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                           llvm                                   py-xopen
ack                              llvm-lld                               py-xpyb
activeharmony                    llvm-openmp-ompt                       py-xvfbwrapper
adept-utils                      lmdb                                   py-yapf
adios                            lmod                                   py-yt
adlbx                            lndir                                  py-zmq
adol-c                           log4cxx                                python
allinea-forge                    lrslib                                 qbank
allinea-reports                  lrzip                                  qhull
alquimia                         lua                                    qrupdate
ant                              lua-jit                                qt
antlr                            lua-luafilesystem                      qt-creator
ape                              lua-luaposix                           qthreads
apex                             luit                                   r
applewmproto                     lulesh                                 r-abind
appres                           lwgrp                                  r-adabag
apr                              lwm2                                   r-assertthat
apr-util                         lz4                                    r-base64enc
archer                           lzma                                   r-bh
armadillo                        lzo                                    r-biocgenerics
arpack                           m4                                     r-biocinstaller
arpack-ng                        mad-numdiff                            r-bitops
asciidoc                         mafft                                  r-boot
astra                            magics                                 r-brew
astyle                           magma                                  r-c50
atk                              makedepend                             r-car
atlas                            mallocmc                               r-caret
atompaw                          mariadb                                r-catools
atop                             matio                                  r-checkpoint
autoconf                         matlab                                 r-chron
autogen                          maven                                  r-class
automaded                        mawk                                   r-cluster
automake                         mbedtls                                r-coda
bamtools                         mdtest                                 r-codetools
bash                             meep                                   r-coin
bash-completion                  memaxes                                r-colorspace
bats                             meme                                   r-corrplot
bazel                            mercurial                              r-crayon
bbcp                             mesa                                   r-cubature
bcftools                         mesa-glu                               r-cubist
bcl2fastq2                       mesquite                               r-curl
bdftopcf                         metis                                  r-data-table
bdw-gc                           mfem                                   r-dbi
bear                             miniconda2                             r-deoptim
bedtools2                        miniconda3                             r-deoptimr
beforelight                      mitos                                  r-devtools
benchmark                        mkfontdir                              r-diagrammer
bertini                          mkfontscale                            r-dichromat
bib2xhtml                        moab                                   r-digest
bigreqsproto                     mosh                                   r-domc
binutils                         mozjs                                  r-doparallel
bison                            mpc                                    r-dplyr
bitmap                           mpe2                                   r-dt
blast-plus                       mpfr                                   r-dygraphs
blat                             mpibash                                r-e1071
blaze                            mpich                                  r-ellipse
bliss                            mpifileutils                           r-ergm
blitz                            mpileaks                               r-evaluate
boost                            mpip                                   r-filehash
boostmplcartesianproduct         mpir                                   r-foreach
bowtie                           mrnet                                  r-foreign
bowtie2                          msgpack-c                              r-formatr
boxlib                           multiverso                             r-formula
bpp-core                         mummer                                 r-gdata
bpp-phyl                         mumps                                  r-geosphere
bpp-seq                          munge                                  r-ggmap
bpp-suite                        muparser                               r-ggplot2
brigand                          muster                                 r-ggvis
bwa                              mvapich2                               r-gistr
bzip2                            mxml                                   r-git2r
c-blosc                          nag                                    r-glmnet
caffe                            nano                                   r-gmp
cairo                            nasm                                   r-googlevis
caliper                          nauty                                  r-gridbase
callpath                         nccl                                   r-gridextra
cantera                          nccmp                                  r-gtable
cask                             ncdu                                   r-gtools
catch                            ncftp                                  r-hexbin
cbench                           ncl                                    r-highr
cblas                            nco                                    r-htmltools
cbtf                             ncurses                                r-htmlwidgets
cbtf-argonavis                   ncview                                 r-httpuv
cbtf-krell                       ndiff                                  r-httr
cbtf-lanl                        netcdf                                 r-igraph
ccache                           netcdf-cxx                             r-influencer
cdd                              netcdf-cxx4                            r-inline
cddlib                           netcdf-fortran                         r-ipred
cdo                              netgauge                               r-irdisplay
cereal                           netlib-lapack                          r-irkernel
cfitsio                          netlib-scalapack                       r-irlba
cgal                             nettle                                 r-iterators
cgm                              nextflow                               r-jpeg
cgns                             nfft                                   r-jsonlite
charm                            nginx                                  r-kernlab
chombo                           ninja                                  r-kernsmooth
cityhash                         nmap                                   r-kknn
cleverleaf                       node-js                                r-knitr
