Basic Usage

The spack command has many subcommands. You’ll only need a small subset of them for typical usage.

Note that Spack colorizes output. less -R should be used with Spack to maintain this colorization. E.g.:

$ spack find | less -R

It is recommended that the following be put in your .bashrc file:

alias less='less -R'

Listing available packages

To install software with Spack, you need to know what software is available. You can see a list of available package names at the Package List webpage, or using the spack list command.

spack list

The spack list command prints out a list of all of the packages Spack can install:

$ spack list
abinit                           muscle                                 r-broom
abyss                            muse                                   r-bsgenome
accfft                           muster                                 r-bumphunter
ack                              mvapich2                               r-c50
activeharmony                    mxml                                   r-cairo
adept-utils                      mxnet                                  r-callr
adios                            nag                                    r-car
adios2                           nalu                                   r-caret
adlbx                            nalu-wind                              r-category
adol-c                           namd                                   r-catools
aegean                           nano                                   r-cdcfluview
aida                             nanoflann                              r-cellranger
albany                           nanopb                                 r-checkmate
albert                           nasm                                   r-checkpoint
alglib                           nauty                                  r-chemometrics
allinea-forge                    ncbi-magicblast                        r-chron
allinea-reports                  ncbi-rmblastn                          r-circlize
allpaths-lg                      ncbi-toolkit                           r-class
alquimia                         nccl                                   r-classint
alsa-lib                         nccmp                                  r-cli
aluminum                         ncdu                                   r-clipr
amg                              ncftp                                  r-cluster
amg2013                          ncl                                    r-clustergeneration
amp                              nco                                    r-clusterprofiler
ampliconnoise                    ncurses                                r-cner
amrex                            ncview                                 r-coda
amrvis                           ndiff                                  r-codetools
andi                             nek5000                                r-coin
angsd                            nekbone                                r-colorspace
ant                              nekcem                                 r-combinat
antlr                            nektar                                 r-complexheatmap
ants                             neovim                                 r-compositions
ape                              nest                                   r-convevol
aperture-photometry              netcdf                                 r-corpcor
apex                             netcdf-cxx                             r-corrplot
apple-libunwind                  netcdf-cxx4                            r-covr
applewmproto                     netcdf-fortran                         r-cowplot
appres                           netgauge                               r-crayon
apr                              netgen                                 r-crosstalk
apr-util                         netlib-lapack                          r-ctc
aragorn                          netlib-scalapack                       r-cubature
archer                           netlib-xblas                           r-cubist
argobots                         nettle                                 r-curl
argp-standalone                  neuron                                 r-data-table
argtable                         nextflow                               r-dbi
arlecore                         nfft                                   r-dbplyr
armadillo                        nghttp2                                r-delayedarray
arpack-ng                        nginx                                  r-deldir
arrow                            ngmlr                                  r-dendextend
ascent                           ninja                                  r-deoptim
asciidoc                         ninja-fortran                          r-deoptimr
asciidoctor                      nlohmann-json                          r-deseq
aspa                             nlopt                                  r-deseq2
aspcud                           nmap                                   r-desolve
aspect                           nnvm                                   r-devtools
aspell                           node-js                                r-diagrammer
aspell6-de                       notmuch                                r-dicekriging
aspell6-en                       npb                                    r-dichromat
aspell6-es                       npm                                    r-diffusionmap
aspera-cli                       npth                                   r-digest
assimp                           nspr                                   r-diptest
astra                            numactl                                r-dirichletmultinomial
astral                           numdiff                                r-dismo
astyle                           nut                                    r-diversitree
at-spi2-atk                      nvptx-tools                            r-dnacopy
at-spi2-core                     nwchem                                 r-do-db
atk                              nyancat                                r-domc
atlas                            ocaml                                  r-doparallel
atom-dft                         occa                                   r-dorng
atompaw                          oce                                    r-dose
atop                             oclint                                 r-downloader
augustus                         oclock                                 r-dplyr
autoconf                         octave                                 r-dt
autodock-vina                    octave-optim                           r-dtw
autofact                         octave-splines                         r-dygraphs
autogen                          octave-struct                          r-e1071
automaded                        octopus                                r-edger
automake                         of-adios-write                         r-ellipse
axel                             of-precice                             r-energy
axl                              omega-h                                r-ensembldb
bamdst                           ompss                                  r-ergm
bamtools                         ompt-openmp                            r-evaluate
bamutil                          oniguruma                              r-expint
barrnap                          ont-albacore                           r-expm
bash                             opa-psm2                               r-factoextra
bash-completion                  opam                                   r-factominer
bats                             opari2                                 r-fastcluster
bazel                            openbabel                              r-fastmatch
bbcp                             openblas                               r-ff
bbmap                            opencoarrays                           r-fftwtools
bc                               opencv                                 r-fgsea
bcftools                         openexr                                r-filehash
bcl2fastq2                       openfast                               r-findpython
bdftopcf                         openfoam-com                           r-fit-models
bdw-gc                           openfoam-org                           r-flashclust
bear                             openfst                                r-flexclust
beast1                           opengl                                 r-flexmix
beast2                           openglu                                r-fnn
bedops                           openimageio                            r-forcats
bedtools2                        openjpeg                               r-foreach
beforelight                      openmc                                 r-forecast
benchmark                        openmpi                                r-foreign
berkeley-db                      opennurbs                              r-formatr
bertini                          openpmd-api                            r-formula
bib2xhtml                        openscenegraph                         r-fpc
bigreqsproto                     openslide                              r-fracdiff
binutils                         openspeedshop                          r-futile-logger
bioawk                           openspeedshop-utils                    r-futile-options
biobloom                         openssh                                r-gbm
biopieces                        openssl                                r-gcrma
bismark                          opium                                  r-gdata
bison                            optional-lite                          r-gdsfmt
bitmap                           opus                                   r-geiger
blasr                            orca                                   r-genefilter
blasr-libcpp                     orfm                                   r-genelendatabase
blast-plus                       orthofinder                            r-geneplotter
blat                             orthomcl                               r-genie3
blaze                            osu-micro-benchmarks                   r-genomeinfodb
blis                             otf                                    r-genomeinfodbdata
bliss                            otf2                                   r-genomicalignments
blitz                            p4est                                  r-genomicfeatures
bmake                            p7zip                                  r-genomicranges
bml                              pacbio-daligner                        r-gensa
bohrium                          pacbio-damasker                        r-geomorph
bolt                             pacbio-dazz-db                         r-geoquery
bookleaf-cpp                     pacbio-dextractor                      r-geor
boost                            packmol                                r-geosphere
boostmplcartesianproduct         pacvim                                 r-getopt
bowtie                           pagit                                  r-getoptlong
bowtie2                          pagmo                                  r-ggally
boxlib                           paml                                   r-ggbio
bpp-core                         panda                                  r-ggdendro
bpp-phyl                         pandaseq                               r-ggjoy
bpp-seq                          pango                                  r-ggmap
bpp-suite                        pangomm                                r-ggplot2
bracken                          papi                                   r-ggpubr
braker                           papyrus                                r-ggrepel
branson                          paradiseo                              r-ggridges
breakdancer                      parallel                               r-ggsci
breseq                           parallel-netcdf                        r-ggvis
brigand                          paraver                                r-gistr
bsseeker2                        paraview                               r-git2r
bucky                            parmetis                               r-glimma
bumpversion                      parmgridgen                            r-glmnet
busco                            parquet                                r-globaloptions
butter                           parsimonator                           r-glue
bwa                              parsplice                              r-gmodels
bwtool                           partitionfinder                        r-gmp
byobu                            patch                                  r-go-db
bzip2                            patchelf                               r-googlevis
c-blosc                          pathfinder                             r-goplot
c-lime                           pax-utils                              r-gosemsim
cabana                           pbbam                                  r-goseq
caffe                            pbmpi                                  r-gostats
cairo                            pbsuite                                r-gplots
cairomm                          pcma                                   r-graph
caliper                          pcre                                   r-gridbase
callpath                         pcre2                                  r-gridextra
camellia                         pdf2svg                                r-gseabase
candle-benchmarks                pdftk                                  r-gss
cantera                          pdsh                                   r-gsubfn
canu                             pdt                                    r-gtable
cap3                             pegtl                                  r-gtools
cares                            pennant                                r-gtrellis
cask                             percept                                r-gviz
casper                           perl                                   r-haven
catalyst                         perl-algorithm-diff                    r-hexbin
catch                            perl-app-cmd                           r-highr
cbench                           perl-array-utils                       r-hmisc
cblas                            perl-b-hooks-endofscope                r-hms
cbtf                             perl-bio-perl                          r-htmltable
cbtf-argonavis                   perl-bit-vector                        r-htmltools
cbtf-argonavis-gui               perl-cairo                             r-htmlwidgets
cbtf-krell                       perl-capture-tiny                      r-httpuv
cbtf-lanl                        perl-carp-clan                         r-httr
ccache                           perl-cgi                               r-hwriter
cctools                          perl-class-data-inheritable            r-hypergraph
cdbfasta                         perl-class-inspector                   r-ica
cdd                              perl-class-load                        r-igraph
cddlib                           perl-class-load-xs                     r-illuminaio
cdhit                            perl-clone                             r-impute
cdo                              perl-compress-raw-bzip2                r-influencer
ceed                             perl-compress-raw-zlib                 r-inline
cereal                           perl-config-general                    r-interactivedisplaybase
ceres-solver                     perl-contextual-return                 r-ipred
cfitsio                          perl-cpan-meta-check                   r-iranges
cgal                             perl-data-optlist                      r-irdisplay
cgm                              perl-data-stag                         r-irkernel
cgns                             perl-dbd-mysql                         r-irlba
channelflow                      perl-dbd-sqlite                        r-iso
charliecloud                     perl-dbfile                            r-iterators
charmpp                          perl-dbi                               r-janitor
chatterbug                       perl-devel-cycle                       r-jaspar2018
check                            perl-devel-globaldestruction           r-jomo
chlorop                          perl-devel-overloadinfo                r-jpeg
chombo                           perl-devel-stacktrace                  r-jsonlite
chrpath                          perl-digest-md5                        r-kegg-db
circos                           perl-dist-checkconflicts               r-kegggraph
cistem                           perl-encode-locale                     r-keggrest
citcoms                          perl-eval-closure                      r-kernlab
cityhash                         perl-exception-class                   r-kernsmooth
clamr                            perl-exporter-tiny                     r-kknn
clapack                          perl-extutils-config                   r-knitr
claw                             perl-extutils-depends                  r-ks
cleaveland4                      perl-extutils-helpers                  r-labeling
cleverleaf                       perl-extutils-installpaths             r-lambda-r
clfft                            perl-extutils-makemaker                r-laplacesdemon
clhep                            perl-extutils-pkgconfig                r-lars
clingo                           perl-file-copy-recursive               r-lattice
cloc                             perl-file-listing                      r-latticeextra
cloog                            perl-file-pushd                        r-lava
cloverleaf                       perl-file-sharedir-install             r-lazyeval
cloverleaf3d                     perl-file-slurp-tiny                   r-leaflet
clp                              perl-file-slurper                      r-leaps
clustalo                         perl-file-which                        r-learnbayes
clustalw                         perl-font-ttf                          r-lhs
cmake                            perl-gd                                r-limma
cmocka                           perl-gd-graph                          r-lme4
cmor                             perl-gd-text                           r-lmtest
cnmem                            perl-gdgraph-histogram                 r-locfit
cnpy                             perl-graph                             r-log4r
cntk                             perl-graph-readwrite                   r-lpsolve
cntk1bitsgd                      perl-html-parser                       r-lsei
codar-cheetah                    perl-html-tagset                       r-lubridate
codes                            perl-http-cookies                      r-magic
coevp                            perl-http-daemon                       r-magrittr
cohmm                            perl-http-date                         r-makecdfenv
coinhsl                          perl-http-message                      r-maldiquant
colm                             perl-http-negotiate                    r-manipulatewidget
colordiff                        perl-inline                            r-mapproj
comd                             perl-inline-c                          r-maps
commons-lang                     perl-intervaltree                      r-maptools
commons-lang3                    perl-io-compress                       r-markdown
commons-logging                  perl-io-html                           r-mass
compiz                           perl-io-sessiondata                    r-matr
compositeproto                   perl-io-socket-ssl                     r-matrix
conduit                          perl-io-string                         r-matrixmodels
constype                         perl-json                              r-matrixstats
converge                         perl-libwww-perl                       r-mclust
coreutils                        perl-list-moreutils                    r-mcmcglmm
corset                           perl-log-log4perl                      r-mco
