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                           listres                                r-adabag
ack                              llvm                                   r-assertthat
activeharmony                    llvm-lld                               r-base64enc
adept-utils                      llvm-openmp-ompt                       r-bh
adios                            lmdb                                   r-biocgenerics
adlbx                            lmod                                   r-biocinstaller
adol-c                           lndir                                  r-bitops
allinea-forge                    log4cxx                                r-boot
allinea-reports                  lrslib                                 r-brew
ant                              lrzip                                  r-c50
antlr                            lua                                    r-car
ape                              lua-jit                                r-caret
apex                             lua-luafilesystem                      r-catools
applewmproto                     lua-luaposix                           r-checkpoint
appres                           luit                                   r-chron
apr                              lulesh                                 r-class
apr-util                         lwgrp                                  r-cluster
archer                           lwm2                                   r-codetools
armadillo                        lz4                                    r-coin
arpack                           lzma                                   r-colorspace
arpack-ng                        lzo                                    r-corrplot
asciidoc                         m4                                     r-crayon
astra                            mafft                                  r-cubature
astyle                           magics                                 r-cubist
atk                              magma                                  r-curl
atlas                            makedepend                             r-data-table
atompaw                          mariadb                                r-dbi
atop                             matio                                  r-deoptim
autoconf                         matlab                                 r-devtools
autogen                          maven                                  r-diagrammer
automaded                        mawk                                   r-dichromat
automake                         mbedtls                                r-digest
bamtools                         mdtest                                 r-domc
bash                             meep                                   r-doparallel
bash-completion                  memaxes                                r-dplyr
bats                             mercurial                              r-dt
bazel                            mesa                                   r-dygraphs
bbcp                             metis                                  r-e1071
bcftools                         mfem                                   r-ellipse
bdftopcf                         miniconda2                             r-evaluate
bdw-gc                           miniconda3                             r-filehash
bear                             mitos                                  r-foreach
bedtools2                        mkfontdir                              r-foreign
beforelight                      mkfontscale                            r-formatr
bertini                          moab                                   r-formula
bib2xhtml                        mosh                                   r-gdata
bigreqsproto                     mozjs                                  r-geosphere
binutils                         mpc                                    r-ggmap
bison                            mpe2                                   r-ggplot2
bitmap                           mpfr                                   r-ggvis
blast-plus                       mpibash                                r-gistr
blat                             mpich                                  r-git2r
bliss                            mpileaks                               r-glmnet
blitz                            mpip                                   r-googlevis
boost                            mpir                                   r-gridbase
bowtie2                          mrnet                                  r-gridextra
boxlib                           msgpack-c                              r-gtable
bpp-core                         mummer                                 r-gtools
bpp-phyl                         mumps                                  r-hexbin
bpp-seq                          munge                                  r-highr
bpp-suite                        muparser                               r-htmltools
bwa                              muster                                 r-htmlwidgets
bzip2                            mvapich2                               r-httpuv
c-blosc                          mxml                                   r-httr
caffe                            nag                                    r-igraph
cairo                            nano                                   r-influencer
caliper                          nasm                                   r-inline
callpath                         nauty                                  r-ipred
cantera                          nccl                                   r-irdisplay
cask                             nccmp                                  r-irkernel
catch                            ncdu                                   r-irlba
cblas                            ncftp                                  r-iterators
cbtf                             ncl                                    r-jpeg
