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-crayon
abyss                            nag                                    r-crosstalk
ack                              nalu                                   r-cubature
activeharmony                    namd                                   r-cubist
adept-utils                      nano                                   r-curl
adios                            nanoflann                              r-data-table
adios2                           nasm                                   r-dbi
adlbx                            nauty                                  r-dbplyr
adol-c                           ncbi-rmblastn                          r-delayedarray
albert                           nccl                                   r-deldir
alglib                           nccmp                                  r-dendextend
allinea-forge                    ncdu                                   r-deoptim
allinea-reports                  ncftp                                  r-deoptimr
allpaths-lg                      ncl                                    r-deseq
alquimia                         nco                                    r-deseq2
alsa-lib                         ncurses                                r-desolve
amg                              ncview                                 r-devtools
amg2013                          ndiff                                  r-diagrammer
amp                              nek5000                                r-dichromat
ampliconnoise                    nekbone                                r-diffusionmap
amr-exp-parabolic                nekcem                                 r-digest
amrex                            neovim                                 r-diptest
andi                             netcdf                                 r-dnacopy
angsd                            netcdf-cxx                             r-do-db
ant                              netcdf-cxx4                            r-domc
antlr                            netcdf-fortran                         r-doparallel
ape                              netgauge                               r-dorng
apex                             netgen                                 r-dose
applewmproto                     netlib-lapack                          r-downloader
appres                           netlib-scalapack                       r-dplyr
apr                              netlib-xblas                           r-dt
apr-util                         nettle                                 r-dtw
archer                           neuron                                 r-dygraphs
argp-standalone                  nextflow                               r-e1071
argtable                         nfft                                   r-edger
arlecore                         nghttp2                                r-ellipse
armadillo                        nginx                                  r-ensembldb
arpack-ng                        ngmlr                                  r-ergm
ascent                           ninja                                  r-evaluate
asciidoc                         ninja-fortran                          r-expm
aspa                             nlopt                                  r-factoextra
aspell                           nmap                                   r-factominer
aspell6-de                       nnvm                                   r-ff
aspell6-en                       node-js                                r-fftwtools
aspell6-es                       notmuch                                r-fgsea
assimp                           npb                                    r-filehash
astra                            npm                                    r-flashclust
astral                           npth                                   r-flexmix
astyle                           nspr                                   r-fnn
atk                              numactl                                r-forcats
atlas                            numdiff                                r-foreach
atom-dft                         nut                                    r-forecast
atompaw                          nwchem                                 r-foreign
atop                             ocaml                                  r-formatr
augustus                         oce                                    r-formula
autoconf                         oclint                                 r-fpc
autodock-vina                    oclock                                 r-fracdiff
autogen                          octave                                 r-futile-logger
automaded                        octave-optim                           r-futile-options
automake                         octave-splines                         r-gbm
bamtools                         octave-struct                          r-gcrma
bamutil                          octopus                                r-gdata
barrnap                          of-adios-write                         r-gdsfmt
bash                             ompss                                  r-geiger
bash-completion                  ompt-openmp                            r-genefilter
bats                             oniguruma                              r-geneplotter
bazel                            ont-albacore                           r-genomeinfodb
bbcp                             opa-psm2                               r-genomeinfodbdata
bbmap                            opam                                   r-genomicalignments
bcftools                         opari2                                 r-genomicfeatures
bcl2fastq2                       openbabel                              r-genomicranges
bdftopcf                         openblas                               r-geomorph
bdw-gc                           opencoarrays                           r-geoquery
bear                             opencv                                 r-geosphere
beast2                           openexr                                r-getopt
bedtools2                        openfast                               r-getoptlong
beforelight                      openfoam-com                           r-ggally
benchmark                        openfoam-org                           r-ggbio
berkeley-db                      openfst                                r-ggdendro
bertini                          opengl                                 r-ggjoy
bib2xhtml                        openjpeg                               r-ggmap
bigreqsproto                     openmc                                 r-ggplot2
binutils                         openmpi                                r-ggpubr
bioawk                           opennurbs                              r-ggrepel
biopieces                        openscenegraph                         r-ggridges
bison                            openspeedshop                          r-ggsci
bitmap                           openssh                                r-ggvis
blast-plus                       openssl                                r-gistr
blat                             opium                                  r-git2r
blaze                            opus                                   r-glmnet
bliss                            orfm                                   r-globaloptions
blitz                            orthomcl                               r-glue
bmake                            osu-micro-benchmarks                   r-gmodels
bml                              otf                                    r-gmp
bohrium                          otf2                                   r-go-db
boost                            p4est                                  r-googlevis
boostmplcartesianproduct         p7zip                                  r-gosemsim
bowtie                           pacbio-daligner                        r-gostats
bowtie2                          pacbio-damasker                        r-gplots
boxlib                           pacbio-dazz-db                         r-graph