cosmomc                          perl-lwp                               r-mda
cosp2                            perl-lwp-mediatypes                    r-memoise
cp2k                             perl-lwp-protocol-https                r-mergemaid
cppad                            perl-math-bezier                       r-methodss3
cppcheck                         perl-math-cdf                          r-mgcv
cppgsl                           perl-math-cephes                       r-mgraster
cpprestsdk                       perl-math-matrixreal                   r-mice
cppunit                          perl-math-round                        r-mime
cppzmq                           perl-math-vecstat                      r-minfi
cpu-features                     perl-module-build                      r-miniui
cpuinfo                          perl-module-build-tiny                 r-minqa
cram                             perl-module-implementation             r-misc3d
cryptopp                         perl-module-runtime                    r-mitml
cscope                           perl-module-runtime-conflicts          r-mixtools
csdp                             perl-moose                             r-mlbench
ctffind                          perl-mozilla-ca                        r-mlinterfaces
cub                              perl-mro-compat                        r-mlr
cube                             perl-namespace-clean                   r-mlrmbo
cubelib                          perl-net-http                          r-mmwrweek
cubew                            perl-net-scp-expect                    r-mnormt
cuda                             perl-net-ssleay                        r-modelmetrics
cuda-memtest                     perl-number-format                     r-modelr
cudnn                            perl-package-deprecationmanager        r-modeltools
cufflinks                        perl-package-stash                     r-mpm
cups                             perl-package-stash-xs                  r-msnbase
curl                             perl-padwalker                         r-multcomp
cvs                              perl-parallel-forkmanager              r-multicool
czmq                             perl-params-util                       r-multtest
dakota                           perl-params-validate                   r-munsell
daligner                         perl-parse-recdescent                  r-mvtnorm
damageproto                      perl-pdf-api2                          r-mzid
damaris                          perl-pegex                             r-mzr
damselfly                        perl-perl4-corelibs                    r-nanotime
darshan-runtime                  perl-perl6-slurp                       r-ncbit
darshan-util                     perl-perlio-gzip                       r-ncdf4
dash                             perl-perlio-utf8-strict                r-network
datamash                         perl-readonly                          r-networkd3
dataspaces                       perl-regexp-common                     r-nlme
davix                            perl-scalar-list-utils                 r-nloptr
dbcsr                            perl-scalar-util-numeric               r-nmf
dbus                             perl-set-intspan                       r-nnet
dcmtk                            perl-soap-lite                         r-nnls
dealii                           perl-star-fusion                       r-nor1mix
dealii-parameter-gui             perl-statistics-basic                  r-np
deconseq-standalone              perl-statistics-descriptive            r-numderiv
dejagnu                          perl-statistics-pca                    r-oligoclasses
delly2                           perl-sub-exporter                      r-oo
denovogear                       perl-sub-exporter-progressive          r-openssl
dftfe                            perl-sub-identify                      r-optparse
dia                              perl-sub-install                       r-org-hs-eg-db
dialign-tx                       perl-sub-name                          r-organismdbi
diamond                          perl-sub-uplevel                       r-packrat
diffsplice                       perl-svg                               r-pacman
diffutils                        perl-swissknife                        r-paleotree
direnv                           perl-task-weaken                       r-pamr
discovar                         perl-term-readkey                      r-pan
discovardenovo                   perl-test-cleannamespaces              r-parallelmap
dislin                           perl-test-deep                         r-paramhelpers
diy                              perl-test-differences                  r-party
dlpack                           perl-test-exception                    r-partykit
dmd                              perl-test-fatal                        r-pathview
dmlc-core                        perl-test-memory-cycle                 r-pbapply
dmtcp                            perl-test-most                         r-pbdzmq
dmxproto                         perl-test-needs                        r-pbkrtest
docbook-xml                      perl-test-requires                     r-pcamethods
docbook-xsl                      perl-test-requiresinternet             r-pcapp
dos2unix                         perl-test-warn                         r-permute
dotnet-core-sdk                  perl-test-warnings                     r-pfam-db
double-conversion                perl-text-csv                          r-phangorn
doxygen                          perl-text-diff                         r-phantompeakqualtools
dri2proto                        perl-text-format                       r-phyloseq
dri3proto                        perl-text-simpletable                  r-phytools
dsdp                             perl-text-soundex                      r-picante
dsrc                             perl-text-unidecode                    r-pkgconfig
dtcmp                            perl-time-hires                        r-pkgmaker
dyninst                          perl-time-piece                        r-plogr
ea-utils                         perl-try-tiny                          r-plot3d
easybuild                        perl-uri                               r-plotly
ebms                             perl-uri-escape                        r-plotrix
eccodes                          perl-version                           r-pls
ecflow                           perl-want                              r-plyr
eclipse-gcj-parser               perl-www-robotrules                    r-pmcmr
ecp-proxy-apps                   perl-xml-parser                        r-png
ed                               perl-xml-parser-lite                   r-powerlaw
editres                          perl-xml-simple                        r-prabclus
eigen                            perl-yaml-libyaml                      r-praise
elasticsearch                    petsc                                  r-preprocesscore
elemental                        pexsi                                  r-prettyunits
elfutils                         pfft                                   r-processx
elk                              pflotran                               r-prodlim
elpa                             pfunit                                 r-progress
elsd                             pgdspider                              r-protgenerics
elsdc                            pgi                                    r-proto
emacs                            pgmath                                 r-proxy
ember                            phantompeakqualtools                   r-pryr
emboss                           phast                                  r-ps
encodings                        phasta                                 r-psych
energyplus                       phist                                  r-ptw
environment-modules              phylip                                 r-purrr
eospac                           phyluce                                r-quadprog
er                               picard                                 r-quantmod
erne                             picsar                                 r-quantreg
es                               picsarlite                             r-quantro
esmf                             pidx                                   r-qvalue
essl                             pigz                                   r-r6
ethminer                         pilon                                  r-randomfields
etsf-io                          pindel                                 r-randomfieldsutils
everytrace                       piranha                                r-randomforest
everytrace-example               pism                                   r-ranger
evieext                          pixman                                 r-rappdirs
exabayes                         pkg-config                             r-raster
examinimd                        pkgconf                                r-rbgl
exampm                           planck-likelihood                      r-rbokeh
exasp2                           plasma                                 r-rcolorbrewer
exchanger                        platypus                               r-rcpp
exmcutils                        plink                                  r-rcpparmadillo
exodusii                         plplot                                 r-rcppblaze
exonerate                        plumed                                 r-rcppcctz
expat                            pmgr-collective                        r-rcppcnpy
expect                           pmix                                   r-rcppeigen
express                          pnfft                                  r-rcppprogress
extrae                           pngwriter                              r-rcurl
exuberant-ctags                  pnmpi                                  r-rda
eztrace                          poamsa                                 r-readr
f18                              pocl                                   r-readxl
f90cache                         polymake                               r-registry
fabtests                         poppler                                r-rematch
falcon                           poppler-data                           r-reordercluster
fast-global-file-status          porta                                  r-reportingtools
fasta                            portage                                r-repr
fastjar                          portcullis                             r-reprex
fastmath                         postgresql                             r-reshape
fastme                           ppl                                    r-reshape2
fastphase                        pplacer                                r-rex
fastq-screen                     prank                                  r-rgdal
fastqc                           precice                                r-rgenoud
fastqvalidator                   presentproto                           r-rgeos
fasttree                         preseq                                 r-rgl
fastx-toolkit                    price                                  r-rgooglemaps
fenics                           primer3                                r-rgraphviz
fermi                            prinseq-lite                           r-rhdf5
fermikit                         printproto                             r-rhtslib
fermisciencetools                prng                                   r-rinside
ferret                           probconsrna                            r-rjags
ffmpeg                           prodigal                               r-rjava
fftw                             proj                                   r-rjson
figtree                          protobuf                               r-rjsonio
fimpute                          proxymngr                              r-rlang
findutils                        pruners-ninja                          r-rmarkdown
fio                              ps-lite                                r-rminer
fish                             psi4                                   r-rmpfr
fixesproto                       pslib                                  r-rmpi
flac                             psm                                    r-rmysql
flang                            psmc                                   r-rngtools
flann                            pstreams                               r-robustbase
flash                            pugixml                                r-rocr
flatbuffers                      pumi                                   r-rodbc
flatcc                           pv                                     r-rots
flecsale                         pvm                                    r-roxygen2
flecsi                           pxz                                    r-rpart
flex                             py-3to2                                r-rpart-plot
flint                            py-4suite-xml                          r-rpostgresql
flit                             py-abipy                               r-rprojroot
fltk                             py-adios                               r-rrpp
flux-core                        py-affine                              r-rsamtools
flux-sched                       py-alabaster                           r-rsnns
fluxbox                          py-apache-libcloud                     r-rsolnp
fmt                              py-apipkg                              r-rsqlite
foam-extend                      py-appdirs                             r-rstan
folly                            py-appnope                             r-rstudioapi
font-adobe-100dpi                py-apscheduler                         r-rtracklayer
font-adobe-75dpi                 py-argcomplete                         r-rtsne
font-adobe-utopia-100dpi         py-argparse                            r-rvcheck
font-adobe-utopia-75dpi          py-ase                                 r-rvest
font-adobe-utopia-type1          py-asn1crypto                          r-rzmq
font-alias                       py-astroid                             r-s4vectors
font-arabic-misc                 py-astropy                             r-samr
font-bh-100dpi                   py-atomicwrites                        r-sandwich
font-bh-75dpi                    py-attrs                               r-scales
font-bh-lucidatypewriter-100dpi  py-autopep8                            r-scatterplot3d
font-bh-lucidatypewriter-75dpi   py-avro                                r-sdmtools
font-bh-ttf                      py-avro-json-serializer                r-segmented
font-bh-type1                    py-babel                               r-selectr
font-bitstream-100dpi            py-backcall                            r-seqinr
font-bitstream-75dpi             py-backports-abc                       r-seqlogo
font-bitstream-speedo            py-backports-functools-lru-cache       r-seurat
font-bitstream-type1             py-backports-shutil-get-terminal-size  r-sf
font-cronyx-cyrillic             py-backports-ssl-match-hostname        r-sfsmisc
font-cursor-misc                 py-basemap                             r-shape
font-daewoo-misc                 py-bcbio-gff                           r-shiny
font-dec-misc                    py-beautifulsoup4                      r-shinydashboard
font-ibm-type1                   py-binwalk                             r-shortread
font-isas-misc                   py-biom-format                         r-siggenes
font-jis-misc                    py-biopython                           r-simpleaffy
font-micro-misc                  py-bitarray                            r-sm
font-misc-cyrillic               py-bitstring                           r-smoof
font-misc-ethiopic               py-bleach                              r-sn
font-misc-meltho                 py-blessings                           r-snow
font-misc-misc                   py-bokeh                               r-snowfall
font-mutt-misc                   py-boltons                             r-snprelate
font-schumacher-misc             py-bottleneck                          r-som
font-screen-cyrillic             py-breakseq2                           r-somaticsignatures
font-sony-misc                   py-brian                               r-sourcetools
font-sun-misc                    py-brian2                              r-sp
font-util                        py-bsddb3                              r-sparsem
font-winitzki-cyrillic           py-bx-python                           r-spdep
font-xfree86-type1               py-cartopy                             r-speedglm
fontcacheproto                   py-cclib                               r-spem
fontconfig                       py-cdat-lite                           r-splancs
fontsproto                       py-cdo                                 r-splitstackshape
fonttosfnt                       py-certifi                             r-sqldf
fp16                             py-cffi                                r-squash
fpc                              py-chardet                             r-sseq
fr-hit                           py-checkm-genome                       r-stanheaders
freebayes                        py-cheetah                             r-statmod
freeglut                         py-click                               r-statnet-common
freetype                         py-click-plugins                       r-stringi
freexl                           py-cligj                               r-stringr
fseq                             py-cloudpickle                         r-strucchange
fsl                              py-cogent                              r-subplex
fslsfonts                        py-colorama                            r-summarizedexperiment
fstobdf                          py-colormath                           r-survey
fstrack                          py-configparser                        r-survival
ftgl                             py-counter                             r-sva
funhpc                           py-coverage                            r-tarifx
fyba                             py-cpuinfo                             r-tclust
gapbs                            py-crispresso                          r-tensora
gapcloser                        py-cryptography                        r-testit
gapfiller                        py-csvkit                              r-testthat
gasnet                           py-current                             r-tfbstools
gatk                             py-cutadapt                            r-tfmpvalue
gaussian                         py-cvxopt                              r-th-data
gawk                             py-cycler                              r-threejs
gblocks                          py-cython                              r-tibble
gcc                              py-dask                                r-tidycensus
gccmakedep                       py-dateutil                            r-tidyr
gccxml                           py-dbf                                 r-tidyselect
gconf                            py-decorator                           r-tidyverse
gcta                             py-deeptools                           r-tiff
gdal                             py-dendropy                            r-tigris
gdb                              py-descartes                           r-timedate
gdbm                             py-dill                                r-tmixclust
gdk-pixbuf                       py-discover                            r-topgo
gdl                              py-dlcpar                              r-trimcluster
geant4                           py-docopt                              r-truncnorm
gearshifft                       py-docutils                            r-trust
gemmlowp                         py-doxypy                              r-tseries
genemark-et                      py-doxypypy                            r-tsne
genomefinisher                   py-dryscrape                           r-ttr
