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| author | Kevin Brandstatter <kjbrandstatter@gmail.com> | 2015-02-26 14:42:12 -0600 |
|---|---|---|
| committer | Kevin Brandstatter <kjbrandstatter@gmail.com> | 2015-02-26 14:42:12 -0600 |
| commit | 2f2eab0e157b7ebced80772d9bc81b205d69d620 (patch) | |
| tree | 2e7fc63859631b84f68aeeb14d8414a5ecb01f9c | |
| parent | bbfc519ee5631efa4224d852d9c63446a60a8c07 (diff) | |
| parent | ffdb90f39a56e5f0dacefd19ccf85ddd0e7a01c0 (diff) | |
| download | spack-2f2eab0e157b7ebced80772d9bc81b205d69d620.tar.gz spack-2f2eab0e157b7ebced80772d9bc81b205d69d620.tar.bz2 spack-2f2eab0e157b7ebced80772d9bc81b205d69d620.tar.xz spack-2f2eab0e157b7ebced80772d9bc81b205d69d620.zip | |
Merge branch 'develop' of github.com:kev40293/spack into develop
115 files changed, 4338 insertions, 812 deletions
@@ -36,16 +36,19 @@ Authors ---------------- Spack was written by Todd Gamblin, tgamblin@llnl.gov. -Significant contributions were also made by the following awesome -people: +Significant contributions were also made by: * David Beckingsale * David Boehme + * Alfredo Gimenez * Luc Jaulmes * Matt Legendre * Greg Lee * Adam Moody + * Saravan Pantham + * Joachim Protze * Bob Robey + * Justin Too Release ---------------- @@ -58,14 +58,16 @@ parser = argparse.ArgumentParser( description='Spack: the Supercomputing PACKage Manager.') parser.add_argument('-V', '--version', action='version', version="%s" % spack.spack_version) -parser.add_argument('-v', '--verbose', action='store_true', dest='verbose', +parser.add_argument('-v', '--verbose', action='store_true', help="Print additional output during builds") -parser.add_argument('-d', '--debug', action='store_true', dest='debug', +parser.add_argument('-d', '--debug', action='store_true', help="Write out debug logs during compile") -parser.add_argument('-k', '--insecure', action='store_true', dest='insecure', +parser.add_argument('-k', '--insecure', action='store_true', help="Do not check ssl certificates when downloading archives.") -parser.add_argument('-m', '--mock', action='store_true', dest='mock', +parser.add_argument('-m', '--mock', action='store_true', help="Use mock packages instead of real ones.") +parser.add_argument('-p', '--profile', action='store_true', + help="Profile execution using cProfile.") # each command module implements a parser() function, to which we pass its # subparser for setup. @@ -85,42 +87,49 @@ if len(sys.argv) == 1: # actually parse the args. args = parser.parse_args() -# Set up environment based on args. -tty.set_verbose(args.verbose) -tty.set_debug(args.debug) -spack.debug = args.debug - -spack.spack_working_dir = working_dir -if args.mock: - from spack.packages import PackageDB - spack.db = PackageDB(spack.mock_packages_path) - -# If the user asked for it, don't check ssl certs. -if args.insecure: - tty.warn("You asked for --insecure, which does not check SSL certificates or checksums.") - spack.curl.add_default_arg('-k') - -# Try to load the particular command asked for and run it -command = spack.cmd.get_command(args.command) -try: - return_val = command(parser, args) -except SpackError, e: - if spack.debug: - # In debug mode, raise with a full stack trace. - raise - elif e.long_message: - tty.die(e.message, e.long_message) +def main(): + # Set up environment based on args. + tty.set_verbose(args.verbose) + tty.set_debug(args.debug) + spack.debug = args.debug + + spack.spack_working_dir = working_dir + if args.mock: + from spack.packages import PackageDB + spack.db = PackageDB(spack.mock_packages_path) + + # If the user asked for it, don't check ssl certs. + if args.insecure: + tty.warn("You asked for --insecure, which does not check SSL certificates or checksums.") + spack.curl.add_default_arg('-k') + + # Try to load the particular command asked for and run it + command = spack.cmd.get_command(args.command) + try: + return_val = command(parser, args) + except SpackError, e: + if spack.debug: + # In debug mode, raise with a full stack trace. + raise + elif e.long_message: + tty.die(e.message, e.long_message) + else: + tty.die(e.message) + + except KeyboardInterrupt: + sys.stderr.write('\n') + tty.die("Keyboard interrupt.") + + # Allow commands to return values if they want to exit with some ohter code. + if return_val is None: + sys.exit(0) + elif isinstance(return_val, int): + sys.exit(return_val) else: - tty.die(e.message) - -except KeyboardInterrupt: - sys.stderr.write('\n') - tty.die("Keyboard interrupt.") + tty.die("Bad return value from command %s: %s" % (args.command, return_val)) -# Allow commands to return values if they want to exit with some ohter code. -if return_val is None: - sys.exit(0) -elif isinstance(return_val, int): - sys.exit(return_val) +if args.profile: + import cProfile + cProfile.run('main()', sort='tottime') else: - tty.die("Bad return value from command %s: %s" % (args.command, return_val)) + main() diff --git a/lib/spack/docs/.gitignore b/lib/spack/docs/.gitignore index 7701dd9f12..26c343d3eb 100644 --- a/lib/spack/docs/.gitignore +++ b/lib/spack/docs/.gitignore @@ -1,3 +1,4 @@ package_list.rst +command_index.rst spack*.rst _build diff --git a/lib/spack/docs/Makefile b/lib/spack/docs/Makefile index a660e1255d..00203b5b61 100644 --- a/lib/spack/docs/Makefile +++ b/lib/spack/docs/Makefile @@ -28,6 +28,18 @@ package_list: spack package-list > package_list.rst # +# Generate a command index +# +command_index: + cp command_index.in command_index.rst + echo >> command_index.rst + grep -ho '.. _spack-.