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 1848 mainline packages:

abinit llvm-lld py-xmlrunner
abyss llvm-openmp-ompt py-xopen
ack lmdb py-xpyb
activeharmony lmod py-xvfbwrapper
adept-utils lndir py-yapf
adios log4cxx py-yt
adios2 lrslib py-zmq
adlbx lrzip python
adol-c lua qbank
albert lua-bitlib qbox
alglib lua-jit qhull
allinea-forge lua-lpeg qmd-progress
allinea-reports lua-luafilesystem qrupdate
allpaths-lg lua-luaposix qt
alquimia lua-mpack qt-creator
alsa-lib luit qtgraph
amg2013 lulesh qthreads
ampliconnoise lwgrp quinoa
amr-exp-parabolic lwm2 qwt
amrex lz4 r
andi lzma r-abind
angsd lzo r-ada
ant m4 r-adabag
antlr mad-numdiff r-ade4
ape mafft r-adegenet
apex magics r-affyio
applewmproto magma r-ape
appres makedepend r-assertthat
apr mallocmc r-base64enc
apr-util man-db r-bh
archer mariadb r-biobase
argtable matio r-biocgenerics
armadillo matlab r-biocinstaller
arpack-ng maven r-bit
asciidoc maverick r-bitops
aspa mawk r-boot
astra mbedtls r-brew
astral mcl r-c50
astyle mdtest r-car
atk meep r-caret
atlas memaxes r-catools
atompaw meme r-checkpoint
atop mercurial r-chron
augustus mesa r-class
autoconf mesa-glu r-cluster
autogen meshkit r-coda
automaded meson r-codetools
automake mesquite r-coin
bamtools metis r-colorspace
bamutil mfem r-corpcor
bash microbiomeutil r-corrplot
bash-completion miniaero r-crayon
bats miniamr r-cubature
bazel miniconda2 r-cubist
bbcp miniconda3 r-curl
bbmap minife r-data-table
bcftools minighost r-dbi
bcl2fastq2 minigmg r-deldir
bdftopcf minimd r-dendextend
bdw-gc minismac2d r-deoptim
bear minixyce r-deoptimr
beast2 mirdeep r-devtools
bedtools2 mitofates r-diagrammer
beforelight mitos r-dichromat
benchmark mkfontdir r-digest
berkeley-db mkfontscale r-diptest
bertini mlhka r-domc
bib2xhtml moab r-doparallel
bigreqsproto molcas r-dplyr
binutils mono r-dt
bioawk mosh r-dygraphs
bison mothur r-e1071
bitmap mozjs r-ellipse
blast-plus mpc r-ergm
blat mpe2 r-evaluate
blaze mpest r-expm
bliss mpfr r-factoextra
blitz mpibash r-factominer
bml mpiblast r-filehash
boost mpich r-flashclust
boostmplcartesianproduct mpifileutils r-flexmix
bowtie mpileaks r-foreach
bowtie2 mpip r-foreign
boxlib mpir r-formatr
bpp-core mpix-launch-swift r-formula
bpp-phyl mrbayes r-fpc
bpp-seq mrnet r-gdata
bpp-suite msgpack-c r-geosphere
braker multiverso r-ggmap
brigand mummer r-ggplot2
bsseeker2 mumps r-ggpubr
bucky munge r-ggrepel
busco muparser r-ggsci
butter muscle r-ggvis
bwa muse r-gistr
bzip2 muster r-git2r
c-blosc mvapich2 r-glmnet
caffe mxml r-gmodels
cairo nag r-gmp
caliper nalu r-googlevis
callpath namd r-gridbase
cantera nano r-gridextra
canu nanoflann r-gtable
cap3 nasm r-gtools
cares nauty r-hexbin
cask nccl r-highr
catch nccmp r-htmltools
cbench ncdu r-htmlwidgets
cblas ncftp r-httpuv
cbtf ncl r-httr
cbtf-argonavis nco r-igraph
cbtf-argonavis-gui ncurses r-influencer
cbtf-krell ncview r-inline
cbtf-lanl ndiff r-ipred
ccache nekbone r-irdisplay
cctools neovim r-irkernel
cdbfasta netcdf r-irlba
cdd netcdf-cxx r-iterators
cddlib netcdf-cxx4 r-jpeg
cdhit netcdf-fortran r-jsonlite
cdo netgauge r-kernlab
cereal netgen r-kernsmooth
cfitsio netlib-lapack r-kknn
cgal netlib-scalapack r-knitr
cgm nettle r-labeling
cgns nextflow r-laplacesdemon
charm nfft r-lattice
check nginx r-lava
chlorop ngmlr r-lazyeval
chombo ninja r-leaflet
cityhash ninja-fortran r-leaps
clamr nmap r-learnbayes
cleaveland4 node-js r-lme4
cleverleaf notmuch r-lmtest
clfft npb r-lpsolve
clhep npm r-lubridate
cloog npth r-magic
cloverleaf nspr r-magrittr
cloverleaf3d numactl r-mapproj
clustalo numdiff r-maps
clustalw nut r-maptools
cmake nwchem r-markdown
cmocka ocaml r-mass
cmor oce r-matrix
cnmem oclock r-matrixmodels
cnpy octave r-mclust
cns-nospec octave-splines r-mda
cntk octopus r-memoise
cntk1bitsgd of-adios-write r-mgcv
codar-cheetah ompss r-mime
cohmm ompt-openmp r-minqa
coinhsl oniguruma r-mlbench
comd ont-albacore r-modelmetrics
compiz opari2 r-modeltools
compositeproto openbabel r-mpm
conduit openblas r-multcomp
constype opencoarrays r-munsell
converge opencv r-mvtnorm
coreutils openexr r-ncdf4
corset openfoam-com r-network
cosmomc openfoam-org r-networkd3
cosp2 openfst r-nlme
cp2k openjpeg r-nloptr
cppad openmc r-nmf
cppcheck openmpi r-nnet
cpprestsdk openscenegraph r-np
cppunit openspeedshop r-numderiv
cppzmq openssh r-openssl
cram openssl r-packrat
cryptopp opium r-pacman
cscope opus r-party
csdp orfm r-partykit
cub orthomcl r-pbdzmq
cube osu-micro-benchmarks r-pbkrtest
cuda otf r-permute
cuda-memtest otf2 r-pkgmaker
cudnn p4est r-plotrix
cufflinks p7zip r-pls
cups pacbio-daligner r-plyr
curl pacbio-damasker r-png
cvs pacbio-dazz-db r-prabclus
czmq pacbio-dextractor r-praise
dakota pagit r-preprocesscore
daligner pagmo r-prodlim
damageproto paml r-proto
damselfly panda r-pryr
darshan-runtime pango r-quadprog
darshan-util papi r-quantmod
dash paradiseo r-quantreg
datamash parallel r-r6
dataspaces parallel-netcdf r-randomforest
dbus paraver r-raster
dealii paraview r-rbokeh
dejagnu parmetis r-rcolorbrewer
dia parmgridgen r-rcpp
dialign-tx parsimonator r-rcppeigen
direnv parsplice r-registry
discovar partitionfinder r-repr
dmxproto patch r-reshape2
docbook-xml patchelf r-rgl
docbook-xsl pathfinder r-rgooglemaps
dos2unix pax-utils r-rinside
double-conversion pbmpi r-rjava
doxygen pcma r-rjson
dri2proto pcre r-rjsonio
dri3proto pcre2 r-rmarkdown
dtcmp pdsh r-rminer
dyninst pdt r-rmpfr
ea-utils pegtl r-rmpi
easybuild pennant r-rmysql
ebms perl r-rngtools
eccodes perl-dbfile r-robustbase
editres perl-dbi r-rodbc
eigen perl-devel-cycle r-roxygen2
elemental perl-extutils-makemaker r-rpart
elfutils perl-font-ttf r-rpart-plot
elk perl-intervaltree r-rpostgresql
elpa perl-math-cdf r-rsnns
emacs perl-module-build r-rsqlite
emboss perl-padwalker r-rstan
encodings perl-pdf-api2 r-rstudioapi
environment-modules perl-star-fusion r-rzmq
es perl-sub-uplevel r-s4vectors
