.. _basic-usage: =========== Basic Usage =========== The ``spack`` command has many *subcommands*. You'll only need a small subset of them for typical usage. Note that Spack colorizes output. ``less -R`` should be used with Spack to maintain this colorization. E.g.: .. code-block:: console $ spack find | less -R It is recommended that the following be put in your ``.bashrc`` file: .. code-block:: sh alias less='less -R' -------------------------- Listing available packages -------------------------- To install software with Spack, you need to know what software is available. You can see a list of available package names at the :ref:`package-list` webpage, or using the ``spack list`` command. .. _cmd-spack-list: ^^^^^^^^^^^^^^ ``spack list`` ^^^^^^^^^^^^^^ The ``spack list`` command prints out a list of all of the packages Spack can install: .. command-output:: spack list The packages are listed by name in alphabetical order. A pattern to match with no wildcards, ``*`` or ``?``, will be treated as though it started and ended with ``*``, so ``util`` is equivalent to ``*util*``. All patterns will be treated as case-insensitive. You can also add the ``-d`` to search the description of the package in addition to the name. Some examples: All packages whose names contain "sql": .. command-output:: spack list sql All packages whose names or descriptions contain documentation: .. command-output:: spack list --search-description documentation .. _cmd-spack-info: ^^^^^^^^^^^^^^ ``spack info`` ^^^^^^^^^^^^^^ To get more information on a particular package from `spack list`, use `spack info`. Just supply the name of a package: .. command-output:: spack info mpich Most of the information is self-explanatory. The *safe versions* are versions that Spack knows the checksum for, and it will use the checksum to verify that these versions download without errors or viruses. :ref:`Dependencies ` and :ref:`virtual dependencies ` are described in more detail later. .. _cmd-spack-versions: ^^^^^^^^^^^^^^^^^^ ``spack versions`` ^^^^^^^^^^^^^^^^^^ To see *more* available versions of a package, run ``spack versions``. For example: .. command-output:: spack versions libelf 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 --------------------------- .. _cmd-spack-install: ^^^^^^^^^^^^^^^^^ ``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: .. code-block:: console $ 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: .. code-block:: console $ 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: .. code-block:: console $ 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 :ref:`sec-specs`. .. _cmd-spack-uninstall: ^^^^^^^^^^^^^^^^^^^ ``spack uninstall`` ^^^^^^^^^^^^^^^^^^^ To uninstall a package, type ``spack uninstall ``. This will ask the user for confirmation before completely removing the directory in which the package was installed. .. code-block:: console $ 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. .. code-block:: console $ 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 .. code-block:: console $ 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 .. code-block:: console $ 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. .. _nondownloadable: ^^^^^^^^^^^^^^^^^^^^^^^^^ 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 (``jdk`` and ``galahad``). #. 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 :ref:`mirrors`): #. Create a directory for the mirror. You can create this directory anywhere you like, it does not have to be inside ``~/.spack``: .. code-block:: console $ mkdir ~/.spack/manual_mirror #. Register the mirror with Spack by creating ``~/.spack/mirrors.yaml``: .. code-block:: yaml mirrors: manual: file://~/.spack/manual_mirror #. Put your tarballs in it. Tarballs should be named ``/-.tar.gz``. For example: .. code-block:: console $ ls -l manual_mirror/galahad -rw-------. 1 me me 11657206 Jun 21 19:25 galahad-2.60003.tar.gz #. Install as usual: .. code-block:: console $ 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? .. _cmd-spack-find: ^^^^^^^^^^^^^^ ``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: .. code-block:: console $ 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 `` 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: .. code-block:: console $ 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``: .. code-block:: console $ 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``: .. code-block:: console $ 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: .. code-block:: console $ 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: .. code-block:: console $ 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: .. code-block:: console $ 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 :ref:`sec-specs`. .. _sec-specs: -------------------- 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: .. code-block:: none mpileaks @1.2:1.4 %gcc@4.7.5 +debug -qt arch=bgq_os ^callpath @1.1 %gcc@4.7.2 If provided to ``spack install``, this will install the ``mpileaks`` library at some