genometools                      py-dxchange                            r-udunits2
geopm                            py-dxfile                              r-units
geos                             py-easybuild-easyblocks                r-utils
gettext                          py-easybuild-easyconfigs               r-uuid
gflags                           py-easybuild-framework                 r-variantannotation
ghost                            py-edffile                             r-varselrf
ghostscript                      py-editdistance                        r-vcd
ghostscript-fonts                py-elasticsearch                       r-vegan
giflib                           py-elephant                            r-vgam
git                              py-emcee                               r-vipor
git-imerge                       py-entrypoints                         r-viridis
git-lfs                          py-enum34                              r-viridislite
gl2ps                            py-epydoc                              r-visnetwork
glew                             py-espresso                            r-vsn
glfmultiples                     py-espressopp                          r-webshot
glib                             py-et-xmlfile                          r-whisker
glibmm                           py-eventlet                            r-withr
glimmer                          py-execnet                             r-xde
glm                              py-fastaindex                          r-xgboost
global                           py-fasteners                           r-xlconnect
globalarrays                     py-faststructure                       r-xlconnectjars
globus-toolkit                   py-filelock                            r-xlsx
glog                             py-fiona                               r-xlsxjars
gloo                             py-fiscalyear                          r-xmapbridge
glpk                             py-flake8                              r-xml
glproto                          py-flake8-polyfill                     r-xml2
glvis                            py-flask                               r-xtable
gmake                            py-flask-compress                      r-xts
gmap-gsnap                       py-flask-socketio                      r-xvector
gmime                            py-flexx                               r-yaml
gmodel                           py-fn                                  r-yapsa
gmp                              py-fparser                             r-yaqcaffy
gmsh                             py-funcsigs                            r-yarn
gmt                              py-functools32                         r-zlibbioc
gnat                             py-future                              r-zoo
gnu-prolog                       py-futures                             racon
gnupg                            py-fypp                                raft
gnuplot                          py-gdbgui                              ragel
gnutls                           py-genders                             raja
go                               py-genshi                              randfold
go-bootstrap                     py-geopandas                           random123
gobject-introspection            py-gevent                              randrproto
googletest                       py-git-review                          range-v3
gotcha                           py-git2                                rankstr
gource                           py-gnuplot                             rapidjson
gperf                            py-goatools                            ravel
gperftools                       py-gpaw                                raxml
gplates                          py-greenlet                            ray
grackle                          py-griddataformats                     rclone
gradle                           py-guidata                             rdma-core
grandr                           py-guiqwt                              rdp-classifier
graph500                         py-h5glance                            re2c
graphicsmagick                   py-h5py                                readfq
graphlib                         py-hdfs                                readline
graphmap                         py-hepdata-validator                   recordproto
graphviz                         py-html2text                           redset
grass                            py-html5lib                            redundans
grib-api                         py-htseq                               regcm
grnboost                         py-httpbin                             relion
groff                            py-hypothesis                          rempi
gromacs                          py-idna                                rename
gsl                              py-igraph                              rendercheck
gslib                            py-illumina-utils                      renderproto
gtkmm                            py-imageio                             repeatmasker
gtkorvo-atl                      py-imagesize                           resourceproto
gtkorvo-cercs-env                py-iminuit                             revbayes
gtkorvo-dill                     py-importlib                           rgb
gtkorvo-enet                     py-ipaddress                           rhash
gtkplus                          py-ipdb                                rlwrap
gts                              py-ipykernel                           rmats
guidance                         py-ipython                             rmlab
guile                            py-ipython-genutils                    rna-seqc
gurobi                           py-ipywidgets                          rngstreams
h5hut                            py-isort                               rockstar
h5part                           py-itsdangerous                        root
h5utils                          py-jdcal                               rose
h5z-zfp                          py-jedi                                ross
hacckernels                      py-jinja2                              rr
hadoop                           py-joblib                              rsbench
halc                             py-jprops                              rsem
hapcut2                          py-jpype                               rstart
hapdip                           py-jsonschema                          rsync
haploview                        py-junit-xml                           rtags
harfbuzz                         py-jupyter-client                      rtax
harminv                          py-jupyter-console                     ruby
hc                               py-jupyter-core                        ruby-gnuplot
hdf                              py-jupyter-notebook                    ruby-narray
hdf5                             py-keras                               ruby-ronn
hdf5-blosc                       py-kiwisolver                          ruby-rubyinline
help2man                         py-lark-parser                         ruby-svn2git
henson                           py-latexcodec                          ruby-terminal-table
hepmc                            py-lazy                                rust
heppdt                           py-lazy-object-proxy                   rust-bindgen
hic-pro                          py-lazy-property                       sabre
highfive                         py-lazyarray                           sailfish
highwayhash                      py-libconf                             salmon
hiop                             py-libensemble                         sambamba
hisat2                           py-line-profiler                       samblaster
hisea                            py-linecache2                          samrai
hmmer                            py-lit                                 samtools
homer                            py-llvmlite                            sandbox
hoomd-blue                       py-lmfit                               sas
hpccg                            py-localcider                          satsuma2
hpctoolkit                       py-locket                              savanna
hpgmg                            py-lockfile                            saws
hpl                              py-logilab-common                      sbt
hpx                              py-lrudict                             scala
hpx5                             py-lxml                                scalasca
hsakmt                           py-lzstring                            scallop
hstr                             py-macholib                            scalpel
htop                             py-machotools                          scan-for-matches
htslib                           py-macs2                               scons
httpie                           py-maestrowf                           scorec-core
hub                              py-mako                                scorep
hunspell                         py-mappy                               scotch
hwloc                            py-markdown                            scr
hybpiper                         py-markupsafe                          screen
hydra                            py-matplotlib                          scripts
hydrogen                         py-mccabe                              scrnsaverproto
hypre                            py-mdanalysis                          sctk
i3                               py-meep                                sdl2
ibmisc                           py-memory-profiler                     sdl2-image
iceauth                          py-merlin                              sdsl-lite
icedtea                          py-methylcode                          sed
icet                             py-mg-rast-tools                       sentieon-genomics
ico                              py-misopy                              seqan
icu4c                            py-mistune                             seqprep
id3lib                           py-mock                                seqtk
idba                             py-moltemplate                         serf
igraph                           py-mongo                               sessreg
igvtools                         py-monotonic                           setxkbmap
ilmbase                          py-monty                               sga
image-magick                     py-more-itertools                      shapeit
imake                            py-mpi4py                              shared-mime-info
imp                              py-mpmath                              shiny-server
impute2                          py-multiprocess                        shocklibs
infernal                         py-multiqc                             shoremap
inputproto                       py-munch                               shortbred
intel                            py-mx                                  shortstack
intel-daal                       py-mxnet                               showfont
intel-gpu-tools                  py-myhdl                               shuffile
intel-ipp                        py-mysqldb1                            sickle
intel-mkl                        py-natsort                             siesta
intel-mkl-dnn                    py-nbconvert                           signalp
intel-mpi                        py-nbformat                            signify
intel-parallel-studio            py-neo                                 silo
intel-tbb                        py-nestle                              simplemoc
intel-xed                        py-netcdf4                             simul
intltool                         py-netifaces                           simulationio
ior                              py-networkx                            singularity
iozone                           py-nose                                skilion-onedrive
iperf2                           py-nosexcover                          sleef
iperf3                           py-numba                               slepc
ipopt                            py-numexpr                             slurm
isaac                            py-numexpr3                            smalt
isaac-server                     py-numpy                               smproxy
isl                              py-numpydoc                            snakemake
itstool                          py-olefile                             snap
itsx                             py-ont-fast5-api                       snap-berkeley
jackcess                         py-openpmd-validator                   snap-korf
jags                             py-openpyxl                            snappy
jansson                          py-openslide-python                    snbone
jasper                           py-opentuner                           sniffles
jbigkit                          py-ordereddict                         snpeff
jchronoss                        py-oset                                snphylo
jdk                              py-owslib                              snptest
jellyfish                        py-packaging                           soap2
jemalloc                         py-palettable                          soapdenovo-trans
jmol                             py-pandas                              soapdenovo2
jq                               py-paramiko                            soapindel
json-c                           py-partd                               soapsnp
json-cwx                         py-pathlib2                            sofa-c
json-glib                        py-pathos                              somatic-sniper
jsoncpp                          py-pathspec                            sortmerna
judy                             py-patsy                               sosflow
julia                            py-pbr                                 sowing
k8                               py-pep8-naming                         sox
kahip                            py-perf                                spades
kaiju                            py-performance                         span-lite
kaks-calculator                  py-periodictable                       spark
kaldi                            py-petsc4py                            sparsehash
kallisto                         py-pexpect                             sparta
karma                            py-phonopy                             spdlog
kbproto                          py-pickleshare                         spectrum-mpi
kdiff3                           py-picrust                             speex
kealib                           py-pil                                 spglib
kentutils                        py-pillow                              sph2pipe
kibana                           py-pint                                spherepack
kim-api                          py-pip                                 spindle
kmergenie                        py-pipits                              spm
kokkos                           py-pkgconfig                           spot
kraken                           py-plotly                              sqlite
krb5                             py-pluggy                              sqlitebrowser
krims                            py-ply                                 squid
kripke                           py-pmw                                 sra-toolkit
kvasir-mpl                       py-poster                              ssht
kvtree                           py-pox                                 sspace-longread
laghos                           py-ppft                                sspace-standard
lammps                           py-prettytable                         sst-core
last                             py-progress                            sst-dumpi
lastz                            py-projectq                            sst-macro
latte                            py-prompt-toolkit                      stacks
launchmon                        py-protobuf                            staden-io-lib
lazyten                          py-psutil                              star
lbann                            py-psyclone                            star-ccm-plus
lbxproxy                         py-psycopg2                            startup-notification
lbzip2                           py-ptyprocess                          stat
lcals                            py-pudb                                stc
lcms                             py-py                                  steps
ldc                              py-py2bit                              stow
ldc-bootstrap                    py-py2cairo                            strace
legion                           py-py2neo                              stream
lemon                            py-py4j                                strelka
leveldb                          py-pyani                               stress
lftp                             py-pyarrow                             string-view-lite
libaec                           py-pyasn1                              stringtie
libaio                           py-pybigwig                            structure
libapplewm                       py-pybind11                            strumpack
libarchive                       py-pybtex                              sublime-text
libassuan                        py-pybtex-docutils                     subread
libatomic-ops                    py-pycairo                             subversion
libbeagle                        py-pychecker                           suite-sparse
libbeato                         py-pycodestyle                         sumaclust
libbsd                           py-pycparser                           sundials
libbson                          py-pycrypto                            superlu
libcanberra                      py-pycurl                              superlu-dist
libcap                           py-pydatalog                           superlu-mt
libceed                          py-pydispatcher                        supernova
libcerf                          py-pydot                               sw4lite
libcheck                         py-pyelftools                          swap-assembler
libcint                          py-pyepsg                              swarm
libcircle                        py-pyfasta                             swfft
libconfig                        py-pyfftw                              swiftsim
libcroco                         py-pyflakes                            swig
libctl                           py-pygdbmi                             symengine
libdivsufsort                    py-pygments                            sympol
libdmx                           py-pygobject                           sz
libdrm                           py-pygpu                               tabix
libdwarf                         py-pygresql                            talass
libedit                          py-pygtk                               talloc
libelf                           py-pylint                              tantan
libemos                          py-pymatgen                            tar
libepoxy                         py-pyminifier                          targetp
libev                            py-pymol                               task
libevent                         py-pympler                             taskd
libevpath                        py-pymysql                             tasmanian
libfabric                        py-pynn                                tassel
libffi                           py-pypar                               tau
libffs                           py-pyparsing                           tcl
libfontenc                       py-pypeflow                            tcl-itcl
libfs                            py-pyprof2html                         tcl-tcllib
libgcrypt                        py-pyproj                              tcl-tclxml
libgd                            py-pyqi                                tclap