esmf perl-term-readkey r-sandwich
espresso perl-test-exception r-scales
espressopp perl-test-memory-cycle r-scatterplot3d
etsf-io perl-uri-escape r-segmented
everytrace perl-xml-parser r-seqinr
everytrace-example petsc r-shiny
evieext pexsi r-snow
exabayes pfft r-sp
exmcutils pflotran r-sparsem
exodusii pgdspider r-spdep
exonerate pgi r-stanheaders
expat phasta r-statnet-common
expect phylip r-stringi
extrae picard r-stringr
exuberant-ctags pidx r-strucchange
f90cache pigz r-survey
falcon piranha r-survival
farmhash pixman r-tarifx
fastjar pkg-config r-testit
fastmath pkgconf r-testthat
fastphase planck-likelihood r-th-data
fastqc plink r-threejs
fastx-toolkit plumed r-tibble
fenics pmgr-collective r-tidyr
ferret pmix r-trimcluster
ffmpeg pnfft r-trust
fftw pngwriter r-ttr
fimpute poamsa r-uuid
findutils pocl r-vcd
fio polymake r-vegan
fish porta r-viridis
fixesproto portage r-viridislite
flac postgresql r-visnetwork
flann ppl r-whisker
flash prank r-withr
flecsale presentproto r-xgboost
flecsi preseq r-xlconnect
flex price r-xlconnectjars
flint primer3 r-xlsx
fltk printproto r-xlsxjars
flux probconsrna r-xml
fmt proj r-xtable
foam-extend protobuf r-xts
folly proxymngr r-xvector
font-adobe-100dpi pruners-ninja r-yaml
font-adobe-75dpi psi4 r-zlibbioc
font-adobe-utopia-100dpi pstreams r-zoo
font-adobe-utopia-75dpi pugixml raft
font-adobe-utopia-type1 pumi raja
font-alias pvm randfold
font-arabic-misc py-3to2 random123
font-bh-100dpi py-4suite-xml randrproto
font-bh-75dpi py-abipy ravel
font-bh-lucidatypewriter-100dpi py-alabaster raxml
font-bh-lucidatypewriter-75dpi py-apache-libcloud ray
font-bh-ttf py-apipkg rdp-classifier
font-bh-type1 py-appdirs readline
font-bitstream-100dpi py-appnope recordproto
font-bitstream-75dpi py-apscheduler redundans
font-bitstream-speedo py-argcomplete relion
font-bitstream-type1 py-argparse rempi
font-cronyx-cyrillic py-ase rename
font-cursor-misc py-asn1crypto rendercheck
font-daewoo-misc py-astroid renderproto
font-dec-misc py-astropy resourceproto
font-ibm-type1 py-attrs revbayes
font-isas-misc py-autopep8 rgb
font-jis-misc py-babel rhash
font-micro-misc py-backports-abc rockstar
font-misc-cyrillic py-backports-shutil-get-terminal-size root
font-misc-ethiopic py-backports-ssl-match-hostname rose
font-misc-meltho py-basemap rr
font-misc-misc py-beautifulsoup4 rsbench
font-mutt-misc py-binwalk rsem
font-schumacher-misc py-biom-format rstart
font-screen-cyrillic py-biopython rsync
font-sony-misc py-bleach rtags
font-sun-misc py-blessings rtax
font-util py-bokeh ruby
font-winitzki-cyrillic py-boltons rust
font-xfree86-type1 py-bottleneck rust-bindgen
fontcacheproto py-brian sabre
fontconfig py-brian2 salmon
fontsproto py-bsddb3 sambamba
fonttosfnt py-cclib samrai
freebayes py-cdat-lite samtools
freetype py-cdo sas
fseq py-certifi satsuma2
fslsfonts py-cffi savanna
fstobdf py-chardet saws
funhpc py-click sbt
gapcloser py-colorama scala
gapfiller py-colormath scalasca
gasnet py-configparser scons
gaussian py-counter scorec-core
gawk py-coverage scorep
gblocks py-cpuinfo scotch
gcc py-cryptography scr
gccmakedep py-csvkit screen
gccxml py-current scripts
gconf py-cutadapt scrnsaverproto
gdal py-cycler sctk
gdb py-cython sdl2
gdbm py-dask sdl2-image
gdk-pixbuf py-dateutil sed
geant4 py-dbf seqprep
gearshifft py-decorator seqtk
gemmlowp py-deeptools serf
genemark-et py-dev sessreg
genometools py-dill setxkbmap
geos py-docutils sga
gettext py-doxypy shapeit
gflags py-doxypypy shared-mime-info
ghostscript py-dryscrape shiny-server
ghostscript-fonts py-dxchange shortstack
giflib py-dxfile showfont
git py-easybuild-easyblocks sickle
git-lfs py-easybuild-easyconfigs signalp
gl2ps py-easybuild-framework silo
glew py-edffile simplemoc
glib py-elasticsearch simul
glm py-elephant simulationio
global py-emcee singularity
globalarrays py-entrypoints slepc
globus-toolkit py-enum34 slurm
glog py-epydoc smalt
glpk py-et-xmlfile smc
glproto py-execnet smproxy
gmake py-fastaindex snakemake
gmap-gsnap py-fasteners snap
gmime py-faststructure snap-berkeley
gmp py-fiscalyear snappy
gmsh py-flake8 snbone
gnat py-flask sniffles
gnu-prolog py-flexx snptest
gnupg py-funcsigs soap2
gnuplot py-functools32 soapindel
gnutls py-future soapsnp
go py-futures somatic-sniper
go-bootstrap py-genders sortmerna
gobject-introspection py-genshi sowing
googletest py-git-review sox
gource py-git2 spades
gperf py-gnuplot spark
gperftools py-griddataformats sparsehash
grackle py-guidata sparta
gradle py-guiqwt spdlog
grandr py-h5py spectrum-mpi
graphlib py-html2text speex
graphmap py-html5lib sph2pipe
graphviz py-httpbin spherepack
grib-api py-hypothesis spindle
groff py-idna spot
gromacs py-igraph sqlite
gsl py-imagesize squid
gtkorvo-atl py-iminuit sspace-longread
gtkorvo-cercs-env py-importlib sspace-standard
gtkorvo-dill py-ipaddress sst-dumpi
gtkorvo-enet py-ipdb sst-macro
gtkplus py-ipykernel stacks
gts py-ipython staden-io-lib
guile py-ipython-genutils star
h5hut py-ipywidgets star-ccm-plus
h5part py-itsdangerous stat
h5utils py-jdcal stc
h5z-zfp py-jedi stream
hadoop py-jinja2 stress
hapcut2 py-joblib stringtie
haploview py-jpype structure
harfbuzz py-jsonschema sublime-text
harminv py-junit-xml subread
hdf py-jupyter-client subversion
hdf5 py-jupyter-console suite-sparse
hdf5-blosc py-jupyter-core sumaclust
help2man py-jupyter-notebook sundials
hepmc py-keras superlu
heppdt py-latexcodec superlu-dist
highfive py-lazy superlu-mt
highwayhash py-lazyarray swarm
hmmer py-libconf swiftsim
hoomd-blue py-line-profiler swig
hpccg py-lit symengine
hpctoolkit py-lmfit sympol
hpctoolkit-externals py-lockfile sz
hpl py-logilab-common tabix
hpx py-lxml talloc
hpx5 py-lzstring tar
hsakmt py-macholib targetp
hstr py-machotools task
htop py-macs2 taskd
htslib py-mako tau
httpie py-markdown tcl
hub py-markupsafe tcoffee
hunspell py-matplotlib tealeaf
