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

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-mysqldb1  py-sqlalchemy  r-rmysql  r-rpostgresql  r-rsqlite  r-sqldf  sqlite

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:  
    3.2        http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz

Safe versions:  
    develop    [git] git://github.com/pmodels/mpich
    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:
    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 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:
        set:
          LD_LIBRARY_PATH : /opt/gcc/lib
      extra_rpaths:
      - /path/to/some/compiler/runtime/directory
      - /path/to/some/other/compiler/runtime/directory

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:  
    3.2        http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz

Safe versions:  
    develop    [git] git://github.com/pmodels/mpich
    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:
    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
    intel-mpi                  mpich     mpich@3:  mvapich2@1.9   openmpi        openmpi@1.7.5:  spectrum-mpi
    intel-parallel-studio+mpi  mpich@1:  mvapich2  mvapich2@2.0:  openmpi@1.6.5  openmpi@2.0.0:

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
    intel-mpi                  mpich     mvapich2      mvapich2@2.0:  openmpi@1.6.5   openmpi@2.0.0:
    intel-parallel-studio+mpi  mpich@3:  mvapich2@1.9  openmpi        openmpi@1.7.5:  spectrum-mpi

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
>>>

Extensions & Environment Modules

There are two 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

It is often desirable to have certain packages always available as part of a Python installation. Spack offers a more permanent solution for this case. Instead of requiring users to load particular environment modules, you can activate the package within the Python installation:

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 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, 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

Spack currently 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 may be mounted without flock support enabled. You can determine how your filesystems are mounted with mount -p. The output for a Lustre filesystem might look like this:

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

Note the flock option on both Lustre mounts. If you do not see this or a similar option for your filesystem, you may need ot ask your system administrator to enable flock.

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 [-hkVcolor] <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

environment:
  load                  add package to environment using `module load`
  module                manipulate module files
  unload                remove package from environment using `module unload`
  view                  produce a single-rooted directory view of packages

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 is auto

more help:
  spack help --all       list all available commands
  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 [-h] [--only {package,dependencies}] [-j JOBS]
                     [--overwrite] [--keep-prefix] [--keep-stage]
                     [--dont-restage] [--use-cache] [--show-log-on-error]
                     [--source] [-n] [-v] [--fake] [-f SPEC_YAML_FILE]
                     [--clean | --dirty] [--test {root,all} | --run-tests]
                     [--log-format {junit}] [--log-file LOG_FILE] [-y]
                     ...

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
  --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
  --show-log-on-error   print full build log to stderr if build fails
  --source              install source files in prefix
  -n, --no-checksum     do not check packages against checksum
  -v, --verbose         display verbose build output while installing
  --fake                fake install for debug purposes.
  -f SPEC_YAML_FILE, --file SPEC_YAML_FILE
                        install from file. Read specs to install from .yaml
                        files
  --clean               sanitize the environment from variables that can
                        affect how packages find libraries or headers
  --dirty               maintain the current environment without trying to
                        sanitize it
  --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 {junit}  format to be used for log files
  --log-file LOG_FILE   filename for the log file. if not passed a default
                        will be used
  -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.