libgeotiff                       py-pyqt                                tcoffee
libgit2                          py-pyrad                               tcptrace
libgpg-error                     py-pysam                               tcsh
libgpuarray                      py-pyscaf                              tealeaf
libgridxc                        py-pyserial                            templight
libgtextutils                    py-pyshp                               templight-tools
libharu                          py-pyside                              tetgen
libhio                           py-pysocks                             tethex
libiberty                        py-pyspark                             texinfo
libice                           py-pysqlite                            texlive
libiconv                         py-pytables                            tfel
libint                           py-pytest                              the-platinum-searcher
libjpeg                          py-pytest-cov                          the-silver-searcher
libjpeg-turbo                    py-pytest-flake8                       thornado-mini
libksba                          py-pytest-httpbin                      thrift
liblbxutil                       py-pytest-mock                         thrust
liblockfile                      py-pytest-runner                       tig
libmatheval                      py-pytest-xdist                        time
libmaxminddb                     py-pythia                              tinyxml
libmesh                          py-python-daemon                       tinyxml2
libmng                           py-python-engineio                     tioga
libmongoc                        py-python-gitlab                       tk
libmonitor                       py-python-htmlgen                      tldd
libnbc                           py-python-levenshtein                  tmalign
libnl                            py-python-socketio                     tmhmm
libnova                          py-pythonqwt                           tmux
libogg                           py-pytorch                             tmuxinator
liboldx                          py-pytz                                tophat
libpcap                          py-pyutilib                            tppred
libpciaccess                     py-pywavelets                          tracer
libpfm4                          py-pyyaml                              transabyss
libpipeline                      py-qtawesome                           transdecoder
libpng                           py-qtconsole                           transposome
libpsl                           py-qtpy                                transset
libpthread-stubs                 py-quantities                          trapproto
libquo                           py-quast                               tree
librom                           py-radical-utils                       treesub
libsharp                         py-ranger                              trf
libshm                           py-rasterio                            triangle
libsigcpp                        py-readme-renderer                     trilinos
libsigsegv                       py-regex                               trimal
libsm                            py-reportlab                           trimgalore
libsodium                        py-requests                            trimmomatic
libspatialindex                  py-requests-toolbelt                   trinity
libspatialite                    py-restview                            trinotate
libsplash                        py-rope                                trnascan-se
libssh                           py-rpy2                                turbine
libssh2                          py-rsa                                 turbomole
libsvm                           py-rseqc                               tut
libszip                          py-rtree                               twm
libtermkey                       py-saga-python                         tycho2
libtiff                          py-scandir                             typhon
libtool                          py-scientificpython                    typhonio
libunistring                     py-scikit-image                        uberftp
libunwind                        py-scikit-learn                        ucx
libuuid                          py-scipy                               udunits2
libuv                            py-seaborn                             ufo-core
libvorbis                        py-setuptools                          ufo-filters
libvterm                         py-setuptools-git                      umpire
libwebsockets                    py-setuptools-scm                      unblur
libwindowswm                     py-sfepy                               uncrustify
libx11                           py-sh                                  unibilium
libxau                           py-shapely                             unifycr
libxaw                           py-shiboken                            unison
libxaw3d                         py-simplegeneric                       units
libxc                            py-simplejson                          unixodbc
libxcb                           py-singledispatch                      unuran
libxcomposite                    py-sip                                 unzip
libxcursor                       py-six                                 usearch
libxdamage                       py-slepc4py                            util-linux
libxdmcp                         py-slurm-pipeline                      util-macros
libxevie                         py-sncosmo                             uuid
libxext                          py-snowballstemmer                     valgrind
libxfixes                        py-snuggs                              vampirtrace
libxfont                         py-spectra                             vardictjava
libxfont2                        py-spefile                             varscan
libxfontcache                    py-spglib                              vc
libxft                           py-sphinx                              vcftools
libxi                            py-sphinx-bootstrap-theme              vcsh
libxinerama                      py-sphinx-rtd-theme                    vdt
libxkbcommon                     py-sphinxcontrib-bibtex                vecgeom
libxkbfile                       py-sphinxcontrib-programoutput         veclibfort
libxkbui                         py-sphinxcontrib-websupport            vegas2
libxml2                          py-spyder                              veloc
libxmu                           py-spykeutils                          velvet
libxp                            py-sqlalchemy                          verilator
libxpm                           py-statsmodels                         verrou
libxpresent                      py-stevedore                           videoproto
libxprintapputil                 py-storm                               viennarna
libxprintutil                    py-subprocess32                        viewres
libxrandr                        py-symengine                           vim
libxrender                       py-symfit                              virtualgl
libxres                          py-sympy                               visit
libxscrnsaver                    py-tabulate                            vizglow
libxshmfence                     py-tappy                               vmatch
libxslt                          py-terminado                           voropp
libxsmm                          py-testinfra                           votca-csg
libxstream                       py-tetoolkit                           votca-ctp
libxt                            py-theano                              votca-tools
libxtrap                         py-tifffile                            votca-xtp
libxtst                          py-toml                                vpfft
libxv                            py-tomopy                              vpic
libxvmc                          py-toolz                               vsearch
libxxf86dga                      py-tornado                             vt
libxxf86misc                     py-tqdm                                vtk
libxxf86vm                       py-traceback2                          vtkh
libyogrt                         py-traitlets                           vtkm
libzip                           py-tuiview                             wannier90
lighttpd                         py-twisted                             warpx
likwid                           py-typing                              wcslib
linkphase3                       py-tzlocal                             wget
linux-headers                    py-udunits                             wgsim
listres                          py-umi-tools                           windowswmproto
llvm                             py-unittest2                           wireshark
llvm-openmp-ompt                 py-unittest2py3k                       workrave
lmdb                             py-urllib3                             wt
lmod                             py-urwid                               wx
lndir                            py-vcversioner                         wxpropgrid
log4cplus                        py-virtualenv                          x11perf
log4cxx                          py-virtualenv-clone                    xapian-core
loki                             py-virtualenvwrapper                   xauth
lordec                           py-vsc-base                            xbacklight
lrslib                           py-vsc-install                         xbiff
lrzip                            py-wcsaxes                             xbitmaps
lsof                             py-wcwidth                             xbraid
ltrace                           py-webkit-server                       xcalc
lua                              py-weblogo                             xcb-demo
lua-bitlib                       py-werkzeug                            xcb-proto
lua-jit                          py-wheel                               xcb-util
lua-lpeg                         py-widgetsnbextension                  xcb-util-cursor
lua-luafilesystem                py-wrapt                               xcb-util-errors
lua-luaposix                     py-xarray                              xcb-util-image
lua-mpack                        py-xattr                               xcb-util-keysyms
luit                             py-xdot                                xcb-util-renderutil
lulesh                           py-xlrd                                xcb-util-wm
lumpy-sv                         py-xlsxwriter                          xcb-util-xrm
lwgrp                            py-xmlrunner                           xclip
lwm2                             py-xopen                               xclipboard
lz4                              py-xpyb                                xclock
lzma                             py-xvfbwrapper                         xcmiscproto
lzo                              py-yamlreader                          xcmsdb
m4                               py-yapf                                xcompmgr
macsio                           py-yt                                  xconsole
mad-numdiff                      py-ytopt                               xcursor-themes
mafft                            py-zmq                                 xcursorgen
magics                           py-zope-event                          xdbedizzy
magma                            py-zope-interface                      xditview
makedepend                       pythia6                                xdm
mallocmc                         python                                 xdpyinfo
man-db                           qbank                                  xdriinfo
manta                            qbox                                   xedit
maq                              qca                                    xerces-c
mariadb                          qhull                                  xeus
masa                             qjson                                  xev
masurca                          qmcpack                                xextproto
matio                            qmd-progress                           xeyes
matlab                           qorts                                  xf86bigfontproto
maven                            qrupdate                               xf86dga
maverick                         qt                                     xf86dgaproto
mawk                             qt-creator                             xf86driproto
mbedtls                          qtgraph                                xf86miscproto
mc                               qthreads                               xf86rushproto
mcl                              quantum-espresso                       xf86vidmodeproto
mdtest                           quinoa                                 xfd
med                              qwt                                    xfindproxy
meep                             r                                      xfontsel
mefit                            r-a4                                   xfs
megahit                          r-a4base                               xfsinfo
memaxes                          r-a4classif                            xfwp
meme                             r-a4core                               xgamma
memkind                          r-a4preproc                            xgc
meraculous                       r-a4reporting                          xhmm
mercurial                        r-abadata                              xhost
mercury                          r-abaenrichment                        xineramaproto
mesa                             r-abind                                xinit
mesa-glu                         r-absseq                               xinput
meshkit                          r-acde                                 xios
meson                            r-acepack                              xkbcomp
mesquite                         r-acgh                                 xkbdata
metabat                          r-acme                                 xkbevd
metaphysicl                      r-ada                                  xkbprint
metis                            r-adabag                               xkbutils
mfem                             r-ade4                                 xkeyboard-config
microbiomeutil                   r-adegenet                             xkill
migrate                          r-adsplit                              xload
minced                           r-aer                                  xlogo
mindthegap                       r-affxparser                           xlsatoms
miniaero                         r-affy                                 xlsclients
miniamr                          r-affycomp                             xlsfonts
miniasm                          r-affycompatible                       xmag
miniconda2                       r-affycontam                           xman
miniconda3                       r-affycoretools                        xmessage
minife                           r-affydata                             xmh
minighost                        r-affyexpress                          xmlf90
minigmg                          r-affyilm                              xmlto
minimap2                         r-affyio                               xmodmap
minimd                           r-affypdnn                             xmore
miniqmc                          r-affyplm                              xorg-cf-files
minisign                         r-affyqcreport                         xorg-docs
minismac2d                       r-affyrnadegradation                   xorg-gtest
minitri                          r-agdex                                xorg-server
minivite                         r-agilp                                xorg-sgml-doctools
minixyce                         r-agimicrorna                          xphelloworld
minuit                           r-aims                                 xplor-nih
mira                             r-aldex2                               xplsprinters
mirdeep2                         r-allelicimbalance                     xpr
mitofates                        r-alpine                               xprehashprinterlist
mitos                            r-als                                  xprop
mixcr                            r-alsace                               xproto
mkfontdir                        r-altcdfenvs                           xproxymanagementprotocol
mkfontscale                      r-amap                                 xqilla
mlhka                            r-ampliqueso                           xrandr
moab                             r-analysispageserver                   xrdb
modern-wheel                     r-anaquin                              xrefresh
mofem-cephas                     r-aneufinder                           xrootd
mofem-fracture-module            r-aneufinderdata                       xrx
mofem-minimal-surface-equation   r-animation                            xsbench
mofem-users-modules              r-annaffy                              xscope
molcas                           r-annotate                             xsd
mongo-cxx-driver                 r-annotationdbi                        xsdk
mono                             r-annotationfilter                     xsdktrilinos
mosh                             r-annotationforge                      xset
mothur                           r-annotationhub                        xsetmode
motif                            r-ape                                  xsetpointer
motioncor2                       r-argparse                             xsetroot
mount-point-attributes           r-assertthat                           xsimd
mozjs                            r-backports                            xsm
mpark-variant                    r-bamsignals                           xstdcmap
mpc                              r-base64                               xtensor
mpe2                             r-base64enc                            xtensor-python
mpest                            r-bayesm                               xterm
mpfr                             r-bbmisc                               xtl
mpibash                          r-beanplot                             xtrans
mpiblast                         r-bh                                   xtrap
mpich                            r-biasedurn                            xts
mpifileutils                     r-bindr                                xvidtune
mpilander                        r-bindrcpp                             xvinfo
mpileaks                         r-biobase                              xwd
mpip                             r-biocgenerics                         xwininfo
mpir                             r-biocinstaller                        xwud
mpix-launch-swift                r-biocparallel                         xxhash
mrbayes                          r-biocstyle                            xz
mrnet                            r-biom-utils                           yajl
mrtrix3                          r-biomart                              yambo
mscgen                           r-biomformat                           yaml-cpp
msgpack-c                        r-biostrings                           yasm
mshadow                          r-biovizbase                           yorick
msmc                             r-bit                                  z3
multitail                        r-bit64                                zeromq
multitime                        r-bitops                               zfp
multiverso                       r-blob                                 zip
mummer                           r-blockmodeling                        zlib
mumps                            r-bookdown                             zoltan
munge                            r-boot                                 zsh
muparser                         r-brew                                 zstd

