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 3563 mainline packages:

abinit ntpoly r-base64
abyss numactl r-base64enc
accfft numdiff r-bayesm
ace nut r-bbmisc
ack nvptx-tools r-beanplot
activeharmony nwchem r-bfast
acts-core nyancat r-bfastspatial
adept-utils ocaml r-bglr
adiak occa r-bh
adios oce r-biasedurn
adios2 oclint r-bibtex
adlbx oclock r-bindr
adol-c octave r-bindrcpp
aegean octave-optim r-biobase
aida octave-splines r-biocgenerics
alan octave-struct r-biocinstaller
albany octopus r-biocparallel
albert of-catalyst r-biocstyle
alglib of-precice r-biom-utils
allpaths-lg omega-h r-biomart
alquimia ompss r-biomformat
alsa-lib ompt-openmp r-biostrings
aluminum oniguruma r-biovizbase
amber ont-albacore r-bit
amg opa-psm2 r-bit64
amg2013 opam r-bitops
aml opari2 r-blob
amp openbabel r-blockmodeling
ampliconnoise openblas r-bookdown
amrex opencoarrays r-boot
amrvis opencv r-brew
andi openexr r-broom
angsd openfast r-bsgenome
ant openfdtd r-bumphunter
antlr openfoam r-c50
ants openfoam-org r-cairo
aoflagger openfst r-callr
aom opengl r-car
ape openglu r-cardata
aperture-photometry openimageio r-caret
apex openjdk r-caroline
apple-libunwind openjpeg r-category
applewmproto openkim-models r-catools
appres openldap r-cdcfluview
apr openmc r-cellranger
apr-util openmpi r-checkmate
aragorn openmx r-checkpoint
arborx opennurbs r-chemometrics
archer openpa r-chron
argobots openpmd-api r-circlize
argp-standalone openscenegraph r-class
argtable openslide r-classint
aria2 openspeedshop r-cli
arm-forge openspeedshop-utils r-clipr
armadillo openssh r-clisymbols
arpack-ng openssl r-cluster
arrow openstf r-clustergeneration
asagi opium r-clusterprofiler
ascent optional-lite r-cner
asciidoc optipng r-coda
asciidoctor opus r-codetools
aspa orca r-coin
aspcud orfm r-colorspace
aspect orthofiller r-combinat
aspell orthofinder r-commonmark
aspell6-de orthomcl r-complexheatmap
aspell6-en osmctools r-compositions
aspell6-es osqp r-construct
aspera-cli osu-micro-benchmarks r-convevol
assimp otf r-corhmm
astra otf2 r-corpcor
astral p4est r-corrplot
astyle p7zip r-covr
at-spi2-atk pacbio-daligner r-cowplot
at-spi2-core pacbio-damasker r-crayon
athena pacbio-dazz-db r-crosstalk
atk pacbio-dextractor r-crul
atlas packmol r-ctc
atom-dft pacvim r-cubature
atompaw pagit r-cubist
atop pagmo r-curl
attr pal r-data-table
augustus paml r-dbi
autoconf panda r-dbplyr
autodock-vina pandaseq r-debugme
autofact pandoc r-delayedarray
autogen pango r-deldir
automaded pangomm r-dendextend
automake papi r-deoptim
awscli papyrus r-deoptimr
axel paradiseo r-desc
axl parallel r-deseq
bamdst parallel-netcdf r-deseq2
bamtools paraver r-desolve
bamutil paraview r-devtools
barrnap parmetis r-diagrammer
bash parmgridgen r-dicekriging
bash-completion parquet r-dichromat
bats parsimonator r-diffusionmap
bazel parsplice r-digest
bbcp partitionfinder r-diptest
bbmap pasta r-dirichletmultinomial
bc patch r-dismo
bcftools patchelf r-diversitree
bcl2fastq2 pathfinder r-dnacopy
bdftopcf pax-utils r-do-db
bdw-gc pbbam r-domc
bear pbmpi r-doparallel
beast-tracer pbsuite r-dorng
beast1 pcma r-dose
beast2 pcre r-dosnow
bedops pcre2 r-downloader
bedtools2 pdf2svg r-dplyr
beforelight pdftk r-dqrng
benchmark pdsh r-dt
berkeley-db pdt r-dtw
bertini pegtl r-dygraphs
bib2xhtml pennant r-dynamictreecut
bigreqsproto percept r-e1071
binutils perl r-edger
bioawk perl-acme-damn r-ellipse
biobloom perl-algorithm-diff r-ellipsis
biopieces perl-alien-build r-emmli
bismark perl-alien-libxml2 r-energy
bison perl-app-cmd r-ensembldb
bitmap perl-array-utils r-ergm
blasr perl-b-hooks-endofscope r-evaluate
blasr-libcpp perl-bio-perl r-expint
blast-legacy perl-bit-vector r-expm
blast-plus perl-cairo r-factoextra
blast2go perl-capture-tiny r-factominer
blat perl-carp-clan r-fansi
blaze perl-cgi r-fastcluster
blis perl-class-data-inheritable r-fastmatch
bliss perl-class-inspector r-ff
blitz perl-class-load r-fftwtools
bmake perl-class-load-xs r-fgsea
bmi perl-clone r-filehash
bml perl-clone-choose r-findpython
bohrium perl-compress-raw-bzip2 r-fit-models
bolt perl-compress-raw-zlib r-fitdistrplus
bookleaf-cpp perl-config-general r-flashclust
boost perl-contextual-return r-flexclust
boostmplcartesianproduct perl-cpan-meta-check r-flexmix
bowtie perl-data-dumper r-fnn
bowtie2 perl-data-optlist r-forcats
boxlib perl-data-stag r-foreach
bpp-core perl-dbd-mysql r-forecast
bpp-phyl perl-dbd-pg r-foreign
bpp-seq perl-dbd-sqlite r-formatr
bpp-suite perl-dbfile r-formula
bracken perl-dbi r-fpc
braker perl-devel-cycle r-fracdiff
branson perl-devel-globaldestruction r-fs
breakdancer perl-devel-overloadinfo r-futile-logger
breseq perl-devel-stacktrace r-futile-options
bridger perl-devel-symdump r-future
brigand perl-digest-md5 r-future-apply
brotli perl-dist-checkconflicts r-gamlss
bsseeker2 perl-encode-locale r-gamlss-data
bucky perl-error r-gamlss-dist
bumpversion perl-eval-closure r-gbm
busco perl-exception-class r-gbrd
butter perl-exporter-tiny r-gcrma
butterflypack perl-extutils-config r-gdalutils
bwa perl-extutils-depends r-gdata
bwtool perl-extutils-helpers r-gdsfmt
byobu perl-extutils-installpaths r-geiger
bzip2 perl-extutils-makemaker r-genefilter
c-blosc perl-extutils-pkgconfig r-genelendatabase
c-blosc2 perl-ffi-checklib r-geneplotter
c-lime perl-file-chdir r-generics
cabana perl-file-copy-recursive r-genie3
caffe perl-file-homedir r-genomeinfodb
cairo perl-file-listing r-genomeinfodbdata
cairomm perl-file-pushd r-genomicalignments
caliper perl-file-sharedir-install r-genomicfeatures
callpath perl-file-slurp-tiny r-genomicranges
camellia perl-file-slurper r-gensa
camx perl-file-which r-geomorph
candle-benchmarks perl-font-ttf r-geonames
cantera perl-forks r-geoquery
canu perl-gd r-geor
cap3 perl-gd-graph r-geosphere
capstone perl-gd-text r-getopt
cardioid perl-gdgraph-histogram r-getoptlong
cares perl-graph r-ggally
casacore perl-graph-readwrite r-ggbio
cask perl-hash-merge r-ggdendro
casper perl-html-parser r-ggjoy
catalyst perl-html-tagset r-ggmap
catch perl-http-cookies r-ggplot2
cbench perl-http-daemon r-ggpubr
cblas perl-http-date r-ggrepel
cbtf perl-http-message r-ggridges
cbtf-argonavis perl-http-negotiate r-ggsci
cbtf-argonavis-gui perl-inline r-ggsignif
cbtf-krell perl-inline-c r-ggvis
cbtf-lanl perl-intervaltree r-gh
ccache perl-io-all r-gistr
ccfits perl-io-compress r-git2r
ccs-qcd perl-io-html r-glimma
cctools perl-io-prompt r-glmnet
cdbfasta perl-io-sessiondata r-globaloptions
cdd perl-io-socket-ssl r-globals
cddlib perl-io-string r-glue
cdecimal perl-io-stringy r-gmodels
cdhit perl-io-tty r-gmp
cdo perl-ipc-run r-go-db
ceed perl-json r-googlevis
cereal perl-libwww-perl r-goplot
ceres-solver perl-libxml-perl r-gosemsim
cfitsio perl-list-moreutils r-goseq
cgal perl-list-moreutils-xs r-gostats
cgdb perl-log-log4perl r-gower
cgm perl-logger-simple r-gplots
cgns perl-lwp r-graph
channelflow perl-lwp-mediatypes r-grbase
chapel perl-lwp-protocol-https r-gridbase
charliecloud perl-mailtools r-gridextra
charmpp perl-math-bezier r-gsa
chatterbug perl-math-cdf r-gseabase
check perl-math-cephes r-gss
chill perl-math-matrixreal r-gsubfn
chlorop perl-math-round r-gtable
chombo perl-math-vecstat r-gtools
chrpath perl-module-build r-gtrellis
cinch perl-module-build-tiny r-gviz
circos perl-module-implementation r-gwmodel
cistem perl-module-runtime r-haven
citcoms perl-module-runtime-conflicts r-hdf5r
cityhash perl-moose r-hexbin
clamav perl-mozilla-ca r-highr
clamr perl-mro-compat r-hmisc
clapack perl-namespace-clean r-hms
claw perl-net-http r-hoardr
cleaveland4 perl-net-scp-expect r-htmltable
cleverleaf perl-net-ssleay r-htmltools
clfft perl-number-format r-htmlwidgets
clhep perl-object-insideout r-httpcode
clingo perl-package-deprecationmanager r-httpuv
cln perl-package-stash r-httr
cloc perl-package-stash-xs r-hwriter
cloog perl-padwalker r-hypergraph
cloverleaf perl-parallel-forkmanager r-ica
cloverleaf3d perl-params-util r-igraph
clp perl-params-validate r-illuminaio
clustalo perl-parse-recdescent r-impute
clustalw perl-path-tiny r-influencer
cmake perl-pdf-api2 r-ini
cmocka perl-pegex r-inline
cmor perl-perl-unsafe-signals r-interactivedisplaybase
cnmem perl-perl4-corelibs r-intervals
cnpy perl-perl6-slurp r-inum
cntk perl-perlio-gzip r-ipred
cntk1bitsgd perl-perlio-utf8-strict r-iranges
cnvnator perl-readonly r-irdisplay
codar-cheetah perl-regexp-common r-irkernel
codes perl-scalar-list-utils r-irlba
coevp perl-scalar-util-numeric r-isdparser
cohmm perl-set-intspan r-iso
coinhsl perl-set-scalar r-iterators
colm perl-soap-lite r-janitor
colordiff perl-star-fusion r-jaspar2018
comd perl-statistics-basic r-jomo
commons-lang perl-statistics-descriptive r-jpeg
commons-lang3 perl-statistics-pca r-jsonlite
commons-logging perl-sub-exporter r-kegg-db
compiz perl-sub-exporter-progressive r-kegggraph
compositeproto perl-sub-identify r-keggrest
conduit perl-sub-install r-kernlab
connect-proxy perl-sub-name r-kernsmooth
constype perl-sub-uplevel r-kknn
converge perl-svg r-knitr
coreutils perl-swissknife r-ks
corset perl-sys-sigaction r-labeling
cosmomc perl-task-weaken r-lambda-r
cosp2 perl-term-readkey r-laplacesdemon
cotter perl-test-cleannamespaces r-lars
cowsay perl-test-deep r-later
cp2k perl-test-differences r-lattice
cppad perl-test-exception r-latticeextra
cppcheck perl-test-fatal r-lava
cppgsl perl-test-memory-cycle r-lazyeval
cpprestsdk perl-test-most r-leaflet
cppunit perl-test-needs r-leaps
cppzmq perl-test-requires r-learnbayes
cpu-features perl-test-requiresinternet r-leiden
cpuinfo perl-test-warn r-lhs
cquery perl-test-warnings r-libcoin
cram perl-text-csv r-limma
cromwell perl-text-diff r-listenv
cromwell-womtool perl-text-format r-lme4
cryptopp perl-text-simpletable r-lmtest
cryptsetup perl-text-soundex r-locfit
cscope perl-text-unidecode r-log4r
csdp perl-time-hires r-loo
ctffind perl-time-piece r-lpsolve
cub perl-timedate r-lsei
cube perl-try-tiny r-lubridate
cubelib perl-uri r-magic
cubew perl-version r-magick
cuda perl-want r-magrittr
cuda-memtest perl-www-robotrules r-makecdfenv
cudnn perl-xml-dom r-maldiquant
cufflinks perl-xml-dom-xpath r-manipulatewidget
cups perl-xml-filter-buffertext r-mapproj
curl perl-xml-libxml r-maps
cvs perl-xml-namespacesupport r-maptools
cxxopts perl-xml-parser r-markdown
czmq perl-xml-parser-lite r-mass
dakota perl-xml-quote r-matr
daligner perl-xml-regexp r-matrix
damageproto perl-xml-sax r-matrixmodels
damaris perl-xml-sax-base r-matrixstats
damselfly perl-xml-sax-writer r-mclust
darshan-runtime perl-xml-simple r-mcmcglmm
darshan-util perl-xml-twig r-mco
dash perl-xml-writer r-mda
datamash perl-xml-xpathengine r-memoise
dataspaces perl-yaml r-mergemaid
dateutils perl-yaml-libyaml r-metap
davix petsc r-mgcv
dbcsr pexsi r-mgraster
dbus pfft r-mice
dcmtk pflotran r-mime
dd4hep pfunit r-minfi
dealii pgdspider r-miniui
dealii-parameter-gui pgi r-minqa
deconseq-standalone pgmath r-misc3d
dejagnu phantompeakqualtools r-mitml
delly2 phast r-mitools
denovogear phasta r-mixtools
dftfe phist r-mlbench
dia phrap-crossmatch-swat r-mlinterfaces
dialign phred r-mlr
dialign-tx phylip r-mlrmbo
diamond phyluce r-mmwrweek
diffsplice picard r-mnormt
diffutils picsar r-modelmetrics
dimemas picsarlite r-modelr
direnv pidx r-modeltools
discovar pigz r-mpm
discovardenovo pilon r-msnbase
dislin pindel r-multcomp
diy piranha r-multicool
dlpack pism r-multitaper
dmd pixman r-multtest
dmlc-core pixz r-munsell
dmtcp pkg-config r-mvtnorm
dmxproto pkgconf r-mzid
docbook-xml pktools r-mzr
docbook-xsl planck-likelihood r-nanotime
dos2unix plasma r-ncbit
dotnet-core-sdk platypus r-ncdf4
double-conversion plink r-network
doxygen plplot r-networkd3
draco plumed r-nleqslv
dri2proto pmdk r-nlme
dri3proto pmgr-collective r-nloptr
ds pmix r-nmf
dsdp pmlib r-nmof
dsrc pnfft r-nnet
dtcmp pngquant r-nnls
dyninst pngwriter r-nor1mix
dysco pnmpi r-nortest
ea-utils poamsa r-np
easybuild pocl r-npsurv
ebms polymake r-numderiv
eccodes poppler r-oligoclasses
ecflow poppler-data r-openssl
eclipse-gcj-parser popt r-openxlsx
ecp-io-sdk porta r-optparse
ecp-proxy-apps portage r-ordinal
ecp-viz-sdk portcullis r-org-hs-eg-db
ed postgresql r-organismdbi
editline powerapi r-packrat
editres ppl r-pacman
eem pplacer r-paleotree
eigen prank r-pamr
elasticsearch precice r-pan
elemental presentproto r-parallelmap
elfutils preseq r-paramhelpers
elk price r-party
elmer-fem primer3 r-partykit
elpa prinseq-lite r-pathview
elsd printproto r-pbapply
elsdc prng r-pbdzmq
elsi probconsrna r-pbkrtest
emacs procps r-pcamethods
ember prodigal r-pcapp
emboss proj r-permute
enchant protobuf r-pfam-db
energyplus protobuf-c r-phangorn
entrezdirect proxymngr r-phantompeakqualtools
environment-modules prrte r-phyloseq
eospac pruners-ninja r-phylostratr
eqr ps-lite r-phytools
er psi4 r-picante
erfa pslib r-pillar
ermod psm r-pkgbuild
erne psmc r-pkgconfig
es pstreams r-pkgload
esmf pugixml r-pkgmaker
essl pumi r-plogr
ethminer pv r-plot3d
etsf-io pvm r-plotly
everytrace pxz r-plotrix
everytrace-example py-3to2 r-pls
evieext py-4suite-xml r-plyr
exabayes py-abipy r-pmcmr
examinimd py-absl-py r-png
exampm py-adios r-polynom
exasp2 py-advancedhtmlparser r-popgenome
exchanger py-aenum r-popvar
exiv2 py-affine r-powerlaw
exmcutils py-alabaster r-prabclus
exodusii py-alembic r-praise
exonerate py-altgraph r-preprocesscore
expat py-antlr4-python3-runtime r-prettyunits
expect py-apache-libcloud r-processx
express py-apipkg r-prodlim
extrae py-appdirs r-progress
exuberant-ctags py-appnope r-promises
eztrace py-apscheduler r-protgenerics
f18 py-argcomplete r-proto
f90cache py-argparse r-proxy
fabtests py-asdf r-pryr
falcon py-ase r-ps
fann py-asn1crypto r-psych
faodel py-astor r-ptw
fast-global-file-status py-astroid r-purrr
fasta py-astropy r-qtl
fastjar py-astunparse r-quadprog
fastmath py-async-generator r-quantmod
fastme py-atomicwrites r-quantreg
fastp py-atropos r-quantro
fastphase py-attrs r-qvalue
fastq-screen py-autopep8 r-r-methodss3
fastqc py-avro r-r-oo
fastqvalidator py-avro-json-serializer r-r-utils
fasttree py-babel r-r6
fastx-toolkit py-backcall r-randomfields
fenics py-backports-abc r-randomfieldsutils
fermi py-backports-functools-lru-cache r-randomforest
fermikit py-backports-shutil-get-terminal-size r-randomglm
fermisciencetools py-backports-ssl-match-hostname r-ranger
ferret py-backports-tempfile r-rann
ffmpeg py-backports-weakref r-rappdirs
fftw py-basemap r-raster
fgsl py-bcbio-gff r-rbgl
figtree py-beautifulsoup4 r-rbokeh
fimpute py-bintrees r-rcmdcheck
findutils py-binwalk r-rcolorbrewer
fio py-biom-format r-rcpp
fish py-biomine r-rcppannoy
fixesproto py-biopython r-rcpparmadillo
fl py-bitarray r-rcppblaze
flac py-bitstring r-rcppcctz
flang py-black r-rcppcnpy
flann py-bleach r-rcppeigen
flash py-blessed r-rcppparallel
flatbuffers py-blessings r-rcppprogress
flatcc py-blinker r-rcurl
flecsale py-bokeh r-rda
flecsi py-boltons r-rdpack
flecsph py-boto3 r-readr
flex py-botocore r-readxl
flibcpp py-bottleneck r-recipes
flint py-breakseq2 r-registry
flit py-breathe r-rematch
fltk py-brian r-remotes
flux-core py-brian2 r-reordercluster
flux-sched py-brotlipy r-reportingtools
fluxbox py-bsddb3 r-repr
fmt py-bx-python r-reprex
foam-extend py-bz2file r-reshape
folly py-cachetools r-reshape2
font-util py-cairocffi r-reticulate
fontcacheproto py-cartopy r-rex
fontconfig py-cclib r-rgdal
fontsproto py-cdat-lite r-rgenoud
fonttosfnt py-cdo r-rgeos
fp16 py-cdsapi r-rgexf
fpc py-certifi r-rgl
fpocket py-certipy r-rgooglemaps
fqtrim py-cf-units r-rgraphviz
fr-hit py-cffi r-rhdf5
freebayes py-cftime r-rhmmer
freeglut py-chardet r-rhtslib
freeimage py-checkm-genome r-rinside
freetype py-cheetah r-rio
freexl py-click r-rjags
fribidi py-click-plugins r-rjava
fseq py-cligj r-rjson
fsl py-clipboard r-rjsonio
fslsfonts py-cloudpickle r-rlang
fstobdf py-codecov r-rmarkdown
fstrack py-cogent r-rminer
ftgl py-colorama r-rmpfr
fujitsu-mpi py-colorlog r-rmpi
funhpc py-colormath r-rmutil
fyba py-colorpy r-rmysql
fzf py-configobj r-rngtools
g4abla py-configparser r-rnoaa
g4emlow py-contextlib2 r-robust
g4ensdfstate py-counter r-robustbase
g4ndl py-cov-core r-rocr
g4neutronxs py-coverage r-rodbc
g4photonevaporation py-cpuinfo r-rook
g4pii py-crispresso r-rots
g4radioactivedecay py-crossmap r-roxygen2
g4realsurface py-cryptography r-rpart
g4saiddata py-csvkit r-rpart-plot
g4tendl py-current r-rpostgresql
gams py-cutadapt r-rprojroot
gapbs py-cvxopt r-rrblup
gapcloser py-cycler r-rrcov
gapfiller py-cython r-rrpp
gasnet py-dask r-rsamtools
gatk py-dbf r-rsnns
gaudi py-decorator r-rsolnp
gaussian py-deeptools r-rspectra
gawk py-deeptoolsintervals r-rsqlite
gblocks py-defusedxml r-rstan
gcc py-dendropy r-rstantools
gccmakedep py-descartes r-rstudioapi
gccxml py-dill r-rsvd
gconf py-discover r-rtracklayer
gcta py-dlcpar r-rtsne
gdal py-dnaio r-runit
gdb py-docopt r-rvcheck
gdbm py-docutils r-rvest
gdk-pixbuf py-docutils-stubs r-rzmq
gdl py-doxypy r-s4vectors
geant4 py-doxypypy r-samr
geant4-data py-dryscrape r-sandwich
gearshifft py-dxchange r-scales
gemmlowp py-dxfile r-scatterplot3d
genemark-et py-earthengine-api r-sctransform
genomefinisher py-easybuild-easyblocks r-sdmtools
genometools py-easybuild-easyconfigs r-segmented
geopm py-easybuild-framework r-selectr
geos py-ecdsa r-seqinr
gettext py-edffile r-seqlogo
gflags py-editdistance r-sessioninfo
ghost py-elasticsearch r-seurat
ghostscript py-elephant r-sf
ghostscript-fonts py-emcee r-sfsmisc
giflib py-empy r-shape
ginkgo py-entrypoints r-shiny
git py-enum34 r-shinydashboard
git-fat-git py-epydoc r-shinyfiles
git-imerge py-espresso r-shortread
git-lfs py-espressopp r-siggenes
gl2ps py-et-xmlfile r-simpleaffy
glew py-eventlet r-sitmo
glfmultiples py-execnet r-sm
glib py-exodus r-smoof
glibmm py-fallocate r-sn
glimmer py-fastaindex r-snakecase
glm py-fastcache r-snow
global py-fasteners r-snowfall
globalarrays py-faststructure r-snprelate
glog py-filelock r-som
gloo py-filemagic r-somaticsignatures
glpk py-fiona r-sourcetools
glproto py-fiscalyear r-sp
glvis py-flake8 r-spacetime
gmake py-flake8-import-order r-sparsem
gmap-gsnap py-flake8-polyfill r-spatial
gmime py-flask r-spatialreg