*:' *rst \ + | perl -pe 's/.. _([^:]*):/ * :ref:`\1`/' \ + | sort >> command_index.rst + +custom_targets: package_list command_index + +# # This creates a git repository and commits generated html docs. # It them pushes the new branch into THIS repository as gh-pages. # @@ -77,10 +89,10 @@ help: @echo " doctest to run all doctests embedded in the documentation (if enabled)" clean: - -rm -f package_list.rst + -rm -f package_list.rst command_index.rst -rm -rf $(BUILDDIR)/* $(APIDOC_FILES) -html: apidoc package_list +html: apidoc custom_targets $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index 196b7077f9..ed79790bb9 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -4,18 +4,19 @@ Basic usage ===================== Spack is implemented as a single command (``spack``) with many -*subcommands*, much like ``git``, ``svn``, ``yum``, or ``apt-get``. -Only a small subset of commands are needed for typical usage. - -This section covers a small set of subcommands that should cover most -general use cases for Spack. +*subcommands*. Only a small subset of commands is needed for typical +usage. Listing available packages ------------------------------ -The first thing you will likely want to do with spack is find out what -software is available to install. There are a few relevant commands. +The first thing you likely want to do with spack is to install some +software. Before that, you need to know what's available. You can +see available package names either using the :ref:`package-list`, or +using the commands below. + +.. _spack-list: ``spack list`` ~~~~~~~~~~~~~~~~ @@ -26,45 +27,292 @@ Spack can install: .. command-output:: spack list The packages are listed by name in alphabetical order. You can also -do wildcard searches using ``*``: +do wildcats searches using ``*``: .. command-output:: spack list m* .. command-output:: spack list *util* +.. _spack-info: ``spack info`` ~~~~~~~~~~~~~~~~ -To get information on a particular package from the full list, run -``spack info <package name>``. For example, for ``mpich`` the output -looks like this: +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 -This includes basic information about the package: where to download -it, its dependencies, virtual packages it provides (e.g. an MPI -implementation will provide the MPI interface), and a text -description, if one is available. :ref:`Dependencies -<sec-specs>` and :ref:`virtual dependencies -<sec-virtual-dependencies>` are described in more detail later. +Most of the information is self-explanatory. *Safe versions* are +versions that Spack has a checksum for, and Spack will use the +checksum to ensure they downloaded without any errors or malicious +attacks. :ref:`Dependencies <sec-specs>` and :ref:`virtual +dependencies <sec-virtual-dependencies>`, are described in more detail +later. + +.. _spack-versions: ``spack versions`` ~~~~~~~~~~~~~~~~~~~~~~~~ -To see available versions of a package, run ``spack versions``, for -example: +To see *more* available versions of a package, run ``spack versions``, +for example: .. command-output:: spack versions libelf -Since it has to manage many different software packages, Spack doesn't -place many restrictions on what a package version has to look like. -Packages like ``mpich`` use traditional version numbers like -``3.0.4``. Other packages, like ``libdwarf`` use date-stamp versions -like ``20130729``. Versions can contain numbers, letters, dashes, -underscores, and periods. +There are two sections in the output. *Safe versions* are ones that +have already been checksummed. Spack goes a step further, though, and +also shows you what versions are available out on the web---these are +*remote versions*. Spack gets this information by scraping it +directly from web pages. Depending on the package, Spack may or may +not be able to find any remote versions. + + +Installing and uninstalling +------------------------------ + +Now that you know how to list available packages and versions, you're +ready to start installing things. + +.. _spack-install: + +``spack install`` +~~~~~~~~~~~~~~~~~~~~~ + +``spack install`` will install any package shown by ``spack list``. +To install the latest version of a package, along with all of its +dependencies, simply give it a package name: + +.. code-block:: sh + + $ spack install mpileaks + +If `mpileaks` depends on other packages, Spack will install those +first. It then fetches the tarball for ``mpileaks``, expands it, +verifies that it was downloaded without errors, builds it, and +installs it in its own directory under ``$SPACK_HOME/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:: sh + + $ spack install mpileaks + ==> Installing mpileaks + ==> mpich is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/mpich@3.0.4. + ==> callpath is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/callpath@1.0.2-5dce4318. + ==> adept-utils is already installed in /home/gamblin2/spack/opt/chaos_5_x86_64_ib/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: /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7=chaos_5_x86_64_ib-59f6ad23/mpileaks-1.0.tar.gz + ==> Created stage in /home/gamblin2/spack/var/spack/stage/mpileaks@1.0%gcc@4.4.7=chaos_5_x86_64_ib-59f6ad23. + ==> No patches needed for mpileaks. + ==> Building mpileaks. + + ... build output ... + + ==> Successfully installed mpileaks. + Fetch: 2.16s. Build: 9.82s. Total: 11.98s. + [+] /home/gamblin2/spack/opt/chaos_5_x86_64_ib/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:: sh + + $ 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), 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 special syntax. Spack +calls the descriptor used to refer to a particular package +configuration a **spec**. In the command lines above, both +``mpileaks`` and ``mpileaks@3.0.4`` are specs. Specs are described in +detail in :ref:`sec-specs`. + +.. _spack-uninstall: + +``spack uninstall`` +~~~~~~~~~~~~~~~~~~~~~ + +To uninstall a package, type ``spack uninstall <package>``. This will +completely remove the directory in which the package was installed. + +.. code-block:: sh + + spack uninstall mpich -Compiler Configuration +If there are still installed packages that depend on the package to be +uninstalled, spack will refuse to uninstall it. You can override this +behavior with ``spack uninstall -f <package>``, but you risk breaking +other installed packages. In general, it is safer to remove dependent +packages *before* removing their dependencies. + +A line 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 to provide a version number to remove the +ambiguity. As an example, ``spack uninstall mpich@3.1`` is +unambiguous in this scenario. + + +Seeing installed packages +----------------------------------- + +We know that ``spack list`` shows you the names of available packages, +but how do you figure out which are installed? + +.. _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:: sh + + $ spack find + ==> 74 installed packages. + -- chaos_5_x86_64_ib / 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 + + -- chaos_5_x86_64_ib / 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. + +In some cases, there may be different configurations of the *same* +version of a package installed. For example, there are two +installations of of ``libdwarf@20130729`` above. We can look at them +in more detail using ``spack find -d``, and by asking only to show +``libdwarf`` packages: + +.. code-block:: sh + + $ spack find --deps libdwarf + ==> 2 installed packages. + -- chaos_5_x86_64_ib / 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 -l``: + +.. code-block:: sh + + $ spack find -l libdwarf + ==> 2 installed packages. + -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + libdwarf@20130729-d9b90962 libdwarf@20130729-b52fac98 + +Now the ``libwarf`` 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 -p``: + +.. code-block:: sh + + $ spack find -p + ==> 74 installed packages. + -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + ImageMagick@6.8.9-10 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/ImageMagick@6.8.9-10-4df950dd + adept-utils@1.