Package List

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 2429 mainline packages:

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

abinit

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

abyss

Homepage:
Spack package:
Versions:
2.0.2, 1.5.2
Build Dependencies:
sparsehash, boost, sqlite, mpi, automake, autoconf, libtool
Link Dependencies:
sparsehash, libtool, boost, sqlite, mpi
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.

ack

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

activeharmony

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

adept-utils

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

adios

Homepage:
Spack package:
Versions:
develop, 1.13.0, 1.12.0, 1.11.1, 1.11.0, 1.10.0, 1.9.0
Build Dependencies:
netcdf, hdf5, zlib, libtool, automake, mpi, autoconf, szip, lz4, m4, bzip2, dataspaces, libevpath, zfp, python, c-blosc, sz
Link Dependencies:
netcdf, hdf5, zlib, bzip2, szip, lz4, c-blosc, dataspaces, libevpath, zfp, mpi, sz
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, 2.0.0
Build Dependencies:
py-numpy, zeromq, hdf5, adios, cmake, bzip2, py-mpi4py, python, mpi, zfp
Link Dependencies:
zeromq, hdf5, bzip2, adios, python, mpi, zfp
Run Dependencies:
py-numpy, python, py-mpi4py
Description:
Next generation of ADIOS developed in the Exascale Computing Program

adlbx

Homepage:
Spack package:
Versions:
0.8.0
Build Dependencies:
exmcutils, 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
Build Dependencies:
automake, autoconf, m4, libtool
Description:
A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading.

albert

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

alglib

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

allinea-forge

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

allinea-reports

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

allpaths-lg

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

alquimia

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

alsa-lib

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

amg

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

amg2013

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

amp

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

ampliconnoise

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

amr-exp-parabolic

Homepage:
Spack package:
Versions:
release
Build Dependencies:
gmake, mpi
Link Dependencies:
mpi
Description:
Simplified block-structured adaptive mesh refinement algorithm in two and three dimensions with subcycling in time. The algorithm solves a linear advection diffusion equation with a simple numerical method. This proxy app is intended to capture the communication pattern of an explicit AMR algorithm but does not represent an accurate characterization of floating point effort or relative costs of communication to computation.

amrex

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

andi

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

angsd

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

ant

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

antlr

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

ape

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

apex

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

applewmproto

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

appres

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

apr

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

apr-util

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

archer

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

argp-standalone

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

argtable

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

arlecore

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

armadillo

Homepage:
Spack package:
Versions:
8.100.1, 7.950.1, 7.900.1, 7.500.0, 7.200.2, 7.200.1
Build Dependencies:
arpack-ng, hdf5, superlu, cmake, lapack, blas
Link Dependencies:
superlu, arpack-ng, hdf5, lapack, blas
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:
3.5.0, 3.4.0, 3.3.0
Build Dependencies:
autoconf, libtool, mpi, lapack, automake, cmake, blas
Link Dependencies:
lapack, blas, mpi
Description:
ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Important Features: * Reverse Communication Interface. * Single and Double Precision Real Arithmetic Versions for Symmetric, Non-symmetric, Standard or Generalized Problems. * Single and Double Precision Complex Arithmetic Versions for Standard or Generalized Problems. * Routines for Banded Matrices - Standard or Generalized Problems. * Routines for The Singular Value Decomposition. * Example driver routines that may be used as templates to implement numerous Shift-Invert strategies for all problem types, data types and precision. This project is a joint project between Debian, Octave and Scilab in order to provide a common and maintained version of arpack. Indeed, no single release has been published by Rice university for the last few years and since many software (Octave, Scilab, R, Matlab...) forked it and implemented their own modifications, arpack-ng aims to tackle this by providing a common repository and maintained versions. arpack-ng is replacing arpack almost everywhere.

ascent

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

asciidoc

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

aspa

Homepage:
Spack package:
Versions:
master
Build Dependencies:
lapack, hdf5, blas, mpi
Link Dependencies:
lapack, hdf5, blas, mpi
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.

aspell

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

aspell6-de

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

aspell6-en

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

aspell6-es

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

assimp

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

astra

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

astral

Homepage:
Spack package:
Versions:
4.10.7
Build Dependencies:
java
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:
3.0.1, 2.06, 2.05.1, 2.04
Description:
A Free, Fast, and Small Automatic Formatter for C, C++, C++/CLI, Objective-C, C#, and Java Source Code.

