Basic Installation Tutorial¶
This tutorial will guide you through the process of installing
software using Spack. We will first cover the spack install command,
focusing on the power of the spec syntax and the flexibility it gives
to users. We will also cover the spack find command for viewing
installed packages and the spack uninstall command for uninstalling
them. Finally, we will touch on how Spack manages compilers,
especially as it relates to using Spack-built compilers within Spack.
We will include full output from all of the commands demonstrated,
although we will frequently call attention to only small portions of
that output (or merely to the fact that it succeeded). The provided
output is all from an AWS instance running Ubuntu 18.04.
Installing Spack¶
Spack works out of the box. Simply clone Spack to get going. We will clone Spack and immediately check out the most recent release, v0.17.
$ git clone https://github.com/spack/spack.git ~/spack
Cloning into '/home/spack/spack'...
remote: Enumerating objects: 326481, done.K
remote: Counting objects: 100% (770/770), done.K
remote: Compressing objects: 100% (328/328), done.K
remote:nTotale3264819(delta5343),2reused4706.(delta|316),5pack-reused 325711K
Receiving objects: 100% (326481/326481), 135.26 MiB | 1.34 MiB/s, done.
Resolving deltas: 100% (141483/141483), done.
$ cd ~/spack
$ git checkout releases/v0.17
Branch 'releases/v0.17' set up to track remote branch 'releases/v0.17' from 'origin'.
Switched to a new branch 'releases/v0.17'
Next, add Spack to your path. Spack has some nice command-line
integration tools, so instead of simply appending to your PATH
variable, source the Spack setup script.
$ . share/spack/setup-env.sh
You’re good to go!
What is in Spack?¶
The spack list command shows available packages.
$ spack list
==> 5969 packages.
3dtk intel-oneapi-inspector pexsi py-pygeos r-parallelmap
3proxy intel-oneapi-ipp pfapack py-pygetwindow r-paramhelpers
abduco intel-oneapi-ippcp pfft py-pygit2 r-party
abi-compliance-checker intel-oneapi-mkl pflask py-pygithub r-partykit
The spack list command can also take a query string. Spack
automatically adds wildcards to both ends of the string, or you
can add your own wildcards. For example, we can view all available
Python packages.
$ spack list 'py-*'
==> 1604 packages.
py-3to2 py-cf-units py-gevent py-mpld3 py-pygtk py-simplekml
py-4suite-xml py-cffi py-gf256 py-mpmath py-pygtrie py-singledispatch
py-abcpy py-cfgrib py-gffutils py-mrcfile py-pyh5md py-sip
py-abipy py-cfgv py-git-review py-msal py-pyheadtail py-six
Installing Packages¶
Installing a package with Spack is very simple. To install a piece of
software, simply type spack install <package_name>.
$ spack install zlib
==> Bootstrapping clingo from pre-built binaries
==> Installing zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
==> No binary for zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/c3/c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1.tar.gz
==> No patches needed for zlib
==> zlib: Executing phase: 'install'
==> zlib: Successfully installed zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
Fetch: 1.06s. Build: 3.09s. Total: 4.15s.
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
Spack can install software either from source or from a binary cache. Packages in the binary cache are signed with GPG for security. For the tutorial we have prepared a binary cache so you don’t have to wait on slow compilation from source. To be able to install from the binary cache, we will need to configure Spack with the location of the binary cache and trust the GPG key that the binary cache was signed with.
$ spack mirror add tutorial /mirror
$ spack buildcache keys --install --trust
==> Fetching file:///mirror/build_cache/_pgp/8990E06AC18B52C31C9914C79328D01DE7FB5587.pub
gpg: key 9328D01DE7FB5587: public key "Spack Build Pipeline (Demo Key) <key@spack.demo>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: inserting ownertrust of 6
You’ll learn more about configuring Spack later in the tutorial, but
for now you will be able to install the rest of the packages in the
tutorial from a binary cache using the same spack install
command. By default this will install the binary cached version if it
exists and fall back on installing from source if it does not.
Spack’s spec syntax is the interface by which we can request specific
configurations of the package. The % sigil is used to specify
compilers.
$ spack install zlib %clang
==> Installing zlib-1.2.11-atdrszvduszjw55p5g7fnjezpb5l6veu
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/clang-7.0.0/zlib-1.2.11/linux-ubuntu18.04-x86_64-clang-7.0.0-zlib-1.2.11-atdrszvduszjw55p5g7fnjezpb5l6veu.spack
==> Extracting zlib-1.2.11-atdrszvduszjw55p5g7fnjezpb5l6veu from binary cache
==> Installing patchelf-0.13-2txxradgazf7zvc5kzwmc26oqjuop7ej
==> No binary for patchelf-0.13-2txxradgazf7zvc5kzwmc26oqjuop7ej found: installing from source
==> Using cached archive: /home/spack/spack/var/spack/cache/_source-cache/archive/4c/4c7ed4bcfc1a114d6286e4a0d3c1a90db147a4c3adda1814ee0eee0f9ee917ed.tar.bz2
==> No patches needed for patchelf
==> patchelf: Executing phase: 'autoreconf'
==> patchelf: Executing phase: 'configure'
==> patchelf: Executing phase: 'build'
==> patchelf: Executing phase: 'install'
==> patchelf: Successfully installed patchelf-0.13-2txxradgazf7zvc5kzwmc26oqjuop7ej
Fetch: 0.00s. Build: 7.14s. Total: 7.14s.
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/patchelf-0.13-2txxradgazf7zvc5kzwmc26oqjuop7ej
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/clang-7.0.0/zlib-1.2.11-atdrszvduszjw55p5g7fnjezpb5l6veu
Note that this installation is located separately from the previous one. We will discuss this in more detail later, but this is part of what allows Spack to support arbitrarily versioned software.
You can check for particular versions before requesting them. We will
use the spack versions command to see the available versions, and then
install a different version of zlib.
$ spack versions zlib
==> Safe versions (already checksummed):
1.2.11 1.2.8 1.2.3
==> Remote versions (not yet checksummed):
1.2.10 1.2.7.2 1.2.6.1 1.2.5.2 1.2.4.5 1.2.4.2 1.2.3.9 1.2.3.6 1.2.3.3 1.2.2.4 1.2.2.1 1.2.1.1 1.2.0.7 1.2.0.4 1.2.0.1 1.1.3 1.1.0 1.0.7 1.0.4 1.0-pre 0.94 0.91 0.9
1.2.9 1.2.7.1 1.2.6 1.2.5.1 1.2.4.4 1.2.4.1 1.2.3.8 1.2.3.5 1.2.3.2 1.2.2.3 1.2.2 1.2.1 1.2.0.6 1.2.0.3 1.2.0 1.1.2 1.0.9 1.0.6 1.0.2 0.99 0.93 0.79 0.8
1.2.7.3 1.2.7 1.2.5.3 1.2.5 1.2.4.3 1.2.4 1.2.3.7 1.2.3.4 1.2.3.1 1.2.2.2 1.2.1.2 1.2.0.8 1.2.0.5 1.2.0.2 1.1.4 1.1.1 1.0.8 1.0.5 1.0.1 0.95 0.92 0.71
The @ sigil is used to specify versions, both of packages and of
compilers.
