrap
mpe2 r-biocgenerics xts
mpest r-biocinstaller xvidtune
mpfr r-biocparallel xvinfo
mpibash r-biocstyle xwd
mpiblast r-biom-utils xwininfo
mpich r-biomart xwud
mpifileutils r-biomformat xxhash
mpilander r-biostrings xz
mpileaks r-biovizbase yajl
mpip r-bit yambo
mpir r-bit64 yaml-cpp
mpix-launch-swift r-bitops yasm
mrbayes r-blob yorick
mrnet r-bookdown z3
mrtrix3 r-boot zeromq
mscgen r-brew zfp
msgpack-c r-broom zip
mshadow r-bsgenome zlib
multitail r-bumphunter zoltan
multiverso r-c50 zsh
mummer r-callr zstd

abinit

Homepage:
Spack package:
Versions:
8.8.2, 8.6.3, 8.2.2, 8.0.8b
Build Dependencies:
fftw, lapack, blas, scalapack, netcdf-fortran, libxc, mpi, hdf5
Link Dependencies:
fftw, lapack, blas, scalapack, netcdf-fortran, libxc, mpi, hdf5
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:
libtool, automake, autoconf, sparsehash, boost, mpi, sqlite
Link Dependencies:
libtool, sparsehash, boost, mpi, sqlite
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, fftw, cmake, parallel-netcdf
Link Dependencies:
cuda, fftw, parallel-netcdf
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:
cmake, mpi, boost
Link Dependencies:
mpi, boost
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:
libtool, m4, netcdf, zlib, libevpath, bzip2, automake, c-blosc, python, dataspaces, zfp, autoconf, hdf5, sz, lz4, mpi, szip
Link Dependencies:
netcdf, libevpath, bzip2, lz4, c-blosc, dataspaces, mpi, hdf5, sz, zlib, zfp, szip
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, 2.2.0, 2.1.0, 2.0.0
Build Dependencies:
pkgconfig, zeromq, mpi, hdf5, cmake, bzip2, py-mpi4py, py-numpy, python, zfp, adios
Link Dependencies:
zeromq, mpi, bzip2, hdf5, python, zfp, adios
Run Dependencies:
python, py-mpi4py, py-numpy
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, 2.5.2
Build Dependencies:
autoconf, m4, automake, libtool, boost
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.

aida

Homepage:
Spack package:
Versions:
3.2.1
Description:
Abstract Interfaces for Data Analysis

albany

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
trilinos, cmake, 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, cmake, petsc, 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, 1.1, 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, lapack, petsc, blas, silo, trilinos, cmake, zlib, mpi, hdf5
Link Dependencies:
lapack, petsc, blas, silo, trilinos, boost, zlib, mpi, hdf5
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
Build Dependencies:
python, cmake, mpi
Link Dependencies:
mpi
Description:
AMReX is a publicly available software framework designed for building massively parallel block- structured adaptive mesh refinement (AMR) applications.

amrvis

Homepage:
Spack package:
Versions:
master
Build Dependencies:
libsm, libxpm, libxext, libx11, motif, libxt, mpi, bison, libice, gmake, flex
Link Dependencies:
libsm, libxpm, libxext, libx11, motif, libxt, bison, libice, mpi, flex
Description:
Amrvis is a visualization package specifically designed to read and display output and profiling data from codes built on the AMReX framework.

andi

Homepage:
Spack package:
Versions:
0.10
Build Dependencies:
libtool, m4, gsl, autoconf, libdivsufsort, automake
Link Dependencies:
gsl, libdivsufsort
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:
java, python
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

aperture-photometry

Homepage:
Spack package:
Versions:
2.7.2
Build Dependencies:
java
Link Dependencies:
java
Description:
Aperture Photometry Tool APT is software for astronomical research

apex

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

apple-libunwind

Homepage:
Spack package:
Description:
Placeholder package for Apple's analogue to non-GNU libunwind

applewmproto

Homepage:
Spack package:
Versions:
1.4.2
Build Dependencies:
util-macros, pkgconfig
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:
util-macros, libxt, libx11, 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:
apr, unixodbc, expat, libiconv, openssl, postgresql, gdbm, sqlite
Link Dependencies:
apr, unixodbc, expat, libiconv, openssl, postgresql, gdbm, sqlite
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:
llvm, cmake, ninja, llvm-openmp-ompt
Link Dependencies:
llvm, llvm-openmp-ompt
Description:
ARCHER, a data race detection tool for large OpenMP applications.

argobots

Homepage:
Spack package:
Versions:
1.0b1, 1.0a1
Description:
Argobots, which was developed as a part of the Argo project, is a lightweight runtime system that supports integrated computation and data movement with massive concurrency. It will directly leverage the lowest- level constructs in the hardware and OS: lightweight notification mechanisms, data movement engines, memory mapping, and data placement strategies. It consists of an execution model and a memory model.

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, lapack, blas, cmake, arpack-ng, hdf5
Link Dependencies:
superlu, lapack, arpack-ng, blas, 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, 3.6.2, 3.6.0, 3.5.0, 3.4.0, 3.3.0
Build Dependencies:
libtool, lapack, blas, autoconf, cmake, mpi, automake
Link Dependencies:
lapack, mpi, blas
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.

arrow

Homepage:
Spack package:
Versions:
0.9.0, 0.8.0
Build Dependencies:
flatbuffers, zstd, snappy, rapidjson, cmake, zlib, boost
Link Dependencies:
flatbuffers, zstd, snappy, rapidjson, zlib, boost
Description:
A cross-language development platform for in-memory data. This package contains the C++ bindings.

ascent

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
vtkh, python, py-sphinx, py-numpy, py-mpi4py, cmake, conduit, mpi, adios
Link Dependencies:
vtkh, python, py-mpi4py, cmake, conduit, mpi, adios
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:
libxslt, libxml2, docbook-xsl, docbook-xml
Link Dependencies:
libxslt, libxml2, docbook-xsl, 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:
lapack, blas, mpi, hdf5
Link Dependencies:
lapack, blas, 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:
re2c, cmake, clingo, boost
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, 2.0.1, 2.0.0
Build Dependencies:
dealii, cmake, 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.

aspera-cli

Homepage:
Spack package:
Versions:
3.7.7
Description:
The Aspera CLI client for the Fast and Secure Protocol (FASP).

assimp

Homepage:
Spack package:
Versions:
4.0.1
Build Dependencies:
cmake, boost
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:
java, zip
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.

at-spi2-atk

Homepage:
Spack package:
Versions:
2.26.2, 2.26.1
Build Dependencies:
meson, atk, ninja, at-spi2-core
Link Dependencies:
at-spi2-core, atk
Description:
The At-Spi2 Atk package contains a library that bridges ATK to At-Spi2 D-Bus service.

at-spi2-core

Homepage:
Spack package:
Versions:
2.28.0
Build Dependencies:
ninja, libxi, libx11, dbus, meson, glib
Link Dependencies:
dbus, libx11, glib, libxi
Description:
The At-Spi2 Core package provides a Service Provider Interface for the Assistive Technologies available on the GNOME platform and a library against which applications can be linked.

atk

Homepage:
Spack package:
Versions:
2.28.1, 2.20.0, 2.14.0
Build Dependencies:
python, gobject-introspection, gettext, meson, glib, pkgconfig
Link Dependencies:
python, gobject-introspection, glib, gettext
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:
lapack, libxc, blas
Link Dependencies:
lapack, libxc, blas
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:
zlib, ncurses
Link Dependencies:
zlib, ncurses
Description:
Atop is an ASCII full-screen performance monitor for Linux

augustus

Homepage:
Spack package:
Versions:
3.3.1, 3.3, 3.2.3
Build Dependencies:
bamtools, gsl, zlib, boost
Link Dependencies:
bamtools, gsl, zlib, boost
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:
cmake, mpi, callpath, boost
Link Dependencies:
mpi, callpath, boost
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:
libtool, m4, openssl, pkgconf, gettext, autoconf, automake
Link Dependencies:
openssl, gettext
Description:
Axel is a light command line download accelerator for Linux and Unix

axl

Homepage:
Spack package:
Versions:
0.1.1, master
Build Dependencies:
cmake, kvtree
Link Dependencies:
kvtree
Description:
Asynchronous transfer library

bamdst

Homepage:
Spack package:
Versions:
master
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Bamdst is a a lightweight bam file depth statistical tool.