bpp-core                         pacbio-dextractor                      r-gridbase
bpp-phyl                         pagit                                  r-gridextra
bpp-seq                          pagmo                                  r-gseabase
bpp-suite                        paml                                   r-gsubfn
braker                           panda                                  r-gtable
branson                          pandaseq                               r-gtools
breakdancer                      pango                                  r-gtrellis
breseq                           papi                                   r-gviz
brigand                          paradiseo                              r-haven
bsseeker2                        parallel                               r-hexbin
bucky                            parallel-netcdf                        r-highr
busco                            paraver                                r-hmisc
butter                           paraview                               r-hms
bwa                              parmetis                               r-htmltable
byobu                            parmgridgen                            r-htmltools
bzip2                            parsimonator                           r-htmlwidgets
c-blosc                          parsplice                              r-httpuv
caffe                            partitionfinder                        r-httr
cairo                            patch                                  r-hwriter
caliper                          patchelf                               r-hypergraph
callpath                         pathfinder                             r-ica
candle-benchmarks                pax-utils                              r-igraph
cantera                          pbmpi                                  r-illuminaio
canu                             pcma                                   r-impute
cap3                             pcre                                   r-influencer
cares                            pcre2                                  r-inline
cask                             pdsh                                   r-interactivedisplaybase
casper                           pdt                                    r-ipred
catalyst                         pegtl                                  r-iranges
catch                            pennant                                r-irdisplay
cbench                           percept                                r-irkernel
cblas                            perl                                   r-irlba
cbtf                             perl-algorithm-diff                    r-iso
cbtf-argonavis                   perl-app-cmd                           r-iterators
cbtf-argonavis-gui               perl-array-utils                       r-janitor
cbtf-krell                       perl-b-hooks-endofscope                r-jaspar2018
cbtf-lanl                        perl-bio-perl                          r-jpeg
ccache                           perl-bit-vector                        r-jsonlite
cctools                          perl-capture-tiny                      r-kegg-db
cdbfasta                         perl-carp-clan                         r-kegggraph
cdd                              perl-class-data-inheritable            r-keggrest
cddlib                           perl-class-inspector                   r-kernlab
cdhit                            perl-class-load                        r-kernsmooth
cdo                              perl-class-load-xs                     r-kknn
cereal                           perl-cpan-meta-check                   r-knitr
cfitsio                          perl-data-optlist                      r-labeling
cgal                             perl-data-stag                         r-lambda-r
cgm                              perl-dbd-mysql                         r-laplacesdemon
cgns                             perl-dbfile                            r-lars
charm                            perl-dbi                               r-lattice
check                            perl-devel-cycle                       r-latticeextra
chlorop                          perl-devel-globaldestruction           r-lava
chombo                           perl-devel-overloadinfo                r-lazyeval
cityhash                         perl-devel-stacktrace                  r-leaflet
clamr                            perl-digest-md5                        r-leaps
cleaveland4                      perl-dist-checkconflicts               r-learnbayes
cleverleaf                       perl-encode-locale                     r-limma
clfft                            perl-eval-closure                      r-lme4
clhep                            perl-exception-class                   r-lmtest
clingo                           perl-exporter-tiny                     r-locfit
cloc                             perl-extutils-makemaker                r-log4r
cloog                            perl-extutils-pkgconfig                r-lpsolve
cloverleaf                       perl-file-copy-recursive               r-lsei
cloverleaf3d                     perl-file-listing                      r-lubridate
clustalo                         perl-file-pushd                        r-magic
clustalw                         perl-file-sharedir-install             r-magrittr
cmake                            perl-file-slurp-tiny                   r-makecdfenv
cmocka                           perl-file-which                        r-maldiquant
cmor                             perl-font-ttf                          r-mapproj
cnmem                            perl-gd                                r-maps
cnpy                             perl-gd-graph                          r-maptools
cns-nospec                       perl-gd-text                           r-markdown
cntk                             perl-graph                             r-mass
cntk1bitsgd                      perl-html-parser                       r-matrix
codar-cheetah                    perl-html-tagset                       r-matrixmodels
coevp                            perl-http-cookies                      r-matrixstats
cohmm                            perl-http-daemon                       r-mclust
coinhsl                          perl-http-date                         r-mcmcglmm
comd                             perl-http-message                      r-mda
compiz                           perl-http-negotiate                    r-memoise
compositeproto                   perl-inline                            r-mergemaid
conduit                          perl-inline-c                          r-methodss3
constype                         perl-intervaltree                      r-mgcv
converge                         perl-io-html                           r-mime
coreutils                        perl-io-sessiondata                    r-minfi
corset                           perl-io-socket-ssl                     r-minqa
cosmomc                          perl-io-string                         r-mixtools
cosp2                            perl-list-moreutils                    r-mlbench
cp2k                             perl-log-log4perl                      r-mlinterfaces
cppad                            perl-lwp                               r-mnormt
cppcheck                         perl-lwp-mediatypes                    r-modelmetrics
cpprestsdk                       perl-lwp-protocol-https                r-modelr
cppunit                          perl-math-cdf                          r-modeltools
cppzmq                           perl-module-build                      r-mpm
cram                             perl-module-runtime-conflicts          r-msnbase
cryptopp                         perl-moose                             r-multcomp
cscope                           perl-mozilla-ca                        r-multtest
csdp                             perl-mro-compat                        r-munsell
ctffind                          perl-namespace-clean                   r-mvtnorm
cub                              perl-net-http                          r-mzid