$ spack install zlib@1.2.8
==> Installing zlib-1.2.8-4njczleoib56k2kczohm4gc5gb2b2y5j
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.8/linux-ubuntu18.04-x86_64-gcc-7.5.0-zlib-1.2.8-4njczleoib56k2kczohm4gc5gb2b2y5j.spack
==> Extracting zlib-1.2.8-4njczleoib56k2kczohm4gc5gb2b2y5j from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.8-4njczleoib56k2kczohm4gc5gb2b2y5j
$ spack install zlib %gcc@6.5.0
==> Installing zlib-1.2.11-z4ueaqdxmjyjwftnuw42kmb2gy6xrxn3
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-6.5.0/zlib-1.2.11/linux-ubuntu18.04-x86_64-gcc-6.5.0-zlib-1.2.11-z4ueaqdxmjyjwftnuw42kmb2gy6xrxn3.spack
==> Extracting zlib-1.2.11-z4ueaqdxmjyjwftnuw42kmb2gy6xrxn3 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-6.5.0/zlib-1.2.11-z4ueaqdxmjyjwftnuw42kmb2gy6xrxn3
The spec syntax also includes compiler flags. Spack accepts
cppflags, cflags, cxxflags, fflags, ldflags, and
ldlibs parameters. The values of these fields must be quoted on
the command line if they include spaces. These values are injected
into the compile line automatically by the Spack compiler wrappers.
$ spack install zlib @1.2.8 cppflags=-O3
==> Installing zlib-1.2.8-5wzra4bls7jurzo6knqfa77xhcv6p36l
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.8/linux-ubuntu18.04-x86_64-gcc-7.5.0-zlib-1.2.8-5wzra4bls7jurzo6knqfa77xhcv6p36l.spack
==> Extracting zlib-1.2.8-5wzra4bls7jurzo6knqfa77xhcv6p36l from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.8-5wzra4bls7jurzo6knqfa77xhcv6p36l
The spack find command is used to query installed packages. Note that
some packages appear identical with the default output. The -l flag
shows the hash of each package, and the -f flag shows any non-empty
compiler flags of those packages.
$ spack find
==> 6 installed packages
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
zlib@1.2.11
-- linux-ubuntu18.04-x86_64 / gcc@6.5.0 -------------------------
zlib@1.2.11
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
patchelf@0.13 zlib@1.2.8 zlib@1.2.8 zlib@1.2.11
$ spack find -lf
==> 6 installed packages
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
atdrszv zlib@1.2.11%clang
-- linux-ubuntu18.04-x86_64 / gcc@6.5.0 -------------------------
z4ueaqd zlib@1.2.11%gcc
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
2txxrad patchelf@0.13%gcc 4njczle zlib@1.2.8%gcc 5wzra4b zlib@1.2.8%gcc cppflags="-O3" 3rlgy7y zlib@1.2.11%gcc
Spack generates a hash for each spec. This hash is a function of the full provenance of the package, so any change to the spec affects the hash. Spack uses this value to compare specs and to generate unique installation directories for every combinatorial version. As we move into more complicated packages with software dependencies, we can see that Spack reuses existing packages to satisfy a dependency only when the existing package’s hash matches the desired spec.
$ spack install tcl
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
==> Installing tcl-8.6.11-oysrbhtudfatk3qz655qxf52lpyy32ag
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/tcl-8.6.11/linux-ubuntu18.04-x86_64-gcc-7.5.0-tcl-8.6.11-oysrbhtudfatk3qz655qxf52lpyy32ag.spack
==> Extracting tcl-8.6.11-oysrbhtudfatk3qz655qxf52lpyy32ag from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/tcl-8.6.11-oysrbhtudfatk3qz655qxf52lpyy32ag
Dependencies can be explicitly requested using the ^ sigil. Note that
the spec syntax is recursive. Anything we could specify about the
top-level package, we can also specify about a dependency using ^.
$ spack install tcl ^zlib @1.2.8 %clang
==> Installing zlib-1.2.8-xho2oc7aqwuvxngbnk6pp6msvwta6ki6
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/clang-7.0.0/zlib-1.2.8/linux-ubuntu18.04-x86_64-clang-7.0.0-zlib-1.2.8-xho2oc7aqwuvxngbnk6pp6msvwta6ki6.spack
==> Extracting zlib-1.2.8-xho2oc7aqwuvxngbnk6pp6msvwta6ki6 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/clang-7.0.0/zlib-1.2.8-xho2oc7aqwuvxngbnk6pp6msvwta6ki6
==> Installing tcl-8.6.11-tyatftrqtficqagmmenbyzyuidkkpyxw
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/clang-7.0.0/tcl-8.6.11/linux-ubuntu18.04-x86_64-clang-7.0.0-tcl-8.6.11-tyatftrqtficqagmmenbyzyuidkkpyxw.spack
==> Extracting tcl-8.6.11-tyatftrqtficqagmmenbyzyuidkkpyxw from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/clang-7.0.0/tcl-8.6.11-tyatftrqtficqagmmenbyzyuidkkpyxw
Packages can also be referred to from the command line by their package
hash. Using the spack find -lf command earlier we saw that the hash
of our optimized installation of zlib (cppflags="-O3") began with
5wz. We can now explicitly build with that package without typing
the entire spec, by using the / sigil to refer to it by hash. As with
other tools like Git, you do not need to specify an entire hash on the
command line. You can specify just enough digits to identify a hash
uniquely. If a hash prefix is ambiguous (i.e., two or more installed
packages share the prefix) then Spack will report an error.
$ spack install tcl ^/5wz
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.8-5wzra4bls7jurzo6knqfa77xhcv6p36l
==> Installing tcl-8.6.11-asjutitl4u5c7qnuihi44rk5jxrqfw3h
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/tcl-8.6.11/linux-ubuntu18.04-x86_64-gcc-7.5.0-tcl-8.6.11-asjutitl4u5c7qnuihi44rk5jxrqfw3h.spack
==> Extracting tcl-8.6.11-asjutitl4u5c7qnuihi44rk5jxrqfw3h from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/tcl-8.6.11-asjutitl4u5c7qnuihi44rk5jxrqfw3h
The spack find command can also take a -d flag, which can show
dependency information. Note that each package has a top-level entry,
even if it also appears as a dependency.
$ spack find -ldf
==> 10 installed packages
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
tyatftr tcl@8.6.11%clang
xho2oc7 zlib@1.2.8%clang
xho2oc7 zlib@1.2.8%clang
atdrszv zlib@1.2.11%clang
-- linux-ubuntu18.04-x86_64 / gcc@6.5.0 -------------------------
z4ueaqd zlib@1.2.11%gcc
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
2txxrad patchelf@0.13%gcc
asjutit tcl@8.6.11%gcc
5wzra4b zlib@1.2.8%gcc cppflags="-O3"
oysrbht tcl@8.6.11%gcc
3rlgy7y zlib@1.2.11%gcc
4njczle zlib@1.2.8%gcc
5wzra4b zlib@1.2.8%gcc cppflags="-O3"
3rlgy7y zlib@1.2.11%gcc
Let’s move on to slightly more complicated packages. HDF5 is a good example of a more complicated package, with an MPI dependency. If we install it “out of the box,” it will build with OpenMPI.