atk

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

atlas

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

atom-dft

Homepage:
Spack package:
Versions:
4.2.6
Build Dependencies:
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, libxc, blas
Link Dependencies:
lapack, libxc, blas
Description:
A Projector Augmented Wave (PAW) code for generating atom-centered functions. Official website: http://pwpaw.wfu.edu User's guide: ~/doc/atompaw-usersguide.pdf

atop

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

augustus

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

autoconf

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

autodock-vina

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

autogen

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

automaded

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

automake

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

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
Description:
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.

barrnap

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

bash

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

bash-completion

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

bats

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

bazel

Homepage:
Spack package:
Versions:
0.4.5, 0.4.4, 0.3.1, 0.3.0, 0.2.3, 0.2.2b, 0.2.2
Build Dependencies:
zip, java
Link Dependencies:
zip, java
Description:
Bazel is Google's own build tool

bbcp

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

bbmap

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

bcftools

Homepage:
Spack package:
Versions:
1.6, 1.4, 1.3.1, 1.2
Build Dependencies:
htslib
Link Dependencies:
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:
2.19.1.403, 2.18.0.12, 2.17.1.14
Build Dependencies:
libgcrypt, zlib, boost, libxslt, cmake, libxml2
Link Dependencies:
libgcrypt, zlib, boost, libxslt, cmake, libxml2
Description:
The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files.

bdftopcf

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
pkgconfig, xproto, libxfont, 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:
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.

beast2

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

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

benchmark

Homepage:
Spack package:
Versions:
develop, 1.2.0, 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, mpi, bison, mpfr, gmp
Link Dependencies:
mpi, mpfr, gmp
Description:
Bertini is a general-purpose solver, written in C, that was created for research about polynomial continuation. It solves for the numerical solution of systems of polynomial equations using homotopy continuation.

bib2xhtml

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

bigreqsproto

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

binutils

Homepage:
Spack package:
Versions:
2.29.1, 2.28, 2.27, 2.26, 2.25, 2.24, 2.23.2, 2.20.1
Build Dependencies:
zlib, m4, bison, gettext, flex
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.

bison

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

bitmap

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

blast-plus

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

blat

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

blaze

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

bliss

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

blitz

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

bmake

Homepage:
Spack package:
Versions:
20171207
Description:
bmake: portable BSD make bmake is the BSD make(1) utility ported to several non-BSD systems. It supports GNU's autoconf.

bml

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

bohrium

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

boost

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

boostmplcartesianproduct

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

bowtie

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

bowtie2

Homepage:
Spack package:
Versions:
2.3.1, 2.3.0, 2.2.5
Build Dependencies:
zlib, tbb, readline
Link Dependencies:
zlib, tbb, readline
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:
bpp-seq, cmake, bpp-core
Link Dependencies:
bpp-seq, bpp-core
Description:
Bio++ phylogeny library.

bpp-seq

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

bpp-suite

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

braker

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

branson

Homepage:
Spack package:
Versions:
develop, 1.01
Build Dependencies:
metis, mpi, cmake, boost, parmetis
Link Dependencies:
metis, mpi, boost, 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
Build Dependencies:
cmake, zlib
Link Dependencies:
zlib
Description:
BreakDancer-1.3.6, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs..

breseq

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

brigand

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

bsseeker2

Homepage:
Spack package:
Versions:
2.1.2
Build Dependencies:
py-pysam, python
Run Dependencies:
py-pysam, python
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.

busco

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

butter

Homepage:
Spack package:
Versions:
0.3.3
Build Dependencies:
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.

bwa

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

byobu

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

bzip2

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

c-blosc

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

caffe

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

cairo

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

caliper

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

callpath

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

candle-benchmarks

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

cantera

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

canu

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

cap3

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

cares

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

cask

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

casper

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

catalyst

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

catch

Homepage:
Spack package:
Versions:
2.1.0, 2.0.1, 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
Description:
Catch tests

cbench

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

cblas

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

cbtf

Homepage:
Spack package:
Versions:
1.8
Build Dependencies:
mrnet, cmake, boost, xerces-c, libxml2
Link Dependencies:
mrnet, boost, xerces-c, libxml2
Description:
CBTF project contains the base code for CBTF that supports creating components, component networks and the support to connect these components and component networks into sequential and distributed network tools.