hwloc py-mccabe tetgen
hybpiper py-mdanalysis tethex
hydra py-meep texinfo
hypre py-memory-profiler texlive
ibmisc py-methylcode the-platinum-searcher
iceauth py-misopy the-silver-searcher
icedtea py-mistune thrift
icet py-mock tig
ico py-mongo tinyxml
icu4c py-monotonic tinyxml2
id3lib py-monty tk
idba py-mpi4py tmalign
igraph py-mpmath tmhmm
ilmbase py-multiprocess tmux
image-magick py-multiqc tmuxinator
imake py-mx tophat
impute2 py-myhdl tppred
infernal py-mysqldb1 transabyss
inputproto py-nbconvert transdecoder
intel py-nbformat transposome
intel-daal py-neo transset
intel-gpu-tools py-nestle trapproto
intel-ipp py-netcdf4 tree
intel-mkl py-netifaces triangle
intel-mpi py-networkx trilinos
intel-parallel-studio py-nose trimgalore
intel-tbb py-nosexcover trimmomatic
intltool py-numexpr turbine
ior py-numpy turbomole
iozone py-numpydoc tut
ipopt py-olefile twm
isaac py-ont-fast5-api uberftp
isaac-server py-openpyxl udunits2
isl py-ordereddict uncrustify
itstool py-oset unibilium
itsx py-packaging unison
jags py-palettable units
jansson py-pandas unixodbc
jasper py-paramiko usearch
jdk py-pathlib2 util-linux
jemalloc py-pathos util-macros
jmol py-pathspec uuid
jq py-patsy valgrind
json-c py-pbr vampirtrace
jsoncpp py-periodictable varscan
judy py-petsc4py vc
julia py-pexpect vcftools
kahip py-phonopy vcsh
kaldi py-pickleshare vdt
kallisto py-pil vecgeom
kbproto py-pillow veclibfort
kdiff3 py-pip vegas2
kealib py-pipits velvet
kentutils py-pkgconfig videoproto
kmergenie py-ply viennarna
kokkos py-pmw viewres
kripke py-pox vim
lammps py-ppft virtualgl
last py-prettytable visit
latte py-proj vizglow
launchmon py-prompt-toolkit vmatch
lbann py-protobuf voropp
lbxproxy py-psutil votca-csg
lcals py-ptyprocess votca-ctp
lcms py-pudb votca-moo
ldc py-py votca-tools
ldc-bootstrap py-py2bit votca-xtp
legion py-py2cairo vpfft
leveldb py-py2neo vpic
lftp py-py4j vsearch
libaec py-pyasn1 vtk
libaio py-pybigwig wannier90
libapplewm py-pybind11 wget
libarchive py-pybtex windowswmproto
libassuan py-pybtex-docutils wt
libatomic-ops py-pychecker wx
libbeagle py-pycodestyle wxpropgrid
libbsd py-pycparser x11perf
libbson py-pycrypto xapian-core
libcanberra py-pycurl xauth
libcap py-pydatalog xbacklight
libcerf py-pydispatcher xbiff
libcircle py-pydot xbitmaps
libconfig py-pyelftools xcalc
libctl py-pyfasta xcb-demo
libdivsufsort py-pyfftw xcb-proto
libdmx py-pyflakes xcb-util
libdrm py-pygments xcb-util-cursor
libdwarf py-pygobject xcb-util-errors
libedit py-pygtk xcb-util-image
libelf py-pylint xcb-util-keysyms
libemos py-pymatgen xcb-util-renderutil
libepoxy py-pyminifier xcb-util-wm
libevent py-pympler xclipboard
libevpath py-pynn xclock
libfabric py-pypar xcmiscproto
libffi py-pyparsing xcmsdb
libffs py-pypeflow xcompmgr
libfontenc py-pyprof2html xconsole
libfs py-pyqt xcursor-themes
libgcrypt py-pyrad xcursorgen
libgd py-pysam xdbedizzy
libgit2 py-pyscaf xditview
libgpg-error py-pyserial xdm
libgpuarray py-pyside xdpyinfo
libgtextutils py-pysocks xdriinfo
libharu py-pytables xedit
libhio py-pytest xerces-c
libice py-pytest-cov xev
libiconv py-pytest-flake8 xextproto
libint py-pytest-httpbin xeyes
libjpeg py-pytest-mock xf86bigfontproto
libjpeg-turbo py-pytest-runner xf86dga
libksba py-pytest-xdist xf86dgaproto
liblbxutil py-python-daemon xf86driproto
libmatheval py-python-gitlab xf86miscproto
libmesh py-pythonqwt xf86rushproto
libmng py-pytz xf86vidmodeproto
libmongoc py-pywavelets xfd
libmonitor py-pyyaml xfindproxy
libnbc py-qtawesome xfontsel
libogg py-qtconsole xfs
liboldx py-qtpy xfsinfo
libpciaccess py-quantities xfwp
libpfm4 py-radical-utils xgamma
libpipeline py-ranger xgc
libpng py-readme-renderer xhost
libpsl py-regex xineramaproto
libpthread-stubs py-requests xinit
libquo py-restview xinput
libsigsegv py-rope xkbcomp
libsm py-rpy2 xkbdata
libsodium py-rsa xkbevd
libspatialindex py-rtree xkbprint
libsplash py-saga-python xkbutils
libssh2 py-scientificpython xkeyboard-config
libsvm py-scikit-image xkill
libszip py-scikit-learn xload
libtermkey py-scipy xlogo
libtiff py-seaborn xlsatoms
libtool py-setuptools xlsclients
libunistring py-sh xlsfonts
libunwind py-shiboken xmag
libuuid py-simplegeneric xman
libuv py-simplejson xmessage
libvorbis py-singledispatch xmh
libvterm py-sip xmlto
libwebsockets py-six xmodmap
libwindowswm py-slepc4py xmore
libx11 py-sncosmo xorg-cf-files
libxau py-snowballstemmer xorg-docs
libxaw py-spectra xorg-gtest
libxaw3d py-spefile xorg-server
libxc py-spglib xorg-sgml-doctools
libxcb py-sphinx xphelloworld
libxcomposite py-sphinx-bootstrap-theme xplor-nih
libxcursor py-sphinx-rtd-theme xplsprinters
libxdamage py-sphinxcontrib-bibtex xpr
libxdmcp py-sphinxcontrib-programoutput xprehashprinterlist
libxevie py-sphinxcontrib-websupport xprop
libxext py-spyder xproto
libxfixes py-spykeutils xproxymanagementprotocol
libxfont py-sqlalchemy xqilla
libxfont2 py-statsmodels xrandr
libxfontcache py-storm xrdb
libxft py-subprocess32 xrefresh
libxi py-symengine xrootd
libxinerama py-symfit xrx
libxkbfile py-sympy xsbench
libxkbui py-tabulate xscope
libxml2 py-tappy xsdk
libxmu py-terminado xsdktrilinos
libxp py-theano xset
libxpm py-tifffile xsetmode
libxpresent py-tomopy xsetpointer
libxprintapputil py-tornado xsetroot
libxprintutil py-tqdm xsm
libxrandr py-traitlets xstdcmap
libxrender py-tuiview xterm
libxres py-twisted xtrans
libxscrnsaver py-typing xtrap
libxshmfence py-tzlocal xts
libxslt py-unittest2 xvidtune
libxsmm py-unittest2py3k xvinfo
libxstream py-urllib3 xwd
libxt py-urwid xwininfo
libxtrap py-vcversioner xwud
libxtst py-virtualenv xz
libxv py-vsc-base yaml-cpp
libxvmc py-vsc-install yasm
libxxf86dga py-wcsaxes yorick
libxxf86misc py-wcwidth z3
libxxf86vm py-webkit-server zeromq
libyogrt py-werkzeug zfp
libzip py-wheel zip
likwid py-widgetsnbextension zlib
linux-headers py-wrapt zoltan
listres py-xarray zsh
llvm py-xlrd zstd