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:
readline, ncurses
Link Dependencies:
readline, ncurses
Description:
The GNU Project's Bourne Again SHell.

bash-completion

Homepage:
Spack package:
Versions:
develop, 2.7, 2.3
Build Dependencies:
autoconf, automake, 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:
java, zip
Link Dependencies:
java, zip
Run Dependencies:
java
Description:
Bazel is Google's own build tool

bbcp

Homepage:
Spack package:
Versions:
git
Build Dependencies:
zlib, openssl
Link Dependencies:
zlib, openssl
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:
ed, texinfo
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:
libxslt, libgcrypt, libxml2, cmake, zlib, boost
Link Dependencies:
libxslt, libgcrypt, libxml2, cmake, zlib, boost
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:
fontsproto, libxfont, util-macros, xproto, pkgconfig
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:
1.10.0, 1.8.4
Build Dependencies:
libbeagle
Link Dependencies:
libbeagle
Run Dependencies:
java, libbeagle
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:
libxt, util-macros, libxscrnsaver, libx11, pkgconfig
Link Dependencies:
libxscrnsaver, libx11, libxt
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:
bison, flex, mpfr, mpi, gmp
Link Dependencies:
mpfr, mpi, gmp
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:
util-macros, pkgconfig
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:
2.31.1, 2.29.1, 2.28, 2.27, 2.26, 2.25, 2.24, 2.23.2, 2.20.1
Build Dependencies:
bison, m4, zlib, gettext
Link Dependencies:
zlib, gettext
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:
samtools, bowtie2, perl
Description:
A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bison

Homepage:
Spack package:
Versions:
3.0.5, 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:
libxaw, libx11, libxmu, xbitmaps, util-macros, libxt, xproto, pkgconfig
Link Dependencies:
libxaw, libx11, libxmu, libxt
Description:
bitmap, bmtoa, atobm - X bitmap (XBM) editor and converter utilities.

blasr

Homepage:
Spack package:
Versions:
5.3.1
Build Dependencies:
python, blasr-libcpp, htslib, boost, pbbam, zlib, ncurses, hdf5
Link Dependencies:
blasr-libcpp, htslib, boost, pbbam, zlib, ncurses, hdf5
Description:
The PacBio long read aligner.

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, lzo, python, gnutls, openssl, jpeg, pcre, bzip2, freetype, zlib, perl
Link Dependencies:
libpng, lzo, python, gnutls, openssl, jpeg, pcre, bzip2, freetype, zlib, perl
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.

blis

Homepage:
Spack package:
Versions:
develop, 0.4.0, 0.3.2, 0.3.1, 0.3.0, 0.2.2
Build Dependencies:
python
Run Dependencies:
python
Description:
BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. The framework was designed to isolate essential kernels of computation that, when optimized, immediately enable optimized implementations of most of its commonly used and computationally intensive operations. BLIS is written in ISO C99 and available under a new/modified/3-clause BSD license. While BLIS exports a new BLAS-like API, it also includes a BLAS compatibility layer which gives application developers access to BLIS implementations via traditional BLAS routine calls. An object-based API unique to BLIS is also available.

bliss

Homepage:
Spack package:
Versions:
0.73
Build Dependencies:
libtool, gmp
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, 1.3.0, 1.2.3, 1.2.2, 1.1.0
Build Dependencies:
lapack, cmake, blas, mpi
Link Dependencies:
lapack, blas, 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, 0.9.1, 0.9.0
Build Dependencies:
opencl, blas, py-numpy, boost, swig, cuda, python, netlib-lapack, py-cython, cmake, zlib, opencv
Link Dependencies:
opencl, opencv, python, netlib-lapack, blas, cuda, zlib, boost
Run Dependencies:
py-numpy
Test Dependencies:
python, py-numpy
Description:
Library for automatic acceleration of array operations

bolt

Homepage:
Spack package:
Versions:
1.0b1
Build Dependencies:
cmake
Description:
BOLT targets a high-performing OpenMP implementation, especially specialized for fine-grain parallelism. Unlike other OpenMP implementations, BOLT utilizes a lightweight threading model for its underlying threading mechanism. It currently adopts Argobots, a new holistic, low-level threading and tasking runtime, in order to overcome shortcomings of conventional OS-level threads. The current BOLT implementation is based on the OpenMP runtime in LLVM, and thus it can be used with LLVM/Clang, Intel OpenMP compiler, and GCC.

bookleaf-cpp

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

boost

Homepage:
Spack package:
Versions:
develop, 1.68.0, 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:
python, icu4c, bzip2, py-numpy, zlib, mpi
Link Dependencies:
python, icu4c, bzip2, 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:
readline, tbb, zlib
Link Dependencies:
readline, tbb, 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:
cmake, bpp-core, bpp-seq
Link Dependencies:
bpp-core, bpp-seq
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:
cmake, bpp-seq, bpp-core, texinfo, bpp-phyl
Link Dependencies:
bpp-seq, bpp-core, bpp-phyl
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:
perl-list-moreutils, perl-exporter-tiny, python, perl-parallel-forkmanager, perl
Link Dependencies:
perl-list-moreutils, perl-exporter-tiny, python, perl-parallel-forkmanager, 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:
2.1.0, 1.11
Build Dependencies:
genemark-et, bamtools, augustus, perl, samtools
Link Dependencies:
genemark-et, bamtools, augustus, 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, parmetis, mpi, metis
Link Dependencies:
boost, parmetis, mpi, 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:
1.4.5, master
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Run Dependencies:
perl-statistics-descriptive, perl-math-cdf, perl-gdgraph-histogram, perl-list-moreutils, perl-gd-graph, perl-exporter-tiny
Description:
BreakDancer-1.3.6, released under GPLv3, is a perl/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:
libtool, m4, automake, autoconf
Run Dependencies:
r, bedtools2
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:
hmmer, python, augustus, blast-plus
Link Dependencies:
hmmer, python, augustus, blast-plus
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:
samtools, perl, bowtie
Link Dependencies:
samtools, bowtie
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.

bwtool

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
libbeato
Link Dependencies:
libbeato
Description:
bwtool is a command-line utility for bigWig files.

byobu

Homepage:
Spack package:
Versions:
5.125, 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, cmake, lz4, 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:
glog, blas, gflags, py-numpy, lmdb, leveldb, python, matlab, cuda, protobuf, boost, cmake, opencv, hdf5
Link Dependencies:
glog, blas, gflags, boost, lmdb, hdf5, python, matlab, cuda, protobuf, leveldb, opencv
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:
libpng, python, libxext, libx11, libxcb, fontconfig, pixman, libxrender, freetype, glib, pkgconfig
Link Dependencies:
libpng, libxext, libx11, libxcb, fontconfig, pixman, libxrender, freetype, glib
Description:
Cairo is a 2D graphics library with support for multiple output devices.

cairomm

Homepage:
Spack package:
Versions:
1.6.4, 1.6.2
Build Dependencies:
cairo, libsigcpp
Link Dependencies:
cairo, libsigcpp
Description:
Cairomm is a C++ wrapper for the cairo graphics library.