cube                             perl-net-ssleay                        r-mzr
cuda                             perl-package-deprecationmanager        r-nanotime
cuda-memtest                     perl-package-stash                     r-ncbit
cudnn                            perl-package-stash-xs                  r-ncdf4
cufflinks                        perl-padwalker                         r-network
cups                             perl-params-util                       r-networkd3
curl                             perl-parse-recdescent                  r-nlme
cvs                              perl-pdf-api2                          r-nloptr
czmq                             perl-pegex                             r-nmf
dakota                           perl-perlio-gzip                       r-nnet
daligner                         perl-soap-lite                         r-nnls
damageproto                      perl-star-fusion                       r-nor1mix
damselfly                        perl-statistics-descriptive            r-np
darshan-runtime                  perl-sub-exporter                      r-numderiv
darshan-util                     perl-sub-exporter-progressive          r-oligoclasses
dash                             perl-sub-identify                      r-oo
datamash                         perl-sub-install                       r-openssl
dataspaces                       perl-sub-name                          r-org-hs-eg-db
dbus                             perl-sub-uplevel                       r-organismdbi
dealii                           perl-svg                               r-packrat
dejagnu                          perl-swissknife                        r-pacman
delly2                           perl-task-weaken                       r-pamr
denovogear                       perl-term-readkey                      r-party
dia                              perl-test-cleannamespaces              r-partykit
dialign-tx                       perl-test-deep                         r-pathview
diamond                          perl-test-differences                  r-pbapply
diffsplice                       perl-test-exception                    r-pbdzmq
direnv                           perl-test-fatal                        r-pbkrtest
discovar                         perl-test-memory-cycle                 r-pcamethods
discovardenovo                   perl-test-most                         r-pcapp
dlpack                           perl-test-needs                        r-permute
dmlc-core                        perl-test-requires                     r-pfam-db
dmxproto                         perl-test-requiresinternet             r-phantompeakqualtools
docbook-xml                      perl-test-warn                         r-phyloseq
docbook-xsl                      perl-test-warnings                     r-pkgconfig
dos2unix                         perl-text-diff                         r-pkgmaker
double-conversion                perl-text-unidecode                    r-plogr
doxygen                          perl-time-hires                        r-plotly
dri2proto                        perl-time-piece                        r-plotrix
dri3proto                        perl-try-tiny                          r-pls
dtcmp                            perl-uri                               r-plyr
dyninst                          perl-uri-escape                        r-pmcmr
ea-utils                         perl-version                           r-png
easybuild                        perl-www-robotrules                    r-powerlaw
ebms                             perl-xml-libxml                        r-prabclus
eccodes                          perl-xml-parser                        r-praise
ecp-proxy-apps                   perl-xml-parser-lite                   r-preprocesscore
editres                          perl-xml-simple                        r-prettyunits
eigen                            perl-yaml-libyaml                      r-prodlim
elemental                        petsc                                  r-progress
elfutils                         pexsi                                  r-protgenerics
elk                              pfft                                   r-proto
elpa                             pflotran                               r-proxy
emacs                            pfunit                                 r-pryr
emboss                           pgdspider                              r-psych
encodings                        pgi                                    r-ptw
environment-modules              phantompeakqualtools                   r-purrr
es                               phasta                                 r-quadprog
esmf                             phylip                                 r-quantmod
espresso                         picard                                 r-quantreg
essl                             pidx                                   r-quantro
ethminer                         pigz                                   r-qvalue
etsf-io                          pilon                                  r-r6
everytrace                       piranha                                r-randomforest
everytrace-example               pixman                                 r-ranger
evieext                          pkg-config                             r-rappdirs
exabayes                         pkgconf                                r-raster
exampm                           planck-likelihood                      r-rbgl
exasp2                           plasma                                 r-rbokeh
exmcutils                        plink                                  r-rcolorbrewer
exodusii                         plumed                                 r-rcpp
exonerate                        pmgr-collective                        r-rcpparmadillo
expat                            pmix                                   r-rcppblaze
expect                           pnfft                                  r-rcppcctz
express                          pngwriter                              r-rcppeigen
extrae                           poamsa                                 r-rcppprogress
exuberant-ctags                  pocl                                   r-rcurl
f90cache                         polymake                               r-rda
falcon                           porta                                  r-readr
farmhash                         portage                                r-readxl
fastjar                          postgresql                             r-registry
fastmath                         ppl                                    r-rematch
fastme                           prank                                  r-reordercluster
fastphase                        presentproto                           r-reportingtools
fastq-screen                     preseq                                 r-repr
fastqc                           price                                  r-reprex
fastqvalidator                   primer3                                r-reshape
fasttree                         printproto                             r-reshape2
fastx-toolkit                    probconsrna                            r-rex
fenics                           prodigal                               r-rgdal
ferret                           proj                                   r-rgeos
ffmpeg                           protobuf                               r-rgl
fftw                             proxymngr                              r-rgooglemaps
fimpute                          pruners-ninja                          r-rgraphviz
findutils                        ps-lite                                r-rhdf5
fio                              psi4                                   r-rhtslib
fish                             pstreams                               r-rinside
fixesproto                       pugixml                                r-rjags
flac                             pumi                                   r-rjava
flang                            pvm                                    r-rjson