cbtf-argonavis                   nco                                    r-jsonlite
cbtf-krell                       ncurses                                r-kernlab
cbtf-lanl                        ncview                                 r-kernsmooth
ccache                           ndiff                                  r-kknn
cdd                              netcdf                                 r-knitr
cddlib                           netcdf-cxx                             r-labeling
cdo                              netcdf-cxx4                            r-lattice
cereal                           netcdf-fortran                         r-lava
cfitsio                          netgauge                               r-lazyeval
cgal                             netlib-lapack                          r-leaflet
cgm                              netlib-scalapack                       r-lme4
cgns                             nettle                                 r-lmtest
charm                            nextflow                               r-lubridate
cityhash                         nfft                                   r-magic
cleverleaf                       ninja                                  r-magrittr
clhep                            nmap                                   r-mapproj
cloog                            node-js                                r-maps
cmake                            notmuch                                r-maptools
cmocka                           npm                                    r-markdown
cmor                             nspr                                   r-mass
cnmem                            numdiff                                r-matrix
compiz                           nwchem                                 r-matrixmodels
compositeproto                   ocaml                                  r-mda
conduit                          oce                                    r-memoise
constype                         oclock                                 r-mgcv
converge                         octave                                 r-mime
coreutils                        octave-splines                         r-minqa
cosmomc                          octopus                                r-mlbench
cp2k                             ompss                                  r-modelmetrics
cppad                            ompt-openmp                            r-modeltools
cppcheck                         oniguruma                              r-multcomp
cppunit                          opari2                                 r-munsell
cram                             openblas                               r-mvtnorm
cryptopp                         opencoarrays                           r-ncdf4
cscope                           opencv                                 r-networkd3
cub                              openexr                                r-nlme
cube                             openfst                                r-nloptr
cuda                             openjpeg                               r-nmf
curl                             openmpi                                r-nnet
cvs                              openscenegraph                         r-np
czmq                             openspeedshop                          r-numderiv
daal                             openssl                                r-openssl
dakota                           opium                                  r-packrat
damageproto                      osu-micro-benchmarks                   r-pacman
damselfly                        otf                                    r-party
darshan-runtime                  otf2                                   r-partykit
darshan-util                     p4est                                  r-pbdzmq
datamash                         pagmo                                  r-pbkrtest
dbus                             panda                                  r-pkgmaker
dealii                           pango                                  r-plotrix
dejagnu                          papi                                   r-pls
dia                              paradiseo                              r-plyr
direnv                           parallel                               r-png
dmxproto                         parallel-netcdf                        r-praise
docbook-xml                      paraver                                r-prodlim
docbook-xsl                      paraview                               r-proto
double-conversion                parmetis                               r-pryr
doxygen                          parmgridgen                            r-quantmod
dri2proto                        parpack                                r-quantreg
dri3proto                        patch                                  r-r6
dtcmp                            patchelf                               r-randomforest
dyninst                          pcre                                   r-raster
editres                          pcre2                                  r-rbokeh
eigen                            pdsh                                   r-rcolorbrewer
elemental                        pdt                                    r-rcpp
elfutils                         perl                                   r-rcppeigen
elk                              petsc                                  r-registry
elpa                             pexsi                                  r-repr
emacs                            pfft                                   r-reshape2
encodings                        pflotran                               r-rgooglemaps
environment-modules              pgi                                    r-rinside
es                               pidx                                   r-rjava
esmf                             pigz                                   r-rjson
espresso                         piranha                                r-rjsonio