The packages are listed by name in alphabetical order. A pattern to match with no wildcards, * or ?, will be treated as though it started and ended with *, so util is equivalent to *util*. All patterns will be treated as case-insensitive. You can also add the -d to search the description of the package in addition to the name. Some examples:

All packages whose names contain “sql”:

$ spack list sql
perl-dbd-mysql   postgresql   py-pygresql  py-pysqlite    r-rmysql       r-rsqlite  sqlite
perl-dbd-sqlite  py-mysqldb1  py-pymysql   py-sqlalchemy  r-rpostgresql  r-sqldf    sqlitebrowser

All packages whose names or descriptions contain documentation:

$ spack list --search-description documentation
compositeproto     libxfixes     py-docutils                  r-ggplot2   r-stanheaders
damageproto        libxpresent   py-epydoc                    r-quadprog  sowing
double-conversion  man-db        py-markdown                  r-rcpp      texinfo
doxygen            perl-dbfile   py-sphinx                    r-rinside   xorg-docs
gflags             py-alabaster  py-sphinxcontrib-websupport  r-roxygen2  xorg-sgml-doctools

spack info

To get more information on a particular package from spack list, use spack info. Just supply the name of a package:

$ spack info mpich
AutotoolsPackage:   mpich

Description:
    MPICH is a high performance and widely portable implementation of the
    Message Passing Interface (MPI) standard.

Homepage: http://www.mpich.org

Tags: 
    None

Preferred version:  
    3.3        http://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz

Safe versions:  
    develop    [git] https://github.com/pmodels/mpich.git
    3.3        http://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz
    3.2.1      http://www.mpich.org/static/downloads/3.2.1/mpich-3.2.1.tar.gz
    3.2        http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
    3.1.4      http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz
    3.1.3      http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3.tar.gz
    3.1.2      http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2.tar.gz
    3.1.1      http://www.mpich.org/static/downloads/3.1.1/mpich-3.1.1.tar.gz
    3.1        http://www.mpich.org/static/downloads/3.1/mpich-3.1.tar.gz
    3.0.4      http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz

Variants:
    Name [Default]    Allowed values        Description


    device [ch3]      ch3, ch4              Abstract Device Interface
                                            (ADI) implementation. The ch4
                                            device is currently in
                                            experimental state
    hydra [on]        True, False           Build the hydra process
                                            manager
    netmod [tcp]      tcp, mxm, ofi, ucx    Network module. Only single
                                            netmod builds are supported.
                                            For ch3 device configurations,
                                            this presumes the ch3:nemesis
                                            communication channel.
                                            ch3:sock is not supported by
                                            this spack package at this
                                            time.
    pmi [on]          True, False           Build with PMI support
    romio [on]        True, False           Enable ROMIO MPI I/O
                                            implementation
    verbs [off]       True, False           Build support for OpenFabrics
                                            verbs.

Installation Phases:
    autoreconf    configure    build    install

Build Dependencies:
    findutils  libfabric

Link Dependencies:
    libfabric

Run Dependencies:
    None

Virtual Packages: 
    mpich@3: provides mpi@:3.0
    mpich@1: provides mpi@:1.3
    mpich provides mpi

Most of the information is self-explanatory. The safe versions are versions that Spack knows the checksum for, and it will use the checksum to verify that these versions download without errors or viruses.

Dependencies and virtual dependencies are described in more detail later.

spack versions

To see more available versions of a package, run spack versions. For example:

$ spack versions libelf
==> Safe versions (already checksummed):
  0.8.13  0.8.12
==> Remote versions (not yet checksummed):
  0.8.11  0.8.10  0.8.9  0.8.8  0.8.7  0.8.6  0.8.5  0.8.4  0.8.3  0.8.2  0.8.0  0.7.0  0.6.4  0.5.2

There are two sections in the output. Safe versions are versions for which Spack has a checksum on file. It can verify that these versions are downloaded correctly.

In many cases, Spack can also show you what versions are available out on the web—these are remote versions. Spack gets this information by scraping it directly from package web pages. Depending on the package and how its releases are organized, Spack may or may not be able to find remote versions.

Installing and uninstalling

spack install

spack install will install any package shown by spack list. For example, To install the latest version of the mpileaks package, you might type this:

$ spack install mpileaks

If mpileaks depends on other packages, Spack will install the dependencies first. It then fetches the mpileaks tarball, expands it, verifies that it was downloaded without errors, builds it, and installs it in its own directory under $SPACK_ROOT/opt. You’ll see a number of messages from spack, a lot of build output, and a message that the packages is installed:

$ spack install mpileaks
==> Installing mpileaks
==> mpich is already installed in ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpich@3.0.4.
==> callpath is already installed in ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318.
==> adept-utils is already installed in ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8da.
==> Trying to fetch from https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
######################################################################## 100.0%
==> Staging archive: ~/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23/mpileaks-1.0.tar.gz
==> Created stage in ~/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7 arch=linux-debian7-x86_64-59f6ad23.
==> No patches needed for mpileaks.
==> Building mpileaks.

... build output ...

==> Successfully installed mpileaks.
  Fetch: 2.16s.  Build: 9.82s.  Total: 11.98s.
[+] ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/mpileaks@1.0-59f6ad23

The last line, with the [+], indicates where the package is installed.

Building a specific version

Spack can also build specific versions of a package. To do this, just add @ after the package name, followed by a version:

$ spack install mpich@3.0.4

Any number of versions of the same package can be installed at once without interfering with each other. This is good for multi-user sites, as installing a version that one user needs will not disrupt existing installations for other users.

In addition to different versions, Spack can customize the compiler, compile-time options (variants), compiler flags, and platform (for cross compiles) of an installation. Spack is unique in that it can also configure the dependencies a package is built with. For example, two configurations of the same version of a package, one built with boost 1.39.0, and the other version built with version 1.43.0, can coexist.

This can all be done on the command line using the spec syntax. Spack calls the descriptor used to refer to a particular package configuration a spec. In the commands above, mpileaks and mpileaks@3.0.4 are both valid specs. We’ll talk more about how you can use them to customize an installation in Specs & dependencies.

spack uninstall

To uninstall a package, type spack uninstall <package>. This will ask the user for confirmation before completely removing the directory in which the package was installed.

$ spack uninstall mpich

If there are still installed packages that depend on the package to be uninstalled, spack will refuse to uninstall it.

To uninstall a package and every package that depends on it, you may give the --dependents option.

$ spack uninstall --dependents mpich

will display a list of all the packages that depend on mpich and, upon confirmation, will uninstall them in the right order.

A command like

$ spack uninstall mpich

may be ambiguous if multiple mpich configurations are installed. For example, if both mpich@3.0.2 and mpich@3.1 are installed, mpich could refer to either one. Because it cannot determine which one to uninstall, Spack will ask you either to provide a version number to remove the ambiguity or use the --all option to uninstall all of the matching packages.

You may force uninstall a package with the --force option

$ spack uninstall --force mpich

but you risk breaking other installed packages. In general, it is safer to remove dependent packages before removing their dependencies or use the --dependents option.

Non-Downloadable Tarballs

The tarballs for some packages cannot be automatically downloaded by Spack. This could be for a number of reasons:

  1. The author requires users to manually accept a license agreement before downloading (jdk and galahad).
  2. The software is proprietary and cannot be downloaded on the open Internet.