cbtf-argonavis

Homepage:
Spack package:
Versions:
1.8
Build Dependencies:
cuda, boost, papi, cmake, cbtf-krell, cbtf, mrnet
Link Dependencies:
cuda, boost, papi, cbtf-krell, cbtf, mrnet
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:
0.8.1
Build Dependencies:
openspeedshop, qtgraph, qt, cmake, xerces-c, mrnet, cuda, boost, cbtf-argonavis, graphviz, cbtf-krell, cbtf
Link Dependencies:
cuda, cbtf, openspeedshop, boost, cbtf-argonavis, graphviz, qtgraph, qt, cbtf-krell, xerces-c, mrnet
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:
1.8
Build Dependencies:
libmonitor, libunwind, papi, mpt, openmpi, dyninst, binutils, llvm-openmp-ompt, mvapich2, xerces-c, mrnet, mvapich, boost, mpich, cmake, mpich2, cbtf
Link Dependencies:
libmonitor, libunwind, papi, mpt, openmpi, dyninst, binutils, llvm-openmp-ompt, mvapich2, xerces-c, mrnet, mvapich, boost, mpich, mpich2, cbtf
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:
1.8
Build Dependencies:
xerces-c, cmake, cbtf-krell, cbtf, mrnet
Link Dependencies:
xerces-c, cbtf-krell, cbtf, mrnet
Description:
CBTF LANL project contains a memory tool and data center type system command monitoring tool.

ccache

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

cctools

Homepage:
Spack package:
Versions:
6.1.1
Build Dependencies:
perl, openssl, swig, zlib, python, readline
Link Dependencies:
swig, openssl, zlib, readline
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
Description:
Fast indexing and retrieval of fasta records from flat file databases

cdd

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

cddlib

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

cdhit

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

cdo

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

cereal

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

cfitsio

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

cgal

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

cgm

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

cgns

Homepage:
Spack package:
Versions:
3.3.1, 3.3.0
Build Dependencies:
hdf5, cmake, 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.

charm

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

check

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

chlorop

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

chombo

Homepage:
Spack package:
Versions:
develop, 3.2
Build Dependencies:
lapack, blas, hdf5, gmake, mpi
Link Dependencies:
lapack, hdf5, blas, mpi
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.

cityhash

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

clamr

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

cleaveland4

Homepage:
Spack package:
Versions:
4.4
Build Dependencies:
perl, perl-math-cdf, viennarna, samtools, r, bowtie
Link Dependencies:
viennarna, samtools, bowtie
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:
samrai, hdf5, cmake, 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:
2.4.0.1, 2.4.0.0, 2.3.4.5, 2.3.4.4, 2.3.4.3, 2.3.4.2, 2.3.4.1, 2.3.4.0, 2.3.3.2, 2.3.3.1, 2.3.3.0, 2.3.2.2, 2.3.2.1, 2.3.1.1, 2.3.1.0, 2.3.0.0, 2.2.0.8, 2.2.0.5, 2.2.0.4
Build Dependencies:
cmake
Description:
CLHEP is a C++ Class Library for High Energy Physics.

clingo

Homepage:
Spack package:
Versions:
5.2.2
Build Dependencies:
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.

cloc

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

cloog

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

cloverleaf

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

cloverleaf3d

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

clustalo

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

clustalw

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

cmake

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

cmocka

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

cmor

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

cnmem

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

cnpy

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

cns-nospec

Homepage:
Spack package:
Versions:
master
Build Dependencies:
gmake, mpi
Link Dependencies:
mpi
Description:
A simple, explicit, stencil-based test code for integrating the compressible Navier-Stokes equations. The code uses 8th order finite differences in space and a 3rd order, low-storage TVD RK algorithm in time.

cntk

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

cntk1bitsgd

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

codar-cheetah

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

coevp

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

cohmm

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

coinhsl

Homepage:
Spack package:
Versions:
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

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.

compiz

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

compositeproto

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

conduit

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

constype

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

converge

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

coreutils

Homepage:
Spack package:
Versions:
8.26, 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:
py-numpy, py-pandas, py-scipy, planck-likelihood, mpi, py-matplotlib, python, py-six
Link Dependencies:
python, planck-likelihood, mpi
Run Dependencies:
py-numpy, py-pandas, py-scipy, py-matplotlib, python, py-six
Description:
CosmoMC is a Fortran 2008 Markov-Chain Monte-Carlo (MCMC) engine for exploring cosmological parameter space, together with Fortran and python code for analysing Monte-Carlo samples and importance sampling (plus a suite of scripts for building grids of runs, plotting and presenting results).

cosp2

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

cp2k

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

cppad

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

cppcheck

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

cpprestsdk

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

cppunit

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

cppzmq

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

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.