clhep                            notmuch                                r-labeling
cloog                            npb                                    r-laplacesdemon
cmake                            npm                                    r-lattice
cmocka                           npth                                   r-lava
cmor                             nspr                                   r-lazyeval
cnmem                            numdiff                                r-leaflet
cntk                             nwchem                                 r-lme4
cntk1bitsgd                      ocaml                                  r-lmtest
compiz                           oce                                    r-lpsolve
compositeproto                   oclock                                 r-lubridate
conduit                          octave                                 r-magic
constype                         octave-splines                         r-magrittr
converge                         octopus                                r-mapproj
coreutils                        ompss                                  r-maps
cosmomc                          ompt-openmp                            r-maptools
cp2k                             oniguruma                              r-markdown
cppad                            ont-albacore                           r-mass
cppcheck                         opari2                                 r-matrix
cpprestsdk                       openbabel                              r-matrixmodels
cppunit                          openblas                               r-mda
cram                             opencoarrays                           r-memoise
cryptopp                         opencv                                 r-mgcv
cscope                           openexr                                r-mime
cub                              openfoam-com                           r-minqa
cube                             openfoam-org                           r-mlbench
cuda                             openfst                                r-modelmetrics
cuda-memtest                     openjpeg                               r-modeltools
cudnn                            openmpi                                r-multcomp
curl                             openscenegraph                         r-munsell
cvs                              openspeedshop                          r-mvtnorm
czmq                             openssh                                r-ncdf4
dakota                           openssl                                r-network
damageproto                      opium                                  r-networkd3
damselfly                        opus                                   r-nlme
darshan-runtime                  osu-micro-benchmarks                   r-nloptr
darshan-util                     otf                                    r-nmf
dash                             otf2                                   r-nnet
datamash                         p4est                                  r-np
dbus                             pagmo                                  r-numderiv
dealii                           panda                                  r-openssl
dejagnu                          pango                                  r-packrat
dia                              papi                                   r-pacman
direnv                           paradiseo                              r-party
dmxproto                         parallel                               r-partykit
docbook-xml                      parallel-netcdf                        r-pbdzmq
docbook-xsl                      paraver                                r-pbkrtest
dos2unix                         paraview                               r-pkgmaker
double-conversion                parmetis                               r-plotrix
doxygen                          parmgridgen                            r-pls
dri2proto                        parpack                                r-plyr
dri3proto                        patch                                  r-png
dtcmp                            patchelf                               r-praise
dyninst                          pax-utils                              r-prodlim
easybuild                        pcre                                   r-proto
eccodes                          pcre2                                  r-pryr
editres                          pdsh                                   r-quadprog
eigen                            pdt                                    r-quantmod
elemental                        pegtl                                  r-quantreg
elfutils                         perl                                   r-r6
elk                              perl-dbi                               r-randomforest
elpa                             perl-extutils-makemaker                r-raster
emacs                            perl-module-build                      r-rbokeh
encodings                        perl-term-readkey                      r-rcolorbrewer
environment-modules              perl-xml-parser                        r-rcpp
es                               petsc                                  r-rcppeigen
esmf                             pexsi                                  r-registry
espresso                         pfft                                   r-repr
espressopp                       pflotran                               r-reshape2
etsf-io                          pgi                                    r-rgl
everytrace                       phasta                                 r-rgooglemaps
everytrace-example               pidx                                   r-rinside
evieext                          pigz                                   r-rjava
exmcutils                        piranha                                r-rjson
exodusii                         pixman                                 r-rjsonio
exonerate                        pkg-config                             r-rmarkdown
expat                            planck-likelihood                      r-rminer
expect                           plumed                                 r-rmpfr
extrae                           pmgr-collective                        r-rmpi
exuberant-ctags                  pnfft                                  r-rmysql
f90cache                         pngwriter                              r-rngtools
farmhash                         pocl                                   r-robustbase
fastmath                         polymake                               r-rodbc
fastqc                           porta                                  r-roxygen2
fastx-toolkit                    portage                                r-rpart
fenics                           postgresql                             r-rpart-plot
ferret                           ppl                                    r-rpostgresql
ffmpeg                           prank                                  r-rsnns
fftw                             presentproto                           r-rsqlite
findutils                        printproto                             r-rstan
fio                              proj                                   r-rstudioapi
fish                             protobuf                               r-rzmq
fixesproto                       proxymngr                              r-sandwich
flac                             pruners-ninja                          r-scales
flann                            psi4                                   r-shiny
flash                            pstreams                               r-snow
flecsale                         pugixml                                r-sp
flecsi                           pumi                                   r-sparsem
flex                             pvm                                    r-stanheaders