$ spack install hdf5
==> Installing pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/pkgconf-1.8.0/linux-ubuntu18.04-x86_64-gcc-7.5.0-pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po.spack
==> Extracting pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po
==> Installing berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/berkeley-db-18.1.40/linux-ubuntu18.04-x86_64-gcc-7.5.0-berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb.spack
==> Extracting berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb
==> Installing libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/libiconv-1.16/linux-ubuntu18.04-x86_64-gcc-7.5.0-libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig.spack
==> Extracting libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
==> Installing libsigsegv-2.13-g2vgcnev7aspdihdmfbviefdbinclpy7
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/libsigsegv-2.13/linux-ubuntu18.04-x86_64-gcc-7.5.0-libsigsegv-2.13-g2vgcnev7aspdihdmfbviefdbinclpy7.spack
==> Extracting libsigsegv-2.13-g2vgcnev7aspdihdmfbviefdbinclpy7 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libsigsegv-2.13-g2vgcnev7aspdihdmfbviefdbinclpy7
==> Installing util-macros-1.19.3-h5cf2g4fzeytdsypsm5gsb4h6saddfev
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/util-macros-1.19.3/linux-ubuntu18.04-x86_64-gcc-7.5.0-util-macros-1.19.3-h5cf2g4fzeytdsypsm5gsb4h6saddfev.spack
==> Extracting util-macros-1.19.3-h5cf2g4fzeytdsypsm5gsb4h6saddfev from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/util-macros-1.19.3-h5cf2g4fzeytdsypsm5gsb4h6saddfev
==> Installing xz-5.2.5-nplaapsuxr5djslmxm6sdmaw2xl4d2ti
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/xz-5.2.5/linux-ubuntu18.04-x86_64-gcc-7.5.0-xz-5.2.5-nplaapsuxr5djslmxm6sdmaw2xl4d2ti.spack
==> Extracting xz-5.2.5-nplaapsuxr5djslmxm6sdmaw2xl4d2ti from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/xz-5.2.5-nplaapsuxr5djslmxm6sdmaw2xl4d2ti
==> Installing ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/ncurses-6.2/linux-ubuntu18.04-x86_64-gcc-7.5.0-ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w.spack
==> Extracting ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w
==> Installing diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/diffutils-3.8/linux-ubuntu18.04-x86_64-gcc-7.5.0-diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy.spack
==> Extracting diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy
==> Installing m4-1.4.19-ybvezwzldr6ibw767ihpeoal625y76qb
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/m4-1.4.19/linux-ubuntu18.04-x86_64-gcc-7.5.0-m4-1.4.19-ybvezwzldr6ibw767ihpeoal625y76qb.spack
==> Extracting m4-1.4.19-ybvezwzldr6ibw767ihpeoal625y76qb from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/m4-1.4.19-ybvezwzldr6ibw767ihpeoal625y76qb
==> Installing libxml2-2.9.12-2hw4ddh7dbtl3wcw5hrt4kk2fkwhfuzj
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/libxml2-2.9.12/linux-ubuntu18.04-x86_64-gcc-7.5.0-libxml2-2.9.12-2hw4ddh7dbtl3wcw5hrt4kk2fkwhfuzj.spack
==> Extracting libxml2-2.9.12-2hw4ddh7dbtl3wcw5hrt4kk2fkwhfuzj from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libxml2-2.9.12-2hw4ddh7dbtl3wcw5hrt4kk2fkwhfuzj
==> Installing readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/readline-8.1/linux-ubuntu18.04-x86_64-gcc-7.5.0-readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg.spack
==> Extracting readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg
==> Installing libedit-3.1-20210216-3lzuqwnyuelfhjrxpn45akh7huu3ifr5
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/libedit-3.1-20210216/linux-ubuntu18.04-x86_64-gcc-7.5.0-libedit-3.1-20210216-3lzuqwnyuelfhjrxpn45akh7huu3ifr5.spack
==> Extracting libedit-3.1-20210216-3lzuqwnyuelfhjrxpn45akh7huu3ifr5 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libedit-3.1-20210216-3lzuqwnyuelfhjrxpn45akh7huu3ifr5
==> Installing bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/bzip2-1.0.8/linux-ubuntu18.04-x86_64-gcc-7.5.0-bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3.spack
==> Extracting bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3
==> Installing libtool-2.4.6-2kia6gf4yz6k3vsdqlg5lmp6n5hplrxq
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/libtool-2.4.6/linux-ubuntu18.04-x86_64-gcc-7.5.0-libtool-2.4.6-2kia6gf4yz6k3vsdqlg5lmp6n5hplrxq.spack
==> Extracting libtool-2.4.6-2kia6gf4yz6k3vsdqlg5lmp6n5hplrxq from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libtool-2.4.6-2kia6gf4yz6k3vsdqlg5lmp6n5hplrxq
==> Installing gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/gdbm-1.19/linux-ubuntu18.04-x86_64-gcc-7.5.0-gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn.spack
==> Extracting gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn
==> Installing libpciaccess-0.16-ryhmw2gqeeqclg65uuabqgsgpiac2nm2
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/libpciaccess-0.16/linux-ubuntu18.04-x86_64-gcc-7.5.0-libpciaccess-0.16-ryhmw2gqeeqclg65uuabqgsgpiac2nm2.spack
==> Extracting libpciaccess-0.16-ryhmw2gqeeqclg65uuabqgsgpiac2nm2 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libpciaccess-0.16-ryhmw2gqeeqclg65uuabqgsgpiac2nm2
==> Installing perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/perl-5.34.0/linux-ubuntu18.04-x86_64-gcc-7.5.0-perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv.spack
==> Extracting perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv
==> Installing hwloc-2.6.0-gedgnpght7xquztmkhthmaid6lbhlz4p
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/hwloc-2.6.0/linux-ubuntu18.04-x86_64-gcc-7.5.0-hwloc-2.6.0-gedgnpght7xquztmkhthmaid6lbhlz4p.spack
==> Extracting hwloc-2.6.0-gedgnpght7xquztmkhthmaid6lbhlz4p from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hwloc-2.6.0-gedgnpght7xquztmkhthmaid6lbhlz4p
==> Installing autoconf-2.69-7hurwa7ymeksnawbazxutf7k7qvjm772
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/autoconf-2.69/linux-ubuntu18.04-x86_64-gcc-7.5.0-autoconf-2.69-7hurwa7ymeksnawbazxutf7k7qvjm772.spack
==> Extracting autoconf-2.69-7hurwa7ymeksnawbazxutf7k7qvjm772 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/autoconf-2.69-7hurwa7ymeksnawbazxutf7k7qvjm772
==> Installing openssl-1.1.1l-lygx3cqqbvl5gkyvfkggphorm7xus2ih
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssl-1.1.1l/linux-ubuntu18.04-x86_64-gcc-7.5.0-openssl-1.1.1l-lygx3cqqbvl5gkyvfkggphorm7xus2ih.spack
==> Extracting openssl-1.1.1l-lygx3cqqbvl5gkyvfkggphorm7xus2ih from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssl-1.1.1l-lygx3cqqbvl5gkyvfkggphorm7xus2ih
==> Installing automake-1.16.3-6rqxcsn5r7kffecp45iumner6vnbbmho
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/automake-1.16.3/linux-ubuntu18.04-x86_64-gcc-7.5.0-automake-1.16.3-6rqxcsn5r7kffecp45iumner6vnbbmho.spack
==> Extracting automake-1.16.3-6rqxcsn5r7kffecp45iumner6vnbbmho from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/automake-1.16.3-6rqxcsn5r7kffecp45iumner6vnbbmho
==> Installing openssh-8.7p1-ux36qlbxdga4c5oragb7o5r4y7bsgbpy
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssh-8.7p1/linux-ubuntu18.04-x86_64-gcc-7.5.0-openssh-8.7p1-ux36qlbxdga4c5oragb7o5r4y7bsgbpy.spack
==> Extracting openssh-8.7p1-ux36qlbxdga4c5oragb7o5r4y7bsgbpy from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssh-8.7p1-ux36qlbxdga4c5oragb7o5r4y7bsgbpy