caliper

Homepage:
Spack package:
Versions:
1.7.0, 1.6.0, master
Build Dependencies:
python, gotcha, papi, sosflow, cmake, unwind, dyninst, mpi, libpfm4
Link Dependencies:
gotcha, papi, sosflow, unwind, dyninst, mpi, libpfm4
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:
adept-utils, libdwarf, cmake, dyninst, mpi
Link Dependencies:
libdwarf, adept-utils, elf, mpi, dyninst
Description:
Library for representing callpaths consistently in distributed-memory performance tools.

camellia

Homepage:
Spack package:
Versions:
master
Build Dependencies:
moab, trilinos, cmake, mpi, hdf5
Link Dependencies:
moab, trilinos, mpi, hdf5
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:
0.1, 0.0
Build Dependencies:
py-mpi4py, python, py-requests, py-theano, py-keras, py-tqdm, py-h5py, py-scikit-learn, opencv, py-mdanalysis, py-matplotlib
Link Dependencies:
python, opencv
Run Dependencies:
py-h5py, py-theano, py-requests, py-keras, py-tqdm, py-mpi4py, py-scikit-learn, py-matplotlib, py-mdanalysis
Description:
ECP-CANDLE Benchmarks

cantera

Homepage:
Spack package:
Versions:
2.3.0, 2.2.1
Build Dependencies:
py-3to2, py-cython, googletest, blas, sundials, py-numpy, lapack, boost, eigen, python, fmt, matlab, scons, py-scipy
Link Dependencies:
eigen, python, fmt, googletest, blas, matlab, sundials, lapack, boost
Run Dependencies:
py-3to2, py-numpy, py-scipy
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:
jdk, gnuplot, 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:
jellyfish, boost
Link Dependencies:
jellyfish, boost
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:
python, libx11, libxt, git, mesa, cmake, mpi
Link Dependencies:
python, libx11, libxt, git, mesa, mpi
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:
fftw, lapack, mpi, blas
Link Dependencies:
fftw, lapack, mpi, blas
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, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
boost, mrnet, cmake, xerces-c, libxml2
Link Dependencies:
mrnet, boost, 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, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cbtf, cbtf-krell, papi, cuda, mrnet, cmake, libmonitor, boost
Link Dependencies:
cbtf, cbtf-krell, elf, papi, cuda, mrnet, libmonitor, boost
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:
cbtf, cbtf-argonavis, graphviz, boost, mrnet, cbtf-krell, xerces-c, cuda, qtgraph, cmake, qt, openspeedshop-utils
Link Dependencies:
cbtf, cbtf-krell, xerces-c, openspeedshop-utils, cbtf-argonavis, cuda, graphviz, qtgraph, mrnet, qt, boost
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, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cbtf, mpich, mvapich, gotcha, llvm-openmp-ompt, dyninst, boost, libmonitor, binutils, libunwind, mvapich2, xerces-c, papi, mpt, mrnet, openmpi, cmake, mpich2
Link Dependencies:
cbtf, mpich, mvapich, gotcha, llvm-openmp-ompt, dyninst, boost, libmonitor, binutils, libunwind, mvapich2, xerces-c, papi, mpt, mrnet, openmpi, mpich2
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, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cbtf, cbtf-krell, xerces-c, cmake, mrnet
Link Dependencies:
cbtf, cbtf-krell, xerces-c, mrnet
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:
libxslt, zlib, gperf
Link Dependencies:
libxslt, zlib, gperf
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:
readline, swig, python, openssl, zlib, perl
Link Dependencies:
readline, swig, openssl, 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:
libtool, gmp
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:
1.9.5, 1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.7.2
Build Dependencies:
fftw, grib-api, netcdf, magics, proj, libuuid, hdf5, udunits2, eccodes, libxml2, curl, szip
Link Dependencies:
fftw, grib-api, netcdf, magics, proj, libuuid, hdf5, udunits2, eccodes, libxml2, curl, szip
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:
petsc, occa, laghos, hpgmg, suite-sparse, nekbone, nek5000, nekcem, pumi, mfem, libceed, gslib, magma, hypre
Link Dependencies:
petsc, occa, laghos, hpgmg, suite-sparse, nekbone, nek5000, nekcem, pumi, mfem, libceed, gslib, magma, hypre
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.

ceres-solver

Homepage:
Spack package:
Versions:
1.12.0
Build Dependencies:
eigen, cmake, lapack, glog
Link Dependencies:
eigen, lapack, glog
Description:
Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It can be used to solve Non- linear Least Squares problems with bounds constraints and general unconstrained optimization problems. It is a mature, feature rich, and performant library that has been used in production at Google since 2010.

cfitsio

Homepage:
Spack package:
Versions:
3.450, 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:
mpfr, gmp, cmake, zlib, qt, boost
Link Dependencies:
qt, gmp, zlib, mpfr, boost
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, mpi, hdf5
Link Dependencies:
mpi, hdf5
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.

channelflow

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
fftw, netcdf, eigen, hdf5, cmake, mpi, boost
Link Dependencies:
fftw, netcdf, eigen, hdf5, mpi, boost
Description:
Channelflow is a software system for numerical analysis of the incompressible fluid flow in channel geometries, written in C++.

charliecloud

Homepage:
Spack package:
Versions:
0.9.1, 0.9.0, 0.2.4
Description:
Lightweight user-defined software stacks for HPC.

charmpp

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:
cuda, autoconf, mpi, papi, automake
Link Dependencies:
cuda, autoconf, mpi, papi, automake
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.

chatterbug

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
scorep, mpi
Link Dependencies:
scorep, mpi
Description:
A suite of communication-intensive proxy applications that mimic commonly found communication patterns in HPC codes. These codes can be used as synthetic codes for benchmarking, or for trace generation using Score-P / OTF2.

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:
blas, lapack, gmake, mpi, hdf5
Link Dependencies:
lapack, blas, 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:
fftw, wx
Link Dependencies:
fftw, wx
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:
samtools, perl-math-cdf, r, bowtie, viennarna, perl
Link Dependencies:
samtools, viennarna, bowtie
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:
cmake, hdf5, samrai, boost
Link Dependencies:
hdf5, samrai, boost
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:
opencl, cmake, boost
Link Dependencies:
opencl, boost
Description:
a software library containing FFT functions written in OpenCL

clhep

Homepage:
Spack package:
Versions:
2.4.1.0, 2.4.0.4, 2.4.0.2, 2.4.0.1, 2.4.0.0, 2.3.4.6, 2.3.4.5, 2.3.4.4, 2.3.4.3, 2.3.4.2, 2.3.3.2, 2.3.3.1, 2.3.3.0, 2.3.2.2, 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:
doxygen, cmake, python
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:
isl, gmp
Link Dependencies:
isl, gmp
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:
3.12.2, 3.12.1, 3.12.0, 3.11.4, 3.11.3, 3.11.2, 3.11.1, 3.11.0, 3.10.3, 3.10.2, 3.10.1, 3.10.0, 3.9.6, 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:
qt, xz, py-sphinx, bzip2, expat, libarchive, python, ncurses, rhash, libuv, zlib, curl, openssl
Link Dependencies:
qt, xz, expat, curl, rhash, libuv, openssl, bzip2, libarchive, ncurses, 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, python, netcdf, uuid, py-numpy, hdf5
Link Dependencies:
udunits2, python, netcdf, uuid, 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:
openblas, nccl, multiverso, cudnn, cub, kaldi, libzip, boost, cntk1bitsgd, cuda, protobuf, opencv, mpi
Link Dependencies:
openblas, nccl, multiverso, cudnn, cub, kaldi, libzip, boost, cntk1bitsgd, cuda, protobuf, opencv, mpi
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.

codes

Homepage:
Spack package:
Versions:
develop, 1.0.0
Build Dependencies:
libtool, m4, ross, pkg-config, autoconf, sst-dumpi, bison, automake, mpi, flex
Link Dependencies:
sst-dumpi, ross, mpi
Description:
CO-Design of multi-layer Exascale Storage (CODES) simulation framework

coevp

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
silo, lapack, flann, mpi
Link Dependencies:
silo, lapack, flann, 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:
2015.06.23, 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.