espressopp                       pixman                                 r-rmarkdown
etsf-io                          pkg-config                             r-rminer
everytrace                       planck-likelihood                      r-rmysql
everytrace-example               plumed                                 r-rngtools
evieext                          pmgr-collective                        r-rodbc
exmcutils                        pnfft                                  r-roxygen2
exodusii                         pngwriter                              r-rpart
exonerate                        pocl                                   r-rpart-plot
expat                            polymake                               r-rpostgresql
expect                           porta                                  r-rsnns
extrae                           postgresql                             r-rsqlite
exuberant-ctags                  ppl                                    r-rstan
farmhash                         prank                                  r-rstudioapi
fastqc                           presentproto                           r-rzmq
fastx-toolkit                    printproto                             r-sandwich
fenics                           proj                                   r-scales
ferret                           protobuf                               r-shiny
ffmpeg                           proxymngr                              r-sp
fftw                             psi4                                   r-sparsem
fish                             py-3to2                                r-stanheaders
fixesproto                       py-4suite-xml                          r-stringi
flex                             py-abipy                               r-stringr
flint                            py-alabaster                           r-strucchange
fltk                             py-apache-libcloud                     r-survey
flux                             py-appdirs                             r-survival
foam-extend                      py-appnope                             r-tarifx
font-adobe-100dpi                py-apscheduler                         r-testit
font-adobe-75dpi                 py-argcomplete                         r-testthat
font-adobe-utopia-100dpi         py-argparse                            r-th-data
font-adobe-utopia-75dpi          py-astroid                             r-threejs
font-adobe-utopia-type1          py-astropy                             r-tibble
font-alias                       py-attrs                               r-tidyr
font-arabic-misc                 py-autopep8                            r-ttr
font-bh-100dpi                   py-babel                               r-uuid
font-bh-75dpi                    py-backports-abc                       r-vcd
font-bh-lucidatypewriter-100dpi  py-backports-shutil-get-terminal-size  r-visnetwork
font-bh-lucidatypewriter-75dpi   py-backports-ssl-match-hostname        r-whisker
font-bh-ttf                      py-basemap                             r-withr
font-bh-type1                    py-beautifulsoup4                      r-xgboost
font-bitstream-100dpi            py-biopython                           r-xlconnect
font-bitstream-75dpi             py-bleach                              r-xlconnectjars
font-bitstream-speedo            py-blessings                           r-xlsx
font-bitstream-type1             py-bokeh                               r-xlsxjars
font-cronyx-cyrillic             py-boltons                             r-xml
font-cursor-misc                 py-bottleneck                          r-xtable
font-daewoo-misc                 py-brian                               r-xts
font-dec-misc                    py-brian2                              r-yaml
font-ibm-type1                   py-cclib                               r-zoo
font-isas-misc                   py-cdo                                 raja
font-jis-misc                    py-certifi                             random123
font-micro-misc                  py-cffi                                randrproto
font-misc-cyrillic               py-chardet                             ravel
font-misc-ethiopic               py-click                               readline
font-misc-meltho                 py-colorama                            recordproto
font-misc-misc                   py-configparser                        rename
font-mutt-misc                   py-coverage                            rendercheck
font-schumacher-misc             py-cpuinfo                             renderproto
font-screen-cyrillic             py-csvkit                              resourceproto
font-sony-misc                   py-current                             rgb
font-sun-misc                    py-cycler                              root
font-util                        py-cython                              rose
font-winitzki-cyrillic           py-dask                                rstart
font-xfree86-type1               py-dateutil                            rsync
fontcacheproto                   py-dbf                                 ruby
fontconfig                       py-decorator                           rust
fontsproto                       py-dev                                 rust-bindgen
fonttosfnt                       py-dill                                samrai
freetype                         py-docutils                            samtools
fslsfonts                        py-doxypy                              saws
fstobdf                          py-doxypypy                            sbt
funhpc                           py-elasticsearch                       scalasca
gasnet                           py-elephant                            scons
gawk                             py-emcee                               scorec-core
gbenchmark                       py-entrypoints                         scorep