cryptopp

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

cscope

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

csdp

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

ctffind

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

cub

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

cube

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

cuda

Homepage:
Spack package:
Versions:
9.1.85, 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: http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details.

cuda-memtest

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

cudnn

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

cups

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

curl

Homepage:
Spack package:
Versions:
7.56.0, 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, nghttp2, zlib
Link Dependencies:
openssl, nghttp2, zlib
Description:
cURL is an open source command line tool and library for transferring data with URL syntax

cvs

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

czmq

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

dakota

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

daligner

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

damageproto

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

damselfly

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

darshan-runtime

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

darshan-util

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

datamash

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

dataspaces

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

dbus

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

dealii

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

dejagnu

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

delly2

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

denovogear

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

dia

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

dialign-tx

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

diamond

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

direnv

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

discovar

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

discovardenovo

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

dlpack

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

dmlc-core

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

dmxproto

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

docbook-xml

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

docbook-xsl

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

dos2unix

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

double-conversion

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

doxygen

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

dri2proto

Homepage:
Spack package:
Versions:
2.8
Build Dependencies:
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.

dtcmp

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

dyninst

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

ea-utils

Homepage:
Spack package:
Versions:
1.04.807
Build Dependencies:
zlib, subversion, gsl, bamtools, perl
Link Dependencies:
zlib, subversion, 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:
3.1.2
Build Dependencies:
python
Link Dependencies:
python
Run Dependencies:
python, py-easybuild-easyblocks, py-easybuild-easyconfigs, py-easybuild-framework
Description:
EasyBuild is a software build and installation framework for (scientific) software on HPC systems.

ebms

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

eccodes

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

ecp-proxy-apps

Homepage:
Spack package:
Versions:
1.0
Build Dependencies:
macsio, minife, candle-benchmarks, miniamr, comd, sw4lite, xsbench, nekbone, laghos, minitri, swfft, amg
Link Dependencies:
macsio, minife, candle-benchmarks, miniamr, comd, sw4lite, xsbench, nekbone, laghos, minitri, swfft, amg
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.

editres

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

eigen

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

elemental

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

elfutils

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

elk

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

elpa

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

emacs

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

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

encodings

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

environment-modules

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

es

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

esmf

Homepage:
Spack package:
Versions:
7.0.1
Build Dependencies:
netcdf, netcdf-fortran, zlib, mpi, lapack, parallel-netcdf, xerces-c, libxml2
Link Dependencies:
netcdf, netcdf-fortran, zlib, mpi, lapack, parallel-netcdf, xerces-c, libxml2
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.

espresso

Homepage:
Spack package:
Versions:
6.1.0, 5.4.0, 5.3.0
Build Dependencies:
fftw, elpa, mpi, lapack, scalapack, hdf5, blas
Link Dependencies:
fftw, elpa, mpi, lapack, scalapack, hdf5, blas
Description:
Quantum-ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

essl

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

ethminer

Homepage:
Spack package:
Versions:
0.12.0
Build Dependencies:
cuda, json-c, zlib, boost, python, curl, cmake, mesa
Link Dependencies:
cuda, json-c, zlib, boost, curl, python, 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, 0.2.0
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, openmpi, everytrace
Link Dependencies:
openmpi, everytrace
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.

exampm

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

exasp2

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

exmcutils

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

exodusii

Homepage:
Spack package:
Versions:
2016-08-09
Build Dependencies:
netcdf, hdf5, cmake, mpi
Link Dependencies:
netcdf, hdf5, mpi
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:
2.2.2, 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, autoconf, m4, libtool, automake
Link Dependencies:
tcl
Description:
Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.

express

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

extrae

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

exuberant-ctags

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

f90cache

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

falcon

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

farmhash

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

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:
hypre, pumi, phasta, sundials, mesquite, mpi, moab, boxlib, arpack-ng, trilinos, petsc, superlu-dist, chombo, zoltan
Link Dependencies:
hypre, pumi, phasta, sundials, mesquite, mpi, moab, boxlib, arpack-ng, trilinos, petsc, superlu-dist, chombo, 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:
automake, autoconf, m4, libtool
Description:
FastME is a distance based phylogeny reconstruction program that works on distance matrices and, as of v2.0, sequence data.

fastphase

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

fastq-screen

Homepage:
Spack package:
Versions:
0.11.2
Build Dependencies:
bowtie2, samtools, bwa, bowtie
Link Dependencies:
bowtie2, samtools, bwa, bowtie
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:
0.11.5, 0.11.4
Build Dependencies:
perl
Link Dependencies:
perl
Run Dependencies:
java
Description:
A quality control tool for high throughput sequence data.