gmodel py-flask-compress r-spdata
gmp py-flask-socketio r-spdep
gmsh py-flexx r-speedglm
gmt py-flye r-spem
gmtsar py-fn r-splancs
gnat py-fortranformat r-splitstackshape
gnome-common py-fparser r-sqldf
gnu-prolog py-freezegun r-squarem
gnupg py-fsspec r-squash
gnuplot py-funcsigs r-sseq
gnutls py-functools32 r-stanheaders
go py-future r-statmod
go-bootstrap py-futures r-statnet-common
go-md2man py-fypp r-stringi
gobject-introspection py-gast r-stringr
googletest py-gdbgui r-strucchange
gotcha py-gdc-client r-subplex
gource py-gee-asset-manager r-summarizedexperiment
gperf py-geeadd r-survey
gperftools py-geeup r-survival
gpgme py-genders r-sva
gplates py-genshi r-sys
gpu-burn py-gensim r-tarifx
grackle py-geoalchemy2 r-taxizedb
gradle py-geopandas r-tclust
grandr py-gevent r-tensora
graph500 py-git-review r-testit
graphicsmagick py-git2 r-testthat
graphlib py-gnuplot r-tfbstools
graphmap py-goatools r-tfmpvalue
graphviz py-google-api-core r-th-data
grass py-google-api-python-client r-threejs
grib-api py-google-auth r-tibble
grnboost py-google-auth-httplib2 r-tidycensus
groff py-google-cloud-core r-tidyr
gromacs py-google-cloud-storage r-tidyselect
grpc py-google-resumable-media r-tidyverse
gsl py-googleapis-common-protos r-tiff
gslib py-gpaw r-tigris
gtkmm py-graphviz r-timedate
gtkorvo-atl py-greenlet r-tinytex
gtkorvo-cercs-env py-grequests r-tmixclust
gtkorvo-dill py-griddataformats r-topgo
gtkorvo-enet py-guidata r-triebeard
gtkplus py-guiqwt r-trimcluster
gtksourceview py-h5glance r-truncnorm
gts py-h5py r-trust
guidance py-hdfs r-tseries
guile py-hepdata-validator r-tsne
gurobi py-hpccm r-ttr
h5hut py-html2text r-ucminf
h5part py-html5lib r-udunits2
h5utils py-htseq r-units
h5z-zfp py-httpbin r-urca
hacckernels py-httplib2 r-urltools
hadoop py-humanize r-usethis
halc py-hypothesis r-utf8
hapcut2 py-idna r-uuid
hapdip py-igraph r-uwot
haploview py-illumina-utils r-variantannotation
harfbuzz py-imageio r-varselrf
harminv py-imagesize r-vcd
hc py-iminuit r-vctrs
hdf py-importlib r-vegan
hdf5 py-importlib-metadata r-vfs
hdf5-blosc py-iniparse r-vgam
heaptrack py-invoke r-vipor
help2man py-ipaddress r-viridis
henson py-ipdb r-viridislite
hepmc py-ipykernel r-visnetwork
heppdt py-ipython r-vsn
hic-pro py-ipython-genutils r-webshot
highfive py-ipywidgets r-wgcna
highwayhash py-isort r-whisker
hiop py-itsdangerous r-withr
hisat2 py-jdcal r-xde
hisea py-jedi r-xfun
hmmer py-jinja2 r-xgboost
homer py-jmespath r-xlconnect
hoomd-blue py-joblib r-xlconnectjars
hotspot py-jplephem r-xlsx
hpccg py-jprops r-xlsxjars
hpctoolkit py-jpype r-xmapbridge
hpcviewer py-jsonpatch r-xml
hpgmg py-jsonpointer r-xml2
hpl py-jsonschema r-xnomial
hpx py-junit-xml r-xopen
hpx5 py-jupyter-client r-xtable
hsakmt py-jupyter-console r-xts
hstr py-jupyter-core r-xvector
htop py-jupyter-notebook r-yaml
htslib py-jupyterhub r-yapsa
httpie py-keras r-yaqcaffy
hub py-keras-applications r-yarn
hugo py-keras-preprocessing r-zeallot
hunspell py-kitchen r-zip
hwloc py-kiwisolver r-zlibbioc
hybpiper py-kmodes r-zoo
hydra py-lark-parser r3d
hydrogen py-latexcodec racon
hyphy py-lazy raft
hypre py-lazy-object-proxy ragel
i3 py-lazy-property raja
ibm-java py-lazyarray randfold
ibmisc py-libconf random123
iceauth py-libensemble randrproto
icedtea py-ligo-segments range-v3
icet py-line-profiler rankstr
ico py-linecache2 rapidjson
icu4c py-lit ravel
id3lib py-llvmlite raxml
idba py-lmfit ray
iegenlib py-localcider rclone
igraph py-locket rdma-core
igvtools py-lockfile rdp-classifier
ilmbase py-logilab-common rdptools
image-magick py-lrudict re2c
imake py-lscsoft-glue readfq
imp py-luigi readline
impute2 py-lxml recon
infernal py-lzstring recordproto
inputproto py-m2r redis
intel py-macholib redset
intel-daal py-machotools redundans
intel-gpu-tools py-macs2 regcm
intel-ipp py-maestrowf relax
intel-mkl py-mako relion
intel-mkl-dnn py-markdown rempi
intel-mpi py-markupsafe rename
intel-parallel-studio py-matplotlib rendercheck
intel-pin py-mccabe renderproto
intel-tbb py-mdanalysis repeatmasker
intel-xed py-mechanize repeatmodeler
interproscan py-meep repeatscout
intltool py-memory-profiler resourceproto
ioapi py-merlin revbayes
ior py-metasv rgb
iozone py-methylcode rhash
iperf2 py-mg-rast-tools rlwrap
iperf3 py-misopy rmats
ipopt py-mistune rmlab
isaac py-mlxtend rna-seqc
isaac-server py-mo-pack rngstreams
isl py-mock rocksdb
iso-codes py-modred rockstar
itstool py-moltemplate rodinia
itsx py-mongo root
jackcess py-monotonic rose
jags py-monty ross
jansson py-more-itertools routino
jasper py-mpi4py rpcsvc-proto
jbigkit py-mpld3 rr
jchronoss py-mpmath rsbench
jdk py-multi-key-dict rsem
jellyfish py-multiprocess rstart
jemalloc py-multiqc rsync
jmol py-munch rtags
jq py-mx rtax
json-c py-myhdl ruby
json-cwx py-mypy ruby-gnuplot
json-fortran py-mypy-extensions ruby-narray
json-glib py-mysql-connector ruby-ronn
jsoncpp py-mysqlclient ruby-rubyinline
jube py-mysqldb1 ruby-svn2git
judy py-natsort ruby-terminal-table
julia py-nbconvert rust
k8 py-nbformat rust-bindgen
kahip py-nc-time-axis sabre
kaiju py-neo saga-gis
kaks-calculator py-nestle sailfish
kaldi py-netcdf4 salmon
kallisto py-netifaces sambamba
karma py-networkx samblaster
kbproto py-nose samrai
kdiff3 py-nose2 samtools
kealib py-nosexcover sandbox
kentutils py-numba sas
kibana py-numexpr satsuma2
kim-api py-numexpr3 savanna
kitty py-numpy saws
kmergenie py-numpydoc sbt
kokkos py-oauth2client scala
kokkos-kernels py-oauthlib scalasca
kraken py-olefile scallop
krb5 py-onnx scalpel
krims py-ont-fast5-api scan-for-matches
kripke py-openpmd-validator scons
kvasir-mpl py-openpyxl scorec-core
kvtree py-openslide-python scorep
ladot py-opentuner scotch
laghos py-opppy scr
lame py-ordereddict screen
lammps py-oset scripts
last py-overpy scrnsaverproto
lastz py-owslib sctk
laszip py-packaging sdl2
latte py-palettable sdl2-image
launchmon py-pamela sdsl-lite
lazyten py-pandas seacas
lbann py-paramiko sed
lbxproxy py-partd sentieon-genomics
lbzip2 py-path-py seqan
lcals py-pathlib seqkit
lcms py-pathlib2 seqprep
ldc py-pathos seqtk
ldc-bootstrap py-pathspec serf
legion py-patsy sessreg
lemon py-pauvre setxkbmap
leveldb py-pbr sga
lftp py-pep8-naming shadow
libaec py-perf shapeit
libaio py-performance shared-mime-info
libapplewm py-periodictable shiny-server
libarchive py-petsc4py shocklibs
libassuan py-pexpect shoremap
libatomic-ops py-phonopy shortbred
libbeagle py-pickleshare shortstack
libbeato py-picrust showfont
libbsd py-pil shuffile
libbson py-pillow sickle
libcanberra py-pint siesta
libcap py-pip signalp
libceed py-pipits signify
libcerf py-pispino silo
libcheck py-pkgconfig simgrid
libcint py-pkginfo simplemoc
libcircle py-planar simul
libconfig py-plotly simulationio
libcroco py-pluggy singularity
libctl py-ply singularity-legacy
libdivsufsort py-pmw sirius
libdmx py-poster skilion-onedrive
libdrm py-pox skopeo
libdwarf py-ppft sl
libeatmydata py-prettytable slate
libedit py-progress sleef
libelf py-progressbar2 slepc
libemos py-projectq slurm
libepoxy py-prometheus-client smalt
libev py-prompt-toolkit smof
libevent py-protobuf smproxy
libevpath py-psutil snakemake
libfabric py-psyclone snap
libffi py-psycopg2 snap-berkeley
libffs py-ptyprocess snap-korf
libfive py-pudb snappy
libflame py-py snbone
libfontenc py-py2bit sniffles
libfs py-py2cairo snpeff
libgcrypt py-py2neo snphylo
libgd py-py4j snptest
libgeotiff py-pyani soapdenovo-trans
libgit2 py-pyarrow soapdenovo2
libglvnd py-pyasn1 sofa-c
libgpg-error py-pyasn1-modules somatic-sniper
libgpuarray py-pybedtools sortmerna
libgridxc py-pybigwig sosflow
libgtextutils py-pybind11 sowing
libharu py-pybtex sox
libhio py-pybtex-docutils spades
libiberty py-pycairo span-lite
libibumad py-pycares spark
libice py-pycbc sparsehash
libiconv py-pychecker sparta
libidn2 py-pycodestyle spdlog
libint py-pycparser spectrum-mpi
libjpeg py-pycrypto speex
libjpeg-turbo py-pycuda spglib
libkml py-pycurl sph2pipe
libksba py-pydatalog spherepack
liblas py-pydispatcher spindle
liblbxutil py-pydot spm
liblockfile py-pydot2 spot
libmad py-pydotplus sqlite
libmatheval py-pydv sqlitebrowser
libmaxminddb py-pyelftools squashfs
libmesh py-pyepsg squid
libmng py-pyfaidx sra-toolkit
libmo-unpack py-pyfasta ssht
libmongoc py-pyfftw sspace-longread
libmonitor py-pyflakes sspace-standard
libnbc py-pygdal sst-core
libnl py-pygdbmi sst-dumpi
libnova py-pyglet sst-macro
libnrm py-pygments stacks
libnsl py-pygobject staden-io-lib
libogg py-pygpu star
liboldx py-pygresql star-ccm-plus
libpcap py-pygtk startup-notification
libpciaccess py-pyjwt stat
libpeas py-pyke stata
libpfm4 py-pykml stc
libpipeline py-pykwalify steps
libplist py-pyliblzma stow
libpmemobj-cpp py-pylint strace
libpng py-pymatgen stream
libpsl py-pyminifier strelka
libpthread-stubs py-pymol stress
libquo py-pymongo string-view-lite
librom py-pymorph stringtie
librsvg py-pympler structure
libseccomp py-pymysql strumpack
libsecret py-pynio sublime-text
libsharp py-pynn subread
libshm py-pyodbc subversion
libsigcpp py-pyomo suite-sparse
libsigsegv py-pyopenssl sumaclust
libsm py-pypar sundials
libsodium py-pyparsing superlu
libspatialindex py-pypeflow superlu-dist
libspatialite py-pyperclip superlu-mt
libsplash py-pyprof2html supernova
libssh py-pyproj sw4lite
libssh2 py-pyqi swap-assembler
libsvm py-pyqt4 swarm
libszip py-pyqt5 swfft
libtasn1 py-pyrad swftools
libtermkey py-pyrosar swiftsim
libtiff py-pysam swig
libtirpc py-pyscaf symengine
libtomlc99 py-pyserial sympol
libtool py-pyshp sz
libunistring py-pyside tabix
libunwind py-pysmartdl talass
libusb py-pysocks talloc
libusbmuxd py-pyspark tantan
libuuid py-pysqlite tar
libuv py-pytailf targetp
libvdwxc py-pytest task
libvorbis py-pytest-cache taskd
libvterm py-pytest-cov tasmanian
libwebp py-pytest-flake8 tassel
libwebsockets py-pytest-forked tau
libwindowswm py-pytest-httpbin tcl
libx11 py-pytest-isort tcl-itcl
libxau py-pytest-mock tcl-tcllib
libxaw py-pytest-runner tcl-tclxml
libxaw3d py-pytest-xdist tclap
libxc py-pythia tcoffee
libxcb py-python-daemon tcptrace
libxcomposite py-python-dateutil tcsh
libxcursor py-python-editor tealeaf
libxdamage py-python-engineio tecplot
libxdmcp py-python-gitlab templight
libxevie py-python-htmlgen templight-tools
libxext py-python-jenkins tetgen
libxfixes py-python-ldap tethex
libxfont py-python-levenshtein texinfo
libxfont2 py-python-magic texlive
libxfontcache py-python-mapnik texstudio
libxft py-python-memcached textparser
libxi py-python-oauth2 tfel
libxinerama py-python-socketio the-platinum-searcher
libxkbcommon py-python-utils the-silver-searcher
libxkbfile py-pythonqwt thornado-mini
libxkbui py-pytools thrift
libxml2 py-pytz thrust
libxmu py-pyudev tig
libxp py-pyugrid time
libxpm py-pyutilib tinyxml
libxpresent py-pyvcf tinyxml2
libxprintapputil py-pywavelets tioga
libxprintutil py-pyyaml tippecanoe
libxrandr py-qtawesome tix
libxrender py-qtconsole tk
libxres py-qtpy tldd
libxscrnsaver py-quantities tmalign
libxshmfence py-quast tmhmm
libxslt py-queryablelist tmux
libxsmm py-radical-utils tmuxinator
libxstream py-ranger tophat
libxt py-rasterio tppred
libxtrap py-ratelim tracer
libxtst py-raven transabyss
libxv py-readme-renderer transdecoder
libxvmc py-redis transposome
libxxf86dga py-regex transset
libxxf86misc py-reportlab trapproto
libxxf86vm py-repoze-lru tree
libyaml py-requests treesub
libyogrt py-requests-futures trf
libzip py-requests-oauthlib triangle
liggghts py-requests-toolbelt trilinos
lighttpd py-restview trilinos-catalyst-ioss-adapter
likwid py-retrying trimal
linkphase3 py-rope trimgalore
linux-headers py-rpy2 trimmomatic
listres py-rsa trinity
llvm py-rseqc trinotate
llvm-openmp py-rtree trnascan-se
llvm-openmp-ompt py-ruamel-yaml turbine
lm-sensors py-s3transfer turbomole
lmdb py-saga-python tut
lmod py-scandir twm
lndir py-scientificpython tycho2
log4cplus py-scikit-image typhon
log4cxx py-scikit-learn typhonio
loki py-scikit-optimize ucx
lordec py-scipy udunits2
lrslib py-scoop ufo-core
lrzip py-scp ufo-filters
lsf py-seaborn umap
lsof py-selenium umoci
ltrace py-semantic-version umpire
lua py-send2trash unblur
lua-bitlib py-setuptools uncrustify
lua-jit py-setuptools-git unibilium
lua-lpeg py-setuptools-scm unifyfs
lua-luafilesystem py-sfepy unison
lua-luaposix py-sgp4 units
lua-mpack py-sh unittest-cpp
luit py-shapely unixodbc
lulesh py-shiboken unrar
lumpy-sv py-simplegeneric unuran
lvm2 py-simplejson unzip
lwgrp py-simplekml upcxx
lwm2 py-singledispatch uriparser
lz4 py-sip usearch
lzma py-six utf8proc
lzo py-slepc4py util-linux
m4 py-slurm-pipeline util-macros
macsio py-smart-open uuid
mad-numdiff py-sncosmo uvw
mafft py-snowballstemmer valgrind
magics py-snuggs vampirtrace
magma py-sortedcontainers vardictjava
makedepend py-soupsieve varscan
maker py-spatialist vc
mallocmc py-spectra vcftools
man-db py-spefile vcsh
manta py-spglib vdt
mapnik py-sphinx vecgeom
mapserver py-sphinx-bootstrap-theme veclibfort
maq py-sphinx-rtd-theme vegas2
margo py-sphinxautomodapi veloc
mariadb py-sphinxcontrib-applehelp velvet
mariadb-c-client py-sphinxcontrib-bibtex verilator
masa py-sphinxcontrib-devhelp verrou
masurca py-sphinxcontrib-htmlhelp vesta
mathematica py-sphinxcontrib-jsmath videoproto
matio py-sphinxcontrib-programoutput viennarna
matlab py-sphinxcontrib-qthelp viewres
maven py-sphinxcontrib-serializinghtml vigra
maverick py-sphinxcontrib-websupport vim
mawk py-spyder virtualgl
mbedtls py-spykeutils visit
mc py-sqlalchemy vizglow
mcl py-statsmodels vmatch
mdtest py-stevedore voropp
med py-storm votca-csg
meep py-stratify votca-ctp
mefit py-subprocess32 votca-tools
megadock py-symengine votca-xtp
megahit py-symfit vpfft
memaxes py-sympy vpic
meme py-systemd-python vsearch
memkind py-tables vt
memsurfer py-tabulate vtk
meraculous py-tappy vtkh
mercurial py-tblib vtkm
mercury py-termcolor wannier90
mesa py-terminado warpx
mesa-glu py-testinfra watch
meshkit py-tetoolkit wcslib
meson py-texttable wget
mesquite py-theano wgsim
metabat py-tifffile windowswmproto
metaphysicl py-toml wireshark
metis py-tomopy wordnet
mfem py-toolz workrave
mgis py-torch wt
microbiomeutil py-torchvision wtdbg2
migrate py-tornado wxpropgrid
mii py-tqdm wxwidgets
minced py-traceback2 x11perf
mindthegap py-traitlets xapian-core
miniaero py-treehash xauth
miniamr py-tuiview xbacklight
miniasm py-twine xbiff
miniconda2 py-twisted xbitmaps
miniconda3 py-typed-ast xbraid
minife py-typesentry xcalc
minighost py-typing xcb-demo
minigmg py-typing-extensions xcb-proto
minimap2 py-tzlocal xcb-util
minimd py-udunits xcb-util-cursor
miniqmc py-umi-tools xcb-util-errors
minisign py-unicycler xcb-util-image
minismac2d py-unittest2 xcb-util-keysyms
minitri py-unittest2py3k xcb-util-renderutil
minivite py-uritemplate xcb-util-wm
minixyce py-urllib3 xcb-util-xrm
minizip py-urwid xclip
minuit py-usgs xclipboard
mira py-vcversioner xclock
mirdeep2 py-virtualenv xcmiscproto
mitofates py-virtualenv-clone xcmsdb
mitos py-virtualenvwrapper xcompmgr
mixcr py-vsc-base xconsole
mkfontdir py-vsc-install xcursor-themes
mkfontscale py-wand xcursorgen
mlhka py-warlock xdbedizzy
mmg py-wcsaxes xditview
moab py-wcwidth xdm
modern-wheel py-weave xdmf3
mofem-cephas py-webencodings xdpyinfo
mofem-fracture-module py-webkit-server xdriinfo
mofem-minimal-surface-equation py-weblogo xedit
mofem-users-modules py-werkzeug xerces-c
molcas py-whatshap xeus
mongo-cxx-driver py-wheel xev
mono py-widgetsnbextension xextproto
montage py-wrapt xeyes
mosh py-wxpython xf86bigfontproto
mothur py-xarray xf86dga
motif py-xattr xf86dgaproto
motioncor2 py-xdot xf86driproto
mount-point-attributes py-xenv xf86miscproto
mozjs py-xlrd xf86rushproto
mpark-variant py-xlsxwriter xf86vidmodeproto
mpc py-xmlrunner xfd
mpdecimal py-xopen xfindproxy
mpe2 py-xpyb xfontsel
mpest py-xvfbwrapper xfs
mpfr py-yamlreader xfsinfo
mpibash py-yapf xfwp
mpich py-yt xgamma
mpifileutils py-ytopt xgboost
mpilander py-zipp xgc
mpileaks py-zmq xhmm
mpip py-zope-event xhost
mpir py-zope-interface xineramaproto
mpix-launch-swift pythia6 xinit
mrbayes python xinput
mrnet qbank xios
mrtrix3 qbox xkbcomp
mscgen qca xkbdata
msgpack-c qhull xkbevd
mshadow qjson xkbprint
msmc qmcpack xkbutils
multitail qmd-progress xkeyboard-config
multitime qorts xkill
multiverso qrupdate xload
mummer qt xlogo
mumps qt-creator xlsatoms
munge qtgraph xlsclients
muparser qthreads xlsfonts
muscle qtkeychain xmag
muse quantum-espresso xman
musl quinoa xmessage
muster qwt xmh
mutationpp qwtpolar xmlf90
mvapich2 r xmlto
mxml r-a4 xmodmap
mxnet r-a4base xmore
mysql r-a4classif xorg-cf-files
nag r-a4core xorg-docs
nalu r-a4preproc xorg-gtest
nalu-wind r-a4reporting xorg-server
namd r-abadata xorg-sgml-doctools
nano r-abaenrichment xphelloworld
nanoflann r-abind xplor-nih
nanopb r-absseq xplsprinters
nasm r-acde xpr
nauty r-acepack xprehashprinterlist
ncbi-magicblast r-acgh xprop
ncbi-rmblastn r-acme xproto
ncbi-toolkit r-ada xproxymanagementprotocol
nccl r-adabag xqilla
nccmp r-ade4 xrandr
ncdu r-adegenet xrdb
ncftp r-adsplit xrefresh
ncl r-aer xrootd
nco r-affxparser xrx
ncurses r-affy xsbench
ncview r-affycomp xscope
ndiff r-affycompatible xsd
nek5000 r-affycontam xsdk
nekbone r-affycoretools xsdktrilinos
nekcem r-affydata xset
nektar r-affyexpress xsetmode
nektools r-affyilm xsetpointer
neovim r-affyio xsetroot
nest r-affypdnn xsimd
netcdf r-affyplm xsm
netcdf-cxx r-affyqcreport xssp
netcdf-cxx4 r-affyrnadegradation xstdcmap
netcdf-fortran r-agdex xtensor
netgauge r-agilp xtensor-python
netgen r-agimicrorna xterm
netlib-lapack r-aims xtl
netlib-scalapack r-aldex2 xtrans
netlib-xblas r-allelicimbalance xtrap
nettle r-alpine xts
neuron r-als xvidtune
nextflow r-alsace xvinfo
nfft r-altcdfenvs xwd
nghttp2 r-amap xwininfo
nginx r-ampliqueso xwud
ngmlr r-analysispageserver xxhash
nim r-anaquin xz
ninja r-aneufinder yajl
ninja-fortran r-aneufinderdata yambo
nix r-animation yaml-cpp
nlohmann-json r-annaffy yara
nlopt r-annotate yasm
nmap r-annotationdbi yorick
nnvm r-annotationfilter z3
node-js r-annotationforge zeromq
notmuch r-annotationhub zfp
npb r-ape zip
npm r-argparse zlib
npth r-askpass zoltan
nrm r-assertthat zsh
nseg r-backports zstd
nspr r-bamsignals None