To install these packages, one must create a mirror and manually add the tarballs in question to it (see Mirrors):

  1. Create a directory for the mirror. You can create this directory anywhere you like, it does not have to be inside ~/.spack:

    $ mkdir ~/.spack/manual_mirror
    
  2. Register the mirror with Spack by creating ~/.spack/mirrors.yaml:

    mirrors:
      manual: file://~/.spack/manual_mirror
    
  3. Put your tarballs in it. Tarballs should be named <package>/<package>-<version>.tar.gz. For example:

    $ ls -l manual_mirror/galahad
    
    -rw-------. 1 me me 11657206 Jun 21 19:25 galahad-2.60003.tar.gz
    
  4. Install as usual:

    $ spack install galahad
    

Seeing installed packages

We know that spack list shows you the names of available packages, but how do you figure out which are already installed?

spack find

spack find shows the specs of installed packages. A spec is like a name, but it has a version, compiler, architecture, and build options associated with it. In spack, you can have many installations of the same package with different specs.

Running spack find with no arguments lists installed packages:

$ spack find
==> 74 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
ImageMagick@6.8.9-10  libdwarf@20130729  py-dateutil@2.4.0
adept-utils@1.0       libdwarf@20130729  py-ipython@2.3.1
atk@2.14.0            libelf@0.8.12      py-matplotlib@1.4.2
boost@1.55.0          libelf@0.8.13      py-nose@1.3.4
bzip2@1.0.6           libffi@3.1         py-numpy@1.9.1
cairo@1.14.0          libmng@2.0.2       py-pygments@2.0.1
callpath@1.0.2        libpng@1.6.16      py-pyparsing@2.0.3
cmake@3.0.2           libtiff@4.0.3      py-pyside@1.2.2
dbus@1.8.6            libtool@2.4.2      py-pytz@2014.10
dbus@1.9.0            libxcb@1.11        py-setuptools@11.3.1
dyninst@8.1.2         libxml2@2.9.2      py-six@1.9.0
fontconfig@2.11.1     libxml2@2.9.2      python@2.7.8
freetype@2.5.3        llvm@3.0           qhull@1.0
gdk-pixbuf@2.31.2     memaxes@0.5        qt@4.8.6
glib@2.42.1           mesa@8.0.5         qt@5.4.0
graphlib@2.0.0        mpich@3.0.4        readline@6.3
gtkplus@2.24.25       mpileaks@1.0       sqlite@3.8.5
harfbuzz@0.9.37       mrnet@4.1.0        stat@2.1.0
hdf5@1.8.13           ncurses@5.9        tcl@8.6.3
icu@54.1              netcdf@4.3.3       tk@src
jpeg@9a               openssl@1.0.1h     vtk@6.1.0
launchmon@1.0.1       pango@1.36.8       xcb-proto@1.11
lcms@2.6              pixman@0.32.6      xz@5.2.0
libdrm@2.4.33         py-dateutil@2.4.0  zlib@1.2.8

-- linux-debian7-x86_64 / gcc@4.9.2 --------------------------------
libelf@0.8.10  mpich@3.0.4

Packages are divided into groups according to their architecture and compiler. Within each group, Spack tries to keep the view simple, and only shows the version of installed packages.

spack find can filter the package list based on the package name, spec, or a number of properties of their installation status. For example, missing dependencies of a spec can be shown with --missing, packages which were explicitly installed with spack install <package> can be singled out with --explicit and those which have been pulled in only as dependencies with --implicit.

In some cases, there may be different configurations of the same version of a package installed. For example, there are two installations of libdwarf@20130729 above. We can look at them in more detail using spack find --deps, and by asking only to show libdwarf packages:

$ spack find --deps libdwarf
==> 2 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
    libdwarf@20130729-d9b90962
        ^libelf@0.8.12
    libdwarf@20130729-b52fac98
        ^libelf@0.8.13

Now we see that the two instances of libdwarf depend on different versions of libelf: 0.8.12 and 0.8.13. This view can become complicated for packages with many dependencies. If you just want to know whether two packages’ dependencies differ, you can use spack find --long:

$ spack find --long libdwarf
==> 2 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962  libdwarf@20130729-b52fac98

Now the libdwarf installs have hashes after their names. These are hashes over all of the dependencies of each package. If the hashes are the same, then the packages have the same dependency configuration.

If you want to know the path where each package is installed, you can use spack find --paths:

$ spack find --paths
==> 74 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
    ImageMagick@6.8.9-10  ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd
    adept-utils@1.0       ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/adept-utils@1.0-5adef8da
    atk@2.14.0            ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/atk@2.14.0-3d09ac09
    boost@1.55.0          ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/boost@1.55.0
    bzip2@1.0.6           ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/bzip2@1.0.6
    cairo@1.14.0          ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/cairo@1.14.0-fcc2ab44
    callpath@1.0.2        ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/callpath@1.0.2-5dce4318
...

And, finally, you can restrict your search to a particular package by supplying its name:

$ spack find --paths libelf
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
    libelf@0.8.11  ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.11
    libelf@0.8.12  ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.12
    libelf@0.8.13  ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/libelf@0.8.13

spack find actually does a lot more than this. You can use specs to query for specific configurations and builds of each package. If you want to find only libelf versions greater than version 0.8.12, you could say:

$ spack find libelf@0.8.12:
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
    libelf@0.8.12  libelf@0.8.13

Finding just the versions of libdwarf built with a particular version of libelf would look like this:

$ spack find --long libdwarf ^libelf@0.8.12
==> 1 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
libdwarf@20130729-d9b90962

We can also search for packages that have a certain attribute. For example, spack find libdwarf +debug will show only installations of libdwarf with the ‘debug’ compile-time option enabled.

The full spec syntax is discussed in detail in Specs & dependencies.

Specs & dependencies

We know that spack install, spack uninstall, and other commands take a package name with an optional version specifier. In Spack, that descriptor is called a spec. Spack uses specs to refer to a particular build configuration (or configurations) of a package. Specs are more than a package name and a version; you can use them to specify the compiler, compiler version, architecture, compile options, and dependency options for a build. In this section, we’ll go over the full syntax of specs.

Here is an example of a much longer spec than we’ve seen thus far:

mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt arch=bgq_os ^callpath @1.1 %gcc@4.7.2

If provided to spack install, this will install the mpileaks library at some version between 1.2 and 1.4 (inclusive), built using gcc at version 4.7.5 for the Blue Gene/Q architecture, with debug options enabled, and without Qt support. Additionally, it says to link it with the callpath library (which it depends on), and to build callpath with gcc 4.7.2. Most specs will not be as complicated as this one, but this is a good example of what is possible with specs.

More formally, a spec consists of the following pieces:

  • Package name identifier (mpileaks above)
  • @ Optional version specifier (@1.2:1.4)
  • % Optional compiler specifier, with an optional compiler version (gcc or gcc@4.7.3)
  • + or - or ~ Optional variant specifiers (+debug, -qt, or ~qt) for boolean variants
  • name=<value> Optional variant specifiers that are not restricted to boolean variants
  • name=<value> Optional compiler flag specifiers. Valid flag names are cflags, cxxflags, fflags, cppflags, ldflags, and ldlibs.
  • target=<value> os=<value> Optional architecture specifier (target=haswell os=CNL10)
  • ^ Dependency specs (^callpath@1.1)

There are two things to notice here. The first is that specs are recursively defined. That is, each dependency after ^ is a spec itself. The second is that everything is optional except for the initial package name identifier. Users can be as vague or as specific as they want about the details of building packages, and this makes spack good for beginners and experts alike.

To really understand what’s going on above, we need to think about how software is structured. An executable or a library (these are generally the artifacts produced by building software) depends on other libraries in order to run. We can represent the relationship between a package and its dependencies as a graph. Here is the full dependency graph for mpileaks:

digraph { mpileaks -> mpich mpileaks -> callpath -> mpich callpath -> dyninst dyninst -> libdwarf -> libelf dyninst -> libelf }

Each box above is a package and each arrow represents a dependency on some other package. For example, we say that the package mpileaks depends on callpath and mpich. mpileaks also depends indirectly on dyninst, libdwarf, and libelf, in that these libraries are dependencies of callpath. To install mpileaks, Spack has to build all of these packages. Dependency graphs in Spack have to be acyclic, and the depends on relationship is directional, so this is a directed, acyclic graph or DAG.

The package name identifier in the spec is the root of some dependency DAG, and the DAG itself is implicit. Spack knows the precise dependencies among packages, but users do not need to know the full DAG structure. Each ^ in the full spec refers to some dependency of the root package. Spack will raise an error if you supply a name after ^ that the root does not actually depend on (e.g. mpileaks ^emacs@23.3).

Spack further simplifies things by only allowing one configuration of each package within any single build. Above, both mpileaks and callpath depend on mpich, but mpich appears only once in the DAG. You cannot build an mpileaks version that depends on one version of mpich and on a callpath version that depends on some other version of mpich. In general, such a configuration would likely behave unexpectedly at runtime, and Spack enforces this to ensure a consistent runtime environment.

The point of specs is to abstract this full DAG from Spack users. If a user does not care about the DAG at all, she can refer to mpileaks by simply writing mpileaks. If she knows that mpileaks indirectly uses dyninst and she wants a particular version of dyninst, then she can refer to mpileaks ^dyninst@8.1. Spack will fill in the rest when it parses the spec; the user only needs to know package names and minimal details about their relationship.

When spack prints out specs, it sorts package names alphabetically to normalize the way they are displayed, but users do not need to worry about this when they write specs. The only restriction on the order of dependencies within a spec is that they appear after the root package. For example, these two specs represent exactly the same configuration:

mpileaks ^callpath@1.0 ^libelf@0.8.3
mpileaks ^libelf@0.8.3 ^callpath@1.0

You can put all the same modifiers on dependency specs that you would put on the root spec. That is, you can specify their versions, compilers, variants, and architectures just like any other spec. Specifiers are associated with the nearest package name to their left. For example, above, @1.1 and %gcc@4.7.2 associates with the callpath package, while @1.2:1.4, %gcc@4.7.5, +debug, -qt, and target=haswell os=CNL10 all associate with the mpileaks package.

In the diagram above, mpileaks depends on mpich with an unspecified version, but packages can depend on other packages with constraints by adding more specifiers. For example, mpileaks could depend on mpich@1.2: if it can only build with version 1.2 or higher of mpich.

Below are more details about the specifiers that you can add to specs.

Version specifier

A version specifier comes somewhere after a package name and starts with @. It can be a single version, e.g. @1.0, @3, or @1.2a7. Or, it can be a range of versions, such as @1.0:1.5 (all versions between 1.0 and 1.5, inclusive). Version ranges can be open, e.g. :3 means any version up to and including 3. This would include 3.4 and 3.4.2. 4.2: means any version above and including 4.2. Finally, a version specifier can be a set of arbitrary versions, such as @1.0,1.5,1.7 (1.0, 1.5, or 1.7). When you supply such a specifier to spack install, it constrains the set of versions that Spack will install.

If the version spec is not provided, then Spack will choose one according to policies set for the particular spack installation. If the spec is ambiguous, i.e. it could match multiple versions, Spack will choose a version within the spec’s constraints according to policies set for the particular Spack installation.

Details about how versions are compared and how Spack determines if one version is less than another are discussed in the developer guide.

Compiler specifier

A compiler specifier comes somewhere after a package name and starts with %. It tells Spack what compiler(s) a particular package should be built with. After the % should come the name of some registered Spack compiler. This might include gcc, or intel, but the specific compilers available depend on the site. You can run spack compilers to get a list; more on this below.