flann                            py-3to2                                r-rjsonio
flash                            py-4suite-xml                          r-rlang
flecsale                         py-abipy                               r-rmarkdown
flecsi                           py-adios                               r-rminer
flex                             py-alabaster                           r-rmpfr
flint                            py-apache-libcloud                     r-rmpi
flit                             py-apipkg                              r-rmysql
fltk                             py-appdirs                             r-rngtools
flux                             py-appnope                             r-robustbase
fluxbox                          py-apscheduler                         r-rocr
fmt                              py-argcomplete                         r-rodbc
foam-extend                      py-argparse                            r-roxygen2
folly                            py-ase                                 r-rpart
font-adobe-100dpi                py-asn1crypto                          r-rpart-plot
font-adobe-75dpi                 py-astroid                             r-rpostgresql
font-adobe-utopia-100dpi         py-astropy                             r-rprojroot
font-adobe-utopia-75dpi          py-attrs                               r-rsamtools
font-adobe-utopia-type1          py-autopep8                            r-rsnns
font-alias                       py-babel                               r-rsqlite
font-arabic-misc                 py-backports-abc                       r-rstan
font-bh-100dpi                   py-backports-functools-lru-cache       r-rstudioapi
font-bh-75dpi                    py-backports-shutil-get-terminal-size  r-rtracklayer
font-bh-lucidatypewriter-100dpi  py-backports-ssl-match-hostname        r-rtsne
font-bh-lucidatypewriter-75dpi   py-basemap                             r-rvcheck
font-bh-ttf                      py-beautifulsoup4                      r-rvest
font-bh-type1                    py-binwalk                             r-rzmq
font-bitstream-100dpi            py-biom-format                         r-s4vectors
font-bitstream-75dpi             py-biopython                           r-samr
font-bitstream-speedo            py-bitarray                            r-sandwich
font-bitstream-type1             py-bleach                              r-scales
font-cronyx-cyrillic             py-blessings                           r-scatterplot3d
font-cursor-misc                 py-bokeh                               r-sdmtools
font-daewoo-misc                 py-boltons                             r-segmented
font-dec-misc                    py-bottleneck                          r-selectr
font-ibm-type1                   py-brian                               r-seqinr
font-isas-misc                   py-brian2                              r-seqlogo
font-jis-misc                    py-bsddb3                              r-seurat
font-micro-misc                  py-bx-python                           r-sfsmisc
font-misc-cyrillic               py-cclib                               r-shape
font-misc-ethiopic               py-cdat-lite                           r-shiny
font-misc-meltho                 py-cdo                                 r-shortread
font-misc-misc                   py-certifi                             r-siggenes
font-mutt-misc                   py-cffi                                r-simpleaffy
font-schumacher-misc             py-chardet                             r-sn
font-screen-cyrillic             py-checkm-genome                       r-snow
font-sony-misc                   py-click                               r-snprelate
font-sun-misc                    py-cogent                              r-som
font-util                        py-colorama                            r-somaticsignatures
font-winitzki-cyrillic           py-colormath                           r-sourcetools
font-xfree86-type1               py-configparser                        r-sp
fontcacheproto                   py-counter                             r-sparsem
fontconfig                       py-coverage                            r-spdep
fontsproto                       py-cpuinfo                             r-speedglm
fonttosfnt                       py-cryptography                        r-sqldf
fpc                              py-csvkit                              r-stanheaders
fr-hit                           py-current                             r-statmod
freebayes                        py-cutadapt                            r-statnet-common
freetype                         py-cycler                              r-stringi
fseq                             py-cython                              r-stringr
fsl                              py-dask                                r-strucchange
fslsfonts                        py-dateutil                            r-subplex
fstobdf                          py-dbf                                 r-summarizedexperiment
funhpc                           py-decorator                           r-survey
gapbs                            py-deeptools                           r-survival
gapcloser                        py-dendropy                            r-sva
gapfiller                        py-dev                                 r-tarifx
gasnet                           py-dill                                r-tclust
gatk                             py-dlcpar                              r-tensora
gaussian                         py-docutils                            r-testit
gawk                             py-doxypy                              r-testthat
gblocks                          py-doxypypy                            r-tfmpvalue
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-imerge                       py-faststructure                       r-vcd
git-lfs                          py-fiscalyear                          r-vegan
gl2ps                            py-flake8                              r-vgam
glew                             py-flask                               r-viridis
glfmultiples                     py-flexx                               r-viridislite
glib                             py-fparser                             r-visnetwork
glimmer                          py-funcsigs                            r-vsn
glm                              py-functools32                         r-whisker
global                           py-future                              r-withr
globalarrays                     py-futures                             r-xde
globus-toolkit                   py-genders                             r-xgboost
glog                             py-genshi                              r-xlconnect
glpk                             py-git-review                          r-xlconnectjars
glproto                          py-git2                                r-xlsx
gmake                            py-gnuplot                             r-xlsxjars
gmap-gsnap                       py-griddataformats                     r-xmapbridge
gmime                            py-guidata                             r-xml
gmp                              py-guiqwt                              r-xml2
gmsh                             py-h5py                                r-xtable
gnat                             py-html2text                           r-xts
gnu-prolog                       py-html5lib                            r-xvector
gnupg                            py-htseq                               r-yaml
gnuplot                          py-httpbin                             r-yapsa
gnutls                           py-hypothesis                          r-yaqcaffy
go                               py-idna                                r-yarn
go-bootstrap                     py-igraph                              r-zlibbioc
gobject-introspection            py-imagesize                           r-zoo
googletest                       py-iminuit                             raft