abinit

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

abyss

Homepage:
Spack package:
Versions:
2.0.2, 1.5.2
Build Dependencies
sparsehash, boost, sqlite, mpi
Link Dependencies
sparsehash, 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:
2.18, 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, 1.12.0, 1.11.1, 1.11.0, 1.10.0, 1.9.0
Build Dependencies
sz, bzip2, zlib, hdf5, python, zfp, dataspaces, mpi, m4, libtool, szip, autoconf, libevpath, automake, netcdf
Link Dependencies
sz, bzip2, zlib, dataspaces, zfp, mpi, szip, netcdf, libevpath, hdf5
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
bzip2, cmake, hdf5, python, adios, zfp, mpi, zeromq, py-numpy, py-mpi4py
Link Dependencies
bzip2, hdf5, python, adios, zfp, mpi, zeromq
Run Dependencies
python, py-mpi4py, py-numpy
Description:
Next generation of ADIOS developed in the Exascale Computing Program

adlbx

Homepage:
Spack package:
Versions:
0.8.0
Build Dependencies
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
m4, autoconf, libtool, automake
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-0.2.0
Build Dependencies
petsc, mpi, cmake, pflotran, hdf5
Link Dependencies
petsc, mpi, pflotran, hdf5
Description:
Alquimia is an interface that exposes the capabilities of mature geochemistry codes such as CrunchFlow and PFLOTRAN

alsa-lib

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

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.

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

angsd

Homepage:
Spack package:
Versions:
0.919
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, boost, activeharmony, binutils, ompt-openmp
Link Dependencies
boost, activeharmony, binutils, ompt-openmp

Description:


applewmproto

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

appres

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies
util-macros, libx11, xproto, pkg-config, 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
sqlite, postgresql, apr, unixodbc, expat, openssl, libiconv, gdbm
Link Dependencies
sqlite, postgresql, apr, unixodbc, expat, openssl, libiconv, gdbm
Description:
Apache Portable Runtime Utility

archer

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

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.

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
cmake, superlu, lapack, blas, hdf5, arpack-ng
Link Dependencies
lapack, blas, superlu, arpack-ng, hdf5
Description:
Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use.

arpack-ng

Homepage:
Spack package:
Versions:
3.5.0, 3.4.0, 3.3.0
Build Dependencies
cmake, lapack, blas, automake, libtool, autoconf, mpi
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.

asciidoc

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

aspa

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

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
glib, gobject-introspection, pkg-config
Link Dependencies
glib, gobject-introspection
Description:
ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.

atlas

Homepage:
Spack package:
Versions:
3.11.34, 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.

atompaw

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

atop

Homepage:
Spack package:
Versions:
2.2-3
Build Dependencies
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
bamtools, zlib, boost, gsl
Link Dependencies
bamtools, zlib, boost, gsl
Description:
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences

autoconf

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

autogen

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

automaded

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

automake

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

bamtools

Homepage:
Spack package:
Versions:
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.

bash

Homepage:
Spack package:
Versions:
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, 2.3
Build Dependencies
autoconf, libtool, automake
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
java, zip
Link Dependencies
java, zip
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:
1.4, 1.3.1
Build Dependencies
xz, bzip2, zlib
Link Dependencies
xz, bzip2, zlib
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
cmake, libxml2, zlib, libxslt, boost, libgcrypt
Link Dependencies
cmake, libxml2, zlib, libxslt, boost, libgcrypt
Description:
The bcl2fastq2 Conversion Software converts base call (BCL) files from a sequencing run into FASTQ files.

bdftopcf

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

bdw-gc

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

bear

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

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:
2.26.0, 2.25.0
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
util-macros, libx11, libxt, libxscrnsaver, pkg-config
Link Dependencies
libx11, libxt, libxscrnsaver
Description:
The beforelight program is a sample implementation of a screen saver for X servers supporting the MIT-SCREEN-SAVER extension. It is only recommended for use as a code sample, as it does not include features such as screen locking or configurability.

benchmark

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

bib2xhtml

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

bigreqsproto

Homepage:
Spack package:
Versions:
1.1.2
Build Dependencies
util-macros, pkg-config
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:
2.28, 2.27, 2.26, 2.25, 2.24, 2.23.2, 2.20.1
Build Dependencies
m4, zlib, 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
libx11, libxmu, xproto, util-macros, libxt, xbitmaps, libxaw, pkg-config
Link Dependencies
libxmu, libxt, libxaw, libx11
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
pcre, freetype, python, zlib, openssl, jpeg, perl, lzo, libpng, gnutls, bzip2
Link Dependencies
pcre, freetype, python, zlib, openssl, jpeg, perl, lzo, libpng, gnutls, bzip2
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:
3.1, 3.0, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2.0, 1.5, 1.4, 1.3, 1.2, 1.1, 1.0
Description:
Blaze is an open-source, high-performance C++ math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain- specific language with HPC-grade performance, making it one of the most intuitive and fastest C++ math libraries available.

bliss

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

blitz

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

bml

Homepage:
Spack package:
Versions:
develop, 1.1.0
Build Dependencies
lapack, blas, cmake
Link Dependencies
lapack, blas
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.

boost

Homepage:
Spack package:
Versions:
develop, 1.65.1, 1.65.0, 1.64.0, 1.63.0, 1.62.0, 1.61.0, 1.60.0, 1.59.0, 1.58.0, 1.57.0, 1.56.0, 1.55.0, 1.54.0, 1.53.0, 1.52.0, 1.51.0, 1.50.0, 1.49.0, 1.48.0, 1.47.0, 1.46.1, 1.46.0, 1.45.0, 1.44.0, 1.43.0, 1.42.0, 1.41.0, 1.40.0, 1.39.0, 1.38.0, 1.37.0, 1.36.0, 1.35.0, 1.34.1, 1.34.0
Build Dependencies
python, icu4c, bzip2, zlib, mpi
Link Dependencies
python, icu4c, bzip2, zlib, mpi
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, 2.2.5
Build Dependencies
tbb, readline, zlib
Link Dependencies
tbb, readline, zlib
Description:
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

boxlib

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

bpp-core

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

bpp-phyl

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

bpp-seq

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

bpp-suite

Homepage:
Spack package:
Versions:
2.2.0
Build Dependencies
bpp-phyl, cmake, texinfo, bpp-core, bpp-seq
Link Dependencies
bpp-phyl, bpp-core, bpp-seq
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, genemark-et, samtools, augustus, bamtools
Link Dependencies
genemark-et, samtools, augustus, 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

brigand

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

bsseeker2

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

bucky

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

busco

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

butter

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

bwa

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

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:
1.11.1, 1.9.2, 1.9.1, 1.9.0, 1.8.1, 1.8.0
Build Dependencies
snappy, zlib, cmake
Link Dependencies
snappy, zlib
Description:
Blosc, an extremely fast, multi-threaded, meta-compressor library

caffe

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

cairo

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

caliper

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

cantera

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

canu

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

cap3

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

cares

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

cask

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

catch

Homepage:
Spack package:
Versions:
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, blas, fftw, mpi
Link Dependencies
lapack, blas, fftw, mpi
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
cmake, mrnet, boost, xerces-c, libxml2
Link Dependencies
xerces-c, mrnet, boost, 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
cmake, mrnet, cbtf-krell, cuda, papi, boost, cbtf
Link Dependencies
papi, mrnet, cbtf-krell, cuda, boost, cbtf
Description:
CBTF Argo Navis project contains the CUDA collector and supporting libraries that was done as a result of a DOE SBIR grant.