flint                            py-3to2                                r-statnet-common
fltk                             py-4suite-xml                          r-stringi
flux                             py-abipy                               r-stringr
foam-extend                      py-alabaster                           r-strucchange
font-adobe-100dpi                py-apache-libcloud                     r-survey
font-adobe-75dpi                 py-appdirs                             r-survival
font-adobe-utopia-100dpi         py-appnope                             r-tarifx
font-adobe-utopia-75dpi          py-apscheduler                         r-testit
font-adobe-utopia-type1          py-argcomplete                         r-testthat
font-alias                       py-argparse                            r-th-data
font-arabic-misc                 py-asn1crypto                          r-threejs
font-bh-100dpi                   py-astroid                             r-tibble
font-bh-75dpi                    py-astropy                             r-tidyr
font-bh-lucidatypewriter-100dpi  py-attrs                               r-trust
font-bh-lucidatypewriter-75dpi   py-autopep8                            r-ttr
font-bh-ttf                      py-babel                               r-uuid
font-bh-type1                    py-backports-abc                       r-vcd
font-bitstream-100dpi            py-backports-shutil-get-terminal-size  r-visnetwork
font-bitstream-75dpi             py-backports-ssl-match-hostname        r-whisker
font-bitstream-speedo            py-basemap                             r-withr
font-bitstream-type1             py-beautifulsoup4                      r-xgboost
font-cronyx-cyrillic             py-biopython                           r-xlconnect
font-cursor-misc                 py-bleach                              r-xlconnectjars
font-daewoo-misc                 py-blessings                           r-xlsx
font-dec-misc                    py-bokeh                               r-xlsxjars
font-ibm-type1                   py-boltons                             r-xml
font-isas-misc                   py-bottleneck                          r-xtable
font-jis-misc                    py-brian                               r-xts
font-micro-misc                  py-brian2                              r-yaml
font-misc-cyrillic               py-cclib                               r-zoo
font-misc-ethiopic               py-cdat-lite                           raja
font-misc-meltho                 py-cdo                                 random123
font-misc-misc                   py-certifi                             randrproto
font-mutt-misc                   py-cffi                                ravel
font-schumacher-misc             py-chardet                             readline
font-screen-cyrillic             py-click                               recordproto
font-sony-misc                   py-colorama                            relion
font-sun-misc                    py-configparser                        rempi
font-util                        py-coverage                            rename
font-winitzki-cyrillic           py-cpuinfo                             rendercheck
font-xfree86-type1               py-cryptography                        renderproto
fontcacheproto                   py-csvkit                              resourceproto
fontconfig                       py-current                             rgb
fontsproto                       py-cutadapt                            rockstar
fonttosfnt                       py-cycler                              root
freetype                         py-cython                              rose
fslsfonts                        py-dask                                rstart
fstobdf                          py-dateutil                            rsync
funhpc                           py-dbf                                 ruby
gasnet                           py-decorator                           rust
gawk                             py-dev                                 rust-bindgen
gbenchmark                       py-dill                                samrai
gcc                              py-docutils                            samtools
gccmakedep                       py-doxypy                              sas
gccxml                           py-doxypypy                            saws
gconf                            py-dryscrape                           sbt
gdal                             py-easybuild-easyblocks                scala
gdb                              py-easybuild-easyconfigs               scalasca
gdbm                             py-easybuild-framework                 scons
gdk-pixbuf                       py-elasticsearch                       scorec-core
geant4                           py-elephant                            scorep
gemmlowp                         py-emcee                               scotch
geos                             py-entrypoints                         scr
gettext                          py-enum34                              screen
gflags                           py-epydoc                              scripts
ghostscript                      py-et-xmlfile                          scrnsaverproto
ghostscript-fonts                py-fasteners                           sctk
giflib                           py-fiscalyear                          sdl2
git                              py-flake8                              sdl2-image
git-lfs                          py-flask                               sed
gl2ps                            py-flexx                               seqtk
glew                             py-funcsigs                            serf
glib                             py-functools32                         sessreg
glm                              py-future                              setxkbmap
global                           py-futures                             sga
globalarrays                     py-genders                             shiny-server
globus-toolkit                   py-genshi                              showfont
glog                             py-git-review                          silo
glpk                             py-git2                                simul
glproto                          py-gnuplot                             simulationio
gmake                            py-griddataformats                     slepc
gmime                            py-guidata                             smproxy
gmp                              py-guiqwt                              snakemake
gmsh                             py-h5py                                snappy
gnat                             py-html2text                           sowing
gnu-prolog                       py-html5lib                            sox
gnupg                            py-httpbin                             spark
gnuplot                          py-hypothesis                          sparsehash
gnutls                           py-idna                                spdlog
go                               py-imagesize                           spectrum-mpi
go-bootstrap                     py-iminuit                             speex
gobject-introspection            py-importlib                           sph2pipe
googletest                       py-ipaddress                           spherepack
gource                           py-ipdb                                spindle
gperf                            py-ipykernel                           spot
gperftools                       py-ipython                             sqlite
grackle                          py-ipython-genutils                    sst-dumpi
gradle                           py-ipywidgets                          sst-macro
grandr                           py-itsdangerous                        staden-io-lib