gotcha                           py-importlib                           raja
gource                           py-ipaddress                           randfold
gperf                            py-ipdb                                random123
gperftools                       py-ipykernel                           randrproto
grackle                          py-ipython                             ravel
gradle                           py-ipython-genutils                    raxml
grandr                           py-ipywidgets                          ray
graphlib                         py-isort                               rdp-classifier
graphmap                         py-itsdangerous                        re2c
graphviz                         py-jdcal                               readline
grib-api                         py-jedi                                recordproto
groff                            py-jinja2                              redundans
gromacs                          py-joblib                              relion
gsl                              py-jpype                               rempi
gslib                            py-jsonschema                          rename
gtkorvo-atl                      py-junit-xml                           rendercheck
gtkorvo-cercs-env                py-jupyter-client                      renderproto
gtkorvo-dill                     py-jupyter-console                     repeatmasker
gtkorvo-enet                     py-jupyter-core                        resourceproto
gtkplus                          py-jupyter-notebook                    revbayes
gts                              py-keras                               rgb
guidance                         py-latexcodec                          rhash
guile                            py-lazy                                rlwrap
h5hut                            py-lazy-object-proxy                   rmlab
h5part                           py-lazyarray                           rna-seqc
h5utils                          py-libconf                             rockstar
h5z-zfp                          py-libensemble                         root
hacckernels                      py-line-profiler                       rose
hadoop                           py-linecache2                          rr
hapcut2                          py-lit                                 rsbench
haploview                        py-llvmlite                            rsem
harfbuzz                         py-lmfit                               rstart
harminv                          py-localcider                          rsync
hdf                              py-lockfile                            rtags
hdf5                             py-logilab-common                      rtax
hdf5-blosc                       py-lrudict                             ruby
help2man                         py-lxml                                ruby-gnuplot
hepmc                            py-lzstring                            ruby-narray
heppdt                           py-macholib                            ruby-rubyinline
highfive                         py-machotools                          ruby-terminal-table
highwayhash                      py-macs2                               rust
hisat2                           py-mako                                rust-bindgen
hmmer                            py-mappy                               sabre
hoomd-blue                       py-markdown                            sailfish
hpccg                            py-markupsafe                          salmon
hpctoolkit                       py-matplotlib                          sambamba
hpctoolkit-externals             py-mccabe                              samblaster
hpgmg                            py-mdanalysis                          samrai
hpl                              py-meep                                samtools
hpx                              py-memory-profiler                     sandbox
hpx5                             py-methylcode                          sas
hsakmt                           py-misopy                              satsuma2
hstr                             py-mistune                             savanna
htop                             py-mock                                saws
htslib                           py-moltemplate                         sbt
httpie                           py-mongo                               scala
hub                              py-monotonic                           scalasca
hunspell                         py-monty                               scalpel
hwloc                            py-mpi4py                              scan-for-matches
hybpiper                         py-mpmath                              scons
hydra                            py-multiprocess                        scorec-core
hypre                            py-multiqc                             scorep
i3                               py-mx                                  scotch
ibmisc                           py-mxnet                               scr
iceauth                          py-myhdl                               screen
icedtea                          py-mysqldb1                            scripts
icet                             py-nbconvert                           scrnsaverproto
ico                              py-nbformat                            sctk
icu4c                            py-neo                                 sdl2
id3lib                           py-nestle                              sdl2-image
idba                             py-netcdf4                             sed
igraph                           py-netifaces                           seqprep
igv                              py-networkx                            seqtk
igvtools                         py-nose                                serf
ilmbase                          py-nosexcover                          sessreg
image-magick                     py-numba                               setxkbmap
imake                            py-numexpr                             sga
impute2                          py-numpy                               shapeit
infernal                         py-numpydoc                            shared-mime-info
inputproto                       py-olefile                             shiny-server
intel                            py-ont-fast5-api                       shortbred
intel-daal                       py-openpmd-validator                   shortstack
intel-gpu-tools                  py-openpyxl                            showfont
intel-ipp                        py-ordereddict                         sickle
intel-mkl                        py-oset                                siesta
intel-mkl-dnn                    py-packaging                           signalp
intel-mpi                        py-palettable                          signify
intel-parallel-studio            py-pandas                              silo
intel-tbb                        py-paramiko                            simplemoc
intltool                         py-pathlib2                            simul
ior                              py-pathos                              simulationio
iozone                           py-pathspec                            singularity
ipopt                            py-patsy                               slepc
isaac                            py-pbr                                 slurm
isaac-server                     py-periodictable                       smalt
isl                              py-petsc4py                            smc
itstool                          py-pexpect                             smproxy
itsx                             py-phonopy                             snakemake
jags                             py-pickleshare                         snap
jansson                          py-pil                                 snap-berkeley
jasper                           py-pillow                              snap-korf
jbigkit                          py-pip                                 snappy