cbtf-argonavis-gui

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

ccache

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

cctools

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

cdbfasta

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

cdd

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

cddlib

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

cdhit

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

cdo

Homepage:
Spack package:
Versions:
1.9.0, 1.8.2, 1.7.2
Build Dependencies
hdf5, libxml2, fftw, udunits2, netcdf, proj, magics, szip, curl, grib-api
Link Dependencies
hdf5, libxml2, fftw, udunits2, netcdf, proj, magics, szip, curl, grib-api
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:
3.410, 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:
4.9.1, 4.9, 4.7, 4.6.3
Build Dependencies
cmake, qt, zlib, gmp, boost, mpfr
Link Dependencies
gmp, zlib, boost, qt, 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:
3.3.0
Build Dependencies
cmake, hdf5
Link Dependencies
hdf5
Description:
The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.

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

cityhash

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

clamr

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

cleverleaf

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

clfft

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

clhep

Homepage:
Spack package:
Versions:
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.

cloog

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

cloverleaf

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

cloverleaf3d

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

clustalo

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

clustalw

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

cmake

Homepage:
Spack package:
Versions:
3.9.0, 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
py-sphinx, bzip2, zlib, qt, python, expat, openssl, libarchive, xz, ncurses, rhash, curl, libuv
Link Dependencies
bzip2, expat, qt, ncurses, zlib, openssl, libarchive, xz, rhash, curl, libuv
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
uuid, hdf5, python, py-numpy, udunits2, netcdf
Link Dependencies
python, udunits2, netcdf, uuid, hdf5
Run Dependencies
py-numpy
Description:
Climate Model Output Rewriter is used to produce CF-compliant netCDF files. The structure of the files created by the library and the metadata they contain fulfill the requirements of many of the climate community’s standard model experiments.

cnmem

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

cnpy

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

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

cntk1bitsgd

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

codar-cheetah

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

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

compiz

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

compositeproto

Homepage:
Spack package:
Versions:
0.4.2
Build Dependencies
util-macros, pkg-config
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:
0.2.1, 0.2.0, master
Build Dependencies
py-sphinx, doxygen, cmake, hdf5, python, mpi, py-numpy, silo
Link Dependencies
doxygen, cmake, hdf5, python, mpi, silo
Run Dependencies
py-numpy
Description:
Conduit is an open source project from Lawrence Livermore National Laboratory that provides an intuitive model for describing hierarchical scientific data in C++, C, Fortran, and Python. It is used for data coupling between packages in-core, serialization, and I/O tasks.

constype

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies
util-macros, pkg-config
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-scipy, py-pandas, python, py-numpy, py-six, planck-likelihood, mpi, py-matplotlib
Link Dependencies
python, planck-likelihood, mpi
Run Dependencies
py-scipy, py-pandas, python, py-numpy, py-six, py-matplotlib
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:
4.1, 3.0
Build Dependencies
wannier90, libint, python, blas, fftw, elpa, mpi, lapack, plumed, scalapack, pexsi
Link Dependencies
wannier90, libint, lapack, blas, fftw, elpa, mpi, plumed, scalapack, pexsi
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:
1.78, 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
python, cmake, 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
ncurses, flex, bison, pkg-config
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

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
zlib, qt
Link Dependencies
zlib, qt
Description:
Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performance space consisting of the dimensions: - performance metric - call path - system resource

cuda

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

cudnn

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

cvs

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

czmq

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

dakota

Homepage:
Spack package:
Versions:
6.3
Build Dependencies
cmake, lapack, blas, mpi, python, boost
Link Dependencies
lapack, python, blas, 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
util-macros, pkg-config
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
m4, autoconf, libtool, automake
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
m4, autoconf, libtool, automake, 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
zlib, blas, graphviz, netcdf, arpack-ng, bzip2, cmake, lapack, oce, boost, trilinos, muparser, python, p4est, sundials, mpi, suite-sparse, adol-c, tbb, doxygen, nanoflann, hdf5, slepc, metis, petsc, cuda, netcdf-cxx, gsl
Link Dependencies
zlib, blas, graphviz, netcdf, arpack-ng, bzip2, cmake, lapack, oce, boost, trilinos, muparser, python, p4est, sundials, mpi, suite-sparse, adol-c, tbb, doxygen, nanoflann, hdf5, slepc, metis, petsc, cuda, netcdf-cxx, gsl
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.

dia

Homepage:
Spack package:
Versions:
0.97.3
Build Dependencies
freetype, intltool, python, libxml2, swig, libuuid, gtkplus, libxinerama, libxslt, libsm, libxrender
Link Dependencies
freetype, python, libxml2, swig, libuuid, gtkplus, libxinerama, libxslt, libsm, libxrender
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

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.

dmxproto

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

docbook-xml

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

docbook-xsl

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

dos2unix

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

double-conversion

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

doxygen

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

dri2proto

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

dri3proto

Homepage:
Spack package:
Versions:
1.0
Build Dependencies
util-macros, pkg-config
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:
1.0.3
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, boost, libdwarf
Link Dependencies
elf, boost, libdwarf
Description:
API for dynamic binary instrumentation. Modify programs while they are executing without recompiling, re-linking, or re-executing.

ea-utils

Homepage:
Spack package:
Versions:
1.04.807
Build Dependencies
subversion, bamtools, zlib, gsl, perl
Link Dependencies
subversion, bamtools, zlib, gsl
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-framework, py-easybuild-easyconfigs, py-easybuild-easyblocks
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:
2.2.0
Build Dependencies
cmake, python, py-numpy, netcdf, libpng, openjpeg
Link Dependencies
python, libpng, openjpeg, netcdf, py-numpy
Description:
ecCodes is a package developed by ECMWF for processing meteorological data in GRIB (1/2), BUFR (3/4) and GTS header formats.

editres

Homepage:
Spack package:
Versions:
1.0.6
Build Dependencies
libx11, libxmu, util-macros, libxt, libxaw, pkg-config
Link Dependencies
libxmu, libxt, libxaw, libx11
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, cmake, fftw, suite-sparse, gmp, scotch, mpfr
Link Dependencies
metis, fftw, suite-sparse, gmp, scotch, mpfr
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
Build Dependencies
cmake, mpc, lapack, blas, metis, mpi, python, intel-mkl, gmp, scalapack, openblas, mpfr
Link Dependencies
mpc, lapack, blas, metis, mpi, python, intel-mkl, gmp, scalapack, openblas, mpfr
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
flex, bison, gettext
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, blas, fftw, libxc, mpi
Link Dependencies
lapack, blas, fftw, libxc, mpi
Description:
An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features.

elpa

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

emacs

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

emboss

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

encodings

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies
util-macros, mkfontscale, font-util, pkg-config
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
lapack, libxml2, zlib, xerces-c, mpi, netcdf, netcdf-fortran, parallel-netcdf
Link Dependencies
lapack, libxml2, zlib, xerces-c, mpi, netcdf, netcdf-fortran, parallel-netcdf
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
hdf5, lapack, blas, fftw, elpa, mpi, scalapack
Link Dependencies
hdf5, lapack, blas, fftw, elpa, mpi, scalapack
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.

espressopp

Homepage:
Spack package:
Versions:
develop, 1.9.4.1, 1.9.4
Build Dependencies
py-sphinx, doxygen, cmake, python, fftw, mpi, py-mpi4py, py-numpy, boost, texlive, py-matplotlib
Link Dependencies
python, fftw, boost, mpi
Run Dependencies
py-mpi4py, py-numpy
Description:
ESPResSo++ is an extensible, flexible, fast and parallel simulation software for soft matter research. It is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research

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
everytrace, openmpi, cmake
Link Dependencies
everytrace, openmpi
Description:
Get stack trace EVERY time a program exits.

evieext

Homepage:
Spack package:
Versions:
1.1.1
Build Dependencies
util-macros, pkg-config
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.