commons-lang

Homepage:
Spack package:
Versions:
2.6, 2.4
Build Dependencies:
jdk
Link Dependencies:
jdk
Run Dependencies:
java
Description:
The standard Java libraries fail to provide enough methods for manipulation of its core classes. Apache Commons Lang provides these extra methods. Lang provides a host of helper utilities for the java.lang API, notably String manipulation methods, basic numerical methods, object reflection, concurrency, creation and serialization and System properties. Additionally it contains basic enhancements to java.util.Date and a series of utilities dedicated to help with building methods, such as hashCode, toString and equals.

commons-lang3

Homepage:
Spack package:
Versions:
3.7
Build Dependencies:
jdk
Link Dependencies:
jdk
Run Dependencies:
java
Description:
The standard Java libraries fail to provide enough methods for manipulation of its core classes. Apache Commons Lang provides these extra methods. Lang provides a host of helper utilities for the java.lang API, notably String manipulation methods, basic numerical methods, object reflection, concurrency, creation and serialization and System properties. Additionally it contains basic enhancements to java.util.Date and a series of utilities dedicated to help with building methods, such as hashCode, toString and equals.

commons-logging

Homepage:
Spack package:
Versions:
1.2, 1.1.3, 1.1.1
Build Dependencies:
jdk
Link Dependencies:
jdk
Run Dependencies:
java
Description:
When writing a library it is very useful to log information. However there are many logging implementations out there, and a library cannot impose the use of a particular one on the overall application that the library is a part of. The Logging package is an ultra-thin bridge between different logging implementations. A library that uses the commons-logging API can be used with any logging implementation at runtime. Commons-logging comes with support for a number of popular logging implementations, and writing adapters for others is a reasonably simple task.

compiz

Homepage:
Spack package:
Versions:
0.7.8
Build Dependencies:
libpng, libxslt, libxfixes, libxdamage, libxinerama, libxcb, libxrender, libsm, libxrandr, gconf, libxml2, glib, libice, libxcomposite
Link Dependencies:
libpng, libxslt, libxfixes, libxdamage, libxinerama, libxcb, libxrender, libsm, libxrandr, gconf, libxml2, glib, libice, libxcomposite
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:
util-macros, pkgconfig
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:
py-numpy, python, py-sphinx, silo, doxygen, cmake, mpi, hdf5
Link Dependencies:
python, silo, doxygen, cmake, mpi, hdf5
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:
util-macros, pkgconfig
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:
openmpi, mpi
Link Dependencies:
openmpi, mpi
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:
8.29, 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:
python, py-six, planck-likelihood, py-pandas, py-numpy, py-matplotlib, mpi, py-scipy
Link Dependencies:
planck-likelihood, python, mpi
Run Dependencies:
python, py-six, py-pandas, py-numpy, py-matplotlib, py-scipy
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:
fftw, libint, blas, libxc, python, elpa, lapack, wannier90, plumed, scalapack, pexsi, mpi, libxsmm
Link Dependencies:
fftw, libint, blas, libxc, elpa, lapack, wannier90, plumed, scalapack, pexsi, mpi, libxsmm
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.

cppgsl

Homepage:
Spack package:
Versions:
develop, 2.0.0, 1.0.0
Build Dependencies:
cmake
Description:
C++ Guideline Support Library

cpprestsdk

Homepage:
Spack package:
Versions:
2.9.1
Build Dependencies:
cmake, boost
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:
bison, flex, ncurses, pkgconfig
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:
fftw, wx
Link Dependencies:
fftw, wx
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:
zlib, qt
Link Dependencies:
zlib, qt
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

cubelib

Homepage:
Spack package:
Versions:
4.4
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Component of CubeBundle: General purpose C++ library and tools

cubew

Homepage:
Spack package:
Versions:
4.4
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
Component of CubeBundle: High performance C Writer library

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, nghttp2, libssh2, openssl
Link Dependencies:
zlib, libssh, nghttp2, libssh2, openssl
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:
4.1.1, 4.0.2, 3.0.2
Build Dependencies:
libtool, zeromq, autoconf, pkgconfig, libuuid, automake
Link Dependencies:
zeromq, libuuid
Description:
A C interface to the ZMQ library

dakota

Homepage:
Spack package:
Versions:
6.3
Build Dependencies:
lapack, blas, cmake, python, mpi, boost
Link Dependencies:
mpi, lapack, python, blas, boost
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:
util-macros, pkgconfig
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:
zlib, mpi
Link Dependencies:
zlib, mpi
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, m4, automake, libtool
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:
autoconf, m4, automake, mpi, libtool
Link Dependencies:
mpi
Description:
an extreme scale data management framework.

davix

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

dbus

Homepage:
Spack package:
Versions:
1.12.8, 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:
netcdf, blas, adol-c, graphviz, bzip2, hdf5, nanoflann, gsl, muparser, boost, suite-sparse, arpack-ng, tbb, petsc, netcdf-cxx, assimp, oce, cmake, trilinos, lapack, cuda, slepc, python, gmsh, sundials, mpi, doxygen, p4est, scalapack, zlib, metis
Link Dependencies:
netcdf, blas, adol-c, graphviz, bzip2, hdf5, nanoflann, gsl, muparser, boost, suite-sparse, arpack-ng, tbb, petsc, netcdf-cxx, assimp, oce, cmake, trilinos, lapack, slepc, python, mpi, sundials, cuda, doxygen, p4est, scalapack, zlib, metis
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:
tcl, expect
Link Dependencies:
tcl, expect
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:
bcftools, htslib, boost
Link Dependencies:
bcftools, htslib, boost
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:
eigen, cmake, htslib, boost
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:
libxslt, libxinerama, gtkplus, freetype, libxrender, libuuid, libsm, python, swig, gettext, intltool, pkg-config, libxml2
Link Dependencies:
libsm, libxslt, python, swig, libxinerama, gtkplus, libxrender, freetype, libuuid, 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:
samtools, jemalloc
Link Dependencies:
samtools, jemalloc
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:
motif, mesa
Link Dependencies:
motif, mesa
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.

dmd

Homepage:
Spack package:
Versions:
2.081.1
Build Dependencies:
openssl, curl
Link Dependencies:
openssl, curl
Description:
DMD is the reference compiler for the D programming language.

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.

dmtcp

Homepage:
Spack package:
Versions:
2.5.2
Description:
DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S.

dmxproto

Homepage:
Spack package:
Versions:
2.3.1
Build Dependencies:
util-macros, pkgconfig
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.

dotnet-core-sdk

Homepage:
Spack package:
Versions:
2.1.300
Description:
The .NET Core SDK is a powerful development environment to write applications for all types of infrastructure.