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/adept-utils@1.0-5adef8da + atk@2.14.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/atk@2.14.0-3d09ac09 + boost@1.55.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/boost@1.55.0 + bzip2@1.0.6 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/bzip2@1.0.6 + cairo@1.14.0 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/cairo@1.14.0-fcc2ab44 + callpath@1.0.2 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/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:: sh + + $ spack find -p libelf + -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + libelf@0.8.11 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11 + libelf@0.8.12 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12 + libelf@0.8.13 /home/gamblin2/spack/opt/chaos_5_x86_64_ib/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:: sh + + $ spack find libelf@0.8.12: + -- chaos_5_x86_64_ib / 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:: sh + + $ spack find -l libdwarf ^libelf@0.8.12 + ==> 1 installed packages. + -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + libdwarf@20130729-d9b90962 + +The full spec syntax is discussed in detail in :ref:`sec-specs`. + + +Compiler configuration ----------------------------------- Spack has the ability to build packages with multiple compilers and @@ -72,6 +320,8 @@ compiler versions. Spack searches for compilers on your machine automatically the first time it is run. It does this by inspecting your path. +.. _spack-compilers: + ``spack compilers`` ~~~~~~~~~~~~~~~~~~~~~~~ @@ -98,6 +348,8 @@ compilers`` or ``spack compiler list``:: Any of these compilers can be used to build Spack packages. More on how this is done is in :ref:`sec-specs`. +.. _spack-compiler-add: + ``spack compiler add`` ~~~~~~~~~~~~~~~~~~~~~~~ @@ -110,15 +362,19 @@ where the compiler is installed. For example:: intel@13.0.079 Or you can run ``spack compiler add`` with no arguments to force -autodetection. This is useful if you do not know where compilers -live, but new compilers have been added to your ``PATH``. For -example, using dotkit, you might do this:: +auto-detection. This is useful if you do not know where compilers are +installed, but you know that new compilers have been added to your +``PATH``. For example, using dotkit, you might do this:: - $ use gcc-4.9.0 + $ module load gcc-4.9.0 $ spack compiler add ==> Added 1 new compiler to /Users/gamblin2/.spackconfig gcc@4.9.0 +This loads the environment module for gcc-4.9.0 to get it into the +``PATH``, and then it adds the compiler to Spack. + +.. _spack-compiler-info: ``spack compiler info`` ~~~~~~~~~~~~~~~~~~~~~~~ @@ -126,20 +382,23 @@ example, using dotkit, you might do this:: If you want to see specifics on a particular compiler, you can run ``spack compiler info`` on it:: - $ spack compiler info intel@12.1.3 - intel@12.1.3: - cc = /usr/local/bin/icc-12.1.293 - cxx = /usr/local/bin/icpc-12.1.293 - f77 = /usr/local/bin/ifort-12.1.293 - fc = /usr/local/bin/ifort-12.1.293 + $ spack compiler info intel@15 + intel@15.0.0: + cc = /usr/local/bin/icc-15.0.090 + cxx = /usr/local/bin/icpc-15.0.090 + f77 = /usr/local/bin/ifort-15.0.090 + fc = /usr/local/bin/ifort-15.0.090 This shows which C, C++, and Fortran compilers were detected by Spack. +Notice also that we didn't have to be too specific about the +version. We just said ``intel@15``, and information about the only +matching Intel compiler was displayed. -Manual configuration -~~~~~~~~~~~~~~~~~~~~~~~ +Manual compiler configuration +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -If autodetection fails, you can manually conigure a compiler by +If auto-detection fails, you can manually configure a compiler by editing your ``~/.spackconfig`` file. You can do this by running ``spack config edit``, which will open the file in your ``$EDITOR``. @@ -153,8 +412,8 @@ Each compiler configuration in the file looks like this:: fc = /usr/local/bin/ifort-15.0.024-beta ... -For compilers, like ``clang``, that do not support Fortran, you can simply -put ``None`` for ``f77`` and ``fc``:: +For compilers, like ``clang``, that do not support Fortran, put +``None`` for ``f77`` and ``fc``:: [compiler "clang@3.3svn"] cc = /usr/bin/clang @@ -163,180 +422,18 @@ put ``None`` for ``f77`` and ``fc``:: fc = None Once you save the file, the configured compilers will show up in the -list displayed when you run ``spack compilers``. - - -Seeing installed packages ----------------------------------- - -``spack find`` -~~~~~~~~~~~~~~~~~~~~~~ - -The second thing you're likely to want to do with Spack, and the first -thing users of your system will likely want to do, is to find what -software is already installed and ready to use. You can do that with -``spack find``. - -Running ``spack find`` with no arguments will list all the installed -packages: - -.. code-block:: sh - - $ spack find - == chaos_5_x86_64_ib =========================================== - -- gcc@4.4.7 --------------------------------------------------- - libdwarf@20130207-d9b909 - libdwarf@20130729-d9b909 - libdwarf@20130729-b52fac - libelf@0.8.11 - libelf@0.8.12 - libelf@0.8.13 - -Packages are grouped by architecture, then by the compiler used to -build them, and then by their versions and options. If a package has -dependencies, there will also be a hash at the end of the name -indicating the dependency configuration. Packages with the same hash -have the same dependency configuration. If you want ALL information -about dependencies, as well, then you can supply ``-l`` or ``--long``: - -.. code-block:: sh - - $ spack find -l - == chaos_5_x86_64_ib =========================================== - -- gcc@4.4.7 --------------------------------------------------- - libdwarf@20130207 - ^libelf@0.8.12 - libdwarf@20130729 - ^libelf@0.8.12 - libdwarf@20130729 - ^libelf@0.8.13 - libelf@0.8.11 - libelf@0.8.12 - libelf@0.8.13 - -Now you can see which versions of ``libelf`` each version of -``libdwarf`` was built with. - -If you want to know the path where each of these packages is -installed, do ``spack find -p`` or ``--path``: - -.. code-block:: sh - - $ spack find -p - == chaos_5_x86_64_ib =========================================== - -- gcc@4.4.7 --------------------------------------------------- - libdwarf@20130207-d9b909 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libdwarf@20130207-d9b909 - libdwarf@20130729-d9b909 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libdwarf@20130729-d9b909 - libdwarf@20130729-b52fac /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libdwarf@20130729-b52fac - libelf@0.8.11 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11 - libelf@0.8.12 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12 - libelf@0.8.13 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.13 - - -And, finally, you can restrict your search to a particular package -by supplying its name: - -.. code-block:: sh - - $ spack find -p libelf - == chaos_5_x86_64_ib =========================================== - -- gcc@4.4.7 --------------------------------------------------- - libelf@0.8.11 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.11 - libelf@0.8.12 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/gcc@4.4.7/libelf@0.8.12 - libelf@0.8.13 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/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. The full spec syntax is discussed in detail in -:ref:`sec-specs`. - - - -Installing and uninstalling ------------------------------- - -``spack install`` -~~~~~~~~~~~~~~~~~~~~~ - -``spack install`` will install any package that appears in the output -of ``spack list``. To install the latest version of a pacakge and all -of its dependencies, simply run ``spack install <package>``: - -.. code-block:: sh - - spack install mpileaks - -Spack will fetch the tarball for ``mpileaks``, expand it, verify that -it was downloaded without errors, build it, and install it in its own -directory under ``$SPACK_HOME/opt``. If the requested package depends -on other packages in order to build, Spack fetches them as well, and -installs them before it installs the requested package. Like the main -package, each dependency is also installed in its own directory. - -Spack can also build *specific* configurations of a package. For -example, to install something with a specific version, add ``@`` after -the package name, followed by a version string: - -.. code-block:: sh - - spack install mpich@3.0.4 - -Any number of configurations 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 version configuraitons, Spack can customize the -compiler, compile-time options (variants), 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 special syntax. Spack -calls the descriptor used to refer to a particular package -configuration a **spec**. In the command lines above, both -``mpileaks`` and ``mpileaks@3.0.4`` are specs. To customize -additional properties, simply add more attributes to the spec. Specs -and their syntax are covered in more detail in :ref:`sec-specs`. - - -``spack uninstall`` -~~~~~~~~~~~~~~~~~~~~~ - -To uninstall a package, type ``spack uninstall <package>``. This will -completely remove the directory in which the package was installed. - -.. code-block:: sh - - spack uninstall mpich - -If there are still installed packages that depend on the package to be -uninstalled, spack will refuse to uninstall. If you know what you're -doing, you can override this with ``spack uninstall -f <package>``. -However, running this risks breaking other installed packages. In -general, it is safer to remove dependent packages *before* removing -their dependencies. - -A line 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, it could refer to -either one, and Spack cannot determine which one to uninstall. Spack -will ask you to provide a version number to remove the ambiguity. For -example, ``spack uninstall mpich@3.1`` is unambiguous in the above -scenario. +list displayed by ``spack compilers``. .. _sec-specs: -Specs & Dependencies +Specs & dependencies ------------------------- -We now know that ``spack install`` and ``spack uninstall`` both 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. +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 @@ -499,6 +596,11 @@ based on site policies. Variants ~~~~~~~~~~~~~~~~~~~~~~~ +.. Note:: + + Variants are not yet supported, but will be in the next Spack + release (0.9), due in Q2 2015. + Variants are named options associated with a particular package, and they can be turned on or off. For example, above, supplying ``+debug`` causes ``mpileaks`` to be built with debug flags. The @@ -544,6 +646,11 @@ the command line is provided for convenience and legibility. Architecture specifier ~~~~~~~~~~~~~~~~~~~~~~~ +.. Note:: + + Architecture specifiers are part of specs but are not yet + functional. They will be in Spack version 1.0, due in Q3 2015. + The architecture specifier starts with a ``=`` and also comes after some package name within a spec. It allows a user to specify a particular architecture for the package to be built. This is mostly @@ -627,6 +734,8 @@ any MPI implementation will do. If another package depends on error. Likewise, if you try to plug in some package that doesn't provide MPI, Spack will raise an error. +.. _spack-providers: + ``spack providers`` ~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -646,7 +755,7 @@ versions are now filtered out. .. _shell-support: -Environment Modules +Environment modules ------------------------------- .. note:: @@ -678,10 +787,6 @@ For ``csh`` and ``tcsh`` run: You can put the above code in your ``.bashrc`` or ``.cshrc``, and Spack's shell support will be available on the command line. - -------------------------------- - - When you install a package with Spack, it automatically generates an environment module that lets you add the package to your environment. @@ -698,6 +803,7 @@ The directories are automatically added to your ``MODULEPATH`` and ``DK_NODE`` environment variables when you enable Spack's `shell support <shell-support_>`_. + Using