==> Installing cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4/linux-ubuntu18.04-x86_64-gcc-7.5.0-cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea.spack
==> Extracting cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea from binary cache
==> Warning: patchelf --print-rpath /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea/share/cmake-3.21/Modules/Internal/CPack/CPack.OSXScriptLauncher.in produced an error [Command exited with status 1:
'/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/patchelf-0.13-2txxradgazf7zvc5kzwmc26oqjuop7ej/bin/patchelf' '--print-rpath' '/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea/share/cmake-3.21/Modules/Internal/CPack/CPack.OSXScriptLauncher.in'
patchelf: not an ELF executable
]
==> Warning: patchelf --force-rpath --set-rpath /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea/share/cmake-3.21/Modules/Internal/CPack/CPack.OSXScriptLauncher.in failed with error Command exited with status 1:
'/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/patchelf-0.13-2txxradgazf7zvc5kzwmc26oqjuop7ej/bin/patchelf' '--force-rpath' '--set-rpath' '' '/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea/share/cmake-3.21/Modules/Internal/CPack/CPack.OSXScriptLauncher.in'
patchelf: not an ELF executable
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea
==> Installing libevent-2.1.12-xai6pycqx4h6n2l7f676q3kwql5zjdaw
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/libevent-2.1.12/linux-ubuntu18.04-x86_64-gcc-7.5.0-libevent-2.1.12-xai6pycqx4h6n2l7f676q3kwql5zjdaw.spack
==> Extracting libevent-2.1.12-xai6pycqx4h6n2l7f676q3kwql5zjdaw from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libevent-2.1.12-xai6pycqx4h6n2l7f676q3kwql5zjdaw
==> Installing numactl-2.0.14-3opot4q2nxdmogm7t5pt5wkhvapqex76
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/numactl-2.0.14/linux-ubuntu18.04-x86_64-gcc-7.5.0-numactl-2.0.14-3opot4q2nxdmogm7t5pt5wkhvapqex76.spack
==> Extracting numactl-2.0.14-3opot4q2nxdmogm7t5pt5wkhvapqex76 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/numactl-2.0.14-3opot4q2nxdmogm7t5pt5wkhvapqex76
==> Installing openmpi-4.1.1-p5qicacmcy72pjljd4lfdy66kavxp3tv
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/openmpi-4.1.1/linux-ubuntu18.04-x86_64-gcc-7.5.0-openmpi-4.1.1-p5qicacmcy72pjljd4lfdy66kavxp3tv.spack
==> Extracting openmpi-4.1.1-p5qicacmcy72pjljd4lfdy66kavxp3tv from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openmpi-4.1.1-p5qicacmcy72pjljd4lfdy66kavxp3tv
==> Installing hdf5-1.10.7-vt7sza3ycdsw62lk3f2dtnlvmeyihe3r
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7/linux-ubuntu18.04-x86_64-gcc-7.5.0-hdf5-1.10.7-vt7sza3ycdsw62lk3f2dtnlvmeyihe3r.spack
==> Extracting hdf5-1.10.7-vt7sza3ycdsw62lk3f2dtnlvmeyihe3r from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7-vt7sza3ycdsw62lk3f2dtnlvmeyihe3r
Spack packages can also have build options, called variants. Boolean
variants can be specified using the + (enable) and ~ or -
(disable) sigils. There are two sigils for “disable” to avoid conflicts
with shell parsing in different situations. Variants (boolean or
otherwise) can also be specified using the same syntax as compiler flags.
Here we can install HDF5 without MPI support.
$ spack install hdf5~mpi
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssl-1.1.1l-lygx3cqqbvl5gkyvfkggphorm7xus2ih
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea
==> Installing hdf5-1.10.7-5goewlhuzqaxioxo3enjtrk3354jnqa6
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7/linux-ubuntu18.04-x86_64-gcc-7.5.0-hdf5-1.10.7-5goewlhuzqaxioxo3enjtrk3354jnqa6.spack
==> Extracting hdf5-1.10.7-5goewlhuzqaxioxo3enjtrk3354jnqa6 from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7-5goewlhuzqaxioxo3enjtrk3354jnqa6
We might also want to install HDF5 with a different MPI
implementation. While MPI is not a package itself, packages can depend on
abstract interfaces like MPI. Spack handles these through “virtual
dependencies.” A package, such as HDF5, can depend on the MPI
interface. Other packages (openmpi, mpich, mvapich2, etc.)
provide the MPI interface. Any of these providers can be requested for
an MPI dependency. For example, we can build HDF5 with MPI support
provided by MPICH by specifying a dependency on mpich. Spack also
supports versioning of virtual dependencies. A package can depend on the
MPI interface at version 3, and provider packages specify what version of
the interface they provide. The partial spec ^mpi@3 can be satisfied
by any of several providers.
$ spack install hdf5+hl+mpi ^mpich
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
==> Installing findutils-4.8.0-3susxc457xkcjnq2zuhcsmq7dygrsbiu
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/findutils-4.8.0/linux-ubuntu18.04-x86_64-gcc-7.5.0-findutils-4.8.0-3susxc457xkcjnq2zuhcsmq7dygrsbiu.spack
==> Extracting findutils-4.8.0-3susxc457xkcjnq2zuhcsmq7dygrsbiu from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/findutils-4.8.0-3susxc457xkcjnq2zuhcsmq7dygrsbiu
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libsigsegv-2.13-g2vgcnev7aspdihdmfbviefdbinclpy7
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/util-macros-1.19.3-h5cf2g4fzeytdsypsm5gsb4h6saddfev
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/xz-5.2.5-nplaapsuxr5djslmxm6sdmaw2xl4d2ti
==> Installing libfabric-1.13.2-kwxupt5mfxcdfnymkrjjavkjpkgjzgqm
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/libfabric-1.13.2/linux-ubuntu18.04-x86_64-gcc-7.5.0-libfabric-1.13.2-kwxupt5mfxcdfnymkrjjavkjpkgjzgqm.spack
==> Extracting libfabric-1.13.2-kwxupt5mfxcdfnymkrjjavkjpkgjzgqm from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libfabric-1.13.2-kwxupt5mfxcdfnymkrjjavkjpkgjzgqm
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/m4-1.4.19-ybvezwzldr6ibw767ihpeoal625y76qb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libxml2-2.9.12-2hw4ddh7dbtl3wcw5hrt4kk2fkwhfuzj
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libtool-2.4.6-2kia6gf4yz6k3vsdqlg5lmp6n5hplrxq
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libpciaccess-0.16-ryhmw2gqeeqclg65uuabqgsgpiac2nm2
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hwloc-2.6.0-gedgnpght7xquztmkhthmaid6lbhlz4p
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssl-1.1.1l-lygx3cqqbvl5gkyvfkggphorm7xus2ih
==> Installing mpich-3.4.2-idedbjnr4e4ckjwwnuru5sydxdlrlojt
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/mpich-3.4.2/linux-ubuntu18.04-x86_64-gcc-7.5.0-mpich-3.4.2-idedbjnr4e4ckjwwnuru5sydxdlrlojt.spack
==> Extracting mpich-3.4.2-idedbjnr4e4ckjwwnuru5sydxdlrlojt from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/mpich-3.4.2-idedbjnr4e4ckjwwnuru5sydxdlrlojt
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea
==> Installing hdf5-1.10.7-qbip6imivdrn2fzofyniujqfxp4v5qrq
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7/linux-ubuntu18.04-x86_64-gcc-7.5.0-hdf5-1.10.7-qbip6imivdrn2fzofyniujqfxp4v5qrq.spack
==> Extracting hdf5-1.10.7-qbip6imivdrn2fzofyniujqfxp4v5qrq from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7-qbip6imivdrn2fzofyniujqfxp4v5qrq
We’ll do a quick check in on what we have installed so far.