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:
bison, cmake, flex
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:
util-macros, pkgconfig
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:
util-macros, pkgconfig
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:
lapack, blas
Link Dependencies:
lapack, blas
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, libiberty
Link Dependencies:
libdwarf, boost, elf, libiberty
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:
bamtools, gsl, subversion, zlib, perl
Link Dependencies:
bamtools, gsl, subversion, 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-framework, py-easybuild-easyconfigs
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, python, netcdf, cmake, libaec, py-numpy, jasper, openjpeg
Link Dependencies:
libpng, python, netcdf, libaec, 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:
1.1, 1.0
Build Dependencies:
minitri, miniamr, candle-benchmarks, laghos, xsbench, nekbone, comd, minife, macsio, amg, swfft, sw4lite, examinimd
Link Dependencies:
minitri, miniamr, candle-benchmarks, laghos, xsbench, nekbone, comd, minife, macsio, amg, swfft, sw4lite, examinimd
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, libxt, util-macros, pkgconfig, libxmu
Link Dependencies:
libx11, libxaw, libxmu, libxt
Description:
Dynamic resource editor for X Toolkit applications.

eigen

Homepage:
Spack package:
Versions:
3.3.5, 3.3.4, 3.3.3, 3.3.1, 3.2.10, 3.2.9, 3.2.8, 3.2.7
Build Dependencies:
fftw, scotch, mpfr, suite-sparse, gmp, cmake, metis
Link Dependencies:
fftw, scotch, mpfr, 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:
6.4.0, 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:
openblas, essl, blas, veclibfort, scalapack, lapack, gmp, python, netlib-lapack, intel-mkl, mpfr, mpc, cmake, mpi, metis
Link Dependencies:
openblas, essl, blas, veclibfort, lapack, gmp, python, netlib-lapack, intel-mkl, mpfr, mpc, scalapack, mpi, metis
Description:
Elemental: Distributed-memory dense and sparse-direct linear algebra and optimization library.

elfutils

Homepage:
Spack package:
Versions:
0.173, 0.170, 0.168, 0.163
Build Dependencies:
gettext
Link Dependencies:
xz, bzip2, zlib, 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, lapack, libxc, blas, mpi
Link Dependencies:
fftw, lapack, libxc, blas, mpi
Description:
An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features.

elpa

Homepage:
Spack package:
Versions:
2018.05.001.rc1, 2017.11.001, 2017.05.003, 2017.05.002, 2016.11.001.pre, 2016.05.004, 2016.05.003, 2015.11.001
Build Dependencies:
lapack, scalapack, mpi, blas
Link Dependencies:
lapack, scalapack, mpi, blas
Description:
Eigenvalue solvers for Petaflop-Applications (ELPA)

emacs

Homepage:
Spack package:
Versions:
26.1, 25.3, 25.2, 25.1, 24.5
Build Dependencies:
libpng, libxpm, giflib, pcre, gtkplus, libtiff, gnutls, pkgconfig, libxaw, libx11, zlib, ncurses
Link Dependencies:
libpng, libxpm, giflib, pcre, gtkplus, libx11, gnutls, libtiff, zlib, ncurses, libxaw
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:
mkfontscale, util-macros, font-util, pkgconfig
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.

er

Homepage:
Spack package:
Versions:
0.0.3, master
Build Dependencies:
shuffile, redset, cmake, mpi, kvtree
Link Dependencies:
shuffile, redset, mpi, kvtree
Description:
Encoding and redundancy on a file set

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:
lapack, netcdf, xerces-c, libxml2, parallel-netcdf, zlib, mpi, netcdf-fortran
Link Dependencies:
lapack, netcdf, xerces-c, libxml2, parallel-netcdf, zlib, mpi, netcdf-fortran
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:
Description:
IBM's Engineering and Scientific Subroutine Library (ESSL).

ethminer

Homepage:
Spack package:
Versions:
0.12.0
Build Dependencies:
python, mesa, cuda, json-c, cmake, zlib, curl, boost
Link Dependencies:
python, mesa, cuda, json-c, zlib, curl, boost
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:
openmpi, cmake, everytrace
Link Dependencies:
openmpi, everytrace
Description:
Get stack trace EVERY time a program exits.

evieext

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies:
util-macros, pkgconfig
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:
mpi, kokkos
Link Dependencies:
mpi, kokkos
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, lapack, blas, mpi
Link Dependencies:
bml, lapack, blas, 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:
netcdf, cmake, mpi, hdf5
Link Dependencies:
netcdf, mpi, 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:
glib, pkgconfig
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:
tcl, m4, automake, autoconf, libtool
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:
bamtools, cmake, zlib, boost
Link Dependencies:
bamtools, zlib, boost
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:
mpi, papi, gettext, libdwarf, boost, dyninst, libunwind, binutils, libxml2
Link Dependencies:
elf, papi, gettext, mpi, libdwarf, boost, dyninst, libunwind, binutils, 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:
pacbio-daligner, python, py-networkx, py-setuptools, py-pypeflow, pacbio-dextractor, pacbio-dazz-db, 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:
samtools, python, sabre, parallel, py-cutadapt, py-pyvcf, platypus, bwa
Description:
A bioinformatic pipeline designed to extract a high-quality SNP catalog starting from FASTQ files obtained from sequencing genotyping-by- sequencing (GBS) libraries.

fast-global-file-status

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
mrnet, mpi, mount-point-attributes
Link Dependencies:
mrnet, mpi, mount-point-attributes
Description:
provides a scalable mechanism to retrieve such information of a file, including its degree of distribution or replication and consistency.

fasta

Homepage:
Spack package:
Versions:
36.3.8g
Build Dependencies:
zlib
Link Dependencies:
zlib
Description:
The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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:
boxlib, chombo, superlu-dist, sundials, trilinos, moab, pumi, petsc, arpack-ng, mesquite, phasta, zoltan, hypre, mpi
Link Dependencies:
boxlib, chombo, superlu-dist, sundials, trilinos, moab, pumi, petsc, arpack-ng, mesquite, phasta, zoltan, hypre, mpi
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, m4, automake, libtool
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:
samtools, bwa, bowtie2, bowtie
Link Dependencies:
samtools, bwa, bowtie2, bowtie
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:
petsc, py-six, py-setuptools, cmake, trilinos, py-numpy, parmetis, scotch, swig, slepc, python, mpi, py-sphinx, py-ply, eigen, hdf5, boost, suite-sparse, py-sympy, qt, vtk
Link Dependencies:
petsc, trilinos, boost, parmetis, scotch, slepc, python, mpi, eigen, hdf5, suite-sparse, qt, vtk
Run Dependencies:
swig, py-sympy, py-numpy, py-six, py-ply
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:
readline, hdf5, netcdf, zlib, netcdf-fortran
Link Dependencies:
readline, hdf5, netcdf, zlib, netcdf-fortran
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:
3.3.8, 3.3.7, 3.3.6-pl2, 3.3.5, 3.3.4, 2.1.5
Build Dependencies:
autoconf, automake, 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:
cairo, gtkplus, py-sphinx
Link Dependencies:
cairo, gtkplus
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:
util-macros, pkgconfig
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:
id3lib, libvorbis
Link Dependencies:
id3lib, libvorbis
Description:
Encoder/decoder for the Free Lossless Audio Codec

flang

Homepage:
Spack package:
Versions:
develop, 20180612
Build Dependencies:
llvm, pgmath, cmake
Link Dependencies:
llvm, pgmath
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:
python, matlab, latex, cuda, py-numpy, hdf5, cmake, mpi, boost
Link Dependencies:
python, latex, cuda, hdf5, mpi, boost
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.

flatbuffers

Homepage:
Spack package:
Versions:
1.9.0, 1.8.0
Build Dependencies:
cmake
Description:
Memory Efficient Serialization Library

flecsale

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

flecsi

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, parmetis, legion
Link Dependencies:
parmetis, 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:
libtool, m4, autoconf, bison, help2man, gettext, automake
Description:
Flex is a tool for generating scanners.

flint

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

flit

Homepage:
Spack package:
Versions:
2.0-alpha.1
Run Dependencies:
python, py-numpy, py-matplotlib, py-toml
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-core