version between ``1.2`` and ``1.4`` (inclusive), built using ``gcc`` at version 4.7.5 for the Blue Gene/Q architecture, with debug options enabled, and without Qt support. Additionally, it says to link it with the ``callpath`` library (which it depends on), and to build callpath with ``gcc`` 4.7.2. Most specs will not be as complicated as this one, but this is a good example of what is possible with specs. More formally, a spec consists of the following pieces: * Package name identifier (``mpileaks`` above) * ``@`` Optional version specifier (``@1.2:1.4``) * ``%`` Optional compiler specifier, with an optional compiler version (``gcc`` or ``gcc@4.7.3``) * ``+`` or ``-`` or ``~`` Optional variant specifiers (``+debug``, ``-qt``, or ``~qt``) for boolean variants * ``name=`` Optional variant specifiers that are not restricted to boolean variants * ``name=`` Optional compiler flag specifiers. Valid flag names are ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``. * ``target= os=`` 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``: .. graphviz:: digraph { mpileaks -> mpich mpileaks -> callpath -> mpich callpath -> dyninst dyninst -> libdwarf -> libelf dyninst -> libelf } Each box above is a package and each arrow represents a dependency on some other package. For example, we say that the package ``mpileaks`` *depends on* ``callpath`` and ``mpich``. ``mpileaks`` also depends *indirectly* on ``dyninst``, ``libdwarf``, and ``libelf``, in that these libraries are dependencies of ``callpath``. To install ``mpileaks``, Spack has to build all of these packages. Dependency graphs in Spack have to be acyclic, and the *depends on* relationship is directional, so this is a *directed, acyclic graph* or *DAG*. The package name identifier in the spec is the root of some dependency DAG, and the DAG itself is implicit. Spack knows the precise dependencies among packages, but users do not need to know the full DAG structure. Each ``^`` in the full spec refers to some dependency of the root package. Spack will raise an error if you supply a name after ``^`` that the root does not actually depend on (e.g. ``mpileaks ^emacs@23.3``). Spack further simplifies things by only allowing one configuration of each package within any single build. Above, both ``mpileaks`` and ``callpath`` depend on ``mpich``, but ``mpich`` appears only once in the DAG. You cannot build an ``mpileaks`` version that depends on one version of ``mpich`` *and* on a ``callpath`` version that depends on some *other* version of ``mpich``. In general, such a configuration would likely behave unexpectedly at runtime, and Spack enforces this to ensure a consistent runtime environment. The point of specs is to abstract this full DAG from Spack users. If a user does not care about the DAG at all, she can refer to mpileaks by simply writing ``mpileaks``. If she knows that ``mpileaks`` indirectly uses ``dyninst`` and she wants a particular version of ``dyninst``, then she can refer to ``mpileaks ^dyninst@8.1``. Spack will fill in the rest when it parses the spec; the user only needs to know package names and minimal details about their relationship. When spack prints out specs, it sorts package names alphabetically to normalize the way they are displayed, but users do not need to worry about this when they write specs. The only restriction on the order of dependencies within a spec is that they appear *after* the root package. For example, these two specs represent exactly the same configuration: .. code-block:: none 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=``. 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 `` 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: .. code-block:: sh 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: .. code-block:: sh mpileaks-debug # wrong! mpileaks -debug # right Spack allows the ``-`` character to be part of package names, so the above will be interpreted as a request for the ``mpileaks-debug`` package, not a request for ``mpileaks`` built without ``debug`` options. In this scenario, you should write ``mpileaks~debug`` to avoid ambiguity. When spack normalizes specs, it prints them out with no spaces boolean variants using the backwards compatibility syntax and uses only ``~`` for disabled boolean variants. The ``-`` and spaces on the command line are provided for convenience and legibility. ^^^^^^^^^^^^^^ Compiler Flags ^^^^^^^^^^^^^^ Compiler flags are specified using the same syntax as non-boolean variants, but fulfill a different purpose. While the function of a variant is set by the package, compiler flags are used by the compiler wrappers to inject flags into the compile line of the build. Additionally, compiler flags are inherited by dependencies. ``spack install libdwarf cppflags="-g"`` will install both libdwarf and libelf with the ``-g`` flag injected into their compile line. Notice that the value of the compiler flags must be quoted if it contains any spaces. Any of ``cppflags=-O3``, ``cppflags="-O3"``, ``cppflags='-O3'``, and ``cppflags="-O3 -fPIC"`` are acceptable, but ``cppflags=-O3 -fPIC`` is not. Additionally, if they value of the compiler flags is not the last thing on the line, it must be followed by a space. The commmand ``spack install libelf cppflags="-O3"%intel`` will be interpreted as an attempt to set `cppflags="-O3%intel"``. The six compiler flags are injected in the order of implicit make commands in GNU Autotools. If all flags are set, the order is ``$cppflags $cflags|$cxxflags $ldflags $ldlibs`` for C and C++ and ``$fflags $cppflags $ldflags $ldlibs`` for Fortran. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Compiler environment variables and additional RPATHs ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ In the exceptional case a compiler requires setting special environment variables, like an explicit library load path. These can bet set in an extra section in the compiler configuration. The user can also specify additional ``RPATHs`` that the compiler will add to all executables generated by that compiler. This is useful for forcing certain compilers to RPATH their own runtime libraries, so that executables will run without the need to set ``LD_LIBRARY_PATH``. .. code-block:: yaml compilers: - compiler: spec: gcc@4.9.3 paths: cc: /opt/gcc/bin/gcc c++: /opt/gcc/bin/g++ f77: /opt/gcc/bin/gfortran fc: /opt/gcc/bin/gfortran environment: set: LD_LIBRARY_PATH : /opt/gcc/lib extra_rpaths: - /path/to/some/compiler/runtime/directory - /path/to/some/other/compiler/runtime/directory ^^^^^^^^^^^^^^^^^^^^^^^ Architecture specifiers ^^^^^^^^^^^^^^^^^^^^^^^ The architecture can be specified by using the reserved words ``target`` and/or ``os`` (``target=x86-64 os=debian7``). You can also use the triplet form of platform, operating system and processor. .. code-block:: console $ 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 :ref:`cray-support` .. _sec-virtual-dependencies: -------------------- 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: .. graphviz:: digraph { mpi [color=red] mpileaks -> mpi mpileaks -> callpath -> mpi callpath -> dyninst dyninst -> libdwarf -> libelf dyninst -> libelf } Notice that ``mpich`` has now been replaced with ``mpi``. There is no *real* MPI package, but some packages *provide* the MPI interface, and these packages can be substituted in for ``mpi`` when ``mpileaks`` is built. You can see what virtual packages a particular package provides by getting info on it: .. command-output:: spack info mpich 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: .. code-block:: console $ 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: .. code-block:: console $ 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: .. code-block:: console $ spack install mpileaks ^mpich@3 The ``mpileaks`` package in particular only needs MPI-1 commands, so any MPI implementation will do. If another package depends on ``mpi@2`` and you try to give it an insufficient MPI implementation (e.g., one that provides only ``mpi@:1``), then Spack will raise an error. Likewise, if you try to plug in some package that doesn't provide MPI, Spack will raise an error. ^^^^^^^^^^^^^^^^^^^^^^^^ Specifying Specs by Hash ^^^^^^^^^^^^^^^^^^^^^^^^ Complicated specs can become cumbersome to enter on the command line, especially when many of the qualifications are necessary to distinguish between similar installs, for example when using the ``uninstall`` command. To avoid this, when referencing an existing spec, Spack allows you to reference specs by their hash. We previously discussed the spec hash that Spack computes. In place of a spec in any command, substitute ``/`` where ```` is any amount from the beginning of a spec hash. If the given spec hash is sufficient to be unique, Spack will replace the reference with the spec to which it refers. Otherwise, it will prompt for a more qualified hash. Note that this will not work to reinstall a depencency uninstalled by ``spack uninstall --force``. .. _cmd-spack-providers: ^^^^^^^^^^^^^^^^^^^ ``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: .. command-output:: spack providers mpi And if you *only* wanted to see packages that provide MPI-2, you would add a version specifier to the spec: .. command-output:: spack providers mpi@2 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: .. code-block:: console $ spack find python ==> 1 installed packages. -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- python@2.7.8 .. _cmd-spack-extensions: ^^^^^^^^^^^^^^^^^^^^ ``spack extensions`` ^^^^^^^^^^^^^^^^^^^^ You can find extensions for your Python installation like this: .. code-block:: console $ 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``: .. code-block:: console $ 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``: .. code-block:: console $ 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 "", line 1, in ImportError: No module named numpy >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Extensions & Environment Modules ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ There are two ways