jdk                              py-pipits                              snbone
jellyfish                        py-pkgconfig                           sniffles
jemalloc                         py-plotly                              snptest
jmol                             py-ply                                 soap2
jq                               py-pmw                                 soapindel
json-c                           py-pox                                 soapsnp
json-cwx                         py-ppft                                somatic-sniper
json-glib                        py-prettytable                         sortmerna
jsoncpp                          py-proj                                sosflow
judy                             py-prompt-toolkit                      sowing
julia                            py-protobuf                            sox
kahip                            py-psutil                              spades
kaks-calculator                  py-psyclone                            spark
kaldi                            py-ptyprocess                          sparsehash
kallisto                         py-pudb                                sparta
kbproto                          py-py                                  spdlog
kdiff3                           py-py2bit                              spectrum-mpi
kealib                           py-py2cairo                            speex
kentutils                        py-py2neo                              sph2pipe
kmergenie                        py-py4j                                spherepack
kokkos                           py-pyani                               spindle
kraken                           py-pyasn1                              spot
krims                            py-pybedtools                          sqlite
kripke                           py-pybigwig                            squid
kvasir-mpl                       py-pybind11                            sra-toolkit
laghos                           py-pybtex                              sspace-longread
lammps                           py-pybtex-docutils                     sspace-standard
last                             py-pychecker                           sst-dumpi
latte                            py-pycodestyle                         sst-macro
launchmon                        py-pycparser                           stacks
lazyten                          py-pycrypto                            staden-io-lib
lbann                            py-pycurl                              star
lbxproxy                         py-pydatalog                           star-ccm-plus
lcals                            py-pydispatcher                        startup-notification
lcms                             py-pydot                               stat
ldc                              py-pyelftools                          stc
ldc-bootstrap                    py-pyfasta                             stow
legion                           py-pyfftw                              stream
leveldb                          py-pyflakes                            strelka
lftp                             py-pygments                            stress
libaec                           py-pygobject                           stringtie
libaio                           py-pygtk                               structure
libapplewm                       py-pylint                              sublime-text
libarchive                       py-pymatgen                            subread
libassuan                        py-pyminifier                          subversion
libatomic-ops                    py-pympler                             suite-sparse
libbeagle                        py-pynn                                sumaclust
libbsd                           py-pypar                               sundials
libbson                          py-pyparsing                           superlu
libcanberra                      py-pypeflow                            superlu-dist
libcap                           py-pyprof2html                         superlu-mt
libcerf                          py-pyqt                                sw4lite
libcint                          py-pyrad                               swarm
libcircle                        py-pysam                               swfft
libconfig                        py-pyscaf                              swiftsim
libcroco                         py-pyserial                            swig
libctl                           py-pyside                              symengine
libdivsufsort                    py-pysocks                             sympol
libdmx                           py-pytables                            sz
libdrm                           py-pytest                              tabix
libdwarf                         py-pytest-cov                          talloc
libedit                          py-pytest-flake8                       tantan
libelf                           py-pytest-httpbin                      tar
libemos                          py-pytest-mock                         targetp
libepoxy                         py-pytest-runner                       task
libev                            py-pytest-xdist                        taskd
libevent                         py-python-daemon                       tasmanian
libevpath                        py-python-gitlab                       tassel
libfabric                        py-pythonqwt                           tau
libffi                           py-pytz                                tcl
libffs                           py-pywavelets                          tcoffee
libfontenc                       py-pyyaml                              tcsh
libfs                            py-qtawesome                           tealeaf
libgcrypt                        py-qtconsole                           tetgen
libgd                            py-qtpy                                tethex
libgit2                          py-quantities                          texinfo
libgpg-error                     py-quast                               texlive
libgpuarray                      py-radical-utils                       the-platinum-searcher
libgridxc                        py-ranger                              the-silver-searcher
libgtextutils                    py-readme-renderer                     thrift
libharu                          py-regex                               thrust
libhio                           py-reportlab                           tig
libice                           py-requests                            tinyxml
libiconv                         py-restview                            tinyxml2
libint                           py-rope                                tioga
libjpeg                          py-rpy2                                tk
libjpeg-turbo                    py-rsa                                 tmalign
libksba                          py-rseqc                               tmhmm
liblbxutil                       py-rtree                               tmux
libmatheval                      py-saga-python                         tmuxinator
libmesh                          py-scandir                             tophat
libmng                           py-scientificpython                    tppred
libmongoc                        py-scikit-image                        transabyss
libmonitor                       py-scikit-learn                        transdecoder
libnbc                           py-scipy                               transposome
libogg                           py-seaborn                             transset
liboldx                          py-setuptools                          trapproto
libpcap                          py-setuptools-git                      tree
libpciaccess                     py-setuptools-scm                      trf
libpfm4                          py-sfepy                               triangle
libpipeline                      py-sh                                  trilinos
libpng                           py-shiboken                            trimgalore