abinit

Homepage:
Spack package:
Versions:
8.10.3, 8.8.2, 8.6.3, 8.2.2, 8.0.8b
Build Dependencies:
blas, lapack, mpi, scalapack, fftw, netcdf-fortran, hdf5, libxc
Link Dependencies:
blas, lapack, mpi, scalapack, fftw, netcdf-fortran, hdf5, libxc
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:
2.1.4, 2.0.2, 1.5.2
Build Dependencies:
autoconf, automake, mpi, boost, sparsehash, sqlite, libtool
Link Dependencies:
mpi, boost, sparsehash, sqlite, libtool
Run Dependencies:
bwa
Description:
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.

accfft

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cuda, cmake, fftw, 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

ace

Homepage:
Spack package:
Versions:
6.5.6, 6.5.1, 6.5.0
Description:
ACE is an open-source framework that provides many components and patterns for developing high-performance, distributed real-time and embedded systems. ACE provides powerful, yet efficient abstractions for sockets, demultiplexing loops, threads, synchronization primitives.

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).

acts-core

Homepage:
Spack package:
Versions:
develop, 0.10.4, 0.10.3, 0.10.2, 0.10.1, 0.10.0, 0.09.5, 0.09.4, 0.09.3, 0.09.2, 0.09.1, 0.09.0, 0.08.2, 0.08.1, 0.08.0
Build Dependencies:
cmake, boost, eigen, root, dd4hep
Link Dependencies:
boost, root, dd4hep
Description:
A Common Tracking Software (ACTS) This project contains an experiment- independent set of track reconstruction tools. The main philosophy is to provide high-level track reconstruction modules that can be used for any tracking detector. The description of the tracking detector's geometry is optimized for efficient navigation and quick extrapolation of tracks. Converters for several common geometry description languages exist. Having a highly performant, yet largely customizable implementation of track reconstruction algorithms was a primary objective for the design of this toolset. Additionally, the applicability to real-life HEP experiments plays major role in the development process. Apart from algorithmic code, this project also provides an event data model for the description of track parameters and measurements. Key features of this project include: tracking geometry description which can be constructed from TGeo, DD4Hep, or GDML input, simple and efficient event data model, performant and highly flexible algorithms for track propagation and fitting, basic seed finding algorithms.

adept-utils

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

adiak

Homepage:
Spack package:
Versions:
0.1.1
Build Dependencies:
cmake, mpi
Link Dependencies:
mpi
Description:
Adiak collects metadata about HPC application runs and provides it to 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:
autoconf, automake, m4, libtool, python, mpi, zlib, bzip2, szip, sz, zfp, lz4, c-blosc, hdf5, netcdf, libevpath, dataspaces
Link Dependencies:
mpi, zlib, bzip2, szip, sz, zfp, lz4, c-blosc, hdf5, netcdf, libevpath, dataspaces
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, 2.5.0, 2.4.0, 2.3.1
Build Dependencies:
cmake, pkgconfig, libffi, libfabric, mpi, zeromq, dataspaces, hdf5, c-blosc, bzip2, libpng, zfp, sz, python, py-numpy, py-mpi4py
Link Dependencies:
libffi, libfabric, mpi, zeromq, dataspaces, hdf5, c-blosc, bzip2, libpng, zfp, sz, python
Run Dependencies:
python, py-numpy, py-mpi4py
Description:
The Adaptable Input Output System version 2, developed in the Exascale Computing Program

adlbx

Homepage:
Spack package:
Versions:
master, 0.9.2, 0.9.1
Build Dependencies:
exmcutils, autoconf, automake, libtool, m4, mpi
Link Dependencies:
exmcutils, mpi
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:
automake, autoconf, libtool, m4, 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

alan

Homepage:
Spack package:
Versions:
2.1.1
Description:
Alignment viewer for linux terminal

albany

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, mpi, trilinos
Link Dependencies:
mpi, trilinos
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.