Homepage:
Spack package:
Versions:
0.10.0, 0.9.0, 0.8.0, master
Build Dependencies:
libtool, zeromq, munge, hwloc, yaml-cpp, lua-luaposix, libuuid, jansson, python, py-pylint, asciidoc, autoconf, lua, automake, czmq, py-cffi
Link Dependencies:
zeromq, munge, lua-luaposix, hwloc, czmq, lua, yaml-cpp, jansson, libuuid
Run Dependencies:
python, lua, py-cffi
Description:
A next-generation resource manager (pre-alpha)

flux-sched

Homepage:
Spack package:
Versions:
0.5.0, 0.4.0, master
Build Dependencies:
autoconf, flux-core, boost, libtool, automake
Link Dependencies:
flux-core, boost
Run Dependencies:
flux-core
Description:
A scheduler for flux-core (pre-alpha)

fluxbox

Homepage:
Spack package:
Versions:
1.3.7
Build Dependencies:
expat, libxext, libx11, libxrender, freetype, pkgconfig
Link Dependencies:
libxrender, expat, libxext, libx11, 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:
python, paraview, zlib, flex, parmgridgen, scotch, cmake, parmetis, mpi, metis
Link Dependencies:
python, paraview, zlib, metis, parmetis, mpi, scotch
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:
libtool, m4, pkgconfig, glog, double-conversion, autoconf, gflags, boost, libevent, automake
Link Dependencies:
double-conversion, gflags, glog, libevent, boost
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:
mkfontdir, font-util, fontconfig, bdftopcf, util-macros, pkgconfig
Link Dependencies:
font-util
Description:
X.org adobe-100dpi font.

font-adobe-75dpi

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

font-adobe-utopia-100dpi

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

font-alias

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

font-arabic-misc

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

font-bh-100dpi

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

font-bh-75dpi

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

font-bh-lucidatypewriter-100dpi

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

font-bh-ttf

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

font-bh-type1

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

font-bitstream-100dpi

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

font-bitstream-75dpi

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

font-bitstream-speedo

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

font-bitstream-type1

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

font-cronyx-cyrillic

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

font-cursor-misc

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

font-daewoo-misc

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

font-dec-misc

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

font-ibm-type1

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

font-isas-misc

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

font-jis-misc

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

font-micro-misc

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

font-misc-cyrillic

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

font-misc-ethiopic

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

font-misc-meltho

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

font-misc-misc

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

font-mutt-misc

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

font-schumacher-misc

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

font-screen-cyrillic

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

font-sony-misc

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

font-sun-misc

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

font-util

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

font-winitzki-cyrillic

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

font-xfree86-type1

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
mkfontdir, fontconfig, font-util, mkfontscale, util-macros, pkgconfig
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:
libxml2, pkgconfig, freetype, gperf, font-util
Link Dependencies:
libxml2, freetype, font-util
Description:
Fontconfig is a library for configuring/customizing font access

fontsproto

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

fonttosfnt

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
util-macros, freetype, libfontenc, xproto, pkgconfig
Link Dependencies:
freetype, libfontenc
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:
gl, libxrandr, libx11, libxi, xrandr, cmake, inputproto, glu
Link Dependencies:
gl, libxrandr, libx11, libxi, xrandr, inputproto, glu
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:
libpng, bzip2, pkgconfig
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:
libpng, python, libx11, zlib, sqlite, expat, mesa-glu, boost
Link Dependencies:
libpng, expat, libx11, sqlite, zlib, mesa-glu, boost
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:
util-macros, libfs, xproto, pkgconfig
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:
util-macros, libfs, libx11, xproto, pkgconfig
Link Dependencies:
libfs, libx11
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:
libtool, m4, autoconf, doxygen, pkgconfig, freetype, gl, glu, automake
Link Dependencies:
gl, freetype, 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:
hwloc, googletest, qthreads, cereal, jemalloc, cmake, mpi
Link Dependencies:
hwloc, googletest, qthreads, cereal, jemalloc, mpi
Description:
FunHPC: Functional HPC Programming

fyba

Homepage:
Spack package:
Versions:
4.1.1
Build Dependencies:
autoconf, m4, automake, libtool
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:
1.32.0, 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:
4.0.8.1, 4.0.4.0, 3.8-0
Run Dependencies:
java, python, 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:
readline, libsigsegv, gettext, mpfr, gmp
Link Dependencies:
readline, libsigsegv, gettext, mpfr, 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:
8.2.0, 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:
zip, mpfr, mpc, gnat, isl, zlib, binutils, gmp
Link Dependencies:
mpfr, mpc, gnat, isl, zlib, binutils, gmp
Test Dependencies:
tcl, dejagnu, expect, guile, 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:
glib, libxml2
Link Dependencies:
glib, libxml2
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:
2.3.1, 2.3.0, 2.1.2, 2.0.2, 1.11.5
Build Dependencies:
libpng, libtool, netcdf, libiconv, openssl, xz, libtiff, py-numpy, perl, libgeotiff, opencl, json-c, gmake, xerces-c, cfitsio, fyba, qhull, armadillo, pcre, hdf5, hdf, kealib, libxml2, java, giflib, pkgconfig, zstd, py-setuptools, geos, python, sqlite, unixodbc, expat, cryptopp, curl, postgresql, jpeg, poppler, openjpeg, zlib, proj, jasper
Link Dependencies:
libpng, xz, netcdf, libiconv, openssl, proj, libtiff, fyba, hdf5, opencl, json-c, xerces-c, cfitsio, qhull, armadillo, pcre, hdf, kealib, libxml2, java, giflib, zstd, geos, libgeotiff, python, sqlite, unixodbc, expat, cryptopp, postgresql, jpeg, poppler, openjpeg, zlib, curl, jasper
Run Dependencies:
java, python, py-numpy, jackcess, 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:
8.2, 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:
xz, python, texinfo
Link Dependencies:
xz, python
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:
libpng, gobject-introspection, gettext, jpeg, libtiff, glib, pkgconfig
Link Dependencies:
libpng, gobject-introspection, gettext, jpeg, libtiff, glib
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:
fftw, libsm, netcdf, libx11, proj, wx, pslib, plplot, libxxf86vm, hdf5, readline, python, gsl, graphicsmagick, jpeg, eigen, libxinerama, py-numpy, hdf, cmake, libice
Link Dependencies:
fftw, libsm, netcdf, libx11, proj, wx, pslib, plplot, libxxf86vm, hdf5, readline, python, gsl, graphicsmagick, jpeg, eigen, libxinerama, hdf, libice
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, xerces-c, libx11, libxmu, clhep, mesa, motif, vecgeom, cmake, zlib, qt
Link Dependencies:
expat, xerces-c, libx11, libxmu, clhep, mesa, motif, vecgeom, zlib, qt
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:
opencl, fftw, clfft, cuda, cmake, boost
Link Dependencies:
opencl, fftw, cuda, clfft, boost
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, perl, pango
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:
ruby-ronn, libtool, m4, hwloc, autoconf, doxygen, automake, json-c, mpi, numactl
Link Dependencies:
hwloc, json-c, mpi, numactl
Run Dependencies:
py-natsort, py-pandas, py-numpy, py-matplotlib
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:
swig, ruby, python
Link Dependencies:
ruby, python
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:
xz, libunistring, tar, bzip2, ncurses, libxml2
Link Dependencies:
xz, libunistring, tar, bzip2, ncurses, libxml2
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, blas, hwloc, zoltan, cmake, mpi, scotch
Link Dependencies:
cuda, blas, hwloc, zoltan, cmake, mpi, scotch
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:
libpng, libxext, lcms, jpeg, libtiff, freetype, zlib, pkgconfig
Link Dependencies:
libpng, libxext, lcms, jpeg, libtiff, 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:
2.18.0, 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:
libtool, m4, pcre, openssl, libiconv, perl, automake, expat, tk, gettext, autoconf, zlib, curl
Link Dependencies:
curl, expat, pcre, openssl, tk, gettext, libiconv, zlib, perl
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:
git, python, py-argparse
Link Dependencies:
git, python, py-argparse
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, libxfixes, libxdamage, libdrm, libxi, libxau, libxcb, libxxf86vm, libsm, expat, libxext, libxmu, libxt, libxdmcp, cmake, zlib, libice
Link Dependencies:
libpng, libxfixes, libxdamage, libdrm, libxi, libxau, libxcb, libxxf86vm, libsm, expat, libxext, libxmu, libxt, libxdmcp, zlib, libice
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:
gl, cmake
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:
2.56.2, 2.56.1, 2.56.0, 2.55.1, 2.53.1, 2.49.7, 2.49.4, 2.48.1, 2.42.1
Build Dependencies:
python, pcre, libffi, gettext, pkgconfig, zlib, perl, util-linux
Link Dependencies:
util-linux, pcre, zlib, libffi, gettext
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.

glibmm

Homepage:
Spack package:
Versions:
2.19.3, 2.16.0, 2.4.8
Build Dependencies:
libsigcpp, glib
Link Dependencies:
libsigcpp, glib
Description:
Glibmm is a C++ wrapper for the glib library.

