基本的な使い方¶
spack コマンドには多くの サブコマンド があります。典型的な使い方の場合、その一部を利用することになります。
Spackは出力を色付けしています。この出力の色付けを保つため、 less -R をご利用ください。例:
$ spack find | less -R
ご利用中の環境の .bashrc ファイルに以下を追加することをお勧めします。
alias less='less -R'
利用可能なパッケージの一覧表示¶
Spackでインストール可能なソフトウェアの一覧は、 パッケージ一覧 のウェブページもしくは、 spack list コマンドの出力で確認できます。
spack list¶
spack list コマンドは、Spackがインストール可能なパッケージの一覧を出力します:
$ spack list
abinit multiverso r-blockmodeling
abyss mummer r-bookdown
accfft mumps r-boot
ack munge r-brew
activeharmony muparser r-broom
acts-core muscle r-bsgenome
adept-utils muse r-bumphunter
adios muster r-c50
adios2 mvapich2 r-cairo
adlbx mxml r-callr
...
出力数が多いため、上記は後半を省略していますが、完全な一覧は full list here で確認できます。パッケージ名のアルファベット順に並べられています。ワイルドカードの * と ? なしでの一致は、始めと終わりに * を付けた場合と同じ扱いになります。つまり、 util は、 *util* と同等です。
パッケージ名に "sql" が含まれるもの:
$ spack list sql
mysql postgresql py-pygresql py-sqlalchemy r-rsqlite sqlitebrowser
perl-dbd-mysql py-mysql-connector py-pymysql r-rmysql r-sqldf
perl-dbd-sqlite py-mysqldb1 py-pysqlite r-rpostgresql sqlite
名前か説明に "documentation" を含むすぺてのパッケージ:
$ spack list --search-description documentation
compositeproto libxfixes py-docutils py-sphinxcontrib-websupport r-roxygen2 xorg-sgml-doctools
damageproto libxpresent py-epydoc r-ggplot2 r-stanheaders
double-conversion man-db py-markdown r-quadprog sowing
doxygen perl-dbfile py-sphinx r-rcpp texinfo
gflags py-alabaster py-sphinxautomodapi r-rinside xorg-docs
spack info¶
spack list で表示される特定のパッケージについて更に詳細な情報を得たい場合、 spack info をご利用ください。パッケージ名をコマンドの後につけてください:
$ spack info mpich
AutotoolsPackage: mpich
Description:
MPICH is a high performance and widely portable implementation of the
Message Passing Interface (MPI) standard.
Homepage: http://www.mpich.org
Tags:
None
Preferred version:
3.3 http://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz
Safe versions:
develop [git] https://github.com/pmodels/mpich.git
3.3 http://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz
3.2.1 http://www.mpich.org/static/downloads/3.2.1/mpich-3.2.1.tar.gz
3.2 http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
3.1.4 http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz
3.1.3 http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3.tar.gz
3.1.2 http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2.tar.gz
3.1.1 http://www.mpich.org/static/downloads/3.1.1/mpich-3.1.1.tar.gz
3.1 http://www.mpich.org/static/downloads/3.1/mpich-3.1.tar.gz
3.0.4 http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz
Variants:
Name [Default] Allowed values Description
device [ch3] ch3, ch4 Abstract Device Interface
(ADI) implementation. The ch4
device is currently in
experimental state
hydra [on] True, False Build the hydra process
manager
netmod [tcp] tcp, mxm, ofi, ucx Network module. Only single
netmod builds are supported.
For ch3 device configurations,
this presumes the ch3:nemesis
communication channel.
ch3:sock is not supported by
this spack package at this
time.
pci [on] True, False Support analyzing devices on
PCI bus
pmi [pmi] off, pmi, pmi2, pmix PMI interface.
romio [on] True, False Enable ROMIO MPI I/O
implementation
slurm [off] True, False Enable SLURM support
verbs [off] True, False Build support for OpenFabrics
verbs.
Installation Phases:
autoreconf configure build install
Build Dependencies:
findutils libfabric libpciaccess libxml2 pkgconfig pmix slurm
Link Dependencies:
libfabric libpciaccess libxml2 pmix slurm
Run Dependencies:
None
Virtual Packages:
mpich@3: provides mpi@:3.0
mpich@1: provides mpi@:1.3
mpich provides mpi
多くの情報は一目瞭然でしょう。 安全なバージョン(safe versions) はSpackがchecksumを認識しているバージョンであり、これらのバージョンがエラーやウィルスなしでダンロード可能なことを確認できます。
Dependencies と、 virtual dependencies については後述します。
spack versions¶
To see more available versions of a package, run spack versions.