Modules & Dotkits ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -710,7 +816,7 @@ of installed packages. $ module avail - ------- /g/g21/gamblin2/src/spack/share/spack/modules/chaos_5_x86_64_ib -------- + ------- /home/gamblin2/spack/share/spack/modules/chaos_5_x86_64_ib -------- adept-utils@1.0%gcc@4.4.7-5adef8da libelf@0.8.13%gcc@4.4.7 automaded@1.0%gcc@4.4.7-d9691bb0 libelf@0.8.13%intel@15.0.0 boost@1.55.0%gcc@4.4.7 mpc@1.0.2%gcc@4.4.7-559607f5 @@ -845,6 +951,8 @@ if newer, fancier module support is added to Spack at some later date, you may want to regenerate all the modules to take advantage of these new features. +.. _spack-module: + ``spack module refresh`` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -858,9 +966,226 @@ regenerate all module and dotkit files from scratch: ==> Regenerating tcl module files. ==> Regenerating dotkit module files. + +.. _extensions: + +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 +<https://www.python.org>`_ 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:: sh + + $ spack find python + ==> 1 installed packages. + -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + python@2.7.8 + +.. _spack-extensions: + +``spack extensions`` +~~~~~~~~~~~~~~~~~~~~~~~ + +You can find extensions for your Python installation like this: + +.. code-block:: sh + + $ spack extensions python + ==> python@2.7.8%gcc@4.4.7=chaos_5_x86_64_ib-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: + -- chaos_5_x86_64_ib / 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 -p``: + +.. code-block:: sh + + $ spack find -p py-numpy + ==> 1 installed packages. + -- chaos_5_x86_64_ib / gcc@4.4.7 -------------------------------- + py-numpy@1.9.1 /g/g21/gamblin2/src/spack/opt/chaos_5_x86_64_ib/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:: sh + + $ spack load python + $ python + Python 2.7.8 (default, Feb 17 2015, 01:35:25) + [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2 + Type "help", "copyright", "credits" or "license" for more information. + >>> import numpy + Traceback (most recent call last): + File "<stdin>", line 1, in <module> + ImportError: No module named numpy + >>> + +Extensions & Environment Modules +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +There are two ways to get ``numpy`` working in Python. The first is +to use :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:: sh + + $ spack load python + $ spack load py-numpy + +or, for dotkit: + +.. code-block:: sh + + $ spack use python + $ spack use py-numpy + +Now ``import numpy`` will succeed for as long as you keep your current +session open. + + +Activating Extensions +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +It is often desirable to have certain packages *always* available as +part of a Python installation. Spack offers a more permanent solution +for this case. Instead of requiring users to load particular +environment modules, you can *activate* the package within the Python +installation: + +.. _spack-activate: + +``spack activate`` +^^^^^^^^^^^^^^^^^^^^^^^ + +.. code-block:: sh + + $ spack activate py-numpy + ==> Activated extension py-setuptools@11.3.1%gcc@4.4.7=chaos_5_x86_64_ib-3c74eb69 for python@2.7.8%gcc@4.4.7. + ==> Activated extension py-nose@1.3.4%gcc@4.4.7=chaos_5_x86_64_ib-5f70f816 for python@2.7.8%gcc@4.4.7. + ==> Activated extension py-numpy@1.9.1%gcc@4.4.7=chaos_5_x86_64_ib-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:: sh + + $ spack extensions python + ==> python@2.7.8%gcc@4.4.7=chaos_5_x86_64_ib-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: + -- chaos_5_x86_64_ib / 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: + -- chaos_5_x86_64_ib / 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 -f`` +^^^^^^^^^^^^^^^^^^^^^^^^^ +If, for some reason, you want to activate a package *without* its +dependencies, you can use ``spack activate -f``: + +.. code-block:: sh + + $ spack activate -f py-numpy + ==> Activated extension py-numpy@1.9.1%gcc@4.4.7=chaos_5_x86_64_ib-66733244 for python@2.7.8%gcc@4.4.7. + +.. _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 <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 -f <extension>`` deactivates an extension + regardless of packages that depend on it. + * ``spack deactivate -a <extension>`` deactivates an extension and + all of its dependencies. Use ``-f`` to disregard dependents. + * ``spack deactivate -a <extendee>`` deactivates *all* activated + extensions of a package. For example, to deactivate *all* python + extensions, use:: + + spack deactivate -a python + + Getting Help ----------------------- +.. _spack-help: + ``spack help`` ~~~~~~~~~~~~~~~~~~~~~~ diff --git a/lib/spack/docs/command_index.in b/lib/spack/docs/command_index.in new file mode 100644 index 0000000000..94cdf38109 --- /dev/null +++ b/lib/spack/docs/command_index.in @@ -0,0 +1,10 @@ +.. _command_index: + +Command index +================= + +This is an alphabetical list of commands with links to the places they +appear in the documentation. + +.. hlist:: + :columns: 3 diff --git a/lib/spack/docs/conf.py b/lib/spack/docs/conf.py index b4d49c594d..86df113074 100644 --- a/lib/spack/docs/conf.py +++ b/lib/spack/docs/conf.py @@ -35,7 +35,9 @@ # All configuration values have a default; values that are commented out # serve to show the default. -import sys, os +import sys +import os +import subprocess # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the @@ -43,14 +45,16 @@ import sys, os sys.path.insert(0, os.path.abspath('exts')) # Add the Spack bin directory to the path so that we can use its output in docs. -os.environ['SPACK_ROOT'] = '../../..' +spack_root = '../../..' +os.environ['SPACK_ROOT'] = spack_root os.environ['PATH'] += os.pathsep + '$SPACK_ROOT/bin' +spack_version = subprocess.Popen( + ['spack', '-V'], stderr=subprocess.PIPE).communicate()[1].strip().split('.') + # Set an environment variable so that colify will print output like it would to # a terminal. -os.environ['COLIFY_TTY'] = 'true' -os.environ['COLUMNS'] = '80' -os.environ['LINES'] = '25' +os.environ['COLIFY_SIZE'] = '25x80' # Enable todo items todo_include_todos = True @@ -97,9 +101,9 @@ copyright = u'2013-2014, Lawrence Livermore National Laboratory' # built documents. # # The short X.Y version. -version = '1.0' +version = '.'.join(spack_version[:2]) # The full version, including alpha/beta/rc tags. -release = '1.0' +release = '.'