fastqvalidator

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

fasttree

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

fastx-toolkit

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

fenics

Homepage:
Spack package:
Versions:
2016.1.0, 1.6.0, 1.5.0
Build Dependencies:
py-numpy, hdf5, cmake, parmetis, py-setuptools, qt, mpi, suite-sparse, py-sympy, slepc, trilinos, petsc, boost, py-sphinx, scotch, swig, eigen, py-ply, python, py-six, vtk
Link Dependencies:
hdf5, parmetis, scotch, qt, suite-sparse, slepc, trilinos, petsc, boost, mpi, eigen, python, vtk
Run Dependencies:
py-numpy, swig, py-ply, py-six, py-sympy
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.

ferret

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

ffmpeg

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

fftw

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

fimpute

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

findutils

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

fio

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

fish

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

fixesproto

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

flac

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

flang

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

flann

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

flash

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

flecsale

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

flecsi

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

flex

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

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:
py-numpy, py-matplotlib, python, 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

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

fmt

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

font-adobe-100dpi

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

font-adobe-75dpi

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

font-adobe-utopia-100dpi

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

font-adobe-utopia-75dpi

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

font-adobe-utopia-type1

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

font-alias

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

font-arabic-misc

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

font-bh-100dpi

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

font-bh-75dpi

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

font-bh-lucidatypewriter-100dpi

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

font-bh-lucidatypewriter-75dpi

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

font-bh-ttf

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

font-bh-type1

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

font-bitstream-100dpi

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

font-bitstream-75dpi

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

font-bitstream-speedo

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

font-bitstream-type1

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

font-cronyx-cyrillic

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

font-cursor-misc

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

font-daewoo-misc

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

font-dec-misc

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

font-ibm-type1

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

font-isas-misc

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

font-jis-misc

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

font-micro-misc

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

font-misc-cyrillic

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

font-misc-ethiopic

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

font-misc-meltho

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

font-misc-misc

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

font-mutt-misc

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

font-schumacher-misc

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

font-screen-cyrillic

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

font-sony-misc

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

font-sun-misc

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

font-util

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

font-winitzki-cyrillic

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

font-xfree86-type1

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

fontcacheproto

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

fontconfig

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

fontsproto

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

fonttosfnt

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

fpc

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

fr-hit

Homepage:
Spack package:
Versions:
0.7.1-2013-02-20
Build Dependencies:
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.

freetype

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

fseq

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

fsl

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

fslsfonts

Homepage:
Spack package:
Versions:
1.0.5
Build Dependencies:
pkgconfig, libfs, util-macros, xproto
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:
pkgconfig, libfs, libx11, util-macros, xproto
Link Dependencies:
libfs, libx11
Description:
The fstobdf program reads a font from a font server and prints a BDF file on the standard output that may be used to recreate the font. This is useful in testing servers, debugging font metrics, and reproducing lost BDF files.

funhpc

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

gapbs

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

gapcloser

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

gapfiller

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

gasnet

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

gatk

Homepage:
Spack package:
Versions:
3.8-0
Run Dependencies:
java
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:
libsigsegv, mpfr, gettext, readline, gmp
Link Dependencies:
libsigsegv, mpfr, gettext, readline, 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:
7.3.0, 7.2.0, 7.1.0, 6.4.0, 6.3.0, 6.2.0, 6.1.0, 5.5.0, 5.4.0, 5.3.0, 5.2.0, 5.1.0, 4.9.4, 4.9.3, 4.9.2, 4.9.1, 4.8.5, 4.8.4, 4.7.4, 4.6.4, 4.5.4
Build Dependencies:
gnat, binutils, mpc, isl, zip, mpfr, zlib, gmp
Link Dependencies:
gnat, mpc, mpfr, isl, binutils, zlib, gmp
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.

gdal

Homepage:
Spack package:
Versions:
2.1.2, 2.0.2
Build Dependencies:
netcdf, libpng, openjpeg, hdf5, kealib, geos, zlib, py-numpy, proj, hdf, swig, libtiff, python
Link Dependencies:
netcdf, libpng, openjpeg, hdf5, kealib, geos, zlib, proj, hdf, swig, libtiff, python
Run Dependencies:
py-numpy
Description:
GDAL 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:
8.0.1, 8.0, 7.12.1, 7.11, 7.10.1, 7.10, 7.9.1, 7.9, 7.8.2
Build Dependencies:
python, texinfo
Link Dependencies:
python
Description:
GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes -- or what another program was doing at the moment it crashed.