For example:
$ spack versions libelf
0.8.13
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 ミラー):
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. The - and spaces on the command
line are provided for convenience and legibility.
Compiler Flags¶
Compiler flags are specified using the same syntax as non-boolean variants,
but fulfill a different purpose. While the function of a variant is set by
the package, compiler flags are used by the compiler wrappers to inject
flags into the compile line of the build. Additionally, compiler flags are
inherited by dependencies. spack install libdwarf cppflags="-g" will
install both libdwarf and libelf with the -g flag injected into their
compile line.
Notice that the value of the compiler flags must be quoted if it
contains any spaces. Any of cppflags=-O3, cppflags="-O3",
cppflags='-O3', and cppflags="-O3 -fPIC" are acceptable, but
cppflags=-O3 -fPIC is not. Additionally, if the value of the
compiler flags is not the last thing on the line, it must be followed
by a space. The commmand spack install libelf cppflags="-O3"%intel
will be interpreted as an attempt to set cppflags="-O3%intel".
The six compiler flags are injected in the order of implicit make commands
in GNU Autotools. If all flags are set, the order is
$cppflags $cflags|$cxxflags $ldflags <command> $ldlibs for C and C++ and
$fflags $cppflags $ldflags <command> $ldlibs for Fortran.
Compiler environment variables and additional RPATHs¶
In the exceptional case a compiler requires setting special environment
variables, like an explicit library load path. These can bet set in an
extra section in the compiler configuration (the supported environment
modification commands are: set, unset, append-path, and
prepend-path). 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:
unset:
BAD_VARIABLE: # The colon is required but the value must be empty
set:
GOOD_VARIABLE_NUM: 1
GOOD_VARIABLE_STR: good
prepend-path:
PATH: /path/to/binutils
append-path:
LD_LIBRARY_PATH: /opt/gcc/lib
extra_rpaths:
- /path/to/some/compiler/runtime/directory
- /path/to/some/other/compiler/runtime/directory
注釈
The section environment is interpreted as an ordered dictionary, which means two things. First, environment modification are applied in the order they are specified in the configuration file. Second, you cannot express environment modifications that require mixing different commands, i.e. you cannot set one variable, than prepend-path to another one, and than again set a third one.
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
Description:
MPICH is a high performance and widely portable implementation of the
Message Passing Interface (MPI) standard.
Homepage: http://www.mpich.org
Tags:
None
Preferred version:
3.3 http://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz
Safe versions:
develop [git] https://github.com/pmodels/mpich.git
3.3 http://www.mpich.org/static/downloads/3.3/mpich-3.3.tar.gz
3.2.1 http://www.mpich.org/static/downloads/3.2.1/mpich-3.2.1.tar.gz
3.2 http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
3.1.4 http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz
3.1.3 http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3.tar.gz
3.1.2 http://www.mpich.org/static/downloads/3.1.2/mpich-3.1.2.tar.gz
3.1.1 http://www.mpich.org/static/downloads/3.1.1/mpich-3.1.1.tar.gz
3.1 http://www.mpich.org/static/downloads/3.1/mpich-3.1.tar.gz
3.0.4 http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz
Variants:
Name [Default] Allowed values Description
device [ch3] ch3, ch4 Abstract Device Interface
(ADI) implementation. The ch4
device is currently in
experimental state
hydra [on] True, False Build the hydra process
manager
netmod [tcp] tcp, mxm, ofi, ucx Network module. Only single
netmod builds are supported.
For ch3 device configurations,
this presumes the ch3:nemesis
communication channel.
ch3:sock is not supported by
this spack package at this
time.
pci [on] True, False Support analyzing devices on
PCI bus
pmi [pmi] off, pmi, pmi2, pmix PMI interface.
romio [on] True, False Enable ROMIO MPI I/O
implementation
slurm [off] True, False Enable SLURM support
verbs [off] True, False Build support for OpenFabrics
verbs.