graphlib                         py-jdcal                               star-ccm-plus
graphviz                         py-jedi                                stat
grib-api                         py-jinja2                              stc
gromacs                          py-joblib                              stream
gsl                              py-jpype                               stress
gtkplus                          py-jsonschema                          sublime-text
gts                              py-junit-xml                           subversion
guile                            py-jupyter-client                      suite-sparse
h5hut                            py-jupyter-console                     sundials
h5part                           py-jupyter-core                        superlu
hadoop                           py-jupyter-notebook                    superlu-dist
harfbuzz                         py-keras                               superlu-mt
harminv                          py-lazy                                swiftsim
hdf                              py-lazyarray                           swig
hdf5                             py-libconf                             symengine
hdf5-blosc                       py-lit                                 sympol
help2man                         py-lmfit                               sz
hepmc                            py-lockfile                            szip
heppdt                           py-logilab-common                      talloc
highfive                         py-lxml                                tar
highwayhash                      py-macs2                               task
hmmer                            py-mako                                taskd
hoomd-blue                       py-markdown                            tau
hpctoolkit                       py-markupsafe                          tbb
hpctoolkit-externals             py-matplotlib                          tcl
hpl                              py-mccabe                              tetgen
hpx5                             py-mdanalysis                          tethex
hsakmt                           py-meep                                texinfo
hstr                             py-mistune                             texlive
htop                             py-mock                                the-platinum-searcher
htslib                           py-mongo                               the-silver-searcher
httpie                           py-monotonic                           thrift
hub                              py-monty                               tinyxml
hunspell                         py-mpi4py                              tinyxml2
hwloc                            py-mpmath                              tk
hydra                            py-multiprocess                        tmux
hypre                            py-mx                                  tmuxinator
ibmisc                           py-myhdl                               transset
iceauth                          py-mysqldb1                            trapproto
icet                             py-nbconvert                           tree
ico                              py-nbformat                            triangle
icu4c                            py-neo                                 trilinos
id3lib                           py-nestle                              turbine
ilmbase                          py-netcdf4                             turbomole
image-magick                     py-netifaces                           tut
imake                            py-networkx                            twm
inputproto                       py-nose                                uberftp
intel                            py-nosexcover                          udunits2
intel-daal                       py-numexpr                             uncrustify
intel-gpu-tools                  py-numpy                               unibilium
intel-ipp                        py-numpydoc                            unison
intel-mkl                        py-ont-fast5-api                       units
intel-mpi                        py-openpyxl                            unixodbc
intel-parallel-studio            py-ordereddict                         util-linux
intltool                         py-packaging                           util-macros
ior                              py-palettable                          uuid
iozone                           py-pandas                              valgrind
ipopt                            py-paramiko                            vampirtrace
isaac                            py-pathlib2                            vc
isaac-server                     py-pathos                              vcsh
isl                              py-pathspec                            vdt
itstool                          py-patsy                               vecgeom
jansson                          py-pbr                                 veclibfort
jasper                           py-periodictable                       videoproto
jdk                              py-petsc4py                            viewres
jemalloc                         py-pexpect                             vim
jmol                             py-phonopy                             virtualgl
jpeg                             py-pickleshare                         visit
jq                               py-pil                                 vizglow
json-c                           py-pillow                              voropp
jsoncpp                          py-pip                                 votca-csg
judy                             py-pkgconfig                           votca-tools
julia                            py-ply                                 vtk
kaldi                            py-pmw                                 wannier90
kbproto                          py-pox                                 wget
kdiff3                           py-ppft                                windowswmproto
kealib                           py-prettytable                         wx
kokkos                           py-proj                                wxpropgrid
kripke                           py-prompt-toolkit                      x11perf
lammps                           py-protobuf                            xapian-core
launchmon                        py-psutil                              xauth
lbann                            py-ptyprocess                          xbacklight
lbxproxy                         py-pudb                                xbiff
lcms                             py-py                                  xbitmaps
legion                           py-py2cairo                            xcalc
leveldb                          py-py2neo                              xcb-demo
libaio                           py-py4j                                xcb-proto
libapplewm                       py-pyasn1                              xcb-util
libarchive                       py-pychecker                           xcb-util-cursor
libassuan                        py-pycodestyle                         xcb-util-errors
libatomic-ops                    py-pycparser                           xcb-util-image
libbson                          py-pycrypto                            xcb-util-keysyms
libcanberra                      py-pycurl                              xcb-util-renderutil
libcap                           py-pydatalog                           xcb-util-wm
libcerf                          py-pydispatcher                        xclipboard
libcircle                        py-pydot                               xclock
libconfig                        py-pyelftools                          xcmiscproto
libctl                           py-pyfftw                              xcmsdb
libdmx                           py-pyflakes                            xcompmgr