gcc                              py-enum34                              scotch
gccmakedep                       py-epydoc                              scr
gconf                            py-et-xmlfile                          screen
gdal                             py-fasteners                           scripts
gdb                              py-flake8                              scrnsaverproto
gdk-pixbuf                       py-flask                               sctk
geant4                           py-flexx                               sdl2
gemmlowp                         py-funcsigs                            sdl2-image
geos                             py-functools32                         sed
gettext                          py-future                              seqtk
gflags                           py-futures                             serf
ghostscript                      py-genders                             sessreg
ghostscript-fonts                py-genshi                              setxkbmap
giflib                           py-git-review                          sga
git                              py-git2                                showfont
git-lfs                          py-gnuplot                             silo
gl2ps                            py-guidata                             simul
glew                             py-guiqwt                              simulationio
glib                             py-h5py                                slepc
glm                              py-html2text                           smproxy
global                           py-html5lib                            snakemake
globus-toolkit                   py-httpbin                             snappy
glog                             py-imagesize                           sowing
glpk                             py-iminuit                             spark
glproto                          py-importlib                           sparsehash
gmake                            py-ipdb                                spdlog
gmime                            py-ipykernel                           spectrum-mpi
gmp                              py-ipython                             speex
gmsh                             py-ipython-genutils                    sph2pipe
gnu-prolog                       py-ipywidgets                          spindle
gnuplot                          py-itsdangerous                        spot
gnutls                           py-jdcal                               sqlite
go                               py-jedi                                sst-dumpi
go-bootstrap                     py-jinja2                              sst-macro
gobject-introspection            py-joblib                              staden-io-lib
googletest                       py-jpype                               star-ccm-plus
gource                           py-jsonschema                          stat
gperf                            py-junit-xml                           stc
gperftools                       py-jupyter-client                      stream
grackle                          py-jupyter-console                     sublime-text
gradle                           py-jupyter-core                        subversion
grandr                           py-jupyter-notebook                    suite-sparse
graphlib                         py-keras                               sundials
graphviz                         py-lazy                                superlu
grib-api                         py-lazyarray                           superlu-dist
gromacs                          py-lit                                 superlu-mt
gsl                              py-lmfit                               swiftsim
gtkplus                          py-lockfile                            swig
gts                              py-logilab-common                      symengine
guile                            py-lxml                                sympol
h5hut                            py-macs2                               sz
hadoop                           py-mako                                szip
harfbuzz                         py-markdown                            talloc
harminv                          py-markupsafe                          tar
hdf                              py-matplotlib                          task
hdf5                             py-mccabe                              taskd
hdf5-blosc                       py-meep                                tau
help2man                         py-mistune                             tbb
hepmc                            py-mock                                tcl
heppdt                           py-mongo                               tetgen
highwayhash                      py-monotonic                           tethex
hmmer                            py-monty                               texinfo
hoomd-blue                       py-mpi4py                              texlive
hpctoolkit                       py-mpmath                              the-platinum-searcher
hpctoolkit-externals             py-multiprocess                        the-silver-searcher
hpl                              py-mx                                  thrift
hpx5                             py-myhdl                               tinyxml
hsakmt                           py-mysqldb1                            tinyxml2
htop                             py-nbconvert                           tk
htslib                           py-nbformat                            tmux
httpie                           py-neo                                 tmuxinator
hub                              py-nestle                              transset
hunspell                         py-netcdf4                             trapproto
hwloc                            py-netifaces                           tree
hydra                            py-networkx                            triangle