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:
exuberant-ctags, ncurses
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:
lapack, scalapack, mpi, blas
Link Dependencies:
lapack, scalapack, mpi, blas
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:
gflags, cmake
Link Dependencies:
gflags, cmake
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:
util-macros, pkgconfig
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:
libpng, gl, libx11, glu, fontconfig, libtiff, freetype, mfem
Link Dependencies:
libpng, gl, libx11, glu, fontconfig, libtiff, freetype, mfem
Description:
GLVis: an OpenGL tool for visualization of FEM meshes and functions

gmake

Homepage:
Spack package:
Versions:
4.2.1, 4.0
Build Dependencies:
guile, gettext
Link Dependencies:
guile, gettext
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).

gmodel

Homepage:
Spack package:
Versions:
2.1.0
Build Dependencies:
cmake
Description:
Gmsh model generation library Gmodel is a C++11 library that implements a minimal CAD kernel based on the .geo format used by the Gmsh mesh generation code, and is designed to make it easier for users to quickly construct CAD models for Gmsh.

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, m4, automake, libtool
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:
develop, 4.0.0, 3.0.6, 3.0.1, 2.16.0, 2.15.0, 2.12.0
Build Dependencies:
fltk, petsc, netgen, blas, oce, gmp, slepc, lapack, tetgen, hdf5, cmake, zlib, mpi
Link Dependencies:
fltk, petsc, netgen, blas, oce, gmp, slepc, lapack, tetgen, hdf5, zlib, mpi
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:
libgcrypt, libksba, libassuan, libgpg-error, npth
Link Dependencies:
libgcrypt, libksba, libassuan, libgpg-error, npth
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:
readline, libxpm, libiconv, libgd, wx, pkgconfig, cairo, libcerf, pango
Link Dependencies:
readline, libxpm, libiconv, libgd, wx, cairo, libcerf, pango
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:
nettle, gettext, zlib, pkgconfig
Link Dependencies:
nettle, zlib, gettext
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:
1.11, 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:
python, sed, bison, flex, cairo, 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, 1.0.2, 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, libtool, automake, glew, pcre, glm, sdl2-image, sdl2, boost, autoconf, jpeg, pkgconfig, freetype
Link Dependencies:
libpng, glew, pcre, sdl2-image, jpeg, freetype, sdl2, boost
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:
2.7, 2.4, 2.3
Build Dependencies:
unwind
Link Dependencies:
unwind
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:
cgal, qwt, python, mesa-glu, glew, proj, cmake, gdal, qt, boost
Link Dependencies:
cgal, qwt, python, mesa-glu, glew, proj, gdal, qt, boost
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:
libtool, mpi, hdf5
Link Dependencies:
libtool, mpi, hdf5
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:
4.8.1, 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:
gconf, gtkplus, xrandr
Link Dependencies:
gconf, gtkplus, xrandr
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, xz, ghostscript, libtool, lcms, graphviz, bzip2, jasper, libsm, ghostscript-fonts, jpeg, libtiff, libice, zlib, libxml2
Link Dependencies:
libpng, xz, ghostscript, libtool, lcms, graphviz, bzip2, jasper, libsm, ghostscript-fonts, jpeg, libtiff, libice, zlib, libxml2
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:
libpng, libtool, ghostscript, automake, fontconfig, libgd, pkgconfig, glib, qt, gts, java, gtkplus, bison, cairo, python, flex, swig, expat, autoconf, freetype, zlib, pango
Link Dependencies:
libpng, java, ghostscript, gtkplus, cairo, python, zlib, expat, fontconfig, libgd, gts, freetype, glib, qt, pango
Description:
Graph Visualization Software

grass

Homepage:
Spack package:
Versions:
7.4.1
Build Dependencies:
libpng, netcdf, blas, proj, bzip2, opencl, sqlite, gdal, python, fftw, libx11, geos, zlib, bison, cairo, gl, flex, readline, lapack, mariadb, postgresql, freetype, libtiff, gmake
Link Dependencies:
libpng, fftw, netcdf, libx11, blas, proj, zlib, libtiff, geos, cairo, lapack, gdal, opencl, gl, mariadb, postgresql, readline, sqlite, freetype, bzip2
Run Dependencies:
python
Description:
GRASS GIS (Geographic Resources Analysis Support System), is a free and open source Geographic Information System (GIS) software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization.

grib-api

Homepage:
Spack package:
Versions:
1.24.0, 1.21.0, 1.17.0, 1.16.0
Build Dependencies:
libpng, python, netcdf, cmake, libaec, py-numpy, jasper, openjpeg
Link Dependencies:
libpng, python, netcdf, libaec, 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.

grnboost

Homepage:
Spack package:
Versions:
2017-10-9
Build Dependencies:
java, sbt
Run Dependencies:
java, xgboost, spark
Description:
GRNBoost is a library built on top of Apache Spark that implements a scalable strategy for gene regulatory network (GRN) inference. See https://github.com/aertslab/GRNBoost/blob/master/docs/user_guide.md for the user guide. The location of xgboost4j-<version>.jar and GRNBoost.jar are set to $XGBOOST_JAR and $GRNBOOST_JAR. Path to xgboost4j-<version>.jar is also added to CLASSPATH.

groff

Homepage:
Spack package:
Versions:
1.22.3
Build Dependencies:
sed, ghostscript, gawk, 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, 2018.2, 2018.1, 2018, 2016.5, 2016.4, 2016.3, 5.1.5, 5.1.4, 5.1.2
Build Dependencies:
fftw, cuda, cmake, mpi, plumed
Link Dependencies:
fftw, cuda, mpi, plumed
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:
2.5, 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:
mpi, blas
Link Dependencies:
mpi, blas
Description:
Highly scalable Gather-scatter code with AMG and XXT solvers

gtkmm

Homepage:
Spack package:
Versions:
2.19.7, 2.19.6, 2.19.4, 2.19.2, 2.17.11, 2.17.1, 2.16.0, 2.4.11
Build Dependencies:
atk, glibmm, cairomm, gtkplus, pangomm
Link Dependencies:
atk, glibmm, cairomm, gtkplus, pangomm
Description:
Gtkmm is the official C++ interface for the popular GUI library GTK+.

gtkorvo-atl

Homepage:
Spack package:
Versions:
develop, 2.2, 2.1
Build Dependencies:
gtkorvo-cercs-env, cmake
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, 2.4, 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:
1.3.14, 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:
atk, shared-mime-info, gobject-introspection, gdk-pixbuf, pango, glib, pkgconfig
Link Dependencies:
atk, gobject-introspection, gdk-pixbuf, shared-mime-info, glib, pango
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:
mafft, prank, clustalw, perl-bio-perl, ruby, perl, muscle
Link Dependencies:
clustalw, ruby, muscle, mafft, prank
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:
readline, libtool, libffi, gettext, bdw-gc, gmp, libunistring, pkgconfig
Link Dependencies:
readline, libtool, libffi, gettext, bdw-gc, libunistring, gmp
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, hdf5, hdf, libmatheval, octave
Link Dependencies:
libpng, hdf5, hdf, libmatheval, octave
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.

halc

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
dos2unix
Run Dependencies:
blasr, lordec, python
Description:
HALC is software that makes error correction for long reads with high throughput.