The compiler spec can be followed by an optional compiler version. A compiler version specifier looks exactly like a package version specifier. Version specifiers will associate with the nearest package name or compiler specifier to their left in the spec.

If the compiler spec is omitted, Spack will choose a default compiler based on site policies.

Variants

Variants are named options associated with a particular package. They are optional, as each package must provide default values for each variant it makes available. Variants can be specified using a flexible parameter syntax name=<value>. For example, spack install libelf debug=True will install libelf build with debug flags. The names of particular variants available for a package depend on what was provided by the package author. spack info <package> will provide information on what build variants are available.

For compatibility with earlier versions, variants which happen to be boolean in nature can be specified by a syntax that represents turning options on and off. For example, in the previous spec we could have supplied libelf +debug with the same effect of enabling the debug compile time option for the libelf package.

Depending on the package a variant may have any default value. For libelf here, debug is False by default, and we turned it on with debug=True or +debug. If a variant is True by default you can turn it off by either adding -name or ~name to the spec.

There are two syntaxes here because, depending on context, ~ and - may mean different things. In most shells, the following will result in the shell performing home directory substitution:

mpileaks ~debug   # shell may try to substitute this!
mpileaks~debug    # use this instead

If there is a user called debug, the ~ will be incorrectly expanded. In this situation, you would want to write libelf -debug. However, - can be ambiguous when included after a package name without spaces:

mpileaks-debug     # wrong!
mpileaks -debug    # right

Spack allows the - character to be part of package names, so the above will be interpreted as a request for the mpileaks-debug package, not a request for mpileaks built without debug options. In this scenario, you should write mpileaks~debug to avoid ambiguity.

When spack normalizes specs, it prints them out with no spaces boolean variants using the backwards compatibility syntax and uses only ~ for disabled boolean variants. The - and spaces on the command line are provided for convenience and legibility.

Compiler Flags

Compiler flags are specified using the same syntax as non-boolean variants, but fulfill a different purpose. While the function of a variant is set by the package, compiler flags are used by the compiler wrappers to inject flags into the compile line of the build. Additionally, compiler flags are inherited by dependencies. spack install libdwarf cppflags="-g" will install both libdwarf and libelf with the -g flag injected into their compile line.

Notice that the value of the compiler flags must be quoted if it contains any spaces. Any of cppflags=-O3, cppflags="-O3", cppflags='-O3', and cppflags="-O3 -fPIC" are acceptable, but cppflags=-O3 -fPIC is not. Additionally, if they value of the compiler flags is not the last thing on the line, it must be followed by a space. The commmand spack install libelf cppflags="-O3"%intel will be interpreted as an attempt to set cppflags=”-O3%intel”`.

The six compiler flags are injected in the order of implicit make commands in GNU Autotools. If all flags are set, the order is $cppflags $cflags|$cxxflags $ldflags <command> $ldlibs for C and C++ and $fflags $cppflags $ldflags <command> $ldlibs for Fortran.

Compiler environment variables and additional RPATHs

In the exceptional case a compiler requires setting special environment variables, like an explicit library load path. These can bet set in an extra section in the compiler configuration (the supported environment modification commands are: set, unset, append-path, and prepend-path). The user can also specify additional RPATHs that the compiler will add to all executables generated by that compiler. This is useful for forcing certain compilers to RPATH their own runtime libraries, so that executables will run without the need to set LD_LIBRARY_PATH.

compilers:
  - compiler:
      spec: gcc@4.9.3
      paths:
        cc: /opt/gcc/bin/gcc
        c++: /opt/gcc/bin/g++
        f77: /opt/gcc/bin/gfortran
        fc: /opt/gcc/bin/gfortran
      environment:
        unset:
          BAD_VARIABLE: # The colon is required but the value must be empty
        set:
          GOOD_VARIABLE_NUM: 1
          GOOD_VARIABLE_STR: good
        prepend-path:
          PATH: /path/to/binutils
        append-path:
          LD_LIBRARY_PATH: /opt/gcc/lib
      extra_rpaths:
      - /path/to/some/compiler/runtime/directory
      - /path/to/some/other/compiler/runtime/directory

Note

The section environment is interpreted as an ordered dictionary, which means two things. First, environment modification are applied in the order they are specified in the configuration file. Second, you cannot express environment modifications that require mixing different commands, i.e. you cannot set one variable, than prepend-path to another one, and than again set a third one.

Architecture specifiers

The architecture can be specified by using the reserved words target and/or os (target=x86-64 os=debian7). You can also use the triplet form of platform, operating system and processor.

$ spack install libelf arch=cray-CNL10-haswell

Users on non-Cray systems won’t have to worry about specifying the architecture. Spack will autodetect what kind of operating system is on your machine as well as the processor. For more information on how the architecture can be used on Cray machines, see Spack on Cray

Virtual dependencies

The dependence graph for mpileaks we saw above wasn’t quite accurate. mpileaks uses MPI, which is an interface that has many different implementations. Above, we showed mpileaks and callpath depending on mpich, which is one particular implementation of MPI. However, we could build either with another implementation, such as openmpi or mvapich.

Spack represents interfaces like this using virtual dependencies. The real dependency DAG for mpileaks looks like this:

digraph { mpi [color=red] mpileaks -> mpi mpileaks -> callpath -> mpi callpath -> dyninst dyninst -> libdwarf -> libelf dyninst -> libelf }

Notice that mpich has now been replaced with mpi. There is no real MPI package, but some packages provide the MPI interface, and these packages can be substituted in for mpi when mpileaks is built.

You can see what virtual packages a particular package provides by getting info on it:

$ spack info mpich
AutotoolsPackage:   mpich

Description:
    MPICH is a high performance and widely portable implementation of the
    Message Passing Interface (MPI) standard.

Homepage: http://www.mpich.org

Tags: 
    None

Preferred version:  
    3.3        http://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz

Safe versions:  
    develop    [git] https://github.com/pmodels/mpich.git
    3.3        http://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz
    3.2.1      http://www.mpich.org/static/downloads/3.2.1/mpich-3.2.1.tar.gz
    3.2        http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
    3.1.4      http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz
    3.1.3      http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3.tar.gz
    3.1.2      http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2.tar.gz
    3.1.1      http://www.mpich.org/static/downloads/3.1.1/mpich-3.1.1.tar.gz
    3.1        http://www.mpich.org/static/downloads/3.1/mpich-3.1.tar.gz
    3.0.4      http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz

Variants:
    Name [Default]    Allowed values        Description


    device [ch3]      ch3, ch4              Abstract Device Interface
                                            (ADI) implementation. The ch4
                                            device is currently in
                                            experimental state
    hydra [on]        True, False           Build the hydra process
                                            manager
    netmod [tcp]      tcp, mxm, ofi, ucx    Network module. Only single
                                            netmod builds are supported.
                                            For ch3 device configurations,
                                            this presumes the ch3:nemesis
                                            communication channel.
                                            ch3:sock is not supported by
                                            this spack package at this
                                            time.
    pmi [on]          True, False           Build with PMI support
    romio [on]        True, False           Enable ROMIO MPI I/O
                                            implementation
    verbs [off]       True, False           Build support for OpenFabrics
                                            verbs.

Installation Phases:
    autoreconf    configure    build    install

Build Dependencies:
    findutils  libfabric

Link Dependencies:
    libfabric

Run Dependencies:
    None

Virtual Packages: 
    mpich@3: provides mpi@:3.0
    mpich@1: provides mpi@:1.3
    mpich provides mpi

Spack is unique in that its virtual packages can be versioned, just like regular packages. A particular version of a package may provide a particular version of a virtual package, and we can see above that mpich versions 1 and above provide all mpi interface versions up to 1, and mpich versions 3 and above provide mpi versions up to 3. A package can depend on a particular version of a virtual package, e.g. if an application needs MPI-2 functions, it can depend on mpi@2: to indicate that it needs some implementation that provides MPI-2 functions.

Constraining virtual packages

When installing a package that depends on a virtual package, you can opt to specify the particular provider you want to use, or you can let Spack pick. For example, if you just type this:

$ spack install mpileaks

Then spack will pick a provider for you according to site policies. If you really want a particular version, say mpich, then you could run this instead:

$ spack install mpileaks ^mpich

This forces spack to use some version of mpich for its implementation. As always, you can be even more specific and require a particular mpich version:

$ spack install mpileaks ^mpich@3

The mpileaks package in particular only needs MPI-1 commands, so any MPI implementation will do. If another package depends on mpi@2 and you try to give it an insufficient MPI implementation (e.g., one that provides only mpi@:1), then Spack will raise an error. Likewise, if you try to plug in some package that doesn’t provide MPI, Spack will raise an error.

Specifying Specs by Hash

Complicated specs can become cumbersome to enter on the command line, especially when many of the qualifications are necessary to distinguish between similar installs. To avoid this, when referencing an existing spec, Spack allows you to reference specs by their hash. We previously discussed the spec hash that Spack computes. In place of a spec in any command, substitute /<hash> where <hash> is any amount from the beginning of a spec hash.

For example, lets say that you accidentally installed two different mvapich2 installations. If you want to uninstall one of them but don’t know what the difference is, you can run:

$ spack find --long mvapich2
==> 2 installed packages.
-- linux-centos7-x86_64 / gcc@6.3.0 ----------
qmt35td mvapich2@2.2%gcc
er3die3 mvapich2@2.2%gcc

You can then uninstall the latter installation using:

$ spack uninstall /er3die3

Or, if you want to build with a specific installation as a dependency, you can use:

$ spack install trilinos ^/er3die3

If the given spec hash is sufficiently long as to be unique, Spack will replace the reference with the spec to which it refers. Otherwise, it will prompt for a more qualified hash.

Note that this will not work to reinstall a dependency uninstalled by spack uninstall --force.

spack providers

You can see what packages provide a particular virtual package using spack providers. If you wanted to see what packages provide mpi, you would just run:

$ spack providers mpi
charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:         mpich      mvapich2        openmpi@2.0.0:
charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:         mpich@1:   openmpi         spectrum-mpi
charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:  intel-mpi              mpich@3:   openmpi@1.6.5
charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:  intel-parallel-studio  mpilander  openmpi@1.7.5:

And if you only wanted to see packages that provide MPI-2, you would add a version specifier to the spec:

$ spack providers mpi@2
charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:         mpich      openmpi         spectrum-mpi
charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:         mpich@3:   openmpi@1.6.5
charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:  intel-mpi              mpilander  openmpi@1.7.5:
charmpp@6.7.1:  charmpp@6.7.1:  charmpp@6.7.1:  intel-parallel-studio  mvapich2   openmpi@2.0.0:

Notice that the package versions that provide insufficient MPI versions are now filtered out.

Extensions & Python support

Spack’s installation model assumes that each package will live in its own install prefix. However, certain packages are typically installed within the directory hierarchy of other packages. For example, modules in interpreted languages like Python are typically installed in the $prefix/lib/python-2.7/site-packages directory.