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-0.4.0, xsdk-0.3.0, xsdk-0.2.0
Build Dependencies:
cmake, mpi, hdf5, pflotran, petsc
Link Dependencies:
mpi, hdf5, pflotran, petsc
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.

aluminum

Homepage:
Spack package:
Versions:
master, 0.2.1, 0.2, 0.1
Build Dependencies:
cmake, cuda, mpi, nccl, hwloc, ninja
Link Dependencies:
cuda, mpi, nccl, hwloc
Description:
Aluminum provides a generic interface to high-performance communication libraries, with a focus on allreduce algorithms. Blocking and non- blocking algorithms and GPU-aware algorithms are supported. Aluminum also contains custom implementations of select algorithms to optimize for certain situations.

amber

Homepage:
Spack package:
Versions:
16
Build Dependencies:
cuda, mpi, netcdf-fortran, python, py-numpy, py-scipy, py-matplotlib, zlib
Link Dependencies:
cuda, mpi, netcdf-fortran, zlib
Run Dependencies:
python, py-numpy, py-scipy, py-matplotlib
Description:
Amber is a suite of biomolecular simulation programs. Note: A manual download is required for Amber. 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

amg

Homepage:
Spack package:
Versions:
develop, 1.2, 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.

aml

Homepage:
Spack package:
Versions:
0.1.0
Build Dependencies:
numactl, m4, autoconf, automake, libtool
Link Dependencies:
numactl
Description:
AML: Building Blocks for Memory Management.

amp

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, blas, lapack, boost, petsc, trilinos, hdf5, silo, zlib, mpi
Link Dependencies:
blas, lapack, boost, petsc, trilinos, hdf5, silo, zlib, mpi
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:
mpi, gsl
Link Dependencies:
mpi, gsl
Description:
AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.

amrex

Homepage:
Spack package:
Versions:
develop, 19.10, 19.08, 18.10.1, 18.10, 18.09.1
Build Dependencies:
cmake, mpi, sundials, python
Link Dependencies:
mpi, sundials
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:
gmake, mpi, libsm, libice, libxpm, libx11, libxt, libxext, motif, flex, bison
Link Dependencies:
mpi, libsm, libice, libxpm, libx11, libxt, libxext, motif, flex, bison
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:
m4, autoconf, automake, libtool, gsl, libdivsufsort
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:
1.10.0, 1.9.9, 1.9.8, 1.9.7, 1.9.6
Build Dependencies:
java
Link Dependencies:
java
Description:
Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other

antlr

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

ants

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake
Link Dependencies:
zlib
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.

aoflagger

Homepage:
Spack package:
Versions:
2.10.0
Build Dependencies:
cmake, casacore, fftw, boost, libxml2, lapack, cfitsio
Link Dependencies:
casacore, fftw, boost, libxml2, lapack, cfitsio
Description:
RFI detector and quality analysis for astronomical radio observations.

aom

Homepage:
Spack package:
Versions:
v1.0.0-errata1
Build Dependencies:
cmake, yasm
Link Dependencies:
yasm
Description:
Alliance for Open Media AOM AV1 Codec Library

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:
cmake, binutils, boost, activeharmony, ompt-openmp
Link Dependencies:
binutils, boost, activeharmony, ompt-openmp
Description:
Autonomic Performance Environment for eXascale (APEX).

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

appres

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
libx11, libxt, xproto, pkgconfig, util-macros
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:
1.7.0, 1.6.2, 1.5.2
Description:
Apache portable runtime.

apr-util

Homepage:
Spack package:
Versions:
1.6.1, 1.6.0, 1.5.4
Build Dependencies:
apr, expat, libiconv, openssl, gdbm, postgresql, sqlite, unixodbc
Link Dependencies:
apr, expat, libiconv, openssl, gdbm, postgresql, sqlite, unixodbc
Description:
Apache Portable Runtime Utility

aragorn

Homepage:
Spack package:
Versions:
1.2.38, 1.2.36
Description:
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

arborx

Homepage:
Spack package:
Versions:
master, 0.8-beta2
Build Dependencies:
cmake, cuda, mpi, kokkos
Link Dependencies:
cuda, mpi, kokkos
Description:
ArborX is a performance-portable library for geometric search

archer

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
cmake, llvm, 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:
develop, 1.0rc1, 1.0b1, 1.0a1
Build Dependencies:
m4, autoconf, automake, libtool, valgrind
Link Dependencies:
valgrind
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.

aria2

Homepage:
Spack package:
Versions:
1.34.0
Build Dependencies:
libxml2, libssh2, libgcrypt, zlib, cares, sqlite
Link Dependencies:
libxml2, libssh2, libgcrypt, zlib, cares, sqlite
Description:
An ultra fast download utility

arm-forge

Homepage:
Spack package:
Versions:
19.0.4-linux-ubuntu16.04-x86_64, 19.0.4-linux-ubuntu16.04-aarch64, 19.0.4-linux-ubuntu14.04-x86_64, 19.0.4-linux-sles15-x86_64, 19.0.4-linux-sles12-x86_64, 19.0.4-linux-sles12-aarch64, 19.0.4-linux-sles11-x86_64, 19.0.4-linux-rhel7-x86_64, 19.0.4-linux-rhel7-ppc64le, 19.0.4-linux-rhel7-aarch64, 19.0.4-linux-rhel6-x86_64, 19.0.3-linux-ubuntu16.04-x86_64, 19.0.3-linux-ubuntu16.04-aarch64, 19.0.3-linux-ubuntu14.04-x86_64, 19.0.3-linux-sles12-x86_64, 19.0.3-linux-sles12-aarch64, 19.0.3-linux-sles11-x86_64, 19.0.3-linux-rhel7-x86_64, 19.0.3-linux-rhel7-ppc64le, 19.0.3-linux-rhel7-aarch64, 19.0.3-linux-rhel6-x86_64
Description:
Arm 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.

armadillo

Homepage:
Spack package:
Versions:
8.100.1, 7.950.1
Build Dependencies:
cmake, arpack-ng, blas, lapack, superlu, hdf5
Link Dependencies:
arpack-ng, blas, lapack, superlu, 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, 3.7.0, 3.6.3, 3.6.2, 3.6.0, 3.5.0, 3.4.0, 3.3.0
Build Dependencies:
blas, lapack, automake, autoconf, libtool, cmake, mpi
Link Dependencies:
blas, lapack, mpi
Description:
ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Important Features: * Reverse Communication Interface. * Single and Double Precision Real Arithmetic Versions for Symmetric, Non-symmetric, Standard or Generalized Problems. * Single and Double Precision Complex Arithmetic Versions for Standard or Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. * Example driver routines that may be used as templates to implement numerous Shift-Invert strategies for all problem types, data types and precision. This project is a joint project between Debian, Octave and Scilab in order to provide a common and maintained version of arpack. Indeed, no single release has been published by Rice university for the last few years and since many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifications, arpack-ng aims to tackle this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere.

arrow

Homepage:
Spack package:
Versions:
0.12.1, 0.11.0, 0.9.0, 0.8.0
Build Dependencies:
cmake, boost, flatbuffers, python, py-numpy, rapidjson, snappy, zlib, zstd
Link Dependencies:
boost, flatbuffers, python, py-numpy, rapidjson, snappy, zlib, zstd
Description:
A cross-language development platform for in-memory data. This package contains the C++ bindings.

asagi

Homepage:
Spack package:
Versions:
1.0.1, 1.0
Build Dependencies:
cmake, mpi, netcdf, numactl
Link Dependencies:
mpi, netcdf, numactl
Description:
a pArallel Server for Adaptive GeoInformation.

ascent

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, conduit, python, py-numpy, mpi, py-mpi4py, vtkh, mfem, adios, py-sphinx
Link Dependencies:
conduit, python, mpi, py-mpi4py, vtkh, mfem, 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:
libxml2, libxslt, docbook-xml, docbook-xsl
Link Dependencies:
libxml2, libxslt, docbook-xml, docbook-xsl
Description:
A presentable text document format for writing articles, UNIX man pages and other small to medium sized documents.

asciidoctor

Homepage:
Spack package:
Versions:
1.5.8
Build Dependencies:
ruby
Link Dependencies:
ruby
Description:
Modern asciidoc tool based on ruby

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

aspect

Homepage:
Spack package:
Versions:
develop, 2.0.1, 2.0.0
Build Dependencies:
cmake, dealii, dealii-parameter-gui
Link Dependencies:
dealii, dealii-parameter-gui
Description:
Parallel, extendible finite element code to simulate convection in the Earth's mantle and elsewhere.

aspell

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

aspell6-de

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

aspell6-en

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

aspell6-es

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

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:
5.6.1, 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, ninja, pkgconfig, at-spi2-core, atk
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:
meson, ninja, glib, dbus, gettext, libx11, libxi, libxtst, recordproto, inputproto, fixesproto, pkgconfig, python
Link Dependencies:
glib, dbus, gettext, libx11, 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.

athena

Homepage:
Spack package:
Versions:
master, 4.2
Build Dependencies:
autoconf, automake, libtool, m4, mpi, fftw
Link Dependencies:
mpi, fftw
Description:
Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD). It was developed primarily for studies of the interstellar medium, star formation, and accretion flows.

atk

Homepage:
Spack package:
Versions:
2.30.0, 2.28.1, 2.20.0, 2.14.0
Build Dependencies:
meson, glib, gettext, pkgconfig, gobject-introspection, libffi
Link Dependencies:
glib, gettext, gobject-introspection, libffi
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:
3.11.41, 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:
libgridxc, xmlf90
Link Dependencies:
libgridxc, xmlf90
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, blas, libxc
Link Dependencies:
lapack, blas, libxc
Description:
A Projector Augmented Wave (PAW) code for generating atom-centered functions. Official website: http://pwpaw.wfu.edu User's guide: ~/doc/atompaw-usersguide.pdf

atop

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

attr

Homepage:
Spack package:
Versions:
2.4.47, 2.4.46
Description:
Commands for Manipulating Filesystem Extended Attributes

augustus

Homepage:
Spack package:
Versions:
3.3.2, 3.3.1, 3.3, 3.2.3
Build Dependencies:
perl, bamtools, gsl, boost, zlib, htslib, bcftools, samtools, curl
Link Dependencies:
bamtools, gsl, boost, zlib, htslib, bcftools, samtools, curl
Run Dependencies:
perl
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

autofact

Homepage:
Spack package:
Versions:
3_4
Run Dependencies:
perl, perl-bio-perl, perl-io-string, perl-lwp, blast-legacy
Description:
An Automatic Functional Annotation and Classification Tool

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, boost, callpath
Link Dependencies:
mpi, boost, callpath
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, 1.13.4, 1.11.6
Build Dependencies:
autoconf, perl
Run Dependencies:
perl
Description:
Automake -- make file builder part of autotools

awscli

Homepage:
Spack package:
Versions:
1.16.179
Build Dependencies:
python, py-setuptools, py-docutils, py-colorama, py-rsa, py-pyyaml, py-argparse, py-s3transfer, py-botocore
Link Dependencies:
python
Run Dependencies:
python, py-docutils, py-colorama, py-rsa, py-pyyaml, py-argparse, py-s3transfer, py-botocore
Test Dependencies:
py-nose, py-mock
Description:
This package provides a unified command line interface to Amazon Web Services

axel

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

axl

Homepage:
Spack package:
Versions:
master, 0.1.1
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, 0.7, 0.6
Run Dependencies:
hmmer
Description:
Barrnap predicts the location of ribosomal RNA genes in genomes.

bash

Homepage:
Spack package:
Versions:
5.0, 4.4.12, 4.4, 4.3
Build Dependencies:
ncurses, readline, libiconv
Link Dependencies:
ncurses, readline, libiconv
Description:
The GNU Project's Bourne Again SHell.

bash-completion

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

bats

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

bazel

Homepage:
Spack package:
Versions:
0.17.2, 0.16.1, 0.15.0, 0.14.1, 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
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:
38.63, 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:
1.9, 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
Build Dependencies:
boost, cmake, libxml2, libxslt, libgcrypt, zlib
Link Dependencies:
boost, cmake, libxml2, libxslt, libgcrypt, zlib
Description:
The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files.

bdftopcf

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libxfont, pkgconfig, xproto, fontsproto, util-macros
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:
8.0.0, 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:
cmake, python
Link Dependencies:
python
Description:
Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems.

beast-tracer

Homepage:
Spack package:
Versions:
1.7.1
Build Dependencies:
ant, java
Run Dependencies:
java
Description:
Tracer is a graphical tool for visualization and diagnostics of MCMC output.

beast1

Homepage:
Spack package:
Versions:
1.10.4, 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:
2.5.2, 2.4.6
Build Dependencies:
java
Link Dependencies:
java
Description:
BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time- measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

bedops

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

bedtools2

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

beforelight

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
libx11, libxscrnsaver, libxt, pkgconfig, util-macros
Link Dependencies:
libx11, libxscrnsaver, 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, 1.5.0, 1.4.1, 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:
flex, bison, gmp, mpfr, mpi
Link Dependencies:
gmp, mpfr, mpi
Description:
Bertini is a general-purpose solver, written in C, that was created for research about polynomial continuation. It solves for the numerical solution of systems of polynomial equations using homotopy continuation.

bib2xhtml

Homepage:
Spack package:
Versions:
3.0-79-ge935
Description:
bib2xhtml is a program that converts BibTeX files into HTML.

bigreqsproto

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

binutils

Homepage:
Spack package:
Versions:
2.32, 2.31.1, 2.29.1, 2.28, 2.27, 2.26, 2.25.1, 2.25, 2.24, 2.23.2, 2.20.1
Build Dependencies:
zlib, gettext, m4, bison
Link Dependencies:
zlib, gettext
Description:
GNU binutils, which contain the linker, assembler, objdump and others

bioawk

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
zlib, bison
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.

biobloom

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
boost, sdsl-lite, sparsehash, zlib
Link Dependencies:
boost, sdsl-lite, sparsehash, zlib
Description:
BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorize sequences.

bismark

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

bison

Homepage:
Spack package:
Versions:
3.4.2, 3.0.5, 3.0.4, 2.7
Build Dependencies:
diffutils, m4, perl, help2man
Run Dependencies:
m4
Description:
Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

bitmap

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

blasr

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

blasr-libcpp

Homepage:
Spack package:
Versions:
5.3.1
Build Dependencies:
pbbam, hdf5, python
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-legacy

Homepage:
Spack package:
Versions:
2.2.26
Build Dependencies:
tcsh
Description:
Legacy NCBI BLAST distribution -- no longer supported. Contains older programs including `blastall'

blast-plus

Homepage:
Spack package:
Versions:
2.9.0, 2.8.1, 2.7.1, 2.6.0, 2.2.30
Build Dependencies:
jpeg, libpng, freetype, gnutls, openssl, zlib, bzip2, lzo, pcre, python, perl, lmdb
Link Dependencies:
jpeg, libpng, freetype, gnutls, openssl, zlib, bzip2, lzo, pcre, python, perl, lmdb
Description:
Basic Local Alignment Search Tool.

blast2go

Homepage:
Spack package:
Versions:
5.2.5
Build Dependencies:
bash, java
Run Dependencies:
blast-plus
Description:
Blast2GO is a bioinformatics platform for high-quality functional annotation and analysis of genomic datasets.