.join(spack_version[:2]) # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/lib/spack/docs/developer_guide.rst b/lib/spack/docs/developer_guide.rst index 969ed60b15..db47de80f5 100644 --- a/lib/spack/docs/developer_guide.rst +++ b/lib/spack/docs/developer_guide.rst @@ -50,11 +50,11 @@ as a descriptor for one or more instances of that template. Users express the configuration they want using a spec, and a package turns the spec into a complete build. -The obvious difficulty with this design is that users underspecify +The obvious difficulty with this design is that users under-specify what they want. To build a software package, the package object needs a *complete* specification. In Spack, if a spec describes only one instance of a package, then we say it is **concrete**. If a spec -could describes many instances, (i.e. it is underspecified in one way +could describes many instances, (i.e. it is under-specified in one way or another), then we say it is **abstract**. Spack's job is to take an *abstract* spec from the user, find a @@ -92,7 +92,7 @@ with a high level view of Spack's directory structure:: Spack is designed so that it could live within a `standard UNIX directory hierarchy <http://linux.die.net/man/7/hier>`_, so ``lib``, ``var``, and ``opt`` all contain a ``spack`` subdirectory in case -Spack is installed alongside other software. Most of the insteresting +Spack is installed alongside other software. Most of the interesting parts of Spack live in ``lib/spack``. Files under ``var`` are created as needed, so there is no ``var`` directory when you initially clone Spack from the repository. @@ -123,13 +123,13 @@ Package-related modules Contains the :class:`Package <spack.package.Package>` class, which is the superclass for all packages in Spack. Methods on ``Package`` implement all phases of the :ref:`package lifecycle - <pacakge-lifecycle>` and manage the build process. + <package-lifecycle>` and manage the build process. :mod:`spack.packages` Contains all of the packages in Spack and methods for managing them. Functions like :func:`packages.get <spack.packages.get>` and :func:`class_name_for_package_name - <packages.class_name_for_package_name>` handle mapping packge module + <packages.class_name_for_package_name>` handle mapping package module names to class names and dynamically instantiating packages by name from module files. diff --git a/lib/spack/docs/features.rst b/lib/spack/docs/features.rst index b39dcd3390..fcb810086d 100644 --- a/lib/spack/docs/features.rst +++ b/lib/spack/docs/features.rst @@ -1,4 +1,4 @@ -Feature Overview +Feature overview ================== This is a high-level overview of features that make Spack different diff --git a/lib/spack/docs/index.rst b/lib/spack/docs/index.rst index 73eff43ab7..2382678cc3 100644 --- a/lib/spack/docs/index.rst +++ b/lib/spack/docs/index.rst @@ -46,8 +46,10 @@ Table of Contents getting_started basic_usage packaging_guide + mirrors site_configuration developer_guide + command_index package_list API Docs <spack> diff --git a/lib/spack/docs/mirrors.rst b/lib/spack/docs/mirrors.rst new file mode 100644 index 0000000000..d732a3dd54 --- /dev/null +++ b/lib/spack/docs/mirrors.rst @@ -0,0 +1,217 @@ +.. _mirrors: + +Mirrors +============================ + +Some sites may not have access to the internet for fetching packages. +These sites will need a local repository of tarballs from which they +can get their files. Spack has support for this with *mirrors*. A +mirror is a URL that points to a directory, either on the local +filesystem or on some server, containing tarballs for all of Spack's +packages. + +Here's an example of a mirror's directory structure:: + + mirror/ + cmake/ + cmake-2.8.10.2.tar.gz + dyninst/ + dyninst-8.1.1.tgz + dyninst-8.1.2.tgz + libdwarf/ + libdwarf-20130126.tar.gz + libdwarf-20130207.tar.gz + libdwarf-20130729.tar.gz + libelf/ + libelf-0.8.12.tar.gz + libelf-0.8.13.tar.gz + libunwind/ + libunwind-1.1.tar.gz + mpich/ + mpich-3.0.4.tar.gz + mvapich2/ + mvapich2-1.9.tgz + +The structure is very simple. There is a top-level directory. The +second level directories are named after packages, and the third level +contains tarballs for each package, named after each package. + +.. note:: + + Archives are **not** named exactly they were in the package's fetch + URL. They have the form ``<name>-<version>.<extension>``, where + ``<name>`` is Spack's name for the package, ``<version>`` is the + version of the tarball, and ``<extension>`` is whatever format the + package's fetch URL contains. + + In order to make mirror creation reasonably fast, we copy the + tarball in its original format to the mirror directory, but we do + not standardize on a particular compression algorithm, because this + would potentially require expanding and re-compressing each archive. + +.. _spack-mirror: + +``spack mirror`` +---------------------------- + +Mirrors are managed with the ``spack mirror`` command. The help for +``spack mirror`` looks like this:: + + $ spack mirror -h + usage: spack mirror [-h] SUBCOMMAND ... + + positional arguments: + SUBCOMMAND + create Create a directory to be used as a spack mirror, and fill + it with package archives. + add Add a mirror to Spack. + remove Remove a mirror by name. + list Print out available mirrors to the console. + + optional arguments: + -h, --help show this help message and exit + +The ``create`` command actually builds a mirror by fetching all of its +packages from the internet and checksumming them. + +The other three commands are for managing mirror configuration. They +control the URL(s) from which Spack downloads its packages. + +.. _spack-mirror-create: + +``spack mirror create`` +---------------------------- + +You can create a mirror using the ``spack mirror create`` command, assuming +you're on a machine where you can access the internet. + +The command will iterate through all of Spack's packages and download +the safe ones into a directory structure like the one above. Here is +what it looks like: + + +.. code-block:: bash + + $ spack mirror create libelf libdwarf + ==> Created new mirror in spack-mirror-2014-06-24 + ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz + ########################################################## 81.6% + ==> Checksum passed for libelf@0.8.13 + ==> Added libelf@0.8.13 + ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.12.tar.gz + ###################################################################### 