Spack has support for this type of installation as well. In Spack, a package that can live inside the prefix of another package is called an extension. Suppose you have Python installed like so:

$ spack find python
==> 1 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
python@2.7.8

spack extensions

You can find extensions for your Python installation like this:

$ spack extensions python
==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96
==> 36 extensions:
geos          py-ipython     py-pexpect    py-pyside            py-sip
py-basemap    py-libxml2     py-pil        py-pytz              py-six
py-biopython  py-mako        py-pmw        py-rpy2              py-sympy
py-cython     py-matplotlib  py-pychecker  py-scientificpython  py-virtualenv
py-dateutil   py-mpi4py      py-pygments   py-scikit-learn
py-epydoc     py-mx          py-pylint     py-scipy
py-gnuplot    py-nose        py-pyparsing  py-setuptools
py-h5py       py-numpy       py-pyqt       py-shiboken

==> 12 installed:
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-dateutil@2.4.0    py-nose@1.3.4       py-pyside@1.2.2
py-dateutil@2.4.0    py-numpy@1.9.1      py-pytz@2014.10
py-ipython@2.3.1     py-pygments@2.0.1   py-setuptools@11.3.1
py-matplotlib@1.4.2  py-pyparsing@2.0.3  py-six@1.9.0

==> None activated.

The extensions are a subset of what’s returned by spack list, and they are packages like any other. They are installed into their own prefixes, and you can see this with spack find --paths:

$ spack find --paths py-numpy
==> 1 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
    py-numpy@1.9.1  ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/py-numpy@1.9.1-66733244

However, even though this package is installed, you cannot use it directly when you run python:

$ spack load python
$ python
Python 2.7.8 (default, Feb 17 2015, 01:35:25)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named numpy
>>>

Using Extensions

There are three ways to get numpy working in Python. The first is to use Using module files via Spack. You can simply use or load the module for the extension, and it will be added to the PYTHONPATH in your current shell.

For tcl modules:

$ spack load python
$ spack load py-numpy

or, for dotkit:

$ spack use python
$ spack use py-numpy

Now import numpy will succeed for as long as you keep your current session open.

Activating Extensions in a View

The second way to use extensions is to create a view, which merges the python installation along with the extensions into a single prefix. See Filesystem Views for a more in-depth description of views and spack view for usage of the spack view command.

Activating Extensions Globally

As an alternative to creating a merged prefix with Python and its extensions, and prior to support for views, Spack has provided a means to install the extension into the Spack installation prefix for the extendee. This has typically been useful since extendable packages typically search their own installation path for addons by default.

Global activations are performed with the spack activate command:

spack activate

$ spack activate py-numpy
==> Activated extension py-setuptools@11.3.1%gcc@4.4.7 arch=linux-debian7-x86_64-3c74eb69 for python@2.7.8%gcc@4.4.7.
==> Activated extension py-nose@1.3.4%gcc@4.4.7 arch=linux-debian7-x86_64-5f70f816 for python@2.7.8%gcc@4.4.7.
==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7.

Several things have happened here. The user requested that py-numpy be activated in the python installation it was built with. Spack knows that py-numpy depends on py-nose and py-setuptools, so it activated those packages first. Finally, once all dependencies were activated in the python installation, py-numpy was activated as well.

If we run spack extensions again, we now see the three new packages listed as activated:

$ spack extensions python
==> python@2.7.8%gcc@4.4.7  arch=linux-debian7-x86_64-703c7a96
==> 36 extensions:
geos          py-ipython     py-pexpect    py-pyside            py-sip
py-basemap    py-libxml2     py-pil        py-pytz              py-six
py-biopython  py-mako        py-pmw        py-rpy2              py-sympy
py-cython     py-matplotlib  py-pychecker  py-scientificpython  py-virtualenv
py-dateutil   py-mpi4py      py-pygments   py-scikit-learn
py-epydoc     py-mx          py-pylint     py-scipy
py-gnuplot    py-nose        py-pyparsing  py-setuptools
py-h5py       py-numpy       py-pyqt       py-shiboken

==> 12 installed:
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-dateutil@2.4.0    py-nose@1.3.4       py-pyside@1.2.2
py-dateutil@2.4.0    py-numpy@1.9.1      py-pytz@2014.10
py-ipython@2.3.1     py-pygments@2.0.1   py-setuptools@11.3.1
py-matplotlib@1.4.2  py-pyparsing@2.0.3  py-six@1.9.0

==> 3 currently activated:
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-nose@1.3.4  py-numpy@1.9.1  py-setuptools@11.3.1

Now, when a user runs python, numpy will be available for import without the user having to explicitly loaded. python@2.7.8 now acts like a system Python installation with numpy installed inside of it.

Spack accomplishes this by symbolically linking the entire prefix of the py-numpy into the prefix of the python package. To the python interpreter, it looks like numpy is installed in the site-packages directory.

The only limitation of global activation is that you can only have a single version of an extension activated at a time. This is because multiple versions of the same extension would conflict if symbolically linked into the same prefix. Users who want a different version of a package can still get it by using environment modules or views, but they will have to explicitly load their preferred version.

spack activate --force

If, for some reason, you want to activate a package without its dependencies, you can use spack activate --force:

$ spack activate --force py-numpy
==> Activated extension py-numpy@1.9.1%gcc@4.4.7 arch=linux-debian7-x86_64-66733244 for python@2.7.8%gcc@4.4.7.

spack deactivate

We’ve seen how activating an extension can be used to set up a default version of a Python module. Obviously, you may want to change that at some point. spack deactivate is the command for this. There are several variants:

  • spack deactivate <extension> will deactivate a single extension. If another activated extension depends on this one, Spack will warn you and exit with an error.

  • spack deactivate --force <extension> deactivates an extension regardless of packages that depend on it.

  • spack deactivate --all <extension> deactivates an extension and all of its dependencies. Use --force to disregard dependents.

  • spack deactivate --all <extendee> deactivates all activated extensions of a package. For example, to deactivate all python extensions, use:

    $ spack deactivate --all python
    

Filesystem requirements

By default, Spack needs to be run from a filesystem that supports flock locking semantics. Nearly all local filesystems and recent versions of NFS support this, but parallel filesystems or NFS volumes may be configured without flock support enabled. You can determine how your filesystems are mounted with mount. The output for a Lustre filesystem might look like this:

$ mount | grep lscratch
mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,lazystatfs,flock)
mds2-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,lazystatfs,flock)

Note the flock option on both Lustre mounts.

If you do not see this or a similar option for your filesystem, you have a few options. First, you can move your Spack installation to a filesystem that supports locking. Second, you could ask your system administrator to enable flock for your filesystem.

If none of those work, you can disable locking in one of two ways:

  1. Run Spack with the -L or --disable-locks option to disable locks on a call-by-call basis.
  2. Edit config.yaml and set the locks option to false to always disable locking.

Warning

If you disable locking, concurrent instances of Spack will have no way to avoid stepping on each other. You must ensure that there is only one instance of Spack running at a time. Otherwise, Spack may end up with a corrupted database file, or you may not be able to see all installed packages in commands like spack find.

If you are unfortunate enough to run into this situation, you may be able to fix it by running spack reindex.

This issue typically manifests with the error below:

$ ./spack find
Traceback (most recent call last):
File "./spack", line 176, in <module>
  main()
File "./spack", line 154,' in main
  return_val = command(parser, args)
File "./spack/lib/spack/spack/cmd/find.py", line 170, in find
  specs = set(spack.installed_db.query(\**q_args))
File "./spack/lib/spack/spack/database.py", line 551, in query
  with self.read_transaction():
File "./spack/lib/spack/spack/database.py", line 598, in __enter__
  if self._enter() and self._acquire_fn:
File "./spack/lib/spack/spack/database.py", line 608, in _enter
  return self._db.lock.acquire_read(self._timeout)
File "./spack/lib/spack/llnl/util/lock.py", line 103, in acquire_read
  self._lock(fcntl.LOCK_SH, timeout)   # can raise LockError.
File "./spack/lib/spack/llnl/util/lock.py", line 64, in _lock
  fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
IOError: [Errno 38] Function not implemented

A nicer error message is TBD in future versions of Spack.

Getting Help

spack help

If you don’t find what you need here, the help subcommand will print out out a list of all of spack’s options and subcommands:

$ spack help
usage: spack [-hkV] [--color {always,never,auto}] COMMAND ...

A flexible package manager that supports multiple versions,
configurations, platforms, and compilers.

These are common spack commands:

query packages:
  list                  list and search available packages
  info                  get detailed information on a particular package
  find                  list and search installed packages

build packages:
  install               build and install packages
  uninstall             remove installed packages
  spec                  show what would be installed, given a spec

environments:
  env                   manage virtual environments
  view                  produce a single-rooted directory view of packages

modules:
  load                  add package to environment using `module load`
  module                manipulate module files
  unload                remove package from environment using `module unload`

create packages:
  create                create a new package file
  edit                  open package files in $EDITOR

system:
  arch                  print architecture information about this machine
  compilers             list available compilers

optional arguments:
  -h, --help            show this help message and exit
  -k, --insecure        do not check ssl certificates when downloading
  -V, --version         show version number and exit
  --color {always,never,auto}
                        when to colorize output (default: auto)

more help:
  spack help --all       list all commands and options
  spack help <command>   help on a specific command
  spack help --spec      help on the spec syntax
  spack docs             open http://spack.rtfd.io/ in a browser

Adding an argument, e.g. spack help <subcommand>, will print out usage information for a particular subcommand:

$ spack help install
usage: spack install [-hInvy] [--only {package,dependencies}] [-j JOBS] [--overwrite] [--keep-prefix] [--keep-stage]
                     [--dont-restage] [--use-cache | --no-cache] [--show-log-on-error] [--source] [--fake]
                     [--only-concrete] [-f SPEC_YAML_FILE] [--clean | --dirty] [--test {root,all} | --run-tests]
                     [--log-format {None,junit,cdash}] [--log-file LOG_FILE] [--cdash-upload-url CDASH_UPLOAD_URL]
                     ...

build and install packages

positional arguments:
  package               spec of the package to install

optional arguments:
  -h, --help            show this help message and exit
  --only {package,dependencies}
                        select the mode of installation.
                        the default is to install the package along with all its dependencies.
                        alternatively one can decide to install only the package or only
                        the dependencies
  -j JOBS, --jobs JOBS  explicitly set number of make jobs, default is #cpus.
  -I, --install-status  show install status of packages. packages can be: installed [+], missing and needed by an installed package [-], or not installed (no annotation)
  --overwrite           reinstall an existing spec, even if it has dependents
  --keep-prefix         don't remove the install prefix if installation fails
  --keep-stage          don't remove the build stage if installation succeeds
  --dont-restage        if a partial install is detected, don't delete prior state
  --use-cache           check for pre-built Spack packages in mirrors (default)
  --no-cache            do not check for pre-built Spack packages in mirrors
  --show-log-on-error   print full build log to stderr if build fails
  --source              install source files in prefix
  -n, --no-checksum     do not use checksums to verify downloadeded files (unsafe)
  -v, --verbose         display verbose build output while installing
  --fake                fake install for debug purposes.
  --only-concrete       (with environment) only install already concretized specs
  -f SPEC_YAML_FILE, --file SPEC_YAML_FILE
                        install from file. Read specs to install from .yaml files
  --clean               unset harmful variables in the build environment (default)
  --dirty               preserve user environment in the spack build environment (danger!)
  --test {root,all}     If 'root' is chosen, run package tests during
                        installation for top-level packages (but skip tests for dependencies).
                        if 'all' is chosen, run package tests during installation for all
                        packages. If neither are chosen, don't run tests for any packages.
  --run-tests           run package tests during installation (same as --test=all)
  --log-format {None,junit,cdash}
                        format to be used for log files
  --log-file LOG_FILE   filename for the log file. if not passed a default will be used
  --cdash-upload-url CDASH_UPLOAD_URL
                        CDash URL where reports will be uploaded
  -y, --yes-to-all      assume "yes" is the answer to every confirmation request

Alternately, you can use spack --help in place of spack help, or spack <subcommand> --help to get help on a particular subcommand.