gdbm

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

gdk-pixbuf

Homepage:
Spack package:
Versions:
2.31.2
Build Dependencies:
libpng, gettext, pkgconfig, libtiff, gobject-introspection, glib, jpeg
Link Dependencies:
libpng, gettext, libtiff, gobject-introspection, glib, jpeg
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.

geant4

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

gearshifft

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

gemmlowp

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

genemark-et

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

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.

geos

Homepage:
Spack package:
Versions:
3.5.0, 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
Description:
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

gettext

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

gflags

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

ghostscript

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

ghostscript-fonts

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

giflib

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

git

Homepage:
Spack package:
Versions:
2.15.1, 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:
zlib, libtool, gettext, automake, curl, pcre, perl, autoconf, m4, openssl, libiconv, expat
Link Dependencies:
perl, zlib, gettext, libiconv, openssl, curl, pcre, expat
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-lfs

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

gl2ps

Homepage:
Spack package:
Versions:
1.3.9
Build Dependencies:
libdrm, libxdamage, zlib, libxt, libxfixes, libxmu, cmake, libxxf86vm, libpng, libice, libxext, libsm, libxau, libxdmcp, expat, libxcb, libxi
Link Dependencies:
libdrm, libxdamage, zlib, libxt, libxfixes, libxmu, libxxf86vm, libpng, libice, libxext, libsm, libxau, libxdmcp, expat, libxcb, libxi
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
Description:
The OpenGL Extension Wrangler Library.

glib

Homepage:
Spack package:
Versions:
2.55.1, 2.53.1, 2.49.7, 2.49.4, 2.48.1, 2.42.1
Build Dependencies:
perl, python, zlib, gettext, util-linux, pkgconfig, libffi, pcre
Link Dependencies:
libffi, util-linux, pcre, zlib, gettext
Run Dependencies:
perl, python
Description:
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.

glm

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

global

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

globalarrays

Homepage:
Spack package:
Versions:
master
Build Dependencies:
lapack, blas, cmake, mpi
Link Dependencies:
lapack, blas, mpi
Description:
The Global Arrays (GA) toolkit provides a shared memory style programming environment in the context of distributed array data structures.

globus-toolkit

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

glog

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

glpk

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

glproto

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

gmake

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

gmap-gsnap

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

gmime

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

gmp

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

gmsh

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

gnat

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

gnu-prolog

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

gnupg

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

gnuplot

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

gnutls

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

go

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

go-bootstrap

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

gobject-introspection

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

googletest

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

gotcha

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

gource

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

gperf

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

gperftools

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

grackle

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

gradle

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

grandr

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

graphlib

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

graphmap

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

graphviz

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

grib-api

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

groff

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

gromacs

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

gsl

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

gslib

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

gtkorvo-atl

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

gtkorvo-cercs-env

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

gtkorvo-dill

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

gtkorvo-enet

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

gtkplus

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

gts

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

guidance

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

guile

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

h5hut

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

h5part

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

h5utils

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

h5z-zfp

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

hacckernels

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

hadoop

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

hapcut2

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

haploview

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

harfbuzz

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

harminv

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

hdf

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

hdf5

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

hdf5-blosc

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

help2man

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

hepmc

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

heppdt

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

highfive

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

highwayhash

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

hisat2

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

hmmer

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

hoomd-blue

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

hpccg

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

hpctoolkit

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

hpctoolkit-externals

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

hpgmg

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

hpl

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

hpx

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

hpx5

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

hsakmt

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

hstr

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

htop

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

htslib

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

httpie

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

hub

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

hunspell

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

hwloc

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

hybpiper

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

hydra

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

hypre

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

i3

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

ibmisc

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

iceauth

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

icedtea

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

icet

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

ico

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

icu4c

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

id3lib

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

idba

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

igraph

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

igv

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

ilmbase

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

image-magick

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

imake

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

impute2

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

infernal

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

inputproto

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

intel

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

intel-daal

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

intel-gpu-tools

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

intel-ipp

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

intel-mkl

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

intel-mkl-dnn

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

intel-mpi

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

intel-parallel-studio

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

intel-tbb

Homepage:
Spack package:
Versions:
2018.2, 2018.1, 2018.0, 2017.8, 2017.6, 2017.5, 2017.3, 4.4.4, 4.4.3
Description:
Widely used C++ template library for task parallelism. Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.