hypre                            py-nose                                trilinos
ibmisc                           py-nosexcover                          turbine
iceauth                          py-numexpr                             turbomole
icet                             py-numpy                               twm
ico                              py-numpydoc                            uberftp
icu4c                            py-openpyxl                            udunits2
ilmbase                          py-ordereddict                         uncrustify
image-magick                     py-packaging                           unibilium
imake                            py-palettable                          unison
inputproto                       py-pandas                              units
intel                            py-pathlib2                            unixodbc
intel-gpu-tools                  py-pathos                              util-linux
intel-mkl                        py-pathspec                            util-macros
intel-parallel-studio            py-patsy                               uuid
intltool                         py-pbr                                 valgrind
ior                              py-periodictable                       vc
ipopt                            py-petsc4py                            vcsh
ipp                              py-pexpect                             vdt
isl                              py-phonopy                             vecgeom
itstool                          py-pickleshare                         veclibfort
jansson                          py-pil                                 videoproto
jasper                           py-pillow                              viewres
jdk                              py-pip                                 vim
jemalloc                         py-ply                                 visit
jmol                             py-pmw                                 vizglow
jpeg                             py-pox                                 voropp
jq                               py-ppft                                vtk
jsoncpp                          py-prettytable                         wannier90
judy                             py-proj                                wget
julia                            py-prompt-toolkit                      windowswmproto
kaldi                            py-protobuf                            wx
kbproto                          py-psutil                              wxpropgrid
kdiff3                           py-ptyprocess                          x11perf
kealib                           py-pudb                                xapian-core
kripke                           py-py                                  xauth
lammps                           py-py2cairo                            xbacklight
launchmon                        py-py2neo                              xbiff
lbann                            py-py4j                                xbitmaps
lbxproxy                         py-pychecker                           xcalc
lcms                             py-pycodestyle                         xcb-demo
leveldb                          py-pycparser                           xcb-proto
libaio                           py-pycurl                              xcb-util
libapplewm                       py-pydatalog                           xcb-util-cursor
libarchive                       py-pydispatcher                        xcb-util-errors
libatomic-ops                    py-pydot                               xcb-util-image
libbson                          py-pyelftools                          xcb-util-keysyms
libcanberra                      py-pyfftw                              xcb-util-renderutil
libcap                           py-pyflakes                            xcb-util-wm
libcerf                          py-pygments                            xclipboard
libcircle                        py-pygobject                           xclock
libctl                           py-pygtk                               xcmiscproto
libdmx                           py-pylint                              xcmsdb
libdrm                           py-pymatgen                            xcompmgr
libdwarf                         py-pyminifier                          xconsole
libedit                          py-pympler                             xcursor-themes
libelf                           py-pynn                                xcursorgen
libemos                          py-pypar                               xdbedizzy
libepoxy                         py-pyparsing                           xditview
libevent                         py-pyqt                                xdm
libffi                           py-pyserial                            xdpyinfo
libfontenc                       py-pyside                              xdriinfo
libfs                            py-pysocks                             xedit
libgcrypt                        py-pytables                            xerces-c
libgd                            py-pytest                              xev
libgit2                          py-pytest-cov                          xextproto
libgpg-error                     py-pytest-flake8                       xeyes
libgpuarray                      py-pytest-httpbin                      xf86bigfontproto
libgtextutils                    py-pytest-mock                         xf86dga
libhio                           py-python-daemon                       xf86dgaproto
libice                           py-pythonqwt                           xf86driproto
libiconv                         py-pytz                                xf86miscproto
libint                           py-pyyaml                              xf86rushproto
libjpeg-turbo                    py-qtawesome                           xf86vidmodeproto