Installation Phases:
autoreconf configure build install
Build Dependencies:
findutils libfabric libpciaccess libxml2 pkgconfig pmix slurm
Link Dependencies:
libfabric libpciaccess libxml2 pmix slurm
Run Dependencies:
None
Virtual Packages:
mpich@3: provides mpi@:3.0
mpich@1: provides mpi@:1.3
mpich provides mpi
Spack is unique in that its virtual packages can be versioned, just
like regular packages. A particular version of a package may provide
a particular version of a virtual package, and we can see above that
mpich versions 1 and above provide all mpi interface
versions up to 1, and mpich versions 3 and above provide
mpi versions up to 3. A package can depend on a particular
version of a virtual package, e.g. if an application needs MPI-2
functions, it can depend on mpi@2: to indicate that it needs some
implementation that provides MPI-2 functions.
Constraining virtual packages¶
When installing a package that depends on a virtual package, you can opt to specify the particular provider you want to use, or you can let Spack pick. For example, if you just type this:
$ spack install mpileaks
Then spack will pick a provider for you according to site policies.
If you really want a particular version, say mpich, then you could
run this instead:
$ spack install mpileaks ^mpich
This forces spack to use some version of mpich for its
implementation. As always, you can be even more specific and require
a particular mpich version:
$ spack install mpileaks ^mpich@3
The mpileaks package in particular only needs MPI-1 commands, so
any MPI implementation will do. If another package depends on
mpi@2 and you try to give it an insufficient MPI implementation
(e.g., one that provides only mpi@:1), then Spack will raise an
error. Likewise, if you try to plug in some package that doesn't
provide MPI, Spack will raise an error.
Specifying Specs by Hash¶
Complicated specs can become cumbersome to enter on the command line,
especially when many of the qualifications are necessary to distinguish
between similar installs. To avoid this, when referencing an existing spec,
Spack allows you to reference specs by their hash. We previously
discussed the spec hash that Spack computes. In place of a spec in any
command, substitute /<hash> where <hash> is any amount from
the beginning of a spec hash.
For example, lets say that you accidentally installed two different
mvapich2 installations. If you want to uninstall one of them but don't
know what the difference is, you can run:
$ spack find --long mvapich2
==> 2 installed packages.
-- linux-centos7-x86_64 / gcc@6.3.0 ----------
qmt35td mvapich2@2.2%gcc
er3die3 mvapich2@2.2%gcc
You can then uninstall the latter installation using:
$ spack uninstall /er3die3
Or, if you want to build with a specific installation as a dependency, you can use:
$ spack install trilinos ^/er3die3
If the given spec hash is sufficiently long as to be unique, Spack will replace the reference with the spec to which it refers. Otherwise, it will prompt for a more qualified hash.
Note that this will not work to reinstall a dependency uninstalled by
spack uninstall --force.
spack providers¶
You can see what packages provide a particular virtual package using
spack providers. If you wanted to see what packages provide
mpi, you would just run:
$ spack providers mpi
charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: mpich mvapich2 openmpi@2.0.0:
charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: mpich@1: openmpi spectrum-mpi
charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: intel-mpi mpich@3: openmpi@1.6.5
charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: intel-parallel-studio mpilander openmpi@1.7.5:
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
charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: mpich openmpi spectrum-mpi
charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: mpich@3: openmpi@1.6.5
charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: intel-mpi mpilander openmpi@1.7.5:
charmpp@6.7.1: charmpp@6.7.1: charmpp@6.7.1: intel-parallel-studio mvapich2 openmpi@2.0.0:
Notice that the package versions that provide insufficient MPI versions are now filtered out.
Extensions & Python support¶
Spack's installation model assumes that each package will live in its
own install prefix. However, certain packages are typically installed
within the directory hierarchy of other packages. For example,
modules in interpreted languages like Python are typically installed in the
$prefix/lib/python-2.7/site-packages directory.
Spack has support for this type of installation as well. In Spack, a package that can live inside the prefix of another package is called an extension. Suppose you have Python installed like so:
$ spack find python
==> 1 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
python@2.7.8
spack extensions¶
You can find extensions for your Python installation like this:
$ spack extensions python
==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96
==> 36 extensions:
geos py-ipython py-pexpect py-pyside py-sip
py-basemap py-libxml2 py-pil py-pytz py-six
py-biopython py-mako py-pmw py-rpy2 py-sympy
py-cython py-matplotlib py-pychecker py-scientificpython py-virtualenv
py-dateutil py-mpi4py py-pygments py-scikit-learn
py-epydoc py-mx py-pylint py-scipy
py-gnuplot py-nose py-pyparsing py-setuptools
py-h5py py-numpy py-pyqt py-shiboken
==> 12 installed:
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2
py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10
py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1
py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0
==> None activated.