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:
master, 3.5, 3.4, 3.3, 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
Build Dependencies:
cmake
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:
master, 0.6.0, 0.5.0, 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:
gmp, libtool
Link Dependencies:
gmp
Description:
bliss: A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs

blitz

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

bmake

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

bmi

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
autoconf
Description:
a communications framework and network abstraction layer

bml

Homepage:
Spack package:
Versions:
develop, 1.3.1, 1.3.0, 1.2.3, 1.2.2, 1.1.0
Build Dependencies:
cmake, blas, lapack, mpi
Link Dependencies:
blas, lapack, mpi
Description:
The basic matrix library (bml) is a collection of various matrix data formats (in dense and sparse) and their associated algorithms for basic matrix operations.

bohrium

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

bolt

Homepage:
Spack package:
Versions:
master, 1.0rc2, 1.0rc1, 1.0b1
Build Dependencies:
cmake, argobots, autoconf, automake, libtool
Link Dependencies:
argobots
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, 2.0.2, 2.0.1, 2.0
Build Dependencies:
cmake, caliper, parmetis, silo, typhon, mpi, yaml-cpp
Link Dependencies:
caliper, parmetis, silo, typhon, mpi, yaml-cpp
Description:
BookLeaf is a 2D unstructured hydrodynamics mini-app.

boost

Homepage:
Spack package:
Versions:
develop, 1.70.0, 1.69.0, 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:
icu4c, python, mpi, bzip2, zlib, py-numpy
Link Dependencies:
icu4c, python, mpi, bzip2, 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:
1.2.3, 1.2.2_p1, 1.2.2, 1.2.1.1, 1.2.1, 1.2.0, 1.2
Build Dependencies:
tbb, zlib
Link Dependencies:
tbb, zlib
Description:
Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

bowtie2

Homepage:
Spack package:
Versions:
2.3.5.1, 2.3.5, 2.3.4.1, 2.3.1, 2.3.0, 2.2.5
Build Dependencies:
tbb, readline, zlib
Link Dependencies:
tbb, readline, zlib
Run Dependencies:
perl, python
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, texinfo, bpp-core, bpp-seq, bpp-phyl
Link Dependencies:
bpp-core, bpp-seq, 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, python, perl-exporter-tiny, perl-list-moreutils, perl-parallel-forkmanager
Link Dependencies:
perl, python, perl-exporter-tiny, perl-list-moreutils, perl-parallel-forkmanager
Run Dependencies:
perl, python
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:
2.1.4, 1.11
Build Dependencies:
perl, perl-scalar-util-numeric, perl-parallel-forkmanager, perl-file-which, perl-yaml, perl-hash-merge, perl-logger-simple, perl-file-homedir, augustus, genemark-et, bamtools, samtools, diamond
Link Dependencies:
augustus, genemark-et, bamtools, samtools, diamond
Run Dependencies:
perl, perl-scalar-util-numeric, perl-parallel-forkmanager, perl-file-which, perl-yaml, perl-hash-merge, perl-logger-simple, perl-file-homedir
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, 0.82, 0.81, 0.8
Build Dependencies:
cmake, mpi, boost, metis, parmetis
Link Dependencies:
mpi, boost, metis, parmetis
Description:
Branson's purpose is to study different algorithms for parallel Monte Carlo transport. Currently it contains particle passing and mesh passing methods for domain decomposition.

breakdancer

Homepage:
Spack package:
Versions:
master, 1.4.5
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib, ncurses
Run Dependencies:
perl-statistics-descriptive, perl-math-cdf, perl-gd-graph, perl-gdgraph-histogram, perl-list-moreutils, 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:
0.33.2, 0.33.1, 0.31.1
Build Dependencies:
autoconf, automake, libtool, m4
Link Dependencies:
zlib
Run Dependencies:
bedtools2, r
Description:
breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes.

bridger

Homepage:
Spack package:
Versions:
2014-12-01
Build Dependencies:
boost
Link Dependencies:
boost
Run Dependencies:
perl
Description:
Bridger : An Efficient De novo Transcriptome Assembler For RNA-Seq Data

brigand

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

brotli

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies:
cmake
Description:
Brotli is a generic-purpose lossless compression algorithm

bsseeker2

Homepage:
Spack package:
Versions:
2.1.8, 2.1.5, 2.1.2
Build Dependencies:
python, py-pysam
Run Dependencies:
python, py-pysam
Description:
A versatile aligning pipeline for bisulfite sequencing data.

bucky

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

bumpversion

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

busco

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

butter

Homepage:
Spack package:
Versions:
0.3.3
Build Dependencies:
perl, samtools, 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.

butterflypack

Homepage:
Spack package:
Versions:
master, 1.0.3, 1.0.1, 1.0.0
Build Dependencies:
cmake, mpi, blas, lapack, scalapack, arpack-ng
Link Dependencies:
mpi, blas, lapack, scalapack, arpack-ng
Description:
ButterflyPACK is a mathematical software for rapidly solving large-scale dense linear systems that exhibit off-diagonal rank-deficiency. These systems arise frequently from boundary element methods, or factorization phases in finite-difference/finite-element methods. ButterflyPACK relies on low-rank or butterfly formats under Hierarchical matrix, HODLR or other hierarchically nested frameworks to compress, factor and solve the linear system in quasi-linear time. The computationally most intensive phase, factorization, is accelerated via randomized linear algebras. The butterfly format, originally inspired by the butterfly data flow in fast Fourier Transform, is a linear algebra tool well-suited for compressing matrices arising from high-frequency wave equations or highly oscillatory integral operators.

bwa

Homepage:
Spack package:
Versions:
0.7.17, 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:
5.127, 5.125, 5.123
Build Dependencies:
tmux
Run Dependencies:
tmux
Description:
Byobu: Text-based window manager and terminal multiplexer.

bzip2

Homepage:
Spack package:
Versions:
1.0.8, 1.0.7, 1.0.6
Build Dependencies:
diffutils
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:
1.17.0, 1.16.3, 1.15.0, 1.12.1, 1.11.1, 1.9.2, 1.9.1, 1.9.0, 1.8.1, 1.8.0
Build Dependencies:
cmake, snappy, zlib, zstd, lz4
Link Dependencies:
snappy, zlib, zstd, lz4
Description:
Blosc, an extremely fast, multi-threaded, meta-compressor library

c-blosc2

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, lz4, snappy, zlib, zstd
Link Dependencies:
lz4, snappy, zlib, zstd
Description:
Next generation c-blosc with a new API, a new container and other bells and whistles

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.

cabana

Homepage:
Spack package:
Versions:
develop, 0.1.0-rc0, 0.1.0
Build Dependencies:
cmake, kokkos
Link Dependencies:
kokkos
Description:
The Exascale Co-Design Center for Particle Applications Toolkit

caffe

Homepage:
Spack package:
Versions:
1.0, rc5, rc4, rc3, rc2
Build Dependencies:
cmake, boost, cuda, blas, protobuf, glog, gflags, hdf5, opencv, leveldb, lmdb, python, py-numpy, matlab
Link Dependencies:
boost, cuda, blas, protobuf, glog, gflags, hdf5, opencv, leveldb, lmdb, python, matlab
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:
1.16.0, 1.14.12, 1.14.8, 1.14.0
Build Dependencies:
libx11, libxext, libxrender, libxcb, python, libpng, glib, pixman, freetype, pkgconfig, fontconfig
Link Dependencies:
libx11, libxext, libxrender, libxcb, libpng, glib, pixman, freetype, fontconfig
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:
master, 2.0.1, 1.9.1, 1.9.0, 1.8.0, 1.7.0
Build Dependencies:
cmake, gotcha, dyninst, papi, libpfm4, mpi, unwind, sosflow, python
Link Dependencies:
gotcha, dyninst, papi, libpfm4, mpi, unwind, sosflow
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:
cmake, libdwarf, dyninst, adept-utils, mpi
Link Dependencies:
elf, libdwarf, dyninst, adept-utils, mpi
Description:
Library for representing callpaths consistently in distributed-memory performance tools.

camellia

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

camx

Homepage:
Spack package:
Versions:
6.50
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Comprehensive Air Quality Model with Extensions.

candle-benchmarks

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

cantera

Homepage:
Spack package:
Versions:
2.4.0, 2.3.0, 2.2.1
Build Dependencies:
scons, fmt, googletest, eigen, boost, sundials, blas, lapack, python, py-cython, py-numpy, py-scipy, py-3to2, py-unittest2, py-unittest2py3k, matlab
Link Dependencies:
fmt, googletest, eigen, boost, sundials, blas, lapack, python, matlab
Run Dependencies:
py-numpy, py-scipy, py-3to2, py-unittest2, py-unittest2py3k
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:
1.8, 1.7.1, 1.7, 1.5
Run Dependencies:
gnuplot, jdk, perl
Description:
A single molecule sequence assembler for genomes large and small.

cap3

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

capstone

Homepage:
Spack package:
Versions:
4.0.1
Build Dependencies:
cmake
Description:
Capstone is a lightweight multi-platform, multi-architecture disassembly framework.

cardioid

Homepage:
Spack package:
Versions:
develop, elecfem
Build Dependencies:
cmake, blas, lapack, mpi, cuda, mfem, perl
Link Dependencies:
blas, lapack, mpi, cuda, mfem
Description:
Cardiac simulation suite.

cares

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

casacore

Homepage:
Spack package:
Versions:
2.4.1
Build Dependencies:
cmake, flex, bison, blas, lapack, cfitsio, wcslib, fftw, sofa-c, hdf5, ncurses, python, boost, py-numpy
Link Dependencies:
blas, lapack, cfitsio, wcslib, fftw, sofa-c, hdf5, ncurses, python, boost, py-numpy
Description:
A suite of c++ libraries for radio astronomy data processing.

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:
5.6.0, 5.5.2, 5.5.1, 5.5.0, 5.4.1, 5.4.0, 5.3.0, 5.2.0, 5.1.2, 5.0.1, 4.4.0
Build Dependencies:
cmake, python, git, mpi, py-numpy, py-mpi4py, gl, mesa, glx
Link Dependencies:
python, mpi, gl, mesa, glx
Run Dependencies:
python, py-numpy, py-mpi4py
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:
2.9.1, 2.9.0, 2.8.0, 2.7.2, 2.7.1, 2.7.0, 2.6.1, 2.6.0, 2.5.0, 2.4.2, 2.4.1, 2.4.0, 2.3.0, 2.2.3, 2.2.2, 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:
mpi, blas, lapack, fftw
Link Dependencies:
mpi, blas, lapack, fftw
Description:
Cbench is intended as a relatively straightforward toolbox of tests, benchmarks, applications, utilities, and framework to hold them together with the goal to facilitate scalable testing, benchmarking, and analysis of a Linux parallel compute cluster.

cblas

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

cbtf

Homepage:
Spack package:
Versions:
develop, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cmake, boost, mrnet, xerces-c, libxml2
Link Dependencies:
boost, mrnet, xerces-c, libxml2
Description:
CBTF project contains the base code for CBTF that supports creating components, component networks and the support to connect these components and component networks into sequential and distributed network tools.

cbtf-argonavis

Homepage:
Spack package:
Versions:
develop, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cmake, boost, mrnet, cbtf, libmonitor, papi, cbtf-krell, cuda
Link Dependencies:
elf, boost, mrnet, cbtf, libmonitor, papi, cbtf-krell, cuda
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:
qt, cmake, boost, mrnet, cbtf, cbtf-krell, cbtf-argonavis, cuda, openspeedshop-utils, xerces-c, graphviz, qtgraph
Link Dependencies:
qt, boost, mrnet, cbtf, cbtf-krell, cbtf-argonavis, cuda, openspeedshop-utils, xerces-c, graphviz, qtgraph
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, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cmake, binutils, boost, dyninst, mrnet, xerces-c, cbtf, libmonitor, libunwind, papi, llvm-openmp-ompt, openmpi, mpich, mpich2, mvapich2, mvapich, mpt, python, gotcha
Link Dependencies:
binutils, boost, dyninst, mrnet, xerces-c, cbtf, libmonitor, libunwind, papi, llvm-openmp-ompt, openmpi, mpich, mpich2, mvapich2, mvapich, mpt, gotcha
Run Dependencies:
mrnet, cbtf, python
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, 1.9.3, 1.9.2, 1.9.1.2, 1.9.1.1, 1.9.1.0
Build Dependencies:
cmake, mrnet, xerces-c, cbtf, cbtf-krell
Link Dependencies:
mrnet, xerces-c, cbtf, cbtf-krell
Description:
CBTF LANL project contains a memory tool and data center type system command monitoring tool.

ccache

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

ccfits

Homepage:
Spack package:
Versions:
2.5, 2.4
Build Dependencies:
cfitsio
Link Dependencies:
cfitsio
Description:
CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++. It is written in ANSI C++ and implemented using the C++ Standard Library with namespaces, exception handling, and member template functions.

ccs-qcd

Homepage:
Spack package:
Versions:
master, 1.2.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
This program benchmarks the performance of a linear equation solver with a large sparse coefficient matrix appering in a lattice QCD probrem. Lattice QCD describes the property of protons, neutrons and neucleons in terms of more fundamental interacting elementary particles gluon and quarks.

cctools

Homepage:
Spack package:
Versions:
7.0.18, 6.1.1
Build Dependencies:
openssl, perl, python, readline, swig, zlib
Link Dependencies:
openssl, readline, swig, zlib
Run Dependencies:
perl, python
Description:
The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.

cdbfasta

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

cdd

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

cddlib

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

cdecimal

Homepage:
Spack package:
Versions:
2.3
Description:
cdecimal is a fast drop-in replacement for the decimal module in Python's standard library.

cdhit

Homepage:
Spack package:
Versions:
4.8.1, 4.6.8
Build Dependencies:
perl
Link Dependencies:
zlib
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:
1.9.7.1, 1.9.6, 1.9.5, 1.9.4, 1.9.3, 1.9.2, 1.9.1, 1.9.0, 1.8.2, 1.7.2
Build Dependencies:
pkgconfig, netcdf, hdf5, grib-api, eccodes, szip, udunits2, libxml2, proj, curl, fftw, magics, libuuid
Link Dependencies:
netcdf, hdf5, grib-api, eccodes, szip, udunits2, libxml2, proj, curl, fftw, magics, libuuid
Description:
CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.

ceed

Homepage:
Spack package:
Versions:
2.0.0, 1.0.0
Build Dependencies:
libceed, occa, nek5000, nektools, gslib, nekbone, nekcem, petsc, hpgmg, magma, pumi, mfem, laghos, hypre, suite-sparse
Link Dependencies:
libceed, occa, nek5000, nektools, gslib, nekbone, nekcem, petsc, hpgmg, magma, pumi, mfem, laghos, hypre, suite-sparse
Description:
Ceed is a collection of benchmarks, miniapps, software libraries and APIs for efficient high-order finite element and spectral element discretizations for exascale applications developed in the Department of Energy (DOE) and partially supported by the Exascale Computing Project (ECP). This is a Spack bundle package that installs the CEED software components.

cereal

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

ceres-solver

Homepage:
Spack package:
Versions:
1.12.0
Build Dependencies:
cmake, eigen, 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:
curl, bzip2
Link Dependencies:
curl, 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:
4.13, 4.12, 4.11, 4.9.1, 4.9, 4.7, 4.6.3
Build Dependencies:
cmake, boost, gmp, mpfr, zlib, qt
Link Dependencies:
boost, gmp, mpfr, zlib, qt
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.

cgdb

Homepage:
Spack package:
Versions:
0.7.0
Build Dependencies:
ncurses, readline
Link Dependencies:
ncurses, readline
Description:
A curses front-end to GDB

cgm

Homepage:
Spack package:
Versions:
16.0, 13.1.1, 13.1.0, 13.1
Build Dependencies:
mpi, oce
Link Dependencies:
mpi, oce
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:
develop, master, 3.4.0, 3.3.1, 3.3.0
Build Dependencies:
cmake, hdf5, mpi
Link Dependencies:
hdf5, mpi
Description:
The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.

channelflow

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

chapel

Homepage:
Spack package:
Versions:
1.20.0, 1.19.0, 1.18.0
Description:
Chapel is a modern programming language that is parallel, productive, portable, scalable and open-source.

charliecloud

Homepage:
Spack package:
Versions:
master, 0.11, 0.10, 0.9.10, 0.9.9, 0.9.8, 0.9.7, 0.9.6, 0.9.3, 0.9.2, 0.9.1, 0.9.0, 0.2.4
Build Dependencies:
python, rsync, py-sphinx, py-sphinx-rtd-theme
Run Dependencies:
python, py-lark-parser, skopeo, umoci
Test Dependencies:
bats
Description:
Lightweight user-defined software stacks for HPC.

charmpp

Homepage:
Spack package:
Versions:
develop, 6.9.0, 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:
mpi, papi, cuda, automake, autoconf
Link Dependencies:
mpi, papi, cuda, automake, autoconf
Description:
Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers.

chatterbug

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
mpi, scorep
Link Dependencies:
mpi, scorep
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.