libdrm                           py-pygments                            xconsole
libdwarf                         py-pygobject                           xcursor-themes
libedit                          py-pygtk                               xcursorgen
libelf                           py-pylint                              xdbedizzy
libemos                          py-pymatgen                            xditview
libepoxy                         py-pyminifier                          xdm
libevent                         py-pympler                             xdpyinfo
libffi                           py-pynn                                xdriinfo
libfontenc                       py-pypar                               xedit
libfs                            py-pyparsing                           xerces-c
libgcrypt                        py-pyprof2html                         xev
libgd                            py-pyqt                                xextproto
libgit2                          py-pyserial                            xeyes
libgpg-error                     py-pyside                              xf86bigfontproto
libgpuarray                      py-pysocks                             xf86dga
libgtextutils                    py-pytables                            xf86dgaproto
libhio                           py-pytest                              xf86driproto
libice                           py-pytest-cov                          xf86miscproto
libiconv                         py-pytest-flake8                       xf86rushproto
libint                           py-pytest-httpbin                      xf86vidmodeproto
libjpeg-turbo                    py-pytest-mock                         xfd
libksba                          py-pytest-runner                       xfindproxy
liblbxutil                       py-python-daemon                       xfontsel
libmesh                          py-python-gitlab                       xfs
libmng                           py-pythonqwt                           xfsinfo
libmongoc                        py-pytz                                xfwp
libmonitor                       py-pyyaml                              xgamma
libnbc                           py-qtawesome                           xgc
libogg                           py-qtconsole                           xhost
liboldx                          py-qtpy                                xineramaproto
libpciaccess                     py-quantities                          xinit
libpfm4                          py-radical-utils                       xinput
libpng                           py-ranger                              xkbcomp
libpthread-stubs                 py-readme-renderer                     xkbdata
libquo                           py-requests                            xkbevd
libsigsegv                       py-restview                            xkbprint
libsm                            py-rope                                xkbutils
libsodium                        py-rpy2                                xkeyboard-config
libspatialindex                  py-rtree                               xkill
libsplash                        py-saga-python                         xload
libssh2                          py-scientificpython                    xlogo
libtermkey                       py-scikit-image                        xlsatoms
libtiff                          py-scikit-learn                        xlsclients
libtool                          py-scipy                               xlsfonts
libunistring                     py-seaborn                             xmag
libunwind                        py-setuptools                          xman
libuuid                          py-sh                                  xmessage
libuv                            py-shiboken                            xmh
libvorbis                        py-simplegeneric                       xmlto
libvterm                         py-simplejson                          xmodmap
libwebsockets                    py-singledispatch                      xmore
libwindowswm                     py-sip                                 xorg-cf-files
libx11                           py-six                                 xorg-docs
libxau                           py-slepc4py                            xorg-gtest
libxaw                           py-sncosmo                             xorg-server
libxaw3d                         py-snowballstemmer                     xorg-sgml-doctools
libxc                            py-spglib                              xphelloworld
libxcb                           py-sphinx                              xplsprinters
libxcomposite                    py-sphinx-bootstrap-theme              xpr
libxcursor                       py-sphinx-rtd-theme                    xprehashprinterlist
libxdamage                       py-sphinxcontrib-programoutput         xprop
libxdmcp                         py-sphinxcontrib-websupport            xproto
libxevie                         py-spyder                              xproxymanagementprotocol
libxext                          py-spykeutils                          xqilla
libxfixes                        py-sqlalchemy                          xrandr
libxfont                         py-statsmodels                         xrdb
libxfont2                        py-storm                               xrefresh
libxfontcache                    py-subprocess32                        xrootd
libxft                           py-symengine                           xrx
libxi                            py-symfit                              xscope
libxinerama                      py-sympy                               xsdk
libxkbfile                       py-tabulate                            xsdktrilinos
libxkbui                         py-tappy                               xset
libxml2                          py-terminado                           xsetmode
libxmu                           py-theano                              xsetpointer
libxp                            py-tornado                             xsetroot
libxpm                           py-tqdm                                xsm
libxpresent                      py-traitlets                           xstdcmap
libxprintapputil                 py-tuiview                             xterm
libxprintutil                    py-twisted                             xtrans
libxrandr                        py-typing                              xtrap
libxrender                       py-tzlocal                             xts
libxres                          py-unittest2                           xvidtune
libxscrnsaver                    py-unittest2py3k                       xvinfo
libxshmfence                     py-urllib3                             xwd
libxslt                          py-urwid                               xwininfo
libxsmm                          py-vcversioner                         xwud
libxstream                       py-virtualenv                          xz
libxt                            py-vsc-base                            yaml-cpp
libxtrap                         py-vsc-install                         yasm
libxtst                          py-wcsaxes                             yorick
libxv                            py-wcwidth                             zeromq
libxvmc                          py-webkit-server                       zfp
libxxf86dga                      py-werkzeug                            zip
libxxf86misc                     py-wheel                               zlib
libxxf86vm                       py-widgetsnbextension                  zoltan
libzip                           py-wrapt                               zsh
likwid                           py-xarray                              zstd
linux-headers                    py-xlrd
listres                          py-xmlrunner