$ spack find -ldf
==> 42 installed packages
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
tyatftr tcl@8.6.11%clang
xho2oc7 zlib@1.2.8%clang
xho2oc7 zlib@1.2.8%clang
atdrszv zlib@1.2.11%clang
-- linux-ubuntu18.04-x86_64 / gcc@6.5.0 -------------------------
z4ueaqd zlib@1.2.11%gcc
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
7hurwa7 autoconf@2.69%gcc
ybvezwz m4@1.4.19%gcc
g2vgcne libsigsegv@2.13%gcc
672tzld perl@5.34.0%gcc
ue5lnfm berkeley-db@18.1.40%gcc
55rtzz4 bzip2@1.0.8%gcc
oftaepj gdbm@1.19%gcc
27u6g7p readline@8.1%gcc
d34lizg ncurses@6.2%gcc
3rlgy7y zlib@1.2.11%gcc
6rqxcsn automake@1.16.3%gcc
672tzld perl@5.34.0%gcc
ue5lnfm berkeley-db@18.1.40%gcc
55rtzz4 bzip2@1.0.8%gcc
oftaepj gdbm@1.19%gcc
27u6g7p readline@8.1%gcc
d34lizg ncurses@6.2%gcc
3rlgy7y zlib@1.2.11%gcc
ue5lnfm berkeley-db@18.1.40%gcc
55rtzz4 bzip2@1.0.8%gcc
anj6kcx cmake@3.21.4%gcc
d34lizg ncurses@6.2%gcc
lygx3cq openssl@1.1.1l%gcc
3rlgy7y zlib@1.2.11%gcc
kg5jymj diffutils@3.8%gcc
qi7dxj6 libiconv@1.16%gcc
3susxc4 findutils@4.8.0%gcc
oftaepj gdbm@1.19%gcc
27u6g7p readline@8.1%gcc
d34lizg ncurses@6.2%gcc
5goewlh hdf5@1.10.7%gcc
ucp6vz7 pkgconf@1.8.0%gcc
3rlgy7y zlib@1.2.11%gcc
vt7sza3 hdf5@1.10.7%gcc
p5qicac openmpi@4.1.1%gcc
gedgnpg hwloc@2.6.0%gcc
ryhmw2g libpciaccess@0.16%gcc
2hw4ddh libxml2@2.9.12%gcc
qi7dxj6 libiconv@1.16%gcc
nplaaps xz@5.2.5%gcc
3rlgy7y zlib@1.2.11%gcc
d34lizg ncurses@6.2%gcc
xai6pyc libevent@2.1.12%gcc
lygx3cq openssl@1.1.1l%gcc
3opot4q numactl@2.0.14%gcc
ux36qlb openssh@8.7p1%gcc
3lzuqwn libedit@3.1-20210216%gcc
ucp6vz7 pkgconf@1.8.0%gcc
qbip6im hdf5@1.10.7%gcc
idedbjn mpich@3.4.2%gcc
gedgnpg hwloc@2.6.0%gcc
ryhmw2g libpciaccess@0.16%gcc
2hw4ddh libxml2@2.9.12%gcc
qi7dxj6 libiconv@1.16%gcc
nplaaps xz@5.2.5%gcc
3rlgy7y zlib@1.2.11%gcc
d34lizg ncurses@6.2%gcc
kwxupt5 libfabric@1.13.2%gcc
ucp6vz7 pkgconf@1.8.0%gcc
gedgnpg hwloc@2.6.0%gcc
ryhmw2g libpciaccess@0.16%gcc
2hw4ddh libxml2@2.9.12%gcc
qi7dxj6 libiconv@1.16%gcc
nplaaps xz@5.2.5%gcc
3rlgy7y zlib@1.2.11%gcc
d34lizg ncurses@6.2%gcc
3lzuqwn libedit@3.1-20210216%gcc
d34lizg ncurses@6.2%gcc
xai6pyc libevent@2.1.12%gcc
lygx3cq openssl@1.1.1l%gcc
3rlgy7y zlib@1.2.11%gcc
kwxupt5 libfabric@1.13.2%gcc
qi7dxj6 libiconv@1.16%gcc
ryhmw2g libpciaccess@0.16%gcc
g2vgcne libsigsegv@2.13%gcc
2kia6gf libtool@2.4.6%gcc
2hw4ddh libxml2@2.9.12%gcc
qi7dxj6 libiconv@1.16%gcc
nplaaps xz@5.2.5%gcc
3rlgy7y zlib@1.2.11%gcc
ybvezwz m4@1.4.19%gcc
g2vgcne libsigsegv@2.13%gcc
idedbjn mpich@3.4.2%gcc
gedgnpg hwloc@2.6.0%gcc
ryhmw2g libpciaccess@0.16%gcc
2hw4ddh libxml2@2.9.12%gcc
qi7dxj6 libiconv@1.16%gcc
nplaaps xz@5.2.5%gcc
3rlgy7y zlib@1.2.11%gcc
d34lizg ncurses@6.2%gcc
kwxupt5 libfabric@1.13.2%gcc
d34lizg ncurses@6.2%gcc
3opot4q numactl@2.0.14%gcc
p5qicac openmpi@4.1.1%gcc
gedgnpg hwloc@2.6.0%gcc
ryhmw2g libpciaccess@0.16%gcc
2hw4ddh libxml2@2.9.12%gcc
qi7dxj6 libiconv@1.16%gcc
nplaaps xz@5.2.5%gcc
3rlgy7y zlib@1.2.11%gcc
d34lizg ncurses@6.2%gcc
xai6pyc libevent@2.1.12%gcc
lygx3cq openssl@1.1.1l%gcc
3opot4q numactl@2.0.14%gcc
ux36qlb openssh@8.7p1%gcc
3lzuqwn libedit@3.1-20210216%gcc
ux36qlb openssh@8.7p1%gcc
3lzuqwn libedit@3.1-20210216%gcc
d34lizg ncurses@6.2%gcc
lygx3cq openssl@1.1.1l%gcc
3rlgy7y zlib@1.2.11%gcc
lygx3cq openssl@1.1.1l%gcc
3rlgy7y zlib@1.2.11%gcc
2txxrad patchelf@0.13%gcc
672tzld perl@5.34.0%gcc
ue5lnfm berkeley-db@18.1.40%gcc
55rtzz4 bzip2@1.0.8%gcc
oftaepj gdbm@1.19%gcc
27u6g7p readline@8.1%gcc
d34lizg ncurses@6.2%gcc
3rlgy7y zlib@1.2.11%gcc
ucp6vz7 pkgconf@1.8.0%gcc
27u6g7p readline@8.1%gcc
d34lizg ncurses@6.2%gcc
asjutit tcl@8.6.11%gcc
5wzra4b zlib@1.2.8%gcc cppflags="-O3"
oysrbht tcl@8.6.11%gcc
3rlgy7y zlib@1.2.11%gcc
h5cf2g4 util-macros@1.19.3%gcc
nplaaps xz@5.2.5%gcc
4njczle zlib@1.2.8%gcc
5wzra4b zlib@1.2.8%gcc cppflags="-O3"
3rlgy7y zlib@1.2.11%gcc
Spack models the dependencies of packages as a directed acyclic graph
(DAG). The spack find -d command shows the tree representation of
that graph. We can also use the spack graph command to view the entire
DAG as a graph.