libpsl                           py-simplegeneric                       trimmomatic
libpthread-stubs                 py-simplejson                          turbine
libquo                           py-singledispatch                      turbomole
libsigsegv                       py-sip                                 tut
libsm                            py-six                                 twm
libsodium                        py-slepc4py                            tycho2
libspatialindex                  py-sncosmo                             typhonio
libsplash                        py-snowballstemmer                     uberftp
libssh2                          py-spectra                             ucx
libsvm                           py-spefile                             udunits2
libszip                          py-spglib                              ufo-core
libtermkey                       py-sphinx                              ufo-filters
libtiff                          py-sphinx-bootstrap-theme              unblur
libtool                          py-sphinx-rtd-theme                    uncrustify
libunistring                     py-sphinxcontrib-bibtex                unibilium
libunwind                        py-sphinxcontrib-programoutput         unison
libuuid                          py-sphinxcontrib-websupport            units
libuv                            py-spyder                              unixodbc
libvorbis                        py-spykeutils                          usearch
libvterm                         py-sqlalchemy                          util-linux
libwebsockets                    py-statsmodels                         util-macros
libwindowswm                     py-storm                               uuid
libx11                           py-subprocess32                        valgrind
libxau                           py-symengine                           vampirtrace
libxaw                           py-symfit                              vardictjava
libxaw3d                         py-sympy                               varscan
libxc                            py-tabulate                            vc
libxcb                           py-tappy                               vcftools
libxcomposite                    py-terminado                           vcsh
libxcursor                       py-tetoolkit                           vdt
libxdamage                       py-theano                              vecgeom
libxdmcp                         py-tifffile                            veclibfort
libxevie                         py-toml                                vegas2
libxext                          py-tomopy                              velvet
libxfixes                        py-tornado                             videoproto
libxfont                         py-tqdm                                viennarna
libxfont2                        py-traceback2                          viewres
libxfontcache                    py-traitlets                           vim
libxft                           py-tuiview                             virtualgl
libxi                            py-twisted                             visit
libxinerama                      py-typing                              vizglow
libxkbcommon                     py-tzlocal                             vmatch
libxkbfile                       py-umi-tools                           voropp
libxkbui                         py-unittest2                           votca-csg
libxml2                          py-unittest2py3k                       votca-ctp
libxmu                           py-urllib3                             votca-moo
libxp                            py-urwid                               votca-tools
libxpm                           py-vcversioner                         votca-xtp
libxpresent                      py-virtualenv                          vpfft
libxprintapputil                 py-vsc-base                            vpic
libxprintutil                    py-vsc-install                         vsearch
libxrandr                        py-wcsaxes                             vtk
libxrender                       py-wcwidth                             vtkh
libxres                          py-webkit-server                       vtkm
libxscrnsaver                    py-werkzeug                            wannier90
libxshmfence                     py-wheel                               wget
libxslt                          py-widgetsnbextension                  windowswmproto
libxsmm                          py-wrapt                               wt
libxstream                       py-xarray                              wx
libxt                            py-xattr                               wxpropgrid
libxtrap                         py-xlrd                                x11perf
libxtst                          py-xlsxwriter                          xapian-core
libxv                            py-xmlrunner                           xauth
libxvmc                          py-xopen                               xbacklight
libxxf86dga                      py-xpyb                                xbiff
libxxf86misc                     py-xvfbwrapper                         xbitmaps
libxxf86vm                       py-yapf                                xbraid
libyogrt                         py-yt                                  xcalc
libzip                           py-zmq                                 xcb-demo
likwid                           python                                 xcb-proto
linkphase3                       qbank                                  xcb-util
linux-headers                    qbox                                   xcb-util-cursor
listres                          qhull                                  xcb-util-errors
llvm                             qmcpack                                xcb-util-image
llvm-lld                         qmd-progress                           xcb-util-keysyms
llvm-openmp-ompt                 qrupdate                               xcb-util-renderutil
lmdb                             qt                                     xcb-util-wm
lmod                             qt-creator                             xcb-util-xrm
lndir                            qtgraph                                xclip
log4cplus                        qthreads                               xclipboard
log4cxx                          quinoa                                 xclock
lrslib                           qwt                                    xcmiscproto
lrzip                            r                                      xcmsdb
lua                              r-a4                                   xcompmgr
lua-bitlib                       r-a4base                               xconsole
lua-jit                          r-a4classif                            xcursor-themes
lua-lpeg                         r-a4core                               xcursorgen
lua-luafilesystem                r-a4preproc                            xdbedizzy
lua-luaposix                     r-a4reporting                          xditview
lua-mpack                        r-abadata                              xdm
luit                             r-abaenrichment                        xdpyinfo
lulesh                           r-abind                                xdriinfo
lumpy-sv                         r-absseq                               xedit
lwgrp                            r-acde                                 xerces-c
lwm2                             r-acepack                              xev
lz4                              r-acgh                                 xextproto
lzma                             r-acme                                 xeyes
lzo                              r-ada                                  xf86bigfontproto
m4                               r-adabag                               xf86dga
macsio                           r-ade4                                 xf86dgaproto
mad-numdiff                      r-adegenet                             xf86driproto