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

exonerate

Homepage:
Spack package:
Versions:
2.4.0
Build Dependencies
glib, pkg-config
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
m4, tcl, autoconf, libtool, automake
Link Dependencies
tcl
Description:
Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc.

extrae

Homepage:
Spack package:
Versions:
3.4.1
Build Dependencies
papi, libxml2, dyninst, gettext, mpi, libunwind, boost, binutils, libdwarf
Link Dependencies
papi, libxml2, dyninst, elf, gettext, mpi, libunwind, boost, binutils, libdwarf
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
python, pacbio-dextractor, pacbio-dazz-db, py-pypeflow, pacbio-daligner, pacbio-damasker, py-networkx, 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, chombo, phasta, boxlib, superlu-dist, trilinos, pumi, moab, mpi, petsc, sundials, mesquite, zoltan, arpack-ng
Link Dependencies
hypre, chombo, phasta, boxlib, superlu-dist, trilinos, pumi, moab, mpi, petsc, sundials, mesquite, zoltan, arpack-ng
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.

fastphase

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

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.

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

ferret

Homepage:
Spack package:
Versions:
6.96
Build Dependencies
readline, zlib, netcdf, netcdf-fortran, hdf5
Link Dependencies
readline, zlib, netcdf, netcdf-fortran, hdf5
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:
3.3.6-pl2, 3.3.5, 3.3.4, 2.1.5
Build Dependencies
mpi, autoconf, libtool, automake
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
py-sphinx, gtkplus, cairo
Link Dependencies
cairo, gtkplus
Description:
Flexible I/O Tester.

fish

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

fixesproto

Homepage:
Spack package:
Versions:
5.0
Build Dependencies
util-macros, pkg-config
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

flann

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

flash

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

flecsale

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

flecsi

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

flex

Homepage:
Spack package:
Versions:
2.6.4, 2.6.3, 2.6.1, 2.6.0, 2.5.39
Build Dependencies
gettext, automake, m4, libtool, help2man, bison, autoconf
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).

fltk

Homepage:
Spack package:
Versions:
1.3.3
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:
0.6.0, master
Build Dependencies
hwloc, lua, json-c, czmq, munge, asciidoc, jansson, libtool, py-cffi, libxslt, python, zeromq, autoconf, automake
Link Dependencies
hwloc, lua, json-c, czmq, munge, python, jansson, libxslt, zeromq
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
flex, zlib, cmake, python, metis, mpi, parmgridgen, scotch, parmetis, paraview
Link Dependencies
metis, python, zlib, mpi, paraview, scotch, parmetis
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
gflags, autoconf, automake, m4, libtool, libevent, double-conversion, glog, boost, pkg-config
Link Dependencies
double-conversion, gflags, libevent, boost, glog
Description:
Folly (acronymed loosely after Facebook Open Source Library) is a library of C++11 components designed with practicality and efficiency in mind. Folly contains a variety of core library components used extensively at Facebook. In particular, it’s often a dependency of Facebook’s other open source C++ efforts and place where those projects can share code.

font-adobe-100dpi

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

font-adobe-75dpi

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

font-adobe-utopia-100dpi

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

font-adobe-utopia-75dpi

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

font-adobe-utopia-type1

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

font-alias

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

font-arabic-misc

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

font-bh-100dpi

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

font-bh-75dpi

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

font-bh-lucidatypewriter-100dpi

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

font-bh-lucidatypewriter-75dpi

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

font-bh-ttf

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

font-bh-type1

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

font-bitstream-100dpi

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

font-bitstream-75dpi

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

font-bitstream-speedo

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

font-bitstream-type1

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

font-cronyx-cyrillic

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

font-cursor-misc

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

font-daewoo-misc

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

font-dec-misc

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

font-ibm-type1

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

font-isas-misc

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

font-jis-misc

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

font-micro-misc

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

font-misc-cyrillic

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

font-misc-ethiopic

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

font-misc-meltho

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

font-misc-misc

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

font-mutt-misc

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

font-schumacher-misc

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

font-screen-cyrillic

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

font-sony-misc

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

font-sun-misc

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

font-util

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

font-winitzki-cyrillic

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

font-xfree86-type1

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

fontcacheproto

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

fontconfig

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

fontsproto

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

fonttosfnt

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

freebayes

Homepage:
Spack package:
Versions:
1.1.0
Build Dependencies
zlib, cmake
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, bzip2, pkg-config
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

fslsfonts

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

fstobdf

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

funhpc

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

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:
1.28.2, 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.

gaussian

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

gawk

Homepage:
Spack package:
Versions:
4.1.4
Build Dependencies
readline, gmp, libsigsegv, gettext, mpfr
Link Dependencies
readline, gmp, libsigsegv, gettext, mpfr
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:
7.2.0, 7.1.0, 6.4.0, 6.3.0, 6.2.0, 6.1.0, 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, mpc, zip, zlib, isl, gmp, binutils, mpfr
Link Dependencies
gnat, mpc, zlib, isl, gmp, binutils, mpfr
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
pkg-config
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
libtiff, hdf5, python, swig, zlib, py-numpy, hdf, netcdf, proj, libpng, openjpeg, kealib, geos
Link Dependencies
libtiff, hdf5, python, swig, zlib, hdf, netcdf, proj, libpng, openjpeg, kealib, geos
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:
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:
1.13, 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
glib, gobject-introspection, libtiff, gettext, jpeg, libpng, pkg-config
Link Dependencies
glib, gobject-introspection, libtiff, gettext, jpeg, libpng
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:
10.02.p02, 10.02.p01, 10.01.p03
Build Dependencies
expat, cmake, clhep, zlib, xerces-c, vecgeom, qt
Link Dependencies
expat, clhep, zlib, xerces-c, vecgeom, qt
Description:
Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

gearshifft

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

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
bzip2, tar, libunistring, ncurses, libxml2, xz
Link Dependencies
bzip2, tar, libunistring, ncurses, libxml2, xz
Description:
GNU internationalization (i18n) and localization (l10n) library.

gflags

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

ghostscript

Homepage:
Spack package:
Versions:
9.21, 9.18
Build Dependencies
freetype, zlib, libtiff, jpeg, libpng, lcms, pkg-config
Link Dependencies
freetype, zlib, libtiff, jpeg, libpng, lcms
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:
2.14.1, 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
pcre, expat, zlib, openssl, gettext, perl, libiconv, m4, libtool, curl, autoconf, automake
Link Dependencies
pcre, expat, zlib, openssl, gettext, perl, libiconv, curl
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
libsm, libxdmcp, cmake, libxi, expat, libice, libdrm, libxt, libxext, libxcb, libpng, libxdamage, zlib, libxmu, libxfixes, libxxf86vm, libxau
Link Dependencies
libsm, libxdmcp, libxi, libxmu, libice, libdrm, libxt, libxext, libxcb, libpng, libxdamage, zlib, expat, libxfixes, libxxf86vm, libxau
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:
2.53.1, 2.49.7, 2.49.4, 2.48.1, 2.42.1
Build Dependencies
pcre, zlib, gettext, libffi, util-linux, pkg-config
Link Dependencies
pcre, libffi, util-linux, zlib, gettext
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
ncurses, exuberant-ctags
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:
6.0.1470089956
Description:
The Globus Toolkit is an open source software toolkit used for building grids