to get ``numpy`` working in Python. The first is to use :ref:`shell-support`. You can simply ``use`` or ``load`` the module for the extension, and it will be added to the ``PYTHONPATH`` in your current shell. For tcl modules: .. code-block:: console $ spack load python $ spack load py-numpy or, for dotkit: .. code-block:: console $ spack use python $ spack use py-numpy Now ``import numpy`` will succeed for as long as you keep your current session open. ^^^^^^^^^^^^^^^^^^^^^ Activating Extensions ^^^^^^^^^^^^^^^^^^^^^ It is often desirable to have certain packages *always* available as part of a Python installation. Spack offers a more permanent solution for this case. Instead of requiring users to load particular environment modules, you can *activate* the package within the Python installation: .. _cmd-spack-activate: ^^^^^^^^^^^^^^^^^^ ``spack activate`` ^^^^^^^^^^^^^^^^^^ .. code-block:: console $ 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: .. code-block:: console $ spack extensions python ==> python@2.7.8%gcc@4.4.7 arch=linux-debian7-x86_64-703c7a96 ==> 36 extensions: geos py-ipython py-pexpect py-pyside py-sip py-basemap py-libxml2 py-pil py-pytz py-six py-biopython py-mako py-pmw py-rpy2 py-sympy py-cython py-matplotlib py-pychecker py-scientificpython py-virtualenv py-dateutil py-mpi4py py-pygments py-scikit-learn py-epydoc py-mx py-pylint py-scipy py-gnuplot py-nose py-pyparsing py-setuptools py-h5py py-numpy py-pyqt py-shiboken ==> 12 installed: -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- py-dateutil@2.4.0 py-nose@1.3.4 py-pyside@1.2.2 py-dateutil@2.4.0 py-numpy@1.9.1 py-pytz@2014.10 py-ipython@2.3.1 py-pygments@2.0.1 py-setuptools@11.3.1 py-matplotlib@1.4.2 py-pyparsing@2.0.3 py-six@1.9.0 ==> 3 currently activated: -- linux-debian7-x86_64 / gcc@4.4.7 -------------------------------- py-nose@1.3.4 py-numpy@1.9.1 py-setuptools@11.3.1 Now, when a user runs python, ``numpy`` will be available for import *without* the user having to explicitly loaded. ``python@2.7.8`` now acts like a system Python installation with ``numpy`` installed inside of it. Spack accomplishes this by symbolically linking the *entire* prefix of the ``py-numpy`` into the prefix of the ``python`` package. To the python interpreter, it looks like ``numpy`` is installed in the ``site-packages`` directory. The only limitation of activation is that you can only have a *single* version of an extension activated at a time. This is because multiple versions of the same extension would conflict if symbolically linked into the same prefix. Users who want a different version of a package can still get it by using environment modules, but they will have to explicitly load their preferred version. ^^^^^^^^^^^^^^^^^^^^^^^^^^ ``spack activate --force`` ^^^^^^^^^^^^^^^^^^^^^^^^^^ If, for some reason, you want to activate a package *without* its dependencies, you can use ``spack activate --force``: .. code-block:: console $ 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. .. _cmd-spack-deactivate: ^^^^^^^^^^^^^^^^^^^^ ``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 `` 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 `` deactivates an extension regardless of packages that depend on it. * ``spack deactivate --all `` deactivates an extension and all of its dependencies. Use ``--force`` to disregard dependents. * ``spack deactivate --all `` deactivates *all* activated extensions of a package. For example, to deactivate *all* python extensions, use: .. code-block:: console $ spack deactivate --all python ----------------------- Filesystem requirements ----------------------- Spack currently needs to be run from a filesystem that supports ``flock`` locking semantics. Nearly all local filesystems and recent versions of NFS support this, but parallel filesystems may be mounted without ``flock`` support enabled. You can determine how your filesystems are mounted with ``mount -p``. The output for a Lustre filesystem might look like this: .. code-block:: console $ mount -l | grep lscratch pilsner-mds1-lnet0@o2ib100:/lsd on /p/lscratchd type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock) porter-mds1-lnet0@o2ib100:/lse on /p/lscratche type lustre (rw,nosuid,noauto,_netdev,lazystatfs,flock) Note the ``flock`` option on both Lustre mounts. If you do not see this or a similar option for your filesystem, you may need ot ask your system administrator to enable ``flock``. This issue typically manifests with the error below: .. code-block:: console $ ./spack find Traceback (most recent call last): File "./spack", line 176, in 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 ------------ .. _cmd-spack-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: .. command-output:: spack help Adding an argument, e.g. ``spack help ``, will print out usage information for a particular subcommand: .. command-output:: spack help install Alternately, you can use ``spack --help`` in place of ``spack help``, or ``spack --help`` to get help on a particular subcommand.