The extensions are a subset of what's returned by spack list, and
they are packages like any other. They are installed into their own
prefixes, and you can see this with spack find --paths:
$ spack find --paths py-numpy
==> 1 installed packages.
-- linux-debian7-x86_64 / gcc@4.4.7 --------------------------------
py-numpy@1.9.1 ~/spack/opt/linux-debian7-x86_64/gcc@4.4.7/py-numpy@1.9.1-66733244
However, even though this package is installed, you cannot use it
directly when you run python:
$ spack load python
$ python
Python 2.7.8 (default, Feb 17 2015, 01:35:25)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: No module named numpy
>>>
Using Extensions¶
There are three ways to get numpy working in Python. The first is
to use Using module files via Spack. You can simply use or load the
module for the extension, and it will be added to the PYTHONPATH
in your current shell.
For tcl modules:
$ spack load python
$ spack load py-numpy
or, for dotkit:
$ spack use python
$ spack use py-numpy
Now import numpy will succeed for as long as you keep your current
session open.
Activating Extensions in a View¶
The second way to use extensions is to create a view, which merges the
python installation along with the extensions into a single prefix.
See Filesystem Views for a more in-depth description of views and
spack view for usage of the spack view command.
Activating Extensions Globally¶
As an alternative to creating a merged prefix with Python and its extensions, and prior to support for views, Spack has provided a means to install the extension into the Spack installation prefix for the extendee. This has typically been useful since extendable packages typically search their own installation path for addons by default.
Global activations are performed with the spack activate command:
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 global 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 or views, 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¶
By default, Spack 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 or NFS volumes may
be configured without flock support enabled. You can determine how
your filesystems are mounted with mount. The output for a Lustre
filesystem might look like this:
$ mount | grep lscratch
mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,lazystatfs,flock)
mds2-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,lazystatfs,flock)
Note the flock option on both Lustre mounts.
If you do not see this or a similar option for your filesystem, you have
a few options. First, you can move your Spack installation to a
filesystem that supports locking. Second, you could ask your system
administrator to enable flock for your filesystem.
If none of those work, you can disable locking in one of two ways:
Run Spack with the
-Lor--disable-locksoption to disable locks on a call-by-call basis.Edit config.yaml and set the
locksoption tofalseto always disable locking.
警告
If you disable locking, concurrent instances of Spack will have no way
to avoid stepping on each other. You must ensure that there is only
one instance of Spack running at a time. Otherwise, Spack may end
up with a corrupted database file, or you may not be able to see all
installed packages in commands like spack find.
If you are unfortunate enough to run into this situation, you may be
able to fix it by running spack reindex.
This issue typically manifests with the error below:
$ ./spack find
Traceback (most recent call last):
File "./spack", line 176, in <module>
main()
File "./spack", line 154,' in main
return_val = command(parser, args)
File "./spack/lib/spack/spack/cmd/find.py", line 170, in find
specs = set(spack.installed_db.query(\**q_args))
File "./spack/lib/spack/spack/database.py", line 551, in query
with self.read_transaction():
File "./spack/lib/spack/spack/database.py", line 598, in __enter__
if self._enter() and self._acquire_fn:
File "./spack/lib/spack/spack/database.py", line 608, in _enter
return self._db.lock.acquire_read(self._timeout)
File "./spack/lib/spack/llnl/util/lock.py", line 103, in acquire_read
self._lock(fcntl.LOCK_SH, timeout) # can raise LockError.
File "./spack/lib/spack/llnl/util/lock.py", line 64, in _lock
fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
IOError: [Errno 38] Function not implemented
A nicer error message is TBD in future versions of Spack.
Getting Help¶
spack help¶
If you don't find what you need here, the help subcommand will
print out out a list of all of spack's options and subcommands:
$ spack help
usage: spack [-hkV] [--color {always,never,auto}] COMMAND ...
A flexible package manager that supports multiple versions,
configurations, platforms, and compilers.