intltool

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

ior

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

iozone

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

ipopt

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

isaac

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

isaac-server

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

isl

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

itstool

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

itsx

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

jags

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

jansson

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

jasper

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

jbigkit

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

jdk

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

jellyfish

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

jemalloc

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

jmol

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

jq

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

json-c

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

json-cwx

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

json-glib

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

jsoncpp

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

judy

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

julia

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

kahip

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

kaks-calculator

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

kaldi

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

kallisto

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

kbproto

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

kdiff3

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

kealib

Homepage:
Spack package:
Versions:
1.4.5
Build Dependencies:
hdf5, cmake
Link Dependencies:
hdf5
Description:
An HDF5 Based Raster File Format KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software. Development work on this project has been funded by Landcare Research.

kentutils

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

kmergenie

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

kokkos

Homepage:
Spack package:
Versions:
2.03.00
Build Dependencies:
cuda, hwloc, qthreads
Link Dependencies:
cuda, hwloc, qthreads
Description:
Kokkos implements a programming model in C++ for writing performance portable applications targeting all major HPC platforms.

kraken

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

krims

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

kripke

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

kvasir-mpl

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

laghos

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

lammps

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

last

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

latte

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

launchmon

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

lazyten

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

lbann

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

lbxproxy

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

lcals

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

lcms

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

ldc

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

ldc-bootstrap

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

legion

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

leveldb

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

lftp

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

libaec

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

libaio

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

libapplewm

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

libarchive

Homepage:
Spack package:
Versions:
3.3.2, 3.2.1, 3.1.2, 3.1.1, 3.1.0
Build Dependencies:
openssl, lz4, zlib, xz, bzip2, expat, nettle, lzo, libxml2, lzma
Link Dependencies:
openssl, lz4, zlib, xz, bzip2, expat, nettle, lzo, libxml2, lzma
Description:
libarchive: C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats.

libassuan

Homepage:
Spack package:
Versions:
2.4.5, 2.4.3
Build Dependencies:
libgpg-error
Link Dependencies:
libgpg-error
Description:
Libassuan is a small library implementing the so-called Assuan protocol.

libatomic-ops

Homepage:
Spack package:
Versions:
7.4.4
Description:
This package provides semi-portable access to hardware-provided atomic memory update operations on a number architectures.

libbeagle

Homepage:
Spack package:
Versions:
2.1.2
Build Dependencies:
autoconf, m4, libtool, pkgconfig, automake, subversion
Description:
Beagle performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

libbsd

Homepage:
Spack package:
Versions:
0.8.6
Description:
This library provides useful functions commonly found on BSD systems, and lacking on others like GNU systems, thus making it easier to port projects with strong BSD origins, without needing to embed the same code over and over again on each project.

libbson

Homepage:
Spack package:
Versions:
1.9.1, 1.8.1, 1.8.0, 1.7.0, 1.6.3, 1.6.2, 1.6.1
Build Dependencies:
automake, autoconf, m4, libtool
Description:
libbson is a library providing useful routines related to building, parsing, and iterating BSON documents.

libcanberra

Homepage:
Spack package:
Versions:
0.30
Build Dependencies:
libxcomposite, libxrandr, libxdamage, libxfixes, libxcursor, libxcb, libxext, gtkplus, libxrender, libx11, libvorbis, libxau, libxinerama, pkgconfig
Link Dependencies:
libxcomposite, libxrandr, libxdamage, libxfixes, libxcursor, libxext, gtkplus, libxrender, libx11, libvorbis, libxau, libxinerama, libxcb
Description:
libcanberra is an implementation of the XDG Sound Theme and Name Specifications, for generating event sounds on free desktops, such as GNOME.

libcap

Homepage:
Spack package:
Versions:
2.25
Description:
Libcap implements the user-space interfaces to the POSIX 1003.1e capabilities available in Linux kernels. These capabilities are a partitioning of the all powerful root privilege into a set of distinct privileges.

libcerf

Homepage:
Spack package:
Versions:
1.3
Description:
A self-contained C library providing complex error functions, based on Faddeeva's plasma dispersion function w(z). Also provides Dawson's integral and Voigt's convolution of a Gaussian and a Lorentzian

libcint

Homepage:
Spack package:
Versions:
3.0.4
Build Dependencies:
py-numpy, cmake, python, blas
Link Dependencies:
blas
Test Dependencies:
py-numpy, python
Description:
Library for analytical Gaussian integrals for quantum chemistry.