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:
icu4c, freetype, pkgconfig, cairo, zlib, glib
Link Dependencies:
cairo, icu4c, freetype, zlib, glib
Description:
The Harfbuzz package contains an OpenType text shaping engine.

harminv

Homepage:
Spack package:
Versions:
1.4
Build Dependencies:
lapack, blas
Link Dependencies:
lapack, blas
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:
jpeg, flex, szip, zlib, bison
Link Dependencies:
jpeg, zlib, szip
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:
1.10.3, 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, zlib, mpi, szip
Link Dependencies:
numactl, zlib, mpi, szip
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:
c-blosc, hdf5
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:
r-ggplot2, samtools, python, r, py-pysam, r-rcolorbrewer, py-bx-python, py-numpy, bowtie2, py-scipy
Link Dependencies:
samtools, python, r, bowtie2
Run Dependencies:
r-ggplot2, r-rcolorbrewer, py-pysam, py-bx-python, py-numpy, py-scipy
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:
lapack, cmake, mpi, blas
Link Dependencies:
lapack, mpi, blas
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:
3.2.1, 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:
python, cuda, cmake, doxygen, py-numpy, mpi, pkgconfig
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:
hpctoolkit-externals, papi, mpi
Link Dependencies:
hpctoolkit-externals, papi, mpi
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:
mpi, blas
Link Dependencies:
mpi, blas
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:
hwloc, cmake, boost
Link Dependencies:
hwloc, boost
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:
opencl, libtool, m4, jemalloc, hwloc, autoconf, automake, pkgconfig, mpi, metis
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:
readline, libtool, m4, autoconf, ncurses, automake
Link Dependencies:
readline, ncurses
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:
2.2.0, 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:
1.9, 1.8, 1.7, 1.6, 1.4, 1.3.1, 1.2
Build Dependencies:
xz, m4, libtool, autoconf, bzip2, zlib, automake
Link Dependencies:
xz, m4, libtool, autoconf, bzip2, zlib, automake
Description:
C library for high-throughput sequencing data formats.

httpie

Homepage:
Spack package:
Versions:
0.9.9, 0.9.8
Build Dependencies:
python, py-requests, py-pygments, py-pysocks, py-argparse, py-setuptools
Link Dependencies:
python
Run Dependencies:
python, py-requests, py-pygments, py-pysocks, py-argparse, py-setuptools
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, m4, automake, libtool
Description:
The most popular spellchecking library (sez the author...).

hwloc

Homepage:
Spack package:
Versions:
2.0.2, 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:
libpciaccess, cuda, numactl, cairo, libxml2, pkgconfig
Link Dependencies:
cuda, libxml2, cairo, libpciaccess, numactl
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:
samtools, python, py-biopython, spades, exonerate, blast-plus, bwa, parallel
Link Dependencies:
samtools, parallel, spades, exonerate, blast-plus, bwa
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:
openblas, essl, cudnn, veclibfort, scalapack, mpi, gmp, lapack, netlib-lapack, intel-mkl, mpfr, mpc, cuda, cmake, cub
Link Dependencies:
openblas, essl, cudnn, veclibfort, mpi, gmp, lapack, netlib-lapack, intel-mkl, mpfr, mpc, cuda, 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:
lapack, mpi, blas
Link Dependencies:
lapack, mpi, blas
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:
libtool, m4, yajl, xcb-util-cursor, automake, libxkbcommon, cairo, xcb-util-wm, startup-notification, xcb-util-xrm, autoconf, pkgconfig, libev, xcb-util-keysyms, pango
Link Dependencies:
yajl, pango, xcb-util-cursor, xcb-util-xrm, libev, libxkbcommon, cairo, xcb-util-wm, xcb-util-keysyms, startup-notification
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:
netcdf-cxx4, googletest, everytrace, proj, py-numpy, boost, udunits2, eigen, python, py-cython, doxygen, blitz, cmake
Link Dependencies:
udunits2, python, netcdf-cxx4, everytrace, proj, eigen, blitz, boost
Run Dependencies:
py-cython, py-numpy
Description:
Misc. reusable utilities used by IceBin.

iceauth

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
util-macros, libice, xproto, pkgconfig
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:
giflib, libpng, lcms, alsa-lib, libxtst, libxext, libxt, libxinerama, libxdmcp, cups, libxcomposite, libx11, gtkplus, libxi, libxau, libxrender, xproto, pkgconfig, wget, jpeg, jdk, freetype, zlib, gmake
Link Dependencies:
giflib, libpng, libxcomposite, libx11, gtkplus, libxi, lcms, libxrender, alsa-lib, libxau, xproto, libxtst, libxext, jpeg, libxt, libxinerama, cups, freetype, zlib, libxdmcp
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:
util-macros, libx11, xproto, pkgconfig
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:
autoconf, m4, 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, libtool, ghostscript, jpeg, ghostscript-fonts, fontconfig, libtiff, freetype, pango
Link Dependencies:
libpng, ghostscript-fonts, ghostscript, jpeg, fontconfig, libtiff, freetype, pango
Description:
ImageMagick is a software suite to create, edit, compose, or convert bitmap images.

imake

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

imp

Homepage:
Spack package:
Versions:
2.8.0
Build Dependencies:
swig, python, eigen, hdf5, cmake, boost
Link Dependencies:
swig, eigen, python, hdf5, boost
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:
util-macros, pkgconfig
Description:
X Input Extension. This extension defines a protocol to provide additional input devices management such as graphic tablets.

intel

Homepage:
Spack package:
Versions:
18.0.3, 18.0.2, 18.0.1, 18.0.0, 17.0.7, 17.0.6, 17.0.4, 17.0.3, 17.0.2, 17.0.1, 17.0.0, 16.0.4, 16.0.3, 16.0.2, 15.0.6, 15.0.1
Description:
Intel Compilers.

intel-daal

Homepage:
Spack package:
Versions:
2018.3.222, 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:
python, libdrm, libpciaccess, bison, util-macros, flex, cairo, glib, pkgconfig
Link Dependencies:
cairo, libdrm, glib, libpciaccess
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:
2018.3.222, 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:
2018.3.222, 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:
cmake, intel-mkl
Link Dependencies:
intel-mkl
Description:
Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL- DNN).

intel-mpi

Homepage:
Spack package:
Versions:
2018.3.222, 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.2018.3, professional.2018.2, professional.2018.1, professional.2018.0, professional.2017.7, professional.2017.6, professional.2017.5, 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.2016.1, professional.2016.0, professional.2015.6, professional.2015.1, composer.2018.3, composer.2018.2, composer.2018.1, composer.2018.0, composer.2017.7, composer.2017.6, 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, composer.2015.1, cluster.2018.3, cluster.2018.2, cluster.2018.1, cluster.2018.0, cluster.2017.7, cluster.2017.6, 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.2016.1, cluster.2016.0, cluster.2015.6, cluster.2015.1
Description:
Intel Parallel Studio.

intel-tbb

Homepage:
Spack package:
Versions:
2018.5, 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:
libtool, m4, automake, autoconf, parallel-netcdf, mpi, hdf5
Link Dependencies:
hdf5, mpi, 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.

iperf2

Homepage:
Spack package:
Versions:
2.0.12
Description:
This code is a continuation based from the no longer maintained iperf 2.0.5 code base. Iperf 2.0.5 is still widely deployed and used by many for testing networks and for qualifying networking products.

iperf3

Homepage:
Spack package:
Versions:
3.6
Description:
The iperf series of tools perform active measurements to determine the maximum achievable bandwidth on IP networks. iperf2 is a separately maintained project.

ipopt

Homepage:
Spack package:
Versions:
3.12.10, 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:
lapack, blas, coinhsl, pkgconfig, mumps, metis
Link Dependencies:
lapack, metis, mumps, blas, 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:
icet, cuda, jpeg, jansson, mpi, boost
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 Dependenc