98.6% + ==> Checksum passed for libelf@0.8.12 + ==> Added libelf@0.8.12 + ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130207.tar.gz + ###################################################################### 97.3% + ==> Checksum passed for libdwarf@20130207 + ==> Added libdwarf@20130207 + ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130126.tar.gz + ######################################################## 78.9% + ==> Checksum passed for libdwarf@20130126 + ==> Added libdwarf@20130126 + ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130729.tar.gz + ############################################################# 84.7% + ==> Added libdwarf@20130729 + ==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130729.tar.gz to mirror + ==> Added python@2.7.8. + ==> Successfully updated mirror in spack-mirror-2015-02-24. + Archive stats: + 0 already present + 5 added + 0 failed to fetch. + +Once this is done, you can tar up the ``spack-mirror-2014-06-24`` directory and +copy it over to the machine you want it hosted on. + +Custom package sets +~~~~~~~~~~~~~~~~~~~~~~~ + +Normally, ``spack mirror create`` downloads all the archives it has +checksums for. If you want to only create a mirror for a subset of +packages, you can do that by supplying a list of package specs on the +command line after ``spack mirror create``. For example, this +command:: + + $ spack mirror create libelf@0.8.12: boost@1.44: + +Will create a mirror for libelf versions greater than or equal to +0.8.12 and boost versions greater than or equal to 1.44. + +Mirror files +~~~~~~~~~~~~~~~~~~~~~~~ + +If you have a *very* large number of packages you want to mirror, you +can supply a file with specs in it, one per line:: + + $ cat specs.txt + libdwarf + libelf@0.8.12: + boost@1.44: + boost@1.39.0 + ... + $ spack mirror create -f specs.txt + ... + +This is useful if there is a specific suite of software managed by +your site. + +.. _spack-mirror-add: + +``spack mirror add`` +---------------------------- + +Once you have a mirror, you need to let spack know about it. This is +relatively simple. First, figure out the URL for the mirror. If it's +a file, you can use a file URL like this one:: + + file:///Users/gamblin2/spack-mirror-2014-06-24 + +That points to the directory on the local filesystem. If it were on a +web server, you could use a URL like this one: + + https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24 + +Spack will use the URL as the root for all of the packages it fetches. +You can tell your Spack installation to use that mirror like this: + +.. code-block:: bash + + $ spack mirror add local_filesystem file:///Users/gamblin2/spack-mirror-2014-06-24 + +Each mirror has a name so that you can refer to it again later. + +.. _spack-mirror-list: + +``spack mirror list`` +---------------------------- + +If you want to see all the mirrors Spack knows about you can run ``spack mirror list``:: + + $ spack mirror list + local_filesystem file:///Users/gamblin2/spack-mirror-2014-06-24 + +.. _spack-mirror-remove: + +``spack mirror remove`` +---------------------------- + +And, if you want to remove a mirror, just remove it by name:: + + $ spack mirror remove local_filesystem + $ spack mirror list + ==> No mirrors configured. + +Mirror precedence +---------------------------- + +Adding a mirror really just adds a section in ``~/.spackconfig``:: + + [mirror "local_filesystem"] + url = file:///Users/gamblin2/spack-mirror-2014-06-24 + [mirror "remote_server"] + url = https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24 + +If you want to change the order in which mirrors are searched for +packages, you can edit this file and reorder the sections. Spack will +search the topmost mirror first and the bottom-most mirror last. diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index ec2ca4d099..59ba63fa35 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -5,7 +5,7 @@ Packaging Guide This guide is intended for developers or administrators who want to package software so that Spack can install it. It assumes that you -have at least some familiarty with Python, and that you've read the +have at least some familiarity with Python, and that you've read the :ref:`basic usage guide <basic-usage>`, especially the part about :ref:`specs <sec-specs>`. @@ -16,18 +16,19 @@ There are two key parts of Spack: software according to a spec. Specs allow a user to describe a *particular* build in a way that a -package author can understand. Packages allow a developer to -encapsulate the logic build logic for different versions, compilers, +package author can understand. Packages allow a the packager to +encapsulate the build logic for different versions, compilers, options, platforms, and dependency combinations in one place. +Essentially, a package translates a spec into build logic. Packages in Spack are written in pure Python, so you can do anything in Spack that you can do in Python. Python was chosen as the implementation language for two reasons. First, Python is becoming -ubiquitous in the HPC community due to its use in numerical codes. -Second, it's a modern language and has many powerful features to help -make package writing easy. +ubiquitous in the scientific software community. Second, it's a modern +language and has many powerful features to help make package writing +easy. -Creating & Editing Packages +Creating & editing packages ---------------------------------- .. _spack-create: @@ -35,24 +36,23 @@ Creating & Editing Packages ``spack create`` ~~~~~~~~~~~~~~~~~~~~~ -The ``spack create`` command generates boilerplate package template -from a URL pointing to a tarball or other software archive. In most -cases, you'll only need to run this once, then slightly modify the -boilerplate to get your package working. +The ``spack create`` command generates a boilerplate package template +from a URL. The URL should point to a tarball or other software +archive. In most cases, ``spack create`` plus a few modifications is +all you need to get a package working. -All you need is the URL to a tarball (other archive formats are ok -too) you want to package: +Here's an example: .. code-block:: sh $ spack create http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz -When you run this, Spack looks at the tarball URL and tries to figure -out the name of the package to be created. It also tries to determine -out what version strings look like for this package. Using this -information, it tries to find *additional* versions by spidering the -package's webpage. If it finds multiple versions, Spack prompts you -to tell it how many versions you want to download and checksum. +Spack examines the tarball URL and tries to figure out the name of the +package to be created. It also tries to determine what version strings +look like for this package. Using this information, it will try to +find *additional* versions by spidering the package's webpage. If it +finds multiple versions, Spack prompts you to tell it how many +versions you want to download and checksum: .. code-block:: sh @@ -63,12 +63,6 @@ to tell it how many versions you want to download and checksum. 