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

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

All packages whose names contain “sql”:

$ spack list sql
postgresql  py-mysqldb1  py-sqlalchemy  r-rmysql  r-rpostgresql  r-rsqlite  r-sqldf  sqlite

All packages whose names or descriptions contain documentation:

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

spack info

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

$ spack info mpich
AutotoolsPackage:   mpich

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

Homepage: http://www.mpich.org

Tags: 
    None

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

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

Variants:
    Name [Default]    Allowed values        Description


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

Installation Phases:
    autoreconf    configure    build    install

Build Dependencies:
    libfabric

Link Dependencies:
    libfabric

Run Dependencies:
    None

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

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

Dependencies and virtual dependencies are described in more detail later.

spack versions

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

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

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

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

Installing and uninstalling

spack install

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

$ spack install mpileaks

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

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

... build output ...

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

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

Building a specific version

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

$ spack install mpich@3.0.4

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

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

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

spack uninstall

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

$ spack uninstall mpich

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

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

$ spack uninstall --dependents mpich

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

A command like

$ spack uninstall mpich

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

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

$ spack uninstall --force mpich

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

Non-Downloadable Tarballs

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

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

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

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

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

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

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

    $ spack install galahad
    

Seeing installed packages

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

spack find

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

Running spack find with no arguments lists installed packages:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Specs & dependencies

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

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

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

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

More formally, a spec consists of the following pieces:

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

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

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

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

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

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

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

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

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

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

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

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

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

Version specifier

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

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

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

Compiler specifier

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

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

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

Variants

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

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

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

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

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

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

mpileaks-debug     # wrong!
mpileaks -debug    # right

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

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

Compiler Flags

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

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

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

Compiler environment variables and additional RPATHs

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

compilers:
  - compiler:
      spec: gcc@4.9.3
      paths:
        cc: /opt/gcc/bin/gcc
        c++: /opt/gcc/bin/g++
        f77: /opt/gcc/bin/gfortran
        fc: /opt/gcc/bin/gfortran
      environment:
        set:
          LD_LIBRARY_PATH : /opt/gcc/lib
      extra_rpaths:
      - /path/to/some/compiler/runtime/directory
      - /path/to/some/other/compiler/runtime/directory

Architecture specifiers

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

$ spack install libelf arch=cray-CNL10-haswell

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

Virtual dependencies

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

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

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

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

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

$ spack info mpich
AutotoolsPackage:   mpich

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

Homepage: http://www.mpich.org

Tags: 
    None

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

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

Variants:
    Name [Default]    Allowed values        Description


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

Installation Phases:
    autoreconf    configure    build    install

Build Dependencies:
    libfabric

Link Dependencies:
    libfabric

Run Dependencies:
    None

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

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

Constraining virtual packages

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

$ spack install mpileaks

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

$ spack install mpileaks ^mpich

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

$ spack install mpileaks ^mpich@3

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

Specifying Specs by Hash

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

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

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

You can then uninstall the latter installation using:

$ spack uninstall /er3die3

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

$ spack install trilinos ^/er3die3

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

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

spack providers

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

$ spack providers mpi
    intel-mpi                  mpich     mpich@3:  mvapich2@1.9   openmpi        openmpi@1.7.5:  spectrum-mpi
    intel-parallel-studio+mpi  mpich@1:  mvapich2  mvapich2@2.0:  openmpi@1.6.5  openmpi@2.0.0:

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

$ spack providers mpi@2
    intel-mpi                  mpich     mvapich2      mvapich2@2.0:  openmpi@1.6.5   openmpi@2.0.0:
    intel-parallel-studio+mpi  mpich@3:  mvapich2@1.9  openmpi        openmpi@1.7.5:  spectrum-mpi

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

Extensions & Python support

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

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

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

spack extensions

You can find extensions for your Python installation like this:

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

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

==> None activated.

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

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

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

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

Extensions & Environment Modules

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

For tcl modules:

$ spack load python
$ spack load py-numpy

or, for dotkit:

$ spack use python
$ spack use py-numpy

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

Activating Extensions

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

spack activate

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

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

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

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

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

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

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

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

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

spack activate --force

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

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

spack deactivate

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

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

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

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

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

    $ spack deactivate --all python
    

Filesystem requirements

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

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

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

This issue typically manifests with the error below:

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

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

Getting Help

spack help

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

$ spack help
usage: spack [-hkVcolor] <command> [...]

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

These are common spack commands:

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

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

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

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

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

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

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

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

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

build and install packages

positional arguments:
  package               spec of the package to install

optional arguments:
  -h, --help            show this help message and exit
  --only {package,dependencies}
                        select the mode of installation. the default is to
                        install the package along with all its dependencies.
                        alternatively one can decide to install only the
                        package or only the dependencies
  -j JOBS, --jobs JOBS  explicitly set number of make jobs. default is #cpus
  --overwrite           reinstall an existing spec, even if it has dependents
  --keep-prefix         don't remove the install prefix if installation fails
  --keep-stage          don't remove the build stage if installation succeeds
  --restage             if a partial install is detected, 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, --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.