$ spack graph hdf5+hl+mpi ^mpich
o hdf5
|\
| |\
| | |\
| | | o cmake
| | | |\
| | | o | openssl
| |_|/| |
|/| | | |
| | | o | perl
| |_|/| |
|/| | | |
| | | |\ \
| | | | |\ \
| | o | | | | mpich
| |/| | | | |
| | |\ \ \ \ \
| | | |\ \ \ \ \
| | | | |\ \ \ \ \
| | | | | |\ \ \ \ \
| | | | | o | | | | | hwloc
| | |_|_|/| | | | | |
| |/| |_|/| | | | | |
| | |/| |/| | | | | |
| | | |/| | | | | | |
| | | | | | |_|_|_|/
| | | | | |/| | | |
| | o | | | | | | | libxml2
| |/| | | | | | | |
|/|/| | | | | | | |
| | |\ \ \ \ \ \ \ \
o | | | | | | | | | | zlib
/ / / / / / / / / /
| o | | | | | | | | xz
| / / / / / / / /
| | o | | | | | | libpciaccess
| |/| | | | | | |
|/| | | | | | | |
| | |\ \ \ \ \ \ \
| | o | | | | | | | util-macros
| | / / / / / / /
| | | | | | o | | gdbm
| | | | | | o | | readline
| | | | | |/ / /
| | | | |/| | |
| | | | o | | | ncurses
| |_|_|/ / / /
|/| | | | | |
o | | | | | | pkgconf
/ / / / / /
| o | | | | libtool
| o | | | | m4
| o | | | | libsigsegv
| / / / /
| | | o | bzip2
| | | o | diffutils
| |_|/ /
|/| | |
o | | | libiconv
/ / /
o | | libfabric
/ /
o | findutils
/
o berkeley-db
You may also have noticed that there are some packages shown in the
spack find -d output that we didn’t install explicitly. These are
dependencies that were installed implicitly. A few packages installed
implicitly are not shown as dependencies in the spack find -d
output. These are build dependencies. For example, hdf5 requires
cmake to build. Spack will build cmake as part of the
installation of hdf5, but it does not become a part of the DAG
because it is not linked in at run time. Spack handles build
dependencies differently because of their different (less strict)
consistency requirements. It is entirely possible to have two packages
using different versions of a dependency to build, which obviously cannot
be done with linked dependencies.
HDF5 is more complicated than our basic example of zlib and Tcl, but it’s still within the realm of software that an experienced HPC user could reasonably expect to manually install given a bit of time. Now let’s look at an even more complicated package.
$ spack install trilinos
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libsigsegv-2.13-g2vgcnev7aspdihdmfbviefdbinclpy7
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/util-macros-1.19.3-h5cf2g4fzeytdsypsm5gsb4h6saddfev
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/xz-5.2.5-nplaapsuxr5djslmxm6sdmaw2xl4d2ti
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/m4-1.4.19-ybvezwzldr6ibw767ihpeoal625y76qb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libxml2-2.9.12-2hw4ddh7dbtl3wcw5hrt4kk2fkwhfuzj
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libedit-3.1-20210216-3lzuqwnyuelfhjrxpn45akh7huu3ifr5
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libtool-2.4.6-2kia6gf4yz6k3vsdqlg5lmp6n5hplrxq
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libpciaccess-0.16-ryhmw2gqeeqclg65uuabqgsgpiac2nm2
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hwloc-2.6.0-gedgnpght7xquztmkhthmaid6lbhlz4p
==> Installing openblas-0.3.18-euw6zdupnpuxk3z3fws2qi2n3kl74gsl
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/openblas-0.3.18/linux-ubuntu18.04-x86_64-gcc-7.5.0-openblas-0.3.18-euw6zdupnpuxk3z3fws2qi2n3kl74gsl.spack
==> Extracting openblas-0.3.18-euw6zdupnpuxk3z3fws2qi2n3kl74gsl from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openblas-0.3.18-euw6zdupnpuxk3z3fws2qi2n3kl74gsl
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/autoconf-2.69-7hurwa7ymeksnawbazxutf7k7qvjm772
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssl-1.1.1l-lygx3cqqbvl5gkyvfkggphorm7xus2ih
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/automake-1.16.3-6rqxcsn5r7kffecp45iumner6vnbbmho
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libevent-2.1.12-xai6pycqx4h6n2l7f676q3kwql5zjdaw
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssh-8.7p1-ux36qlbxdga4c5oragb7o5r4y7bsgbpy
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/numactl-2.0.14-3opot4q2nxdmogm7t5pt5wkhvapqex76
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openmpi-4.1.1-p5qicacmcy72pjljd4lfdy66kavxp3tv
==> Installing trilinos-13.0.1-ewdfcj372echxrfaujjtpcnc3ccsezjt
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/trilinos-13.0.1/linux-ubuntu18.04-x86_64-gcc-7.5.0-trilinos-13.0.1-ewdfcj372echxrfaujjtpcnc3ccsezjt.spack
==> Extracting trilinos-13.0.1-ewdfcj372echxrfaujjtpcnc3ccsezjt from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/trilinos-13.0.1-ewdfcj372echxrfaujjtpcnc3ccsezjt
Now we’re starting to see the power of Spack. Trilinos in its default configuration has 23 top level dependencies, many of which have dependencies of their own. Installing more complex packages can take days or weeks even for an experienced user. Although we’ve done a binary installation for the tutorial, a source installation of Trilinos using Spack takes about 3 hours (depending on the system), but only 20 seconds of programmer time.
Spack manages consistency of the entire DAG. Every MPI dependency will be satisfied by the same configuration of MPI, etc. If we install Trilinos again specifying a dependency on our previous HDF5 built with MPICH:
$ spack install trilinos +hdf5 ^hdf5+hl+mpi ^mpich
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/findutils-4.8.0-3susxc457xkcjnq2zuhcsmq7dygrsbiu
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libsigsegv-2.13-g2vgcnev7aspdihdmfbviefdbinclpy7
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/util-macros-1.19.3-h5cf2g4fzeytdsypsm5gsb4h6saddfev
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/xz-5.2.5-nplaapsuxr5djslmxm6sdmaw2xl4d2ti
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libfabric-1.13.2-kwxupt5mfxcdfnymkrjjavkjpkgjzgqm
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/m4-1.4.19-ybvezwzldr6ibw767ihpeoal625y76qb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libxml2-2.9.12-2hw4ddh7dbtl3wcw5hrt4kk2fkwhfuzj
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libtool-2.4.6-2kia6gf4yz6k3vsdqlg5lmp6n5hplrxq
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libpciaccess-0.16-ryhmw2gqeeqclg65uuabqgsgpiac2nm2
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hwloc-2.6.0-gedgnpght7xquztmkhthmaid6lbhlz4p
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openblas-0.3.18-euw6zdupnpuxk3z3fws2qi2n3kl74gsl
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/openssl-1.1.1l-lygx3cqqbvl5gkyvfkggphorm7xus2ih
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/mpich-3.4.2-idedbjnr4e4ckjwwnuru5sydxdlrlojt
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/cmake-3.21.4-anj6kcxdxzhfufoypya56mmsmxlyucea
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7-qbip6imivdrn2fzofyniujqfxp4v5qrq
==> Installing trilinos-13.0.1-qeqaxlemmrjym5bhs3ni747mctvklafz
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/trilinos-13.0.1/linux-ubuntu18.04-x86_64-gcc-7.5.0-trilinos-13.0.1-qeqaxlemmrjym5bhs3ni747mctvklafz.spack
==> Extracting trilinos-13.0.1-qeqaxlemmrjym5bhs3ni747mctvklafz from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/trilinos-13.0.1-qeqaxlemmrjym5bhs3ni747mctvklafz
We see that every package in the Trilinos DAG that depends on MPI now uses MPICH.