libjson-c                        py-qtconsole                           xfd
liblbxutil                       py-qtpy                                xfindproxy
libmesh                          py-quantities                          xfontsel
libmng                           py-radical-utils                       xfs
libmongoc                        py-ranger                              xfsinfo
libmonitor                       py-readme-renderer                     xfwp
libnbc                           py-requests                            xgamma
libogg                           py-restview                            xgc
liboldx                          py-rope                                xhost
libpciaccess                     py-rpy2                                xineramaproto
libpng                           py-rtree                               xinit
libpthread-stubs                 py-saga-python                         xinput
libquo                           py-scientificpython                    xkbcomp
libsigsegv                       py-scikit-image                        xkbdata
libsm                            py-scikit-learn                        xkbevd
libsodium                        py-scipy                               xkbprint
libspatialindex                  py-seaborn                             xkbutils
libsplash                        py-setuptools                          xkeyboard-config
libssh2                          py-sh                                  xkill
libtermkey                       py-shiboken                            xload
libtiff                          py-simplegeneric                       xlogo
libtool                          py-singledispatch                      xlsatoms
libunistring                     py-sip                                 xlsclients
libunwind                        py-six                                 xlsfonts
libuuid                          py-slepc4py                            xmag
libuv                            py-sncosmo                             xman
libvorbis                        py-snowballstemmer                     xmessage
libvterm                         py-spglib                              xmh
libwebsockets                    py-sphinx                              xmlto
libwindowswm                     py-sphinx-bootstrap-theme              xmodmap
libx11                           py-sphinx-rtd-theme                    xmore
libxau                           py-spyder                              xorg-cf-files
libxaw                           py-spykeutils                          xorg-docs
libxaw3d                         py-sqlalchemy                          xorg-gtest
libxc                            py-statsmodels                         xorg-server
libxcb                           py-storm                               xorg-sgml-doctools
libxcomposite                    py-symengine                           xphelloworld
libxcursor                       py-symfit                              xplsprinters
libxdamage                       py-sympy                               xpr
libxdmcp                         py-tabulate                            xprehashprinterlist
libxevie                         py-tappy                               xprop
libxext                          py-terminado                           xproto
libxfixes                        py-theano                              xproxymanagementprotocol
libxfont                         py-tornado                             xrandr
libxfont2                        py-tqdm                                xrdb
libxfontcache                    py-traitlets                           xrefresh
libxft                           py-tuiview                             xrootd
libxi                            py-twisted                             xrx
libxinerama                      py-tzlocal                             xscope
libxkbfile                       py-unittest2                           xsdktrilinos
libxkbui                         py-unittest2py3k                       xset
libxml2                          py-urllib3                             xsetmode
libxmu                           py-urwid                               xsetpointer
libxp                            py-vcversioner                         xsetroot
libxpm                           py-virtualenv                          xsm
libxpresent                      py-wcsaxes                             xstdcmap
libxprintapputil                 py-wcwidth                             xterm
libxprintutil                    py-werkzeug                            xtrans
libxrandr                        py-wheel                               xtrap
libxrender                       py-widgetsnbextension                  xts
libxres                          py-wrapt                               xvidtune
libxscrnsaver                    py-xarray                              xvinfo
libxshmfence                     py-xlrd                                xwd
libxslt                          py-xmlrunner                           xwininfo
libxsmm                          py-xpyb                                xwud
libxstream                       py-yapf                                xz
libxt                            py-yt                                  yaml-cpp
libxtrap                         py-zmq                                 yasm
libxtst                          python                                 yorick
libxv                            qhull                                  zeromq
libxvmc                          qrupdate                               zfp
libxxf86dga                      qt                                     zlib
libxxf86misc                     qt-creator                             zoltan
libxxf86vm                       qthreads                               zsh
likwid                           r                                      zstd
linux-headers                    r-abind

