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 icet printproto r-rjsonio
ack ico proj r-rmarkdown
activeharmony icu4c protobuf r-rmysql
adept-utils ilmbase proxymngr r-rngtools
adios ImageMagick psi4 r-rodbc
adol-c imake py-3to2 r-roxygen2
allinea-forge inputproto py-alabaster r-rpostgresql
allinea-reports intel py-argcomplete r-rsnns
ant intel-gpu-tools py-astroid r-rsqlite
antlr intel-parallel-studio py-astropy r-rstan
ape intltool py-autopep8 r-rstudioapi
apex ior py-babel r-rzmq
applewmproto ipopt py-basemap r-sandwich
appres ipp py-beautifulsoup4 r-scales
apr isl py-biopython r-shiny
apr-util itstool py-blessings r-sp
armadillo jansson py-bottleneck r-sparsem
arpack jasper py-cclib r-stanheaders
arpack-ng jdk py-cdo r-stringi
asciidoc jemalloc py-cffi r-stringr
astyle jpeg py-configparser r-survey
atk jsoncpp py-coverage r-survival
atlas judy py-csvkit r-tarifx
atompaw julia py-cycler r-testit
atop kbproto py-cython r-testthat
autoconf kdiff3 py-dask r-thdata
automaded kealib py-dateutil r-threejs
automake kripke py-dbf r-tibble
bamtools launchmon py-decorator r-tidyr
bash lbxproxy py-docutils r-ttr
bash-completion lcms py-emcee r-uuid
bazel leveldb py-enum34 r-vcd
bbcp libaio py-epydoc r-visnetwork
bcftools libapplewm py-flake8 r-whisker
bdftopcf libarchive py-funcsigs r-withr
bdw-gc libatomic-ops py-genders r-xgboost
bear libcerf py-genshi r-xlconnect
bedtools2 libcircle py-gnuplot r-xlconnectjars
beforelight libctl py-h5py r-xlsx
bertini libdmx py-imagesize r-xlsxjars
bib2xhtml libdrm py-iminuit r-xml
bigreqsproto libdwarf py-ipython r-xtable
binutils libedit py-jdcal r-xts
bison libelf py-jinja2 r-yaml
bitmap libemos py-lockfile r-zoo
bliss libepoxy py-logilab-common raja
blitz libevent py-macs2 randrproto
boost libffi py-mako ravel
bowtie2 libfontenc py-markdown readline
boxlib libfs py-markupsafe recordproto
bpp-core libgcrypt py-matplotlib rename
bpp-phyl libgd py-mccabe rendercheck
bpp-seq libgpg-error py-meep renderproto
bpp-suite libgtextutils py-mistune resourceproto
bwa libhio py-mock rgb
bzip2 libice py-mpi4py root
c-blosc libiconv py-mpmath rose
cairo libint py-mx rstart
caliper libjpeg-turbo py-mysqldb1 rsync
callpath libjson-c py-nestle ruby
cantera liblbxutil py-netcdf rust
cask libmesh py-networkx rust-bindgen
catch libmng py-nose SAMRAI
cblas libmonitor py-numexpr samtools
cbtf libNBC py-numpy sbt
cbtf-argonavis liboldx py-openpyxl scalasca
cbtf-krell libpciaccess py-ordereddict scons
cbtf-lanl libpng py-pandas scorep
cdd libpthread-stubs py-pathspec scotch
cddlib libquo py-pbr scr
cdo libsigsegv py-periodictable screen
cereal libsm py-pexpect scripts
cfitsio libsodium py-phonopy scrnsaverproto
cgal libspatialindex py-pil sdl2
cgm libsplash py-pillow sdl2_image
cgns libtermkey py-ply sed
charm libtiff py-pmw seqtk
cityhash libtool py-prettytable serf
cleverleaf libunistring py-proj sessreg
clhep libunwind py-protobuf setxkbmap
cloog libuuid py-pudb showfont
cmake libuv py-py silo
cmocka libvterm py-py2cairo slepc
cmor libwebsockets py-py2neo smproxy
cnmem libwindowswm py-pychecker snappy
compiz libx11 py-pycodestyle sowing
compositeproto libxau py-pycparser spark
constype libxaw py-pydatalog sparsehash
converge libxaw3d py-pyelftools spdlog
coreutils libxc py-pyflakes spindle
cp2k libxcb py-pygments spot
cppcheck libxcomposite py-pygobject sqlite
cppunit libxcursor py-pygtk star-ccm-plus
cram libxdamage py-pylint stat
cryptopp libxdmcp py-pypar stream
cscope libxevie py-pyparsing sublime-text
cube libxext py-pyqt subversion
cuda libxfixes py-pyside suite-sparse
curl libxfont py-pytables sundials
czmq libxfont2 py-pytest superlu
daal libxfontcache py-python-daemon superlu-dist
dakota libxft py-pytz superlu-mt
damageproto libxi py-pyyaml swiftsim
damselfly libxinerama py-restview swig
darshan-runtime libxkbfile py-rpy2 symengine
darshan-util libxkbui py-rtree sympol
datamash libxml2 py-scientificpython szip
dbus libxmu py-scikit-image tar
dealii libxp py-scikit-learn task
dia libxpm py-scipy taskd
dmxproto libxpresent py-setuptools tau