$ spack find -d trilinos
==> 2 installed packages
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
trilinos@13.0.1
hwloc@2.6.0
libpciaccess@0.16
libxml2@2.9.12
libiconv@1.16
xz@5.2.5
zlib@1.2.11
ncurses@6.2
openblas@0.3.18
openmpi@4.1.1
libevent@2.1.12
openssl@1.1.1l
numactl@2.0.14
openssh@8.7p1
libedit@3.1-20210216
trilinos@13.0.1
hdf5@1.10.7
mpich@3.4.2
hwloc@2.6.0
libpciaccess@0.16
libxml2@2.9.12
libiconv@1.16
xz@5.2.5
zlib@1.2.11
ncurses@6.2
libfabric@1.13.2
pkgconf@1.8.0
openblas@0.3.18
As we discussed before, the spack find -d command shows the
dependency information as a tree. While that is often sufficient, many
complicated packages, including Trilinos, have dependencies that
cannot be fully represented as a tree. Again, the spack graph
command shows the full DAG of the dependency information.
$ spack graph trilinos
o trilinos
|\
| |\
| | |\
o | | | openmpi
|\ \ \ \
| |\ \ \ \
| | |\ \ \ \
| | | |\ \ \ \
| | | | |\ \ \ \
| | | | | |\ \ \ \
| | | | | | | |/ /
| | | | | | |/| |
| | | o | | | | | openssh
| |_|/| | | | | |
|/| | | | | | | |
| | | |\ \ \ \ \ \
| | | | |\ \ \ \ \ \
| | | | | | | o | | | libevent
| | | | |_|_|/ / / /
| | | |/| | | | | |
| | | | | | | | | o cmake
| | | | |_|_|_|_|/|
| | | |/| |_|_|_|/
| | | | |/| | | |
| | | o | | | | | openssl
| |_|/| | | | | |
|/| |/ / / / / /
| | | | | | | o openblas
| | | |_|_|_|/
| | |/| | | |
| | | | | o | numactl
| | | | | |\ \
| | | | | | |\ \
| | | | | | | |\ \
| | | | | | | o | | automake
| | | |_|_|_|/| | |
| | |/| | | | | | |
| | | | | | | |/ /
| | | | | | | o | autoconf
| | | |_|_|_|/| |
| | |/| | | |/ /
| | | | | |/| |
| | o | | | | | perl
| |/| | | | | |
|/| | | | | | |
| | |\ \ \ \ \ \
| | | |\ \ \ \ \ \
| | | | | | | | | o hwloc
| | |_|_|_|_|_|_|/|
| |/| | | | |_|_|/|
| | | | | |/| | | |
| | | | | | | | | |\
| | | | | | | | | o | libxml2
| |_|_|_|_|_|_|_|/| |
|/| |_|_|_|_|_|_|/| |
| |/| | | | | | | | |
| | | | | | | | | |\ \
o | | | | | | | | | | | zlib
/ / / / / / / / / / /
| | | | | | | | o | | xz
| | | | | | | | / /
| | | | | | | | | o libpciaccess
| |_|_|_|_|_|_|_|/|
|/| | | | | | | |/|
| | | | | | | |/| |
| | | | | | | | | o util-macros
| | | | | | | | |
| o | | | | | | | gdbm
| o | | | | | | | readline
| | |_|/ / / / /
| |/| | | | | |
| | | | o | | | libedit
| |_|_|/| | | |
|/| |_|/ / / /
| |/| | | | |
| o | | | | | ncurses
|/ / / / / /
o | | | | | pkgconf
/ / / / /
| | | o | libtool
| | |/ /
| | o | m4
| | o | libsigsegv
| | /
o | | bzip2
o | | diffutils
| |/
|/|
o | libiconv
/
o berkeley-db
You can control how the output is displayed with a number of options.
The ASCII output from spack graph can be difficult to parse for
complicated packages. The output can be changed to the Graphviz
.dot format using the --dot flag.
$ spack graph --dot trilinos | dot -Tpdf > trilinos_graph.pdf
Uninstalling Packages¶
Earlier we installed many configurations each of zlib and Tcl. Now we will go through and uninstall some of those packages that we didn’t really need.
$ spack find -d tcl
==> 3 installed packages
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
tcl@8.6.11
zlib@1.2.8
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
tcl@8.6.11
zlib@1.2.8
tcl@8.6.11
zlib@1.2.11
$ spack find zlib
==> 6 installed packages
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
zlib@1.2.8 zlib@1.2.11
-- linux-ubuntu18.04-x86_64 / gcc@6.5.0 -------------------------
zlib@1.2.11
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
zlib@1.2.8 zlib@1.2.8 zlib@1.2.11
We can uninstall packages by spec using the same syntax as install.
$ spack uninstall zlib %gcc@6.5.0
y
==> The following packages will be uninstalled:
-- linux-ubuntu18.04-x86_64 / gcc@6.5.0 -------------------------
z4ueaqd zlib@1.2.11
==> Do you want to proceed? [y/N]
==> Successfully uninstalled zlib@1.2.11%gcc@6.5.0+optimize+pic+shared arch=linux-ubuntu18.04-x86_64/z4ueaqd
$ spack find -lf zlib
==> 5 installed packages
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
xho2oc7 zlib@1.2.8%clang atdrszv zlib@1.2.11%clang
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
4njczle zlib@1.2.8%gcc 5wzra4b zlib@1.2.8%gcc cppflags="-O3" 3rlgy7y zlib@1.2.11%gcc
We can also uninstall packages by referring only to their hash.
We can use either -f (force) or -R (remove dependents as well) to
remove packages that are required by another installed package.
$ spack uninstall zlib/xho
==> Will not uninstall zlib@1.2.8%clang@7.0.0/xho2oc7
The following packages depend on it:
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
tyatftr tcl@8.6.11
==> Error: There are still dependents.
use `spack uninstall --dependents` to remove dependents too
$ spack uninstall -R zlib/xho
==> The following packages will be uninstalled:
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
tyatftr tcl@8.6.11
xho2oc7 zlib@1.2.8
==> Do you want to proceed? [y/N]
==> Successfully uninstalled tcl@8.6.11%clang@7.0.0 arch=linux-ubuntu18.04-x86_64/tyatftr
==> Successfully uninstalled zlib@1.2.8%clang@7.0.0+optimize+pic+shared arch=linux-ubuntu18.04-x86_64/xho2oc7
Spack will not uninstall packages that are not sufficiently
specified. The -a (all) flag can be used to uninstall multiple
packages at once.
$ spack uninstall trilinos
==> Error: trilinos matches multiple packages:
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
ewdfcj3 trilinos@13.0.1 qeqaxle trilinos@13.0.1
==> Error: You can either:
a) use a more specific spec, or
b) specify the spec by its hash (e.g. `spack uninstall /hash`), or
c) use `spack uninstall --all` to uninstall ALL matching specs.