chill

Homepage:
Spack package:
Versions:
master, 0.3
Build Dependencies:
boost, rose, autoconf, automake, libtool, m4, iegenlib, bison, flex, python
Link Dependencies:
python
Description:
A polyheadral compiler for autotuning

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

chrpath

Homepage:
Spack package:
Versions:
0.16
Description:
chrpath: Modifies the dynamic library load path (rpath and runpath) of compiled programs and libraries.

cinch

Homepage:
Spack package:
Versions:
develop, 1.0
Description:
Cinch is a set of utilities and configuration options designed to make cmake builds easy to use and manage.

cistem

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

citcoms

Homepage:
Spack package:
Versions:
3.3.1, 3.2.0
Build Dependencies:
mpi, zlib, exchanger, py-pythia, hc, cuda, hdf5
Link Dependencies:
mpi, zlib, exchanger, hc, cuda, hdf5
Run Dependencies:
py-pythia
Description:
CitcomS is a finite element code designed to solve compressible thermochemical convection problems relevant to Earth's mantle.

cityhash

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

clamav

Homepage:
Spack package:
Versions:
0.101.2
Build Dependencies:
pkgconfig, json-c, openssl, pcre, yara, zlib, bzip2
Link Dependencies:
json-c, openssl, pcre, yara, zlib, bzip2
Description:
Open source antivirus engine for detecting trojans, viruses, malware & other malicious threats.

clamr

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, mpi, mpe
Link Dependencies:
cmake, mpi, mpe
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.

claw

Homepage:
Spack package:
Versions:
2.0.1, 2.0, 1.2.3, 1.2.2, 1.2.1, 1.2.0, 1.1.0
Build Dependencies:
cmake, java, ant, libxml2, bison
Link Dependencies:
java, ant, libxml2, bison
Description:
CLAW Compiler targets performance portability problem in climate and weather application written in Fortran. From a single source code, it generates architecture specific code decorated with OpenMP or OpenACC

cleaveland4

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

cleverleaf

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, samrai, hdf5, boost
Link Dependencies:
samrai, hdf5, 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:
cmake, opencl, 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:
cmake, doxygen, 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.

cln

Homepage:
Spack package:
Versions:
1.3.4, 1.3.3, 1.3.2, 1.3.1, 1.3.0, 1.2.2, 1.2.1, 1.2.0
Build Dependencies:
autoconf, automake, libtool, m4
Description:
CLN is a library for efficient computations with all kinds of numbers in arbitrary precision. It features number classes for unlimited length integers, rationals, arbitrary precision floating point numbers and much more.

cloc

Homepage:
Spack package:
Versions:
1.80, 1.74
Build Dependencies:
perl
Link Dependencies:
perl
Description:
Count, or compute differences of, physical lines of source code in the given files (may be archives such as compressed tarballs or zip files) and/or recursively below the given directories.

cloog

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

cloverleaf

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
mpi, cuda
Link Dependencies:
mpi, cuda
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.

clp

Homepage:
Spack package:
Versions:
1.16.11
Description:
Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.

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:
3.15.4, 3.15.3, 3.15.2, 3.15.1, 3.15.0, 3.14.5, 3.14.4, 3.14.3, 3.14.2, 3.14.1, 3.14.0, 3.13.4, 3.13.3, 3.13.2, 3.13.1, 3.13.0, 3.12.4, 3.12.3, 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:
curl, expat, zlib, bzip2, xz, libarchive, libuv, rhash, qt, python, py-sphinx, openssl, ncurses
Link Dependencies:
curl, expat, zlib, bzip2, xz, libarchive, libuv, rhash, qt, openssl, ncurses
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
Build Dependencies:
cmake
Description:
Unit-testing framework in pure C

cmor

Homepage:
Spack package:
Versions:
3.4.0, 3.3.0, 3.2.0, 3.1.2
Build Dependencies:
uuid, netcdf, udunits2, hdf5, python, py-numpy
Link Dependencies:
uuid, netcdf, udunits2, hdf5, python
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
Link Dependencies:
zlib
Description:
cnpy: library to read/write .npy and .npz files in C/C++.

cntk

Homepage:
Spack package:
Versions:
master, 2.0
Build Dependencies:
libzip, openblas, mpi, boost, protobuf, kaldi, opencv, cuda, cub, cudnn, nccl, cntk1bitsgd, multiverso
Link Dependencies:
libzip, openblas, mpi, boost, protobuf, kaldi, opencv, cuda, cub, cudnn, nccl, cntk1bitsgd, multiverso
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).

cnvnator

Homepage:
Spack package:
Versions:
0.3.3
Build Dependencies:
samtools, htslib, root, bzip2, curl, lzma, zlib
Link Dependencies:
samtools, htslib, root, bzip2, curl, lzma, zlib
Description:
A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads.

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, 1.1.0, 1.0.0
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, bison, flex, mpi, ross, sst-dumpi
Link Dependencies:
mpi, ross, sst-dumpi
Description:
CO-Design of multi-layer Exascale Storage (CODES) simulation framework

coevp

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

compositeproto

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

conduit

Homepage:
Spack package:
Versions:
master, 0.4.0, 0.3.1, 0.3.0, 0.2.1, 0.2.0
Build Dependencies:
cmake, python, py-numpy, hdf5, silo, adios, mpi, py-sphinx, doxygen
Link Dependencies:
python, hdf5, silo, adios, mpi, doxygen
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.

connect-proxy

Homepage:
Spack package:
Versions:
1.105
Description:
`connect.c` is a simple relaying command to make network connection via SOCKS and https proxy

constype

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

converge

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

coreutils

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

cosp2

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

cotter

Homepage:
Spack package:
Versions:
master, 20190205
Build Dependencies:
cmake, erfa, pal, aoflagger
Link Dependencies:
erfa, pal, aoflagger
Description:
Andre Offringa's cotter pre-processing pipeline.

cowsay

Homepage:
Spack package:
Versions:
3.04
Run Dependencies:
perl
Description:
A program that generates ASCII pictures of a cow with a message.

cp2k

Homepage:
Spack package:
Versions:
develop, 6.1, 5.1, 4.1, 3.0
Build Dependencies:
cuda, python, fftw, openblas, lapack, intel-mkl, libxsmm, pkgconfig, libint, libxc, mpi, scalapack, elpa, plumed, pexsi, sirius, json-fortran, py-numpy, wannier90
Link Dependencies:
cuda, fftw, openblas, lapack, intel-mkl, libxsmm, libint, libxc, mpi, scalapack, elpa, plumed, pexsi, sirius, json-fortran
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:
1.87, 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:
1.14.0, 1.13.2
Description:
Obsolete Unit testing framework for C++

cppzmq

Homepage:
Spack package:
Versions:
develop, 4.3.0, 4.2.2
Build Dependencies:
cmake, zeromq
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.

cquery

Homepage:
Spack package:
Versions:
v20180823
Build Dependencies:
cmake, llvm
Link Dependencies:
llvm
Description:
a C++ header-only library for Nearest Neighbor (NN) search wih KD-trees.

cram

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

cromwell

Homepage:
Spack package:
Versions:
44
Run Dependencies:
java
Description:
Cromwell is a Workflow Management System geared towards scientific workflows.

cromwell-womtool

Homepage:
Spack package:
Versions:
44
Run Dependencies:
java
Description:
Command line utilities for interacting with the Workflow Object Model (WOM).

cryptopp

Homepage:
Spack package:
Versions:
7.0.0, 6.1.0, 6.0.0, 5.6.5, 5.6.4, 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).

cryptsetup

Homepage:
Spack package:
Versions:
2.2.1
Build Dependencies:
libuuid, lvm2, popt, json-c, util-linux, gettext, autoconf, automake, libtool, m4
Link Dependencies:
libuuid, lvm2, popt, json-c, util-linux, gettext
Description:
Cryptsetup and LUKS - open-source disk encryption.

cscope

Homepage:
Spack package:
Versions:
15.8b
Build Dependencies:
ncurses, flex, bison, 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:
wxwidgets, fftw
Link Dependencies:
wxwidgets, fftw
Description:
Fast and accurate defocus estimation from electron micrographs.

cub

Homepage:
Spack package:
Versions:
1.7.1
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, 4.4.3, 4.4.2, 4.4, 4.3.5, 4.3.4, 4.3.3, 4.2.3
Build Dependencies:
cubelib, pkgconfig, dbus, zlib, qt
Link Dependencies:
cubelib, dbus, 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:
4.4.4, 4.4.3, 4.4.2, 4.4
Build Dependencies:
pkgconfig, zlib
Link Dependencies:
zlib
Description:
Component of CubeBundle: General purpose C++ library and tools

cubew

Homepage:
Spack package:
Versions:
4.4.3, 4.4.2, 4.4.1, 4.4
Build Dependencies:
pkgconfig, zlib
Link Dependencies:
zlib
Description:
Component of CubeBundle: High performance C Writer library

cuda

Homepage:
Spack package:
Versions:
10.1.243, 10.0.130, 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:
cmake, cuda
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:
7.5.1-10.1-x86_64, 7.5.1-10.1-ppc64le, 7.5.1-10.0-x86_64, 7.5.1-10.0-ppc64le, 7.5.0-10.1-x86_64, 7.5.0-10.1-ppc64le, 7.5.0-10.0-x86_64, 7.5.0-10.0-ppc64le, 7.3.0, 7.2.1, 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:
7.63.0, 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:
openssl, zlib, nghttp2, libssh2, libssh, krb5
Link Dependencies:
openssl, zlib, nghttp2, libssh2, libssh, krb5
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

cxxopts

Homepage:
Spack package:
Versions:
2.2.0, 2.1.2, 2.1.1, 2.1.0, 2.0.0, 1.4.4, 1.4.3, 1.4.2, 1.4.1, 1.4.0
Build Dependencies:
cmake, icu4c
Link Dependencies:
icu4c
Description:
Lightweight C++ command line option parser

czmq

Homepage:
Spack package:
Versions:
4.1.1, 4.0.2, 3.0.2
Build Dependencies:
libtool, automake, autoconf, pkgconfig, libuuid, zeromq
Link Dependencies:
libuuid, zeromq
Description:
A C interface to the ZMQ library

dakota

Homepage:
Spack package:
Versions:
6.9, 6.3
Build Dependencies:
cmake, netlib-lapack, blas, mpi, python, boost
Link Dependencies:
netlib-lapack, blas, mpi, python, 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:
pkgconfig, util-macros
Description:
X Damage Extension. This package contains header files and documentation for the X Damage extension. Library and server implementations are separate.

damaris

Homepage:
Spack package:
Versions:
master, 1.3.1
Build Dependencies:
cmake, mpi, boost, xsd, xerces-c, hdf5, catalyst, visit
Link Dependencies:
mpi, boost, xsd, xerces-c, hdf5, catalyst, visit
Description:
Damaris is a middleware for I/O and in situ analytics targeting large- scale, MPI-based HPC simulations.

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:
develop, 3.1.7, 3.1.6, 3.1.0, 3.0.0
Build Dependencies:
mpi, zlib
Link Dependencies:
mpi, zlib
Description:
Darshan (runtime) is a scalable HPC I/O characterization tool designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. DarshanRuntime package should be installed on systems where you intend to instrument MPI applications.

darshan-util

Homepage:
Spack package:
Versions:
develop, 3.1.7, 3.1.6, 3.1.0, 3.0.0
Build Dependencies:
zlib, bzip2
Link Dependencies:
zlib, bzip2
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, automake, libtool, m4
Link Dependencies:
libedit
Description:
The Debian Almquist Shell.

datamash

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

dataspaces

Homepage:
Spack package:
Versions:
develop, 1.8.0, 1.6.2
Build Dependencies:
m4, automake, autoconf, libtool, mpi
Link Dependencies:
mpi
Description:
an extreme scale data management framework.

dateutils

Homepage:
Spack package:
Versions:
0.4.6, 0.4.5
Description:
Dateutils are a bunch of tools that revolve around fiddling with dates and times in the command line with a strong focus on use cases that arise when dealing with large amounts of financial data.

davix

Homepage:
Spack package:
Versions:
0.6.8
Build Dependencies:
cmake, pkgconfig, libxml2, libuuid, openssl
Link Dependencies:
libxml2, libuuid, openssl
Description:
High-performance file management over WebDAV/HTTP.

dbcsr

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, blas, lapack, mpi, py-fypp
Link Dependencies:
blas, lapack, mpi, py-fypp
Description:
Distributed Block Compressed Sparse Row matrix library.

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:
pkgconfig, expat, glib
Link Dependencies:
expat, glib
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).

dcmtk

Homepage:
Spack package:
Versions:
3.6.3, 3.6.2
Build Dependencies:
cmake, openssl, zlib, libtiff, libpng, libxml2, libiconv
Link Dependencies:
openssl, zlib, libtiff, libpng, libxml2, libiconv
Description:
DCMTK is a collection of libraries and applications implementing large parts of the DICOM standard.

dd4hep

Homepage:
Spack package:
Versions:
develop, 1.10.0
Build Dependencies:
cmake, root, boost, xerces-c, geant4
Link Dependencies:
root, boost, xerces-c, geant4
Description:
DD4hep is a software framework for providing a complete solution for full detector description (geometry, materials, visualization, readout, alignment, calibration, etc.) for the full experiment life cycle (detector concept development, detector optimization, construction, operation). It offers a consistent description through a single source of detector information for simulation, reconstruction, analysis, etc. It distributed under the LGPLv3 License.

dealii

Homepage:
Spack package:
Versions:
develop, 9.1.1, 9.1.0, 9.0.1, 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:
cuda, cmake, blas, boost, bzip2, lapack, suite-sparse, tbb, zlib, mpi, adol-c, arpack-ng, assimp, doxygen, graphviz, ginkgo, gmsh, gsl, hdf5, metis, muparser, nanoflann, netcdf, netcdf-cxx, oce, p4est, petsc, python, scalapack, slepc, sundials, symengine, trilinos
Link Dependencies:
cuda, blas, boost, bzip2, lapack, suite-sparse, tbb, zlib, mpi, adol-c, arpack-ng, assimp, doxygen, graphviz, ginkgo, gsl, hdf5, metis, muparser, nanoflann, netcdf, netcdf-cxx, oce, p4est, petsc, python, scalapack, slepc, sundials, symengine, trilinos
Run Dependencies:
gmsh
Description:
C++ software library providing well-documented tools to build finite element codes for a broad variety of PDEs.

dealii-parameter-gui

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

deconseq-standalone

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

dejagnu

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

delly2

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

denovogear

Homepage:
Spack package:
Versions:
1.1.1, 1.1.0
Build Dependencies:
cmake, boost, htslib, eigen
Link Dependencies:
zlib
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.

dftfe

Homepage:
Spack package:
Versions:
0.6.0, 0.5.2, 0.5.1, 0.5.0
Build Dependencies:
cmake, mpi, dealii, scalapack, alglib, libxc, spglib, libxml2
Link Dependencies:
mpi, dealii, scalapack, alglib, libxc, spglib, libxml2
Description:
Real-space DFT calculations using Finite Elements

dia

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

dialign

Homepage:
Spack package:
Versions:
2.2.1
Description:
DIALIGN is a software program for multiple sequence alignment developed by Burkhard Morgenstern et al..

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:
0.9.25, 0.9.23, 0.9.22, 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.

diffutils

Homepage:
Spack package:
Versions:
3.7, 3.6
Build Dependencies:
libiconv
Link Dependencies:
libiconv
Description:
GNU Diffutils is a package of several programs related to finding differences between files.

dimemas

Homepage:
Spack package:
Versions:
5.4.1
Build Dependencies:
autoconf, automake, libtool, m4, bison, flex, boost
Link Dependencies:
bison, flex, boost
Run Dependencies:
bison, flex
Description:
High-abstracted network simulator for message-passing programs.

direnv

Homepage:
Spack package:
Versions:
2.20.0, 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:
11.2.linux.i586_64
Build Dependencies:
motif, gl, glx
Link Dependencies:
motif, gl, glx
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.

diy

Homepage:
Spack package:
Versions:
master, 3.5.0
Build Dependencies:
cmake
Description:
Data-parallel out-of-core library

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:
master, 20170508
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:
pkgconfig, util-macros
Description:
Distributed Multihead X (DMX) Extension. This extension defines a protocol for clients to access a front-end proxy X server that controls multiple back-end X servers making up a large display.

docbook-xml

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

docbook-xsl

Homepage:
Spack package:
Versions:
1.79.2
Build Dependencies:
docbook-xml
Link Dependencies:
docbook-xml
Description:
DocBook XSLT 1.0 Stylesheets.