docbook-xml libxprintapputil py-shiboken tbb
docbook-xsl libxprintutil py-sip tcl
doxygen libxrandr py-six tetgen
dri2proto libxrender py-sncosmo tethex
dri3proto libxres py-snowballstemmer texinfo
dtcmp libxscrnsaver py-sphinx texlive
dyninst libxshmfence py-sphinx-rtd-theme the_platinum_searcher
editres libxslt py-SQLAlchemy the_silver_searcher
eigen libxsmm py-storm thrift
elfutils libxstream py-symengine tinyxml
elk libxt py-sympy tinyxml2
elpa libxtrap py-tappy tk
emacs libxtst py-tuiview tmux
encodings libxv py-twisted tmuxinator
environment-modules libxvmc py-unittest2 transset
espresso libxxf86dga py-unittest2py3k trapproto
etsf_io libxxf86misc py-urwid tree
everytrace libxxf86vm py-virtualenv triangle
everytrace-example likwid py-wcsaxes trilinos
evieext listres py-wheel turbomole
exodusii llvm py-xlrd twm
exonerate llvm-lld py-xpyb uberftp
expat lmdb py-yapf udunits2
extrae lmod py-yt uncrustify
exuberant-ctags lndir python unibilium
fastqc lrslib qhull unison
fastx_toolkit lrzip qrupdate unixodbc
fenics lua qt util-linux
ferret lua-luafilesystem qt-creator util-macros
fftw lua-luaposix qthreads uuid
fish LuaJIT R valgrind
fixesproto luit r-abind veclibfort
flex lulesh r-assertthat videoproto
flint lwgrp r-base64enc viewres
fltk lwm2 r-bh vim
flux lz4 r-BiocGenerics visit
foam-extend lzma r-bitops vizglow
font-adobe-100dpi lzo r-boot vtk
font-adobe-75dpi m4 r-brew wannier90
font-adobe-utopia-100dpi mafft r-c50 wget
font-adobe-utopia-75dpi magics r-car windowswmproto
font-adobe-utopia-type1 makedepend r-caret wx
font-alias mariadb r-catools wxpropgrid
font-arabic-misc matio r-chron x11perf
font-bh-100dpi maven r-class xauth
font-bh-75dpi mbedtls r-cluster xbacklight
font-bh-lucidatypewriter-100dpi meep r-codetools xbiff
font-bh-lucidatypewriter-75dpi memaxes r-colorspace xbitmaps
font-bh-ttf mercurial r-crayon xcalc
font-bh-type1 mesa r-cubature xcb-demo
font-bitstream-100dpi metis r-curl xcb-proto
font-bitstream-75dpi mfem r-datatable xcb-util
font-bitstream-speedo Mitos r-dbi xcb-util-cursor
font-bitstream-type1 mkfontdir r-deoptim xcb-util-errors
font-cronyx-cyrillic mkfontscale r-devtools xcb-util-image
font-cursor-misc mkl r-diagrammer xcb-util-keysyms
font-daewoo-misc moab r-dichromat xcb-util-renderutil
font-dec-misc mpc r-digest xcb-util-wm
font-ibm-type1 mpe2 r-doparallel xclipboard
font-isas-misc mpfr r-dplyr xclock
font-jis-misc mpibash r-dt xcmiscproto
font-micro-misc mpich r-dygraphs xcmsdb
font-misc-cyrillic mpileaks r-e1071 xcompmgr
font-misc-ethiopic mpip r-evaluate xconsole
font-misc-meltho mpir r-filehash xcursor-themes
font-misc-misc mrnet r-foreach xcursorgen
font-mutt-misc msgpack-c r-foreign xdbedizzy
font-schumacher-misc mumps r-formatr xditview
font-screen-cyrillic munge r-formula xdm
font-sony-misc muparser r-gdata xdpyinfo
font-sun-misc muster r-geosphere xdriinfo
font-util mvapich2 r-ggmap xedit
font-winitzki-cyrillic mxml r-ggplot2 xerces-c
font-xfree86-type1 nag r-ggvis xev
fontcacheproto nano r-gistr xextproto
fontconfig nasm r-git2r xeyes
fontsproto nauty r-glmnet xf86bigfontproto
fonttosfnt nccmp r-googlevis xf86dga
freetype ncdu r-gridbase xf86dgaproto
fslsfonts ncl r-gridextra xf86driproto
fstobdf nco r-gtable xf86miscproto
gasnet ncurses r-gtools xf86rushproto
gawk ncview r-hexbin xf86vidmodeproto
gbenchmark ndiff r-highr xfd
gcc netcdf r-htmltools xfindproxy
gccmakedep netcdf-cxx r-htmlwidgets xfontsel
gconf netcdf-cxx4 r-httpuv xfs
gdal netcdf-fortran r-httr xfsinfo
gdb netgauge r-igraph xfwp
gdk-pixbuf netlib-lapack r-influencer xgamma
geant4 netlib-scalapack r-inline xgc
geos nettle r-irdisplay xhost
gettext nextflow r-irkernel xineramaproto
gflags nfft r-irlba xinit
ghostscript ninja r-iterators xinput
ghostscript-fonts nmap r-jpeg xkbcomp
giflib numdiff r-jsonlite xkbdata
git nwchem r-knitr xkbevd
git-lfs ocaml r-labeling xkbprint
gl2ps oce r-lattice xkbutils
glew oclock r-lazyeval xkeyboard-config
glib octave r-leaflet xkill
glm octave-splines r-lme4 xload
global octopus r-lmtest xlogo
globus_toolkit ompss r-lubridate xlsatoms