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  sqlite

All packages whose names or descriptions contain documentation:

$ spack list --search-description documentation
compositeproto     doxygen    libxpresent   py-epydoc    r-ggplot2  r-roxygen2     texinfo
damageproto        gflags     py-alabaster  py-markdown  r-rcpp     r-stanheaders  xorg-docs
double-conversion  libxfixes  py-docutils   py-sphinx    r-rinside  sowing         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
Homepage:            http://www.mpich.org

Safe versions:  
    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   Description

    hydra    on        Build the hydra process manager
    pmi      on        Build with PMI support
    romio    on        Enable ROMIO MPI I/O implementation
    verbs    off       Build support for OpenFabrics verbs.

Installation Phases:
    autoreconf    configure    build    install

Build Dependencies:
    None

Link Dependencies:
    None

Run Dependencies:
    None

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

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

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
Homepage:            http://www.mpich.org

Safe versions:  
    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   Description

    hydra    on        Build the hydra process manager
    pmi      on        Build with PMI support
    romio    on        Enable ROMIO MPI I/O implementation
    verbs    off       Build support for OpenFabrics verbs.

Installation Phases:
    autoreconf    configure    build    install

Build Dependencies:
    None

Link Dependencies:
    None

Run Dependencies:
    None

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

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

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, for example when using the uninstall command. 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. If the given spec hash is sufficient 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 depencency 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-parallel-studio@cluster:+mpi  mpich@3:      mvapich2@2.0:  openmpi@1.7.5:  spectrum-mpi
    mpich@1:                            mvapich2@1.9  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-parallel-studio@cluster:+mpi  mvapich2@1.9   openmpi@1.6.5   openmpi@2.0.0:
    mpich@3:                            mvapich2@2.0:  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 Shell support. 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 [-h] [-d] [-D] [-k] [-m] [-p] [-v] [-s] [-V] SUBCOMMAND ...

Spack: the Supercomputing PACKage Manager.

spec expressions:
  PACKAGE [CONSTRAINTS]

    CONSTRAINTS:
      @version
      %compiler  @compiler_version
      +variant
      -variant or ~variant
      =architecture
      [^DEPENDENCY [CONSTRAINTS] ...]

positional arguments:
  SUBCOMMAND
    activate        activate a package extension
    arch            print architecture information about this machine
    bootstrap       create a new installation of spack in another prefix
    build           stops at build stage when installing a package, if possible
    cd              cd to spack directories in the shell
    checksum        checksum available versions of a package
    clean           remove build stage and source tarball for packages
    compiler        manage compilers
    compilers       list available compilers, same as 'spack compiler list'
    config          get and set configuration options
    configure       stops at configuration stage when installing a package, if possible
    create          create a new package file
    deactivate      deactivate a package extension
    debug           debugging commands for troubleshooting Spack
    dependents      show installed packages that depend on another
    diy             do-it-yourself: build from an existing source directory
    doc             run pydoc from within spack
    edit            open package files in $EDITOR
    env             run a command with the install environment for a spec
    extensions      list extensions for package
    fetch           fetch archives for packages
    find            find installed spack packages
    flake8          runs source code style checks on Spack. requires flake8
    graph           generate graphs of package dependency relationships
    help            get help on spack and its commands
    info            get detailed information on a particular package
    install         build and install packages
    list            print available spack packages to stdout in different formats
    load            add package to environment using modules
    location        print out locations of various directories used by Spack
    md5             calculate md5 checksums for files/urls
    mirror          manage mirrors
    module          manipulate module files
    patch           patch expanded archive sources in preparation for install
    pkg             query packages associated with particular git revisions
    providers       list packages that provide a particular virtual package
    purge           remove temporary build files and/or downloaded archives
    python          launch an interpreter as spack would launch a command
    reindex         rebuild Spack's package database
    repo            manage package source repositories
    restage         revert checked out package source code
    setup           create a configuration script and module, but don't build
    spec            print out abstract and concrete versions of a spec
    stage           expand downloaded archive in preparation for install
    test            a thin wrapper around the pytest command
    uninstall       remove an installed package
    unload          remove package from environment using module
    unuse           remove package from environment using dotkit
    url             debugging tool for url parsing
    use             add package to environment using dotkit
    versions        list available versions of a package
    view            produce a single-rooted directory view of a spec

optional arguments:
  -h, --help        show this help message and exit
  -d, --debug       write out debug logs during compile
  -D, --pdb         run spack under the pdb debugger
  -k, --insecure    do not check ssl certificates when downloading
  -m, --mock        use mock packages instead of real ones
  -p, --profile     profile execution using cProfile
  -v, --verbose     print additional output during builds
  -s, --stacktrace  add stacktrace information to all printed statements
  -V, --version     show program's version number and exit

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]
                     [--keep-prefix] [--keep-stage] [-n] [-v] [--fake]
                     [--clean | --dirty] [--run-tests] [--log-format {junit}]
                     [--log-file LOG_FILE]
                     ...

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
  --keep-prefix         don't remove the install prefix if installation fails
  --keep-stage          don't remove the build stage if installation succeeds
  -n, --no-checksum     do not check packages against checksum
  -v, --verbose         display verbose build output while installing
  --fake                fake install. just remove prefix and create a fake
                        file
  --clean               clean environment before installing package
  --dirty               do NOT clean environment before installing
  --run-tests           run package level tests during installation
  --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

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