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:
1.8.15, 1.8.14, 1.8.12, 1.8.11, 1.8.10
Build Dependencies:
cmake, flex, bison
Run Dependencies:
graphviz
Description:
Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D..

draco

Homepage:
Spack package:
Versions:
develop, 7.2.0, 7_1_0, 6_25_0, 6_23_0, 6_22_0, 6_21_0, 6_20_1, 6_20_0
Build Dependencies:
cmake, gsl, mpi, numdiff, python, random123, eospac, lapack, metis, parmetis, qt, superlu-dist
Link Dependencies:
gsl, mpi, eospac, lapack, metis, parmetis, qt, superlu-dist
Run Dependencies:
mpi, python, qt
Description:
Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system.

dri2proto

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

dri3proto

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

ds

Homepage:
Spack package:
Versions:
9.8.0
Build Dependencies:
autoconf, automake, m4, libtool, libx11, libxml2, libxslt, openssl, tcl, tcl-tclxml, tk
Link Dependencies:
libx11, libxml2, libxslt, openssl, tcl, tcl-tclxml, tk
Description:
SAOImage DS9 is an astronomical imaging and data visualization application.

dsdp

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

dsrc

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

dtcmp

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

dyninst

Homepage:
Spack package:
Versions:
develop, 10.1.0, 10.0.0, 9.3.2, 9.3.0, 9.2.0, 9.1.0, 8.2.1
Build Dependencies:
cmake, boost, libiberty, libdwarf, tbb
Link Dependencies:
boost, libiberty, elf, libdwarf, tbb
Description:
API for dynamic binary instrumentation. Modify programs while they are executing without recompiling, re-linking, or re-executing.

dysco

Homepage:
Spack package:
Versions:
1.2
Build Dependencies:
cmake, casacore, gsl, boost
Link Dependencies:
casacore, gsl, boost
Description:
Dysco is a compressing storage manager for Casacore mearement sets.

ea-utils

Homepage:
Spack package:
Versions:
1.04.807
Build Dependencies:
subversion, zlib, gsl, bamtools, perl
Link Dependencies:
subversion, zlib, gsl, bamtools
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:
4.0.0, 3.1.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-easybuild-framework, py-easybuild-easyblocks, 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:
2.13.0, 2.5.0, 2.2.0
Build Dependencies:
cmake, netcdf, openjpeg, jasper, libpng, libaec, python, py-numpy
Link Dependencies:
netcdf, openjpeg, jasper, libpng, libaec, python
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.

ecflow

Homepage:
Spack package:
Versions:
4.11.1
Build Dependencies:
cmake, boost, qt
Link Dependencies:
boost, qt
Description:
ecFlow is a work flow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides tolerance for hardware and software failures, combined with good restart capabilities.

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-io-sdk

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake, adios2, darshan-runtime, darshan-util, faodel, hdf5, mercury, parallel-netcdf, unifyfs, veloc
Link Dependencies:
adios2, darshan-runtime, darshan-util, faodel, hdf5, mercury, parallel-netcdf, unifyfs, veloc
Description:
ECP I/O Services SDK

ecp-proxy-apps

Homepage:
Spack package:
Versions:
2.1, 2.0, 1.1, 1.0
Build Dependencies:
amg, miniamr, ember, miniqmc, minivite, picsarlite, thornado-mini, candle-benchmarks, laghos, macsio, sw4lite, xsbench, examinimd, nekbone, swfft, minife, minitri, comd
Link Dependencies:
amg, miniamr, ember, miniqmc, minivite, picsarlite, thornado-mini, candle-benchmarks, laghos, macsio, sw4lite, xsbench, examinimd, nekbone, swfft, minife, minitri, comd
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.

ecp-viz-sdk

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
cmake, ascent, catalyst, paraview, sz, visit, vtkm, zfp
Link Dependencies:
ascent, catalyst, paraview, sz, visit, vtkm, zfp
Description:
ECP Viz & Analysis SDK

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.

editline

Homepage:
Spack package:
Versions:
1.16.0
Build Dependencies:
autoconf, automake, libtool, m4, ncurses
Link Dependencies:
ncurses
Description:
A readline() replacement for UNIX without termcap (ncurses)

editres

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

eem

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
EEM is a program to extract the gene group and expression modules that are co-expressed in the mRNA expression data.

eigen

Homepage:
Spack package:
Versions:
3.3.7, 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:
cmake, metis, scotch, fftw, suite-sparse, mpfr, gmp
Link Dependencies:
metis, scotch, fftw, suite-sparse, mpfr, gmp
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:
cmake, blas, openblas, intel-mkl, veclibfort, essl, lapack, netlib-lapack, metis, mpi, scalapack, python, gmp, mpc, mpfr
Link Dependencies:
blas, openblas, intel-mkl, veclibfort, essl, lapack, netlib-lapack, metis, mpi, scalapack, python, gmp, mpc, mpfr
Description:
Elemental: Distributed-memory dense and sparse-direct linear algebra and optimization library.

elfutils

Homepage:
Spack package:
Versions:
0.177, 0.176, 0.175, 0.174, 0.173, 0.170, 0.168, 0.163
Build Dependencies:
gettext, m4
Link Dependencies:
bzip2, xz, 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:
blas, lapack, fftw, mpi, libxc
Link Dependencies:
blas, lapack, fftw, mpi, libxc
Description:
An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features.

elmer-fem

Homepage:
Spack package:
Versions:
8.4
Build Dependencies:
cmake, mpi, netcdf-fortran, blas, lapack, mumps, hypre, trilinos, zoltan, lua
Link Dependencies:
mpi, netcdf-fortran, blas, lapack, mumps, hypre, trilinos, zoltan, lua
Description:
Elmer is an open source multiphysical simulation software. It includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics.

elpa

Homepage:
Spack package:
Versions:
2018.11.001, 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:
mpi, blas, lapack, scalapack
Link Dependencies:
mpi, blas, lapack, scalapack
Description:
Eigenvalue solvers for Petaflop-Applications (ELPA)

elsd

Homepage:
Spack package:
Versions:
master
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
ELSD: Ellipse and Line Segment Detector

elsdc

Homepage:
Spack package:
Versions:
master
Build Dependencies:
blas, lapack
Link Dependencies:
blas, lapack
Description:
ELSDc: Ellipse and Line Segment Detector, with Continuous validation.

elsi

Homepage:
Spack package:
Versions:
2.2.1
Build Dependencies:
cmake, mpi, elpa, ntpoly, slepc, petsc, superlu-dist
Link Dependencies:
blas, lapack, mpi, scalapack, elpa, ntpoly, slepc, petsc, superlu-dist
Description:
ELSI provides a unified interface for electronic structure codes to a variety of eigenvalue solvers.

emacs

Homepage:
Spack package:
Versions:
26.2, 26.1, 25.3, 25.2, 25.1, 24.5
Build Dependencies:
pkgconfig, ncurses, pcre, zlib, libtiff, libpng, libxpm, giflib, libx11, libxaw, gtkplus, gnutls, jpeg
Link Dependencies:
ncurses, pcre, zlib, libtiff, libpng, libxpm, giflib, libx11, libxaw, gtkplus, gnutls, jpeg
Description:
The Emacs programmable text editor.

ember

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
Ember Communication Pattern Library The Ember suite provides communication patterns in a simplified setting (simplified by the removal of application calculations, control flow, etc.).

emboss

Homepage:
Spack package:
Versions:
6.6.0
Build Dependencies:
libxpm, libgd, postgresql
Link Dependencies:
libxpm, libgd, 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

enchant

Homepage:
Spack package:
Versions:
2.2.5, 2.2.4, 2.2.3, 2.2.2, 2.2.1, 2.2.0, 2.1.3, 2.1.2, 2.1.1, 2.1.0
Build Dependencies:
glib, aspell, hunspell
Link Dependencies:
glib, aspell, hunspell
Description:
Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface.

energyplus

Homepage:
Spack package:
Versions:
8.9.0
Description:
EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption for heating, cooling, ventilation, lighting and plug and process loads and water use in buildings

entrezdirect

Homepage:
Spack package:
Versions:
10.7.20190114
Run Dependencies:
perl, perl-html-parser, perl-libwww-perl, perl-lwp-protocol-https, perl-http-message, perl-xml-simple
Description:
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.

environment-modules

Homepage:
Spack package:
Versions:
4.3.1, 4.3.0, 4.2.5, 4.2.4, 4.2.3, 4.2.2, 4.2.1, 4.2.0, 4.1.4, 4.1.3, 4.1.2, 4.1.1, 4.1.0, 4.0.0, 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 module files.

eospac

Homepage:
Spack package:
Versions:
6.4.0beta.4, 6.4.0beta.3, 6.4.0beta.2, 6.4.0beta.1, 6.4.0, 6.3.1
Description:
A collection of C routines that can be used to access the Sesame data library.

eqr

Homepage:
Spack package:
Versions:
develop, 1.0
Build Dependencies:
autoconf, automake, libtool, m4, mpi, r-rinside, r-rcpp, r, tcl, swig
Link Dependencies:
mpi, r-rinside, r-rcpp, r, tcl, swig
Description:
EMEWS Queues for R (EQ/R) Installs EQ/R.

er

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

erfa

Homepage:
Spack package:
Versions:
1.4.0
Build Dependencies:
m4, autoconf, automake, libtool
Description:
ERFA(Essential Routines for Fundamental Astronomy) is a C library containing key algorithms for astronomy.

ermod

Homepage:
Spack package:
Versions:
0.3.6, 0.3.5
Build Dependencies:
fftw, blas
Link Dependencies:
fftw, blas
Description:
ERmod (Energy Representation Module) is a program to calculate the solvation free energy based on the energy representation method. The program allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation softwares, such as NAMD, GROMACS and/or AMBER.

erne

Homepage:
Spack package:
Versions:
2.1.1
Build Dependencies:
boost, openmpi
Link Dependencies:
boost
Run Dependencies:
boost, openmpi
Description:
The Extended Randomized Numerical alignEr using BWT

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:
7.1.0r
Build Dependencies:
zlib, libxml2, mpi, lapack, netcdf, netcdf-fortran, parallel-netcdf, xerces-c
Link Dependencies:
zlib, libxml2, mpi, lapack, netcdf, netcdf-fortran, parallel-netcdf, xerces-c
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:
cmake, python, boost, json-c, curl, zlib, cuda, mesa
Link Dependencies:
python, boost, json-c, curl, zlib, cuda, mesa
Description:
The ethminer is an Ethereum GPU mining worker.

etsf-io

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

everytrace

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

everytrace-example

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

evieext

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

exabayes

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

examinimd

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

exampm

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

exasp2

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

exchanger

Homepage:
Spack package:
Versions:
1.0.1
Build Dependencies:
python, py-merlin, py-pythia
Run Dependencies:
python, py-pythia
Description:
Exchanger is a package containing several C++ base classes. These classes, when customized for a solver, can provide communication channels between solvers. This packaged is used by CitcomS for solver coupling.

exiv2

Homepage:
Spack package:
Versions:
0.27.2
Build Dependencies:
cmake
Description:
Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata

exmcutils

Homepage:
Spack package:
Versions:
master, 0.5.7, 0.5.6
Build Dependencies:
m4, autoconf, automake, libtool
Link Dependencies:
m4, autoconf, automake, libtool
Description:
ExM C-Utils: Generic C utility library for ADLB/X and Swift/T

exodusii

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

exonerate

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

expat

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

express

Homepage:
Spack package:
Versions:
1.5.2, 1.5.1
Build Dependencies:
cmake, boost, bamtools, zlib
Link Dependencies:
boost, bamtools, zlib
Description:
eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

extrae

Homepage:
Spack package:
Versions:
3.7.1, 3.4.1
Build Dependencies:
autoconf, automake, libtool, m4, mpi, libunwind, boost, libdwarf, papi, libxml2, numactl, binutils, gettext, dyninst
Link Dependencies:
mpi, libunwind, boost, libdwarf, papi, elf, libxml2, numactl, binutils, gettext, dyninst
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

eztrace

Homepage:
Spack package:
Versions:
1.1-8
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
EZTrace is a tool to automatically generate execution traces of HPC applications.

f18

Homepage:
Spack package:
Versions:
master
Build Dependencies:
cmake, llvm
Link Dependencies:
llvm
Description:
F18 is a front-end for Fortran intended to replace the existing front- end in the Flang compiler

f90cache

Homepage:
Spack package:
Versions:
0.99c, 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. DEPRECATED. Fabtests has merged with the libfabric git repo.

falcon

Homepage:
Spack package:
Versions:
2017-05-30
Build Dependencies:
python, py-networkx
Link Dependencies:
python
Run Dependencies:
python, py-setuptools, py-pypeflow, py-networkx, pacbio-dazz-db, pacbio-daligner, pacbio-dextractor, 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.

fann

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies:
cmake
Description:
Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks. Cross-platform execution in both fixed and floating point are supported. It includes a framework for easy handling of training data sets. It is easy to use, versatile, well documented, and fast. Bindings to more than 20 programming languages are available. An easy to read introduction article and a reference manual accompanies the library with examples and recommendations on how to use the library. Several graphical user interfaces are also available for the library.

faodel

Homepage:
Spack package:
Versions:
1.1906.1, 1.1811.2, 1.1811.1, 1.1803.1
Build Dependencies:
cmake, mpi, boost, hdf5, libfabric, googletest
Link Dependencies:
mpi, boost, hdf5, libfabric
Description:
Flexible, Asynchronous, Object Data-Exchange Libraries

fast-global-file-status

Homepage:
Spack package:
Versions:
1.1
Build Dependencies:
mrnet, mount-point-attributes, mpi
Link Dependencies:
mrnet, mount-point-attributes, mpi
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:
amrex, chombo, hypre, mpi, arpack-ng, petsc, phasta, pumi, sundials, superlu-dist, trilinos, zoltan
Link Dependencies:
amrex, chombo, hypre, mpi, arpack-ng, petsc, phasta, pumi, sundials, superlu-dist, trilinos, zoltan
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, automake, libtool, m4
Description:
FastME is a distance based phylogeny reconstruction program that works on distance matrices and, as of v2.0, sequence data.

fastp

Homepage:
Spack package:
Versions:
0.20.0
Description:
A tool designed to provide fast all-in-one preprocessing for FastQ files.

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:
bowtie, bowtie2, bwa, samtools
Link Dependencies:
bowtie, bowtie2, bwa, samtools
Run Dependencies:
perl, perl-gd-graph
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
Link Dependencies:
zlib
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
Build Dependencies:
cmake, python, eigen, boost, mpi, hdf5, parmetis, scotch, petsc, slepc, trilinos, vtk, suite-sparse, qt, py-ply, py-six, py-numpy, py-sympy, swig, py-setuptools, py-sphinx
Link Dependencies:
python, eigen, boost, mpi, hdf5, parmetis, scotch, petsc, slepc, trilinos, vtk, suite-sparse, qt
Run Dependencies:
py-ply, py-six, py-numpy, py-sympy, swig
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:
7.2, 6.96
Build Dependencies:
hdf5, netcdf, netcdf-fortran, readline, zlib, libx11
Link Dependencies:
hdf5, netcdf, netcdf-fortran, readline, zlib, libx11
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:
4.1.1, 4.1, 3.2.4
Build Dependencies:
yasm, aom
Link Dependencies:
yasm, aom
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:
mpi, automake, autoconf, 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.

fgsl

Homepage:
Spack package:
Versions:
1.3.0, 1.2.0, 1.1.0
Build Dependencies:
autoconf, automake, libtool, m4, gsl
Link Dependencies:
gsl
Description:
Fortran interface to the GNU Scientific Library

figtree

Homepage:
Spack package:
Versions:
1.4.3
Run Dependencies:
java
Description:
FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.