glog

Homepage:
Spack package:
Versions:
0.3.4, 0.3.3
Build Dependencies
gflags, cmake
Link Dependencies
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
util-macros, pkg-config
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
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
m4, autoconf, libtool, automake
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:
3.0.1, 2.16.0, 2.15.0, 2.12.0, 2.11.0
Build Dependencies
cmake, fltk, hdf5, lapack, blas, zlib, oce, mpi, petsc, gmp, slepc
Link Dependencies
fltk, hdf5, lapack, blas, zlib, oce, mpi, petsc, gmp, slepc
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:
2.1.21
Build Dependencies
npth, libksba, libgcrypt, libgpg-error, libassuan
Link Dependencies
npth, libksba, libgcrypt, libgpg-error, libassuan
Description:
GnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880

gnuplot

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

gnutls

Homepage:
Spack package:
Versions:
3.5.13, 3.5.10, 3.5.9, 3.3.9
Build Dependencies
nettle, zlib, gettext, pkg-config
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, 1.8.3, 1.8.1, 1.8, 1.7.5, 1.7.4, 1.6.4
Build Dependencies
git, go-bootstrap
Link Dependencies
git
Run Dependencies
git
Description:
The golang compiler and build environment

go-bootstrap

Homepage:
Spack package:
Versions:
1.4-bootstrap-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
glib, flex, python, cairo, sed, bison, pkg-config
Link Dependencies
glib, python, cairo
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.

gource

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

gperf

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

gperftools

Homepage:
Spack package:
Versions:
2.4, 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:
2.2, 2.0.1
Build Dependencies
mpi, libtool, hdf5
Link Dependencies
mpi, libtool, hdf5
Description:
Grackle is a chemistry and radiative cooling library for astrophysical simulations with interfaces for C, C++, and Fortran codes. It is a generalized and trimmed down version of the chemistry network of the Enzo simulation code

gradle

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

grandr

Homepage:
Spack package:
Versions:
0.1
Build Dependencies
gconf, xrandr, gtkplus
Link Dependencies
gconf, xrandr, gtkplus
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:
2.38.0
Build Dependencies
freetype, ghostscript, java, python, cairo, swig, expat, libtool, libgd, pango, pkg-config
Link Dependencies
freetype, ghostscript, java, python, cairo, swig, expat, libtool, libgd, pango
Description:
Graph Visualization Software

grib-api

Homepage:
Spack package:
Versions:
1.21.0, 1.17.0, 1.16.0
Build Dependencies
libpng, cmake, netcdf, jasper
Link Dependencies
libpng, netcdf, jasper
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
gmake, ghostscript, sed, gawk
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:
2016.4, 2016.3, 5.1.4, 5.1.2
Build Dependencies
mpi, fftw, cmake, cuda, plumed
Link Dependencies
mpi, fftw, cuda, plumed
Description:
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs. It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is released under the GNU Lesser General Public License.

gsl

Homepage:
Spack package:
Versions:
2.3, 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.

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

gts

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

guile

Homepage:
Spack package:
Versions:
2.2.0, 2.0.14, 2.0.11
Build Dependencies
libunistring, gettext, bdw-gc, libtool, libffi, readline, gmp, pkg-config
Link Dependencies
libunistring, gettext, bdw-gc, libtool, libffi, 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
mpi, hdf5
Link Dependencies
mpi, hdf5
Description:
H5hut (HDF5 Utility Toolkit). High-Performance I/O Library for Particle- based Simulations.

h5part

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

h5utils

Homepage:
Spack package:
Versions:
1.12.1
Build Dependencies
libpng, hdf, libmatheval, octave, hdf5
Link Dependencies
libpng, hdf, libmatheval, octave, hdf5
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
zfp, hdf5
Link Dependencies
zfp, hdf5
Description:
A highly flexible floating point and integer compression plugin for the HDF5 library using ZFP compression.

hadoop

Homepage:
Spack package:
Versions:
2.6.4
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
glib, freetype, cairo, zlib, icu4c, pkg-config
Link Dependencies
glib, cairo, freetype, zlib, icu4c
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
szip, zlib, bison, jpeg, flex
Link Dependencies
zlib, szip, jpeg
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
mpi, zlib, szip, numactl
Link Dependencies
mpi, zlib, szip, numactl
Description:
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

hdf5-blosc

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

help2man

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

hepmc

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

highwayhash

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

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

hpccg

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

hpctoolkit

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

hpctoolkit-externals

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

hpl

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

hpx

Homepage:
Spack package:
Versions:
1.0.0
Build Dependencies
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
hwloc, opencl, mpi, metis, autoconf, automake, m4, libtool, jemalloc, pkg-config
Link Dependencies
metis, hwloc, opencl, 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
ncurses, automake, m4, libtool, readline, autoconf
Link Dependencies
ncurses, readline
Description:
hstr(hh) is a shell history suggest box for Bash and Zsh, which enables easy viewing, searching and using your command history.

htop

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

htslib

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

httpie

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

hwloc

Homepage:
Spack package:
Versions:
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
libxml2, libpciaccess, cuda, pkg-config
Link Dependencies
libpciaccess, cuda, 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
samtools, spades, py-biopython, python, parallel, bwa, blast-plus, exonerate
Link Dependencies
samtools, spades, parallel, bwa, blast-plus, exonerate
Run Dependencies
python, py-biopython
Description:
HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads

hydra

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

hypre

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

ibmisc

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

iceauth

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies
libice, util-macros, xproto, pkg-config
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
zlib, jpeg, gmake, libxtst, cups, libxau, libxdmcp, alsa-lib, giflib, libxt, libxinerama, libpng, libxext, freetype, xproto, gtkplus, wget, jdk, libx11, libxcomposite, libxrender, libxi, lcms, pkg-config
Link Dependencies
alsa-lib, freetype, libxdmcp, lcms, libxext, libxcomposite, libx11, libxi, zlib, xproto, jpeg, gtkplus, giflib, libxtst, libxt, libxinerama, libxrender, libpng, cups, libxau
Description:
The IcedTea project provides a harness to build the source code from http://openjdk.java.net using Free Software build tools and adds a number of key features to the upstream OpenJDK codebase. IcedTea requires an existing IcedTea or OpenJDK install to build.

icet

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

ico

Homepage:
Spack package:
Versions:
1.0.4
Build Dependencies
util-macros, libx11, xproto, pkg-config
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:
58.2, 57.1
Description:
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU4C is the C/C++ interface.

id3lib

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

idba

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies
m4, autoconf, libtool, automake
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.