mafft                            r-adsplit                              xf86miscproto
magics                           r-affxparser                           xf86rushproto
magma                            r-affy                                 xf86vidmodeproto
makedepend                       r-affycomp                             xfd
mallocmc                         r-affycompatible                       xfindproxy
man-db                           r-affycontam                           xfontsel
maq                              r-affycoretools                        xfs
mariadb                          r-affydata                             xfsinfo
masa                             r-affyexpress                          xfwp
masurca                          r-affyilm                              xgamma
matio                            r-affyio                               xgc
matlab                           r-affypdnn                             xhost
maven                            r-affyplm                              xineramaproto
maverick                         r-affyqcreport                         xinit
mawk                             r-affyrnadegradation                   xinput
mbedtls                          r-agdex                                xios
mcl                              r-agilp                                xkbcomp
mdtest                           r-agimicrorna                          xkbdata
meep                             r-aims                                 xkbevd
mefit                            r-aldex2                               xkbprint
memaxes                          r-allelicimbalance                     xkbutils
meme                             r-alpine                               xkeyboard-config
meraculous                       r-als                                  xkill
mercurial                        r-alsace                               xload
mesa                             r-altcdfenvs                           xlogo
mesa-glu                         r-ampliqueso                           xlsatoms
meshkit                          r-analysispageserver                   xlsclients
meson                            r-anaquin                              xlsfonts
mesquite                         r-aneufinder                           xmag
metaphysicl                      r-aneufinderdata                       xman
metasv                           r-annaffy                              xmessage
metis                            r-annotate                             xmh
mfem                             r-annotationdbi                        xmlf90
microbiomeutil                   r-annotationfilter                     xmlto
minced                           r-annotationforge                      xmodmap
miniaero                         r-annotationhub                        xmore
miniamr                          r-ape                                  xorg-cf-files
miniconda2                       r-assertthat                           xorg-docs
miniconda3                       r-backports                            xorg-gtest
minife                           r-bamsignals                           xorg-server
minighost                        r-base64                               xorg-sgml-doctools
minigmg                          r-base64enc                            xphelloworld
minimap2                         r-beanplot                             xplor-nih
minimd                           r-bh                                   xplsprinters
miniqmc                          r-bindr                                xpr
minisign                         r-bindrcpp                             xprehashprinterlist
minismac2d                       r-biobase                              xprop
minitri                          r-biocgenerics                         xproto
minixyce                         r-biocinstaller                        xproxymanagementprotocol
mira                             r-biocparallel                         xqilla
mirdeep                          r-biocstyle                            xrandr
mitofates                        r-biomart                              xrdb
mitos                            r-biomformat                           xrefresh
mkfontdir                        r-biostrings                           xrootd
mkfontscale                      r-biovizbase                           xrx
mlhka                            r-bit                                  xsbench
moab                             r-bit64                                xscope
molcas                           r-bitops                               xsdk
mono                             r-blob                                 xsdktrilinos
mosh                             r-bookdown                             xset
mothur                           r-boot                                 xsetmode
motif                            r-brew                                 xsetpointer
motioncor2                       r-broom                                xsetroot
mozjs                            r-bsgenome                             xsimd
mpc                              r-bumphunter                           xsm
mpe2                             r-c50                                  xstdcmap
mpest                            r-callr                                xtensor
mpfr                             r-car                                  xtensor-python
mpibash                          r-caret                                xterm
mpiblast                         r-category                             xtl
mpich                            r-catools                              xtrans
mpifileutils                     r-cellranger                           xtrap
mpileaks                         r-checkmate                            xts
mpip                             r-checkpoint                           xvidtune
mpir                             r-chemometrics                         xvinfo
mpix-launch-swift                r-chron                                xwd
mrbayes                          r-circlize                             xwininfo
mrnet                            r-class                                xwud
mrtrix3                          r-classint                             xz
msgpack-c                        r-cli                                  yajl
mshadow                          r-clipr                                yaml-cpp
multitail                        r-cluster                              yasm
multiverso                       r-clusterprofiler                      yorick
mummer                           r-coda                                 z3
mumps                            r-codetools                            zeromq
munge                            r-coin                                 zfp
muparser                         r-colorspace                           zip
muscle                           r-complexheatmap                       zlib
muse                             r-corpcor                              zoltan
muster                           r-corrplot                             zsh
mvapich2                         r-covr                                 zstd
mxml                             r-cowplot

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 [-hkV] [--color {always,never,auto}] COMMAND ...

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

These are common spack commands:

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

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

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: 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 [-hnvy] [--only {package,dependencies}] [-j JOBS] [--overwrite] [--keep-prefix] [--keep-stage]
                     [--dont-restage] [--use-cache] [--show-log-on-error] [--source] [--fake] [-f SPEC_YAML_FILE]
                     [--clean | --dirty] [--test {root,all} | --run-tests] [--log-format {junit}]
                     [--log-file LOG_FILE]
                     ...

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: #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.