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
Build Dependencies:
autoconf, automake, libtool, m4, texinfo
Description:
The GNU Find Utilities are the basic directory searching utilities of the GNU operating system.

fio

Homepage:
Spack package:
Versions:
3.16, 2.19
Build Dependencies:
gtkplus, cairo, libaio, py-sphinx
Link Dependencies:
gtkplus, cairo, libaio
Description:
Flexible I/O Tester. Fio spawns a number of threads or processes doing a particular type of I/O action as specified by the user. fio takes a number of global parameters, each inherited by the thread unless otherwise parameters given to them overriding that setting is given.

fish

Homepage:
Spack package:
Versions:
3.0.0, 2.7.1, 2.7.0, 2.2.0
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
fish is a smart and user-friendly command line shell for OS X, Linux, and the rest of the family.

fixesproto

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

fl

Homepage:
Spack package:
Versions:
0.79.47
Description:
Fawlty Language is an IDL8 (Interactive Data Language) compatible compiler.

flac

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

flang

Homepage:
Spack package:
Versions:
develop, 20180921, 20180612
Build Dependencies:
cmake, llvm, pgmath
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:
cmake, python, py-numpy, matlab, cuda, mpi, hdf5, boost, latex
Link Dependencies:
python, cuda, mpi, hdf5, boost, latex
Run Dependencies:
py-numpy, matlab
Test Dependencies:
hdf5, gtest
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:
1.10.0, 1.9.0, 1.8.0
Build Dependencies:
cmake
Description:
Memory Efficient Serialization Library

flatcc

Homepage:
Spack package:
Versions:
master, 0.5.3, 0.5.2, 0.5.1, 0.5.0, 0.4.3, 0.4.2, 0.4.1
Build Dependencies:
cmake
Description:
FlatBuffers C Compiler (flatcc), a memory-efficient serialization library, is implemented as a standalone tool instead of extending Googles flatc compiler in order to have a pure portable C library implementation of the schema compiler that is designed to fail graciously on abusive input in long running processes. It is also believed a C version may help provide schema parsing to other language interfaces that find interfacing with C easier than C++.

flecsale

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

flecsi

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, cinch, mpi, gasnet, legion, boost, metis, parmetis, caliper, graphviz, python, llvm
Link Dependencies:
mpi, gasnet, legion, boost, metis, parmetis, caliper, graphviz, python, llvm
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.

flecsph

Homepage:
Spack package:
Versions:
develop
Build Dependencies:
cmake, boost, mpi, hdf5, flecsi, gsl
Link Dependencies:
boost, mpi, hdf5, flecsi, gsl
Description:
FleCSPH is a multi-physics compact application that exercises FleCSI parallel data structures for tree-based particle methods. In particular, FleCSPH implements a smoothed-particle hydrodynamics (SPH) solver for the solution of Lagrangian problems in astrophysics and cosmology. FleCSPH includes support for gravitational forces using the fast multipole method (FMM).

flex

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

flibcpp

Homepage:
Spack package:
Versions:
master, 0.3.1
Build Dependencies:
cmake, swig, py-sphinx
Description:
Fortran bindings to the C++ Standard Library.

flint

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

flit

Homepage:
Spack package:
Versions:
2.0-alpha.1
Run Dependencies:
python, py-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:
master, 0.11.0, 0.10.0, 0.9.0, 0.8.0
Build Dependencies:
zeromq, czmq, hwloc, lua, lua-luaposix, munge, python, py-cffi, py-six, py-pyyaml, py-jsonschema, jansson, pkgconfig, yaml-cpp, lz4, py-pylint, asciidoc, autoconf, automake, libtool
Link Dependencies:
zeromq, czmq, hwloc, lua, lua-luaposix, munge, python, jansson, pkgconfig, yaml-cpp, lz4
Run Dependencies:
lua, python, py-cffi, py-six, py-pyyaml, py-jsonschema
Description:
A next-generation resource manager (pre-alpha)

flux-sched

Homepage:
Spack package:
Versions:
master, 0.7.0, 0.6.0, 0.5.0, 0.4.0
Build Dependencies:
boost, py-pyyaml, libxml2, yaml-cpp, libuuid, pkgconfig, flux-core, autoconf, automake, libtool
Link Dependencies:
boost, py-pyyaml, libxml2, yaml-cpp, libuuid, pkgconfig, flux-core
Run Dependencies:
flux-core
Description:
A scheduler for flux-core (pre-alpha)

fluxbox

Homepage:
Spack package:
Versions:
1.3.7
Build Dependencies:
pkgconfig, freetype, libxrender, libxext, expat, libx11
Link Dependencies:
freetype, libxrender, libxext, expat, libx11
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:
5.3.0, 5.2.1, 5.2.0, 5.1.0, 5.0.0, 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:
mpi, python, zlib, flex, cmake, scotch, metis, parmetis, parmgridgen, paraview
Link Dependencies:
mpi, python, zlib, scotch, metis, parmetis, paraview
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:
m4, autoconf, automake, libtool, pkgconfig, boost, gflags, glog, double-conversion, libevent
Link Dependencies:
boost, gflags, glog, double-conversion, libevent
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-util

Homepage:
Spack package:
Versions:
1.3.2, 1.3.1
Build Dependencies:
autoconf, automake, pkgconfig, util-macros, bdftopcf, mkfontscale, mkfontdir
Description:
X.Org font package creation/installation utilities and fonts.

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:
freetype, gperf, libxml2, pkgconfig, font-util
Link Dependencies:
freetype, libxml2, font-util
Description:
Fontconfig is a library for configuring/customizing font access

fontsproto

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

fonttosfnt

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies:
freetype, libfontenc, xproto, pkgconfig, util-macros
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.

fpocket

Homepage:
Spack package:
Versions:
master
Build Dependencies:
netcdf
Link Dependencies:
netcdf
Description:
fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.

fqtrim

Homepage:
Spack package:
Versions:
0.9.7
Description:
fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing machines.

fr-hit

Homepage:
Spack package:
Versions:
0.7.1-2013-02-20
Build Dependencies:
perl, python
Link Dependencies:
perl, python
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:
cmake, gl, glu, libx11, libxrandr, libxi, xrandr, inputproto
Link Dependencies:
gl, glu, libx11, libxrandr, libxi, xrandr, inputproto
Description:
FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library

freeimage

Homepage:
Spack package:
Versions:
3.18.0
Description:
FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications

freetype

Homepage:
Spack package:
Versions:
2.10.1, 2.9.1, 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.

freexl

Homepage:
Spack package:
Versions:
1.0.5
Description:
FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

fribidi

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
m4, autoconf, automake, libtool
Description:
GNU FriBidi: The Free Implementation of the Unicode Bidirectional Algorithm.

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:
python, expat, libx11, glu, zlib, libpng, boost, sqlite
Link Dependencies:
expat, libx11, glu, zlib, libpng, boost, sqlite
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:
libfs, xproto, pkgconfig, util-macros
Link Dependencies:
libfs
Description:
fslsfonts produces a list of fonts served by an X font server.

fstobdf

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

fstrack

Homepage:
Spack package:
Versions:
0.5.3.092918
Build Dependencies:
gmt, netcdf
Link Dependencies:
gmt, netcdf
Description:
Package with tools to analyze symmetry components of elastic tensors, predict synthetic waveforms and compute automated shear wave splitting along ray paths, and to track finite strain and predict LPO from mantle flow given on GMT/netcdf grds.

ftgl

Homepage:
Spack package:
Versions:
2.1.3-rc5, 2.1.2
Build Dependencies:
autoconf, automake, libtool, m4, pkgconfig, gl, glu, freetype, doxygen
Link Dependencies:
gl, glu, freetype
Description:
Library to use arbitrary fonts in OpenGL applications.

fujitsu-mpi

Homepage:
Spack package:
Description:
Fujitsu MPI implementation only for Fujitsu compiler.

funhpc

Homepage:
Spack package:
Versions:
develop, 1.3.0
Build Dependencies:
cmake, cereal, googletest, hwloc, jemalloc, mpi, qthreads
Link Dependencies:
cereal, googletest, hwloc, jemalloc, mpi, qthreads
Description:
FunHPC: Functional HPC Programming

fyba

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

fzf

Homepage:
Spack package:
Versions:
0.17.5, 0.17.4, 0.17.3, 0.17.1, 0.17.0-2, 0.17.0, 0.16.11, 0.16.10, 0.16.9, 0.16.8
Build Dependencies:
go
Link Dependencies:
go
Description:
fzf is a general-purpose command-line fuzzy finder.

g4abla

Homepage:
Spack package:
Versions:
3.1, 3.0
Description:
Geant4 data for nuclear shell effects in INCL/ABLA hadronic mode

g4emlow

Homepage:
Spack package:
Versions:
7.3, 6.50
Description:
Geant4 data files for low energy electromagnetic processes.

g4ensdfstate

Homepage:
Spack package:
Versions:
2.2, 2.1
Description:
Geant4 data for nuclides properties

g4ndl

Homepage:
Spack package:
Versions:
4.5
Description:
Geant4 Neutron data files with thermal cross sections

g4neutronxs

Homepage:
Spack package:
Versions:
1.4
Description:
Geant4 data for evaluated neutron cross-sections on natural composition of elements

g4photonevaporation

Homepage:
Spack package:
Versions:
5.2, 4.3.2
Description:
Geant4 data for photon evaporation

g4pii

Homepage:
Spack package:
Versions:
1.3
Description:
Geant4 data for shell ionisation cross-sections

g4radioactivedecay

Homepage:
Spack package:
Versions:
5.2, 5.1.1
Description:
Geant4 data files for radio-active decay hadronic processes

g4realsurface

Homepage:
Spack package:
Versions:
2.1.1, 2.1, 1.0
Description:
Geant4 data for measured optical surface reflectance

g4saiddata

Homepage:
Spack package:
Versions:
1.1
Description:
Geant4 data from evaluated cross-sections in SAID data-base

g4tendl

Homepage:
Spack package:
Versions:
1.3.2, 1.3
Description:
Geant4 data for incident particles [optional]

gams

Homepage:
Spack package:
Versions:
27.2
Description:
The General Algebraic Modeling System is a high-level modeling system for mathematical optimization. GAMS is designed for modeling and solving linear, nonlinear, and mixed-integer optimization problems.

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:
2019.3.0, 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:
4.1.0.0, 4.0.12.0, 4.0.11.0, 4.0.8.1, 4.0.4.0, 3.8-1, 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:
gettext, libsigsegv, readline, mpfr, gmp
Link Dependencies:
gettext, libsigsegv, readline, 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:
develop, 9.2.0, 9.1.0, 8.3.0, 8.2.0, 8.1.0, 7.4.0, 7.3.0, 7.2.0, 7.1.0, 6.5.0, 6.4.0, 6.3.0, 6.2.0, 6.1.0, 5.5.0, 5.4.0, 5.3.0, 5.2.0, 5.1.0, 4.9.4, 4.9.3, 4.9.2, 4.9.1, 4.8.5, 4.8.4, 4.7.4, 4.6.4, 4.5.4
Build Dependencies:
gmp, mpfr, mpc, isl, zlib, libiconv, gnat, binutils, zip, cuda
Link Dependencies:
gmp, mpfr, mpc, isl, zlib, libiconv, gnat, binutils, cuda
Test Dependencies:
dejagnu, expect, tcl, autogen, guile
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:
3.0.1, 3.0.0, 2.4.2, 2.4.1, 2.4.0, 2.3.3, 2.3.2, 2.3.1, 2.3.0, 2.1.2, 2.0.2, 1.11.5
Build Dependencies:
python, gmake, pkgconfig, libtiff, libgeotiff, json-c, libtool, zlib, libiconv, xz, zstd, postgresql, cfitsio, libpng, jpeg, giflib, fyba, hdf, hdf5, kealib, netcdf, jasper, openjpeg, xerces-c, expat, libkml, unixodbc, curl, libxml2, sqlite, pcre, geos, qhull, opencl, poppler, proj, perl, py-setuptools, py-numpy, java, armadillo, cryptopp, openssl
Link Dependencies:
python, libtiff, libgeotiff, json-c, zlib, libiconv, xz, zstd, postgresql, cfitsio, libpng, jpeg, giflib, fyba, hdf, hdf5, kealib, netcdf, jasper, openjpeg, xerces-c, expat, libkml, unixodbc, curl, libxml2, sqlite, pcre, geos, qhull, opencl, poppler, proj, java, armadillo, cryptopp, openssl
Run Dependencies:
python, perl, py-numpy, java, jackcess
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:
8.3, 8.2.1, 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:
texinfo, python, xz
Link Dependencies:
python, xz
Description:
GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes -- or what another program was doing at the moment it crashed.

gdbm

Homepage:
Spack package:
Versions:
1.18.1, 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:
2.38.0, 2.31.2
Build Dependencies:
meson, ninja, shared-mime-info, pkgconfig, libxslt, docbook-xsl, gettext, glib, jpeg, libpng, zlib, libtiff, gobject-introspection
Link Dependencies:
gettext, glib, jpeg, libpng, zlib, libtiff, gobject-introspection
Description:
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

gdl

Homepage:
Spack package:
Versions:
0.9.9, 0.9.8
Build Dependencies:
cmake, python, graphicsmagick, hdf, hdf5, libx11, plplot, proj, py-numpy, wxwidgets, eigen, fftw, gsl, jpeg, libice, libsm, libxinerama, libxxf86vm, netcdf, pslib, readline
Link Dependencies:
python, graphicsmagick, hdf, hdf5, libx11, plplot, proj, wxwidgets, eigen, fftw, gsl, jpeg, libice, libsm, libxinerama, libxxf86vm, netcdf, pslib, readline
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
Build Dependencies:
cmake, xerces-c, clhep, vecgeom, expat, zlib, gl, glx, libx11, libxmu, motif, qt, geant4-data
Link Dependencies:
xerces-c, clhep, vecgeom, expat, zlib, gl, glx, libx11, libxmu, motif, qt, geant4-data
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.

geant4-data

Homepage:
Spack package:
Versions:
10.04, 10.03.p03
Build Dependencies:
g4abla, g4emlow, g4ndl, g4neutronxs, g4saiddata, g4ensdfstate, g4photonevaporation, g4pii, g4radioactivedecay, g4realsurface, g4tendl
Link Dependencies:
g4abla, g4emlow, g4ndl, g4neutronxs, g4saiddata, g4ensdfstate, g4photonevaporation, g4pii, g4radioactivedecay, g4realsurface, g4tendl
Description:
An umbrella package to hold Geant4 data packages

gearshifft

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

gemmlowp

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

genemark-et

Homepage:
Spack package:
Versions:
4.46, 4.38
Build Dependencies:
perl, perl-yaml, perl-hash-merge, perl-logger-simple, perl-parallel-forkmanager
Run Dependencies:
perl, perl-yaml, perl-hash-merge, perl-logger-simple, perl-parallel-forkmanager
Description:
Gene Prediction in Bacteria, archaea, Metagenomes and Metatranscriptomes. When downloaded this file is named the same for all versions. 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

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:
perl, cairo, 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, master, 1.0.0-rc2, 1.0.0-rc1, 0.6.1, 0.6.0, 0.5.1, 0.5.0, 0.4.0, 0.3.0
Build Dependencies:
m4, automake, autoconf, libtool, ruby-ronn, doxygen, numactl, mpi, hwloc, json-c
Link Dependencies:
numactl, mpi, hwloc, json-c
Run Dependencies:
py-pandas, py-numpy, py-natsort, 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:
3.7.2, 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:
ruby, python, swig
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:
0.20.1, 0.19.8.1, 0.19.7
Build Dependencies:
ncurses, libxml2, tar, bzip2, xz, libunistring
Link Dependencies:
ncurses, libxml2, tar, bzip2, xz, libunistring
Run Dependencies:
xz
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, cmake, hwloc, blas, mpi, scotch, zoltan
Link Dependencies:
cuda, cmake, hwloc, blas, mpi, scotch, zoltan
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:
9.26, 9.21, 9.18
Build Dependencies:
pkgconfig, freetype, jpeg, lcms, libpng, libtiff, zlib, libxext, gtkplus
Link Dependencies:
freetype, jpeg, lcms, libpng, libtiff, zlib, libxext, gtkplus
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.

ginkgo

Homepage:
Spack package:
Versions:
develop, master, 1.0.0
Build Dependencies:
cuda, cmake
Link Dependencies:
cuda
Description:
High-performance linear algebra library for manycore systems, with a focus on sparse solution of linear systems.

git

Homepage:
Spack package:
Versions:
2.21.0, 2.20.1, 2.19.2, 2.19.1, 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:
curl, expat, gettext, libiconv, openssl, pcre, perl, zlib, autoconf, automake, libtool, m4, tk
Link Dependencies:
curl, expat, gettext, libiconv, openssl, pcre, perl, zlib, tk
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-fat-git

Homepage:
Spack package:
Versions:
2018-08-21
Run Dependencies:
python, git, rsync
Description:
Simple way to handle fat files without committing them to git, supports synchronization using rsync

git-imerge

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

git-lfs

Homepage:
Spack package:
Versions:
2.9.0, 2.8.0, 2.7.2, 2.7.1, 2.7.0, 2.6.1
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:
cmake, freeglut, gl, libice, libsm, libxau, libxdamage, libxdmcp, libxext, libxfixes, libxi, libxmu, libxt, libxxf86vm, libxcb, libdrm, expat, libpng, zlib, texlive
Link Dependencies:
freeglut, gl, libice, libsm, libxau, libxdamage, libxdmcp, libxext, libxfixes, libxi, libxmu, libxt, libxxf86vm, libxcb, libdrm, expat, libpng, zlib
Description:
GL2PS is a C library providing high quality vector output for any OpenGL application.

glew

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

glfmultiples

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

glib

Homepage:
Spack package:
Versions:
2.56.3, 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:
pkgconfig, libffi, zlib, gettext, perl, python, pcre, util-linux, libiconv
Link Dependencies:
libffi, zlib, gettext, pcre, util-linux, libiconv
Run Dependencies:
perl, python
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, 2.1