libcircle

Homepage:
Spack package:
Versions:
0.2.1-rc.1
Build Dependencies:
mpi
Link Dependencies:
mpi
Description:
libcircle provides an efficient distributed queue on a cluster, using self-stabilizing work stealing.

libconfig

Homepage:
Spack package:
Versions:
1.5
Build Dependencies:
automake, autoconf, m4, libtool
Description:
C/C++ Configuration File Library

libcroco

Homepage:
Spack package:
Versions:
0.6.12
Build Dependencies:
glib, libxml2
Link Dependencies:
glib, libxml2
Description:
Libcroco is a standalone css2 parsing and manipulation library.

libctl

Homepage:
Spack package:
Versions:
3.2.2
Build Dependencies:
guile
Link Dependencies:
guile
Description:
libctl is a free Guile-based library implementing flexible control files for scientific simulations.

libdivsufsort

Homepage:
Spack package:
Versions:
2.0.1
Build Dependencies:
cmake
Description:
libdivsufsort is a software library that implements a lightweight suffix array construction algorithm.

libdmx

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies:
libxext, libx11, util-macros, pkgconfig, dmxproto, xextproto
Link Dependencies:
libxext, libx11
Description:
libdmx - X Window System DMX (Distributed Multihead X) extension library.

libdrm

Homepage:
Spack package:
Versions:
2.4.81, 2.4.75, 2.4.70, 2.4.59, 2.4.33
Build Dependencies:
pkgconfig, libpthread-stubs, libpciaccess
Link Dependencies:
libpthread-stubs, libpciaccess
Description:
A userspace library for accessing the DRM, direct rendering manager, on Linux, BSD and other systems supporting the ioctl interface.

libdwarf

Homepage:
Spack package:
Versions:
20160507, 20130729, 20130207, 20130126
Link Dependencies:
zlib, elf
Description:
The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and any one interested in reading or writing DWARF information). It was developed by a committee (known as the PLSIG at the time) starting around 1991. Starting around 1991 SGI developed the libdwarf and dwarfdump tools for internal use and as part of SGI IRIX developer tools. Since that time dwarfdump and libdwarf have been shipped (as an executable and archive respectively, not source) with every release of the SGI MIPS/IRIX C compiler.

libedit

Homepage:
Spack package:
Versions:
3.1-20170329, 3.1-20160903, 3.1-20150325
Build Dependencies:
ncurses
Link Dependencies:
ncurses
Description:
An autotools compatible port of the NetBSD editline library

libelf

Homepage:
Spack package:
Versions:
0.8.13, 0.8.12
Description:
libelf lets you read, modify or create ELF object files in an architecture-independent way. The library takes care of size and endian issues, e.g. you can process a file for SPARC processors on an Intel- based system.

libemos

Homepage:
Spack package:
Versions:
4.5.1, 4.5.0, 4.4.9, 4.4.7, 4.4.2
Build Dependencies:
pkgconfig, grib-api, eccodes, fftw, cmake
Link Dependencies:
grib-api, eccodes, fftw
Description:
The Interpolation library (EMOSLIB) includes Interpolation software and BUFR & CREX encoding/decoding routines.

libepoxy

Homepage:
Spack package:
Versions:
1.3.1
Description:
Epoxy is a library for handling OpenGL function pointer management for you.

libev

Homepage:
Spack package:
Versions:
develop, 4.24
Build Dependencies:
automake, autoconf, m4, libtool
Description:
A full-featured and high-performance event loop that is loosely modelled after libevent, but without its limitations and bugs.

libevent

Homepage:
Spack package:
Versions:
2.0.21, 2.0.20, 2.0.19, 2.0.18, 2.0.17, 2.0.16, 2.0.15, 2.0.14, 2.0.13, 2.0.12
Build Dependencies:
openssl
Link Dependencies:
openssl
Description:
The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

libevpath

Homepage:
Spack package:
Versions:
develop, 4.2.1, 4.1.2, 4.1.1
Build Dependencies:
libffs, cmake
Link Dependencies:
libffs
Description:
EVpath is an event transport middleware layer designed to allow for the easy implementation of overlay networks, with active data processing, routing and management at all points in the overlay. EVPath is designed for high performance systems.

libfabric

Homepage:
Spack package:
Versions:
1.5.0, 1.4.2
Description:
The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications.

libffi

Homepage:
Spack package:
Versions:
3.2.1
Description:
The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time.