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     gflags        py-docutils  py-sphinxcontrib-websupport  r-rinside      texinfo
damageproto        libxfixes     py-epydoc    r-ggplot2                    r-roxygen2     xorg-docs
double-conversion  libxpresent   py-markdown  r-quadprog                   r-stanheaders  xorg-sgml-doctools
doxygen            py-alabaster  py-sphinx    r-rcpp                       sowing

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]    Allowed values    Description


    hydra [on]        True, False       Build the hydra process manager

    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:
    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]    Allowed values    Description


    hydra [on]        True, False       Build the hydra process manager

    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:
    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-mpi                                         mpich@1:  mvapich2@1.9   openmpi@1.6.5   openmpi@2.0.0:
    intel-parallel-studio@cluster.0:cluster.9999+mpi  mpich@3:  mvapich2@2.0:  openmpi@1.7.5:  spectrum-mpi

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@3:      mvapich2@2.0:  openmpi@1.7.5:  spectrum-mpi
    intel-parallel-studio@cluster.0:cluster.9999+mpi  mvapich2@1.9  openmpi@1.6.5  openmpi@2.0.0:

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

Extensions & Python support

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

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

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

spack extensions

You can find extensions for your Python installation like this:

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

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

==> None activated.

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

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

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

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

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 [-hkV] <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

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

build and install packages

positional arguments:
  package               spec of the package to install

optional arguments:
  -h, --help            show this help message and exit
  --only {package,dependencies}
                        select the mode of installation. the default is to
                        install the package along with all its dependencies.
                        alternatively one can decide to install only the
                        package or only the dependencies
  -j JOBS, --jobs JOBS  explicitly set number of make jobs. default 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.