These are common spack commands:
query packages:
list list and search available packages
info get detailed information on a particular package
find list and search installed packages
build packages:
install build and install packages
uninstall remove installed packages
spec show what would be installed, given a spec
environments:
env manage virtual environments
view project packages to a compact naming scheme on the filesystem.
modules:
load add package to environment using `module load`
module manipulate module files
unload remove package from environment using `module unload`
create packages:
create create a new package file
edit open package files in $EDITOR
system:
arch print architecture information about this machine
compilers list available compilers
optional arguments:
-h, --help show this help message and exit
-k, --insecure do not check ssl certificates when downloading
-V, --version show version number and exit
--color {always,never,auto}
when to colorize output (default: auto)
more help:
spack help --all list all commands and options
spack help <command> help on a specific command
spack help --spec help on the spec syntax
spack docs open http://spack.rtfd.io/ in a browser
Adding an argument, e.g. spack help <subcommand>, will print out
usage information for a particular subcommand:
$ spack help install
usage: spack install [-hInvy] [--only {package,dependencies}] [-j JOBS] [--overwrite] [--keep-prefix] [--keep-stage]
[--dont-restage] [--use-cache | --no-cache] [--show-log-on-error] [--source] [--fake]
[--only-concrete] [-f SPEC_YAML_FILE] [--clean | --dirty] [--test {root,all} | --run-tests]
[--log-format {None,junit,cdash}] [--log-file LOG_FILE] [--cdash-upload-url CDASH_UPLOAD_URL]
[--cdash-build CDASH_BUILD] [--cdash-site CDASH_SITE]
[--cdash-track CDASH_TRACK | --cdash-buildstamp CDASH_BUILDSTAMP]
...
build and install packages
positional arguments:
package spec of the package to install
optional arguments:
-h, --help show this help message and exit
--only {package,dependencies}
select the mode of installation.
the default is to install the package along with all its dependencies.
alternatively one can decide to install only the package or only
the dependencies
-j JOBS, --jobs JOBS explicitly set number of parallel jobs
-I, --install-status show install status of packages. packages can be: installed [+], missing and needed by an installed package [-], or not installed (no annotation)
--overwrite reinstall an existing spec, even if it has dependents
--keep-prefix don't remove the install prefix if installation fails
--keep-stage don't remove the build stage if installation succeeds
--dont-restage if a partial install is detected, don't delete prior state
--use-cache check for pre-built Spack packages in mirrors (default)
--no-cache do not check for pre-built Spack packages in mirrors
--show-log-on-error print full build log to stderr if build fails
--source install source files in prefix
-n, --no-checksum do not use checksums to verify downloaded files (unsafe)
-v, --verbose display verbose build output while installing
--fake fake install for debug purposes.
--only-concrete (with environment) only install already concretized specs
-f SPEC_YAML_FILE, --file SPEC_YAML_FILE
install from file. Read specs to install from .yaml files
--clean unset harmful variables in the build environment (default)
--dirty preserve user environment in the spack build environment (danger!)
--test {root,all} If 'root' is chosen, run package tests during
installation for top-level packages (but skip tests for dependencies).
if 'all' is chosen, run package tests during installation for all
packages. If neither are chosen, don't run tests for any packages.
--run-tests run package tests during installation (same as --test=all)
--log-format {None,junit,cdash}
format to be used for log files
--log-file LOG_FILE filename for the log file. if not passed a default will be used
--cdash-upload-url CDASH_UPLOAD_URL
CDash URL where reports will be uploaded
--cdash-build CDASH_BUILD
The name of the build that will be reported to CDash.
Defaults to spec of the package to install.
--cdash-site CDASH_SITE
The site name that will be reported to CDash.
Defaults to current system hostname.
--cdash-track CDASH_TRACK
Results will be reported to this group on CDash.
Defaults to Experimental.
--cdash-buildstamp CDASH_BUILDSTAMP
Instead of letting the CDash reporter prepare the
buildstamp which, when combined with build name, site and project,
uniquely identifies the build, provide this argument to identify
the build yourself. Format: %Y%m%d-%H%M-[cdash-track]
-y, --yes-to-all assume "yes" is the answer to every confirmation request
Alternately, you can use spack --help in place of spack help, or
spack <subcommand> --help to get help on a particular subcommand.