$ spack uninstall /ewd
==> The following packages will be uninstalled:
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
ewdfcj3 trilinos@13.0.1
==> Do you want to proceed? [y/N]
==> Successfully uninstalled trilinos@13.0.1%gcc@7.5.0~adios2+amesos+amesos2+anasazi+aztec~basker+belos~boost~chaco~complex~cuda~cuda_rdc~debug~dtk+epetra+epetraext~epetraextbtf~epetraextexperimental~epetraextgraphreorderings~exodus+explicit_template_instantiation~float+fortran~gtest~hdf5~hypre+ifpack+ifpack2~intrepid~intrepid2~ipo~isorropia+kokkos~mesquite~minitensor+ml+mpi+muelu~mumps~nox~openmp~phalanx~piro~python~rol~rythmos+sacado~scorec~shards+shared~shylu~stk~stokhos~stratimikos~strumpack~suite-sparse~superlu~superlu-dist~teko~tempus+tpetra~trilinoscouplings~wrapper~x11~zoltan~zoltan2 build_type=RelWithDebInfo cuda_arch=none cxxstd=14 gotype=long_long arch=linux-ubuntu18.04-x86_64/ewdfcj3
Advanced spack find Usage¶
We will go over some additional uses for the spack find command not
already covered in the Installing Spack and
Uninstalling Packages sections.
The spack find command can accept what we call “anonymous specs.”
These are expressions in spec syntax that do not contain a package
name. For example, spack find ^mpich will return every installed
package that depends on MPICH, and spack find cppflags="-O3" will
return every package which was built with cppflags="-O3".
$ spack find ^mpich
==> 2 installed packages
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
hdf5@1.10.7 trilinos@13.0.1
$ spack find cppflags=-O3
==> 1 installed package
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
zlib@1.2.8
The find command can also show which packages were installed
explicitly (rather than pulled in as a dependency) using the -x
flag. The -X flag shows implicit installs only. The find command can
also show the path to which a Spack package was installed using the -p
flag.
$ spack find -px
==> 11 installed packages
-- linux-ubuntu18.04-x86_64 / clang@7.0.0 -----------------------
zlib@1.2.11 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/clang-7.0.0/zlib-1.2.11-atdrszvduszjw55p5g7fnjezpb5l6veu
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
hdf5@1.10.7 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7-5goewlhuzqaxioxo3enjtrk3354jnqa6
hdf5@1.10.7 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7-vt7sza3ycdsw62lk3f2dtnlvmeyihe3r
hdf5@1.10.7 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/hdf5-1.10.7-qbip6imivdrn2fzofyniujqfxp4v5qrq
patchelf@0.13 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/patchelf-0.13-2txxradgazf7zvc5kzwmc26oqjuop7ej
tcl@8.6.11 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/tcl-8.6.11-asjutitl4u5c7qnuihi44rk5jxrqfw3h
tcl@8.6.11 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/tcl-8.6.11-oysrbhtudfatk3qz655qxf52lpyy32ag
trilinos@13.0.1 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/trilinos-13.0.1-qeqaxlemmrjym5bhs3ni747mctvklafz
zlib@1.2.8 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.8-4njczleoib56k2kczohm4gc5gb2b2y5j
zlib@1.2.8 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.8-5wzra4bls7jurzo6knqfa77xhcv6p36l
zlib@1.2.11 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
Customizing Compilers¶
Spack manages a list of available compilers on the system, detected
automatically from from the user’s PATH variable. The spack
compilers command is an alias for the command spack compiler list.
$ spack compilers
==> Available compilers
-- clang ubuntu18.04-x86_64 -------------------------------------
clang@7.0.0
-- gcc ubuntu18.04-x86_64 ---------------------------------------
gcc@7.5.0 gcc@6.5.0
The compilers are maintained in a YAML file. Later in the tutorial you will learn how to configure compilers by hand for special cases. Spack also has tools to add compilers, and compilers built with Spack can be added to the configuration.
$ spack install gcc @8.4.0
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libiconv-1.16-qi7dxj6rgdydno5mdjzyolz6applztig
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libsigsegv-2.13-g2vgcnev7aspdihdmfbviefdbinclpy7
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/berkeley-db-18.1.40-ue5lnfmm3yaiwm2jha4pnbg2s4h7jaqb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/pkgconf-1.8.0-ucp6vz7fe6ihtcmqav3vucwgqjwyw7po
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/zlib-1.2.11-3rlgy7ycxtoho44una6o3itgfjltkmpd
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/diffutils-3.8-kg5jymjbqjurpq52nvycbddt5ia5uypy
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/m4-1.4.19-ybvezwzldr6ibw767ihpeoal625y76qb
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/ncurses-6.2-d34lizgt45miuctn4cmx7quklvukdd2w
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/bzip2-1.0.8-55rtzz4s6m4swr6x7exse22ucbmluwl3
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/libtool-2.4.6-2kia6gf4yz6k3vsdqlg5lmp6n5hplrxq
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/readline-8.1-27u6g7pchcquj67llpfzttc6n7e5pfjg
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gdbm-1.19-oftaepjelizkam37ezxwkuw27clnosqn
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/perl-5.34.0-672tzldkvypvrxirrs5okvjrfvhxzyzv
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/autoconf-2.69-7hurwa7ymeksnawbazxutf7k7qvjm772
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/automake-1.16.3-6rqxcsn5r7kffecp45iumner6vnbbmho
==> Installing gmp-6.2.1-7kpzyzgpa54nap7kap6cznbyerseariq
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/gmp-6.2.1/linux-ubuntu18.04-x86_64-gcc-7.5.0-gmp-6.2.1-7kpzyzgpa54nap7kap6cznbyerseariq.spack
==> Extracting gmp-6.2.1-7kpzyzgpa54nap7kap6cznbyerseariq from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gmp-6.2.1-7kpzyzgpa54nap7kap6cznbyerseariq
==> Installing mpfr-3.1.6-z7hztfvtmv3shyltowevqvvz3iemx62g
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/mpfr-3.1.6/linux-ubuntu18.04-x86_64-gcc-7.5.0-mpfr-3.1.6-z7hztfvtmv3shyltowevqvvz3iemx62g.spack
==> Extracting mpfr-3.1.6-z7hztfvtmv3shyltowevqvvz3iemx62g from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/mpfr-3.1.6-z7hztfvtmv3shyltowevqvvz3iemx62g
==> Installing mpc-1.1.0-tjv2csrxbrewtrzd4zygkpho3c3juest
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/mpc-1.1.0/linux-ubuntu18.04-x86_64-gcc-7.5.0-mpc-1.1.0-tjv2csrxbrewtrzd4zygkpho3c3juest.spack
==> Extracting mpc-1.1.0-tjv2csrxbrewtrzd4zygkpho3c3juest from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/mpc-1.1.0-tjv2csrxbrewtrzd4zygkpho3c3juest
==> Installing gcc-8.4.0-jmhauhyule3qqfpkdo54ldx7w7m7vmcv
==> Fetching file:///mirror/build_cache/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.4.0/linux-ubuntu18.04-x86_64-gcc-7.5.0-gcc-8.4.0-jmhauhyule3qqfpkdo54ldx7w7m7vmcv.spack
==> Extracting gcc-8.4.0-jmhauhyule3qqfpkdo54ldx7w7m7vmcv from binary cache
[+] /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.4.0-jmhauhyule3qqfpkdo54ldx7w7m7vmcv
$ spack find -p gcc
==> 1 installed package
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
gcc@8.4.0 /home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.4.0-jmhauhyule3qqfpkdo54ldx7w7m7vmcv
We can add GCC to Spack as an available compiler using the spack
compiler add command. This will allow future packages to build with
gcc@8.4.0. To avoid having to copy and paste GCC’s path, we can use
spack location -i to get the installation prefix.
$ spack compiler add $(spack location -i gcc@8.4.0)
==> Added 1 new compiler to /home/spack/.spack/linux/compilers.yaml
gcc@8.4.0
==> Compilers are defined in the following files:
/home/spack/.spack/linux/compilers.yaml
We can also remove compilers from our configuration using spack compiler remove <compiler_spec>
$ spack compiler remove gcc@8.4.0
==> Removed compiler gcc@8.4.0