glog ompt-openmp r-magic xlsclients
glpk opari2 r-magrittr xlsfonts
glproto openblas r-mapproj xmag
gmake opencoarrays r-maps xman
gmp opencv r-maptools xmessage
gmsh openexr r-markdown xmh
gnu-prolog openjpeg r-mass xmlto
gnuplot openmpi r-matrix xmodmap
gnutls openscenegraph r-matrixmodels xmore
go openspeedshop r-memoise xorg-cf-files
go-bootstrap openssl r-mgcv xorg-docs
gobject-introspection opium r-mime xorg-gtest
googletest osu-micro-benchmarks r-minqa xorg-server
gource otf r-multcomp xorg-sgml-doctools
gperf otf2 r-munsell xphelloworld
gperftools p4est r-mvtnorm xplsprinters
grackle panda r-ncdf4 xpr
grandr pango r-networkd3 xprehashprinterlist
graphlib papi r-nlme xprop
graphviz paradiseo r-nloptr xproto
grib-api parallel r-nmf xproxymanagementprotocol
gromacs parallel-netcdf r-nnet xrandr
gsl paraver r-np xrdb
gtkplus paraview r-openssl xrefresh
gts parmetis r-packrat xrootd
guile parmgridgen r-partykit xrx
h5hut parpack r-pbdzmq xscope
hadoop patch r-pbkrtest xsdktrilinos
harfbuzz patchelf r-pkgmaker xset
harminv pcre r-plotrix xsetmode
hdf pcre2 r-plyr xsetpointer
hdf5 pdt r-png xsetroot
hdf5-blosc perl r-praise xsm
help2man petsc r-proto xstdcmap
hepmc pexsi r-pryr xtrans
heppdt pfft r-quantmod xtrap
hmmer pflotran r-quantreg xts
hoomd-blue pgi r-R6 xvidtune
hpctoolkit pidx r-randomforest xvinfo
hpctoolkit-externals piranha r-raster xwd
hpl pixman r-rbokeh xwininfo
hpx5 pkg-config r-rcolorbrewer xwud
hsakmt plumed r-rcpp xz
htop pmgr_collective r-rcppeigen yaml-cpp
htslib pngwriter r-registry yasm
hub polymake r-repr yorick
hwloc porta r-reshape2 zeromq
hydra postgresql r-rgooglemaps zfp
hypre ppl r-rinside zlib
ibmisc prank r-rjava zoltan
iceauth presentproto r-rjson zsh
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-alabaster py-markdown r-rcpp r-stanheaders xorg-docs
damageproto libxfixes py-docutils py-sphinx r-rinside sowing xorg-sgml-doctools
doxygen libxpresent py-epydoc r-ggplot2 r-roxygen2 texinfo
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:
- The author requires users to manually accept a license agreement
before downloading (
jdkandgalahad). - 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):
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_mirrorRegister the mirror with Spack by creating
~/.spack/mirrors.yaml:mirrors: manual: file://~/.spack/manual_mirror
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
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 (
mpileaksabove) @Optional version specifier (@1.2:1.4)%Optional compiler specifier, with an optional compiler version (gccorgcc@4.7.3)+or-or~Optional variant specifiers (+debug,-qt, or~qt) for boolean variantsname=<value>Optional variant specifiers that are not restricted to boolean variantsname=<value>Optional compiler flag specifiers. Valid flag names arecflags,cxxflags,fflags,cppflags,ldflags, andldlibs.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:
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. We allow - and spaces on the command
line is 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 escape quoted on the
command line. From within python files, the same spec would be specified
libdwarf cppflags="-g". This is necessary because of how the shell
handles the quote symbols.
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:
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:
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:
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--forceto 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:
[0;36m@version[0m
[0;32m%compiler @compiler_version[0m
[0;94m+variant[0m
[0;31m-variant[0m or [0;31m~variant[0m
[0;35m=architecture[0m
[^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 from an archive URL
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.
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-parse Show parsing of a URL, optionally spider web for versions.
urls Inspect urls used by packages in spack.
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.