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
freetype, ghostscript, libtiff, jpeg, fontconfig, libtool, libpng, ghostscript-fonts, pango
Link Dependencies
freetype, ghostscript, libtiff, jpeg, fontconfig, ghostscript-fonts, libpng, pango
Description:
ImageMagick is a software suite to create, edit, compose, or convert bitmap images.

imake

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies
xproto, pkg-config
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
util-macros, pkg-config
Description:
X Input Extension. This extension defines a protocol to provide additional input devices management such as graphic tablets.

intel

Homepage:
Spack package:
Versions:
18.0.0, 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:
2018.0.128, 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
glib, flex, util-macros, python, cairo, libpciaccess, libdrm, bison, pkg-config
Link Dependencies
glib, cairo, libdrm, libpciaccess
Description:
Intel GPU Tools is a collection of tools for development and testing of the Intel DRM driver. There are many macro-level test suites that get used against the driver, including xtest, rendercheck, piglit, and oglconform, but failures from those can be difficult to track down to kernel changes, and many require complicated build procedures or specific testing environments to get useful results. Therefore, Intel GPU Tools includes low-level tools and tests specifically for development and testing of the Intel DRM Driver.

intel-ipp

Homepage:
Spack package:
Versions:
2018.0.128, 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:
2018.0.128, 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-mpi

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

intel-parallel-studio

Homepage:
Spack package:
Versions:
professional.2018.0, 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.2018.0, 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.2018.0, 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:
2018.0, 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-xml-parser, perl
Run Dependencies
perl-xml-parser, perl
Description:
intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.

ior

Homepage:
Spack package:
Versions:
3.0.1
Build Dependencies
hdf5, mpi, m4, libtool, parallel-netcdf, autoconf, automake
Link Dependencies
parallel-netcdf, mpi, hdf5
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:
3.12.7, 3.12.6, 3.12.5, 3.12.4, 3.12.3, 3.12.2, 3.12.1, 3.12.0
Build Dependencies
lapack, blas, metis, coinhsl, mumps, pkg-config
Link Dependencies
lapack, blas, metis, mumps, coinhsl
Description:
Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization.

isaac

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

isaac-server

Homepage:
Spack package:
Versions:
develop, 1.3.1, 1.3.0, master
Build Dependencies
cmake
Link Dependencies
libwebsockets, jansson, boost, jpeg
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
hmmer, perl
Link Dependencies
hmmer
Run Dependencies
perl
Description:
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing

jags

Homepage:
Spack package:
Versions:
4.2.0
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

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.

jemalloc

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

jmol

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

jq

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

json-c

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

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
git, cmake, python, openssl, m4, curl, binutils
Link Dependencies
git, cmake, python, openssl, curl, binutils
Run Dependencies
py-matplotlib, mpi, hdf5
Description:
The Julia Language: A fresh approach to technical computing

kahip

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

kaldi

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

kallisto

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

kbproto

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies
util-macros, pkg-config
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
cmake, hdf5
Link Dependencies
hdf5
Description:
An HDF5 Based Raster File Format KEALib provides an implementation of the GDAL data model. The format supports raster attribute tables, image pyramids, meta-data and in-built statistics while also handling very large files and compression throughout. Based on the HDF5 standard, it also provides a base from which other formats can be derived and is a good choice for long term data archiving. An independent software library (libkea) provides complete access to the KEA image format and a GDAL driver allowing KEA images to be used from any GDAL supported software. Development work on this project has been funded by Landcare Research.

kentutils

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

kmergenie

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

kokkos

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

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.

lammps

Homepage:
Spack package:
Versions:
20170901
Build Dependencies
cmake, lapack, blas, fftw, mpi, netcdf, voropp
Link Dependencies
lapack, blas, fftw, mpi, netcdf, voropp
Description:
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. This package uses patch releases, not stable release. See https://github.com/LLNL/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, blas, cmake, 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
libgpg-error, automake, libtool, spectrum-mpi, autoconf, boost, libgcrypt
Link Dependencies
boost, elf, spectrum-mpi, libgpg-error, libgcrypt
Description:
Software infrastructure that enables HPC run-time tools to co-locate tool daemons with a parallel job.

lbann

Homepage:
Spack package:
Versions:
develop, 0.91
Build Dependencies
hwloc, cmake, protobuf, elemental, mpi, opencv, cnpy, cuda
Link Dependencies
hwloc, protobuf, elemental, mpi, opencv, cnpy, cuda
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
libice, bigreqsproto, libx11, liblbxutil, xtrans, util-macros, xproxymanagementprotocol, libxext, pkg-config
Link Dependencies
libice, libx11, libxext, liblbxutil
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
ldc-bootstrap, cmake, libedit, zlib, llvm, libconfig, curl, binutils
Link Dependencies
ldc-bootstrap, libedit, zlib, llvm, libconfig, curl, 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, cmake, libedit, zlib, libconfig, curl, binutils
Link Dependencies
llvm, libedit, zlib, libconfig, curl, 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, 17.02.0
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
Build Dependencies
expat, ncurses, zlib, openssl, libiconv, readline
Link Dependencies
expat, ncurses, zlib, openssl, libiconv, 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:
1.0.1, 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
xextproto, libx11, util-macros, applewmproto, libxext, pkg-config
Link Dependencies
libx11, libxext
Description:
AppleWM is a simple library designed to interface with the Apple-WM extension. This extension allows X window managers to better interact with the Mac OS X Aqua user interface when running X11 in a rootless mode.

libarchive

Homepage:
Spack package:
Versions:
3.2.1, 3.1.2, 3.1.1, 3.1.0
Build Dependencies
lzma, xz, bzip2, zlib, libxml2, expat, lz4, openssl, nettle, lzo
Link Dependencies
lzma, xz, bzip2, zlib, libxml2, expat, lz4, openssl, nettle, lzo
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:
2.4.3
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
automake, subversion, m4, libtool, autoconf, pkg-config
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:
1.7.0, 1.6.3, 1.6.2, 1.6.1
Build Dependencies
m4, autoconf, libtool, automake
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
libxext, libxrandr, pkg-config, libx11, libxcursor, libxcomposite, libxrender, libxcb, libvorbis, libxdamage, gtkplus, libxfixes, libxinerama, libxau
Link Dependencies
libxext, libxrandr, libx11, libxcursor, libxcomposite, libxrender, libxcb, libvorbis, libxdamage, gtkplus, libxfixes, libxinerama, libxau
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

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
m4, autoconf, libtool, automake
Description:
C/C++ Configuration File 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
xextproto, dmxproto, libx11, util-macros, libxext, pkg-config
Link Dependencies
libx11, libxext
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
libpciaccess, libpthread-stubs, pkg-config
Link Dependencies
libpciaccess, libpthread-stubs
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
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:
4.4.7, 4.4.2
Build Dependencies
fftw, cmake, eccodes, grib-api
Link Dependencies
fftw, eccodes, grib-api
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.

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
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.

libffs

Homepage:
Spack package:
Versions:
develop, 1.1.1, 1.1
Build Dependencies
cmake, gtkorvo-dill, gtkorvo-cercs-env, gtkorvo-atl
Link Dependencies
gtkorvo-dill, gtkorvo-cercs-env, gtkorvo-atl
Description:
FFS is a middleware library for data communication, including representation, processing and marshaling that preserves the performance of traditional approaches while relaxing the requirement of a priori knowledge and providing complex run-time flexibility.

libfontenc

Homepage:
Spack package:
Versions:
1.1.3
Build Dependencies
util-macros, zlib, xproto, pkg-config
Link Dependencies
zlib
Description:
libfontenc - font encoding library.

libfs

Homepage:
Spack package:
Versions:
1.0.7
Build Dependencies
xtrans, util-macros, fontsproto, xproto, pkg-config
Description:
libFS - X Font Service client library. This library is used by clients of X Font Servers (xfs), such as xfsinfo, fslsfonts, and the X servers themselves.

libgcrypt

Homepage:
Spack package:
Versions:
1.7.6, 1.6.2
Build Dependencies
libgpg-error
Link Dependencies
libgpg-error
Description:
Libgcrypt is a general purpose cryptographic library based on the code from GnuPG. It provides functions for all cryptographic building blocks: symmetric ciphers, hash algorithms, MACs, public key algorithms, large integer functions, random numbers and a lot of supporting functions.

libgd

Homepage:
Spack package:
Versions:
2.2.4, 2.2.3, 2.1.1
Build Dependencies
autoconf, libtiff, gettext, automake, libiconv, m4, libtool, jpeg, libpng, fontconfig, pkg-config
Link Dependencies
libiconv, libpng, libtiff, jpeg, fontconfig
Description:
GD is an open source code library for the dynamic creation of images by programmers. GD is written in C, and “wrappers” are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM, BMP images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, o