2.8.12.1 http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz 2.8.12 http://www.cmake.org/files/v2.8/cmake-2.8.12.tar.gz 2.8.11.2 http://www.cmake.org/files/v2.8/cmake-2.8.11.2.tar.gz - 2.8.11.1 http://www.cmake.org/files/v2.8/cmake-2.8.11.1.tar.gz - 2.8.11 http://www.cmake.org/files/v2.8/cmake-2.8.11.tar.gz - 2.8.10.2 http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz - 2.8.10.1 http://www.cmake.org/files/v2.8/cmake-2.8.10.1.tar.gz - 2.8.10 http://www.cmake.org/files/v2.8/cmake-2.8.10.tar.gz - 2.8.9 http://www.cmake.org/files/v2.8/cmake-2.8.9.tar.gz ... 2.8.0 http://www.cmake.org/files/v2.8/cmake-2.8.0.tar.gz @@ -77,10 +71,30 @@ to tell it how many versions you want to download and checksum. Spack will automatically download the number of tarballs you specify (starting with the most recent) and checksum each of them. -Note that you don't need to do everything up front. If your package -is large, you can always choose to download just one tarball for now, -then run :ref:`spack checksum <spack-checksum>` later if you end up -wanting more. Let's say you choose to download 3 tarballs: +You do not *have* to download all of the versions up front. You can +always choose to download just one tarball initially, and run +:ref:`spack checksum <spack-checksum>` later if you need more. + +.. note:: + + If ``spack create`` fails to detect the package name correctly, + you can try supplying it yourself, e.g.:: + + $ spack create --name cmake http://www.cmake.org/files/v2.8/cmake-2.8.12.1.tar.gz + + If it fails entirely, you can get minimal boilerplate by using + :ref:`spack-edit-f`, or you can manually create a directory and + ``package.py`` file for the package in ``var/spack/packages``. + +.. note:: + + Spack can fetch packages from source code repositories, but, + ``spack create`` will *not* currently create a boilerplate package + from a repository URL. You will need to use :ref:`spack-edit-f` + and manually edit the ``version()`` directives to fetch from a + repo. See :ref:`vcs-fetch` for details. + +Let's say you download 3 tarballs: .. code-block:: sh @@ -93,8 +107,8 @@ wanting more. Let's say you choose to download 3 tarballs: ==> Fetching http://www.cmake.org/files/v2.8/cmake-2.8.11.2.tar.gz #################################################################### 95.2% -Now Spack generates boilerplate code and opens the new -``package.py`` file in your favorite ``$EDITOR``: +Now Spack generates boilerplate code and opens a new ``package.py`` +file in your favorite ``$EDITOR``: .. code-block:: python :linenos: @@ -141,12 +155,6 @@ Now Spack generates boilerplate code and opens the new The tedious stuff (creating the class, checksumming archives) has been done for you. -.. note:: - - If ``spack create`` fails to download or to detect the package - version, you can use ``spack edit -f`` to generate simpler - boilerplate. See the next section for more on this. - In the generated package, the download ``url`` attribute is already set. All the things you still need to change are marked with ``FIXME`` labels. The first ``FIXME`` refers to the commented @@ -199,27 +207,30 @@ The ``cmake`` package actually lives in a much simpler shortcut and saves you the trouble of typing the full path. - -``spack edit -f`` -~~~~~~~~~~~~~~~~~~~~ If you try to edit a package that doesn't exist, Spack will recommend -using ``spack create``: +using ``spack create`` or ``spack edit -f``: .. code-block:: sh $ spack edit foo ==> Error: No package 'foo'. Use spack create, or supply -f/--force to edit a new file. -As the output advises, You can use ``spack edit -f/--force`` to force -the creation of a new, *very* simple boilerplate package: +.. _spack-edit-f: + +``spack edit -f`` +~~~~~~~~~~~~~~~~~~~~ + +``spack edit -f`` can be used to create a new, minimal boilerplate +package: .. code-block:: sh $ spack edit -f foo -Unlike ``spack create``, which tries to infer names and versions, and -which actually downloads the tarball and checksums it for you, ``spack -edit -f`` will substitute dummy values for you to fill in yourself: +Unlike ``spack create``, which infers names and versions, and which +actually downloads the tarball and checksums it for you, ``spack edit +-f`` has no such fanciness. It will substitute dummy values for you +to fill in yourself: .. code-block:: python :linenos: @@ -243,9 +254,16 @@ This is useful when ``spack create`` cannot figure out the name and version of your package from the archive URL. -Naming & Directory Structure +Naming & directory structure -------------------------------------- +.. note:: + + Spack's default naming and directory structure will change in + version 0.9. Specifically, 0.9 will stop using directory names + with special characters like ``@``, to avoid interfering with + certain packages that do not handle this well. + This section describes how packages need to be named, and where they live in Spack's directory structure. In general, `spack-create`_ and `spack-edit`_ handle creating package files for you, so you can skip @@ -264,6 +282,7 @@ package: .. command-output:: cd $SPACK_ROOT/var/spack/packages; ls -CF :shell: + :ellipsis: 10 Each directory contains a file called ``package.py``, which is where all the python code for the package goes. For example, the ``libelf`` @@ -280,11 +299,9 @@ Package Names Packages are named after the directory containing ``package.py``. So, ``libelf``'s ``package.py`` lives in a directory called ``libelf``. -The ``package.py`` file contains a class called ``Libelf``, which -extends Spack's ``Package`` class. This is what makes it a Spack -package: - -``var/spack/packages/libelf/package.py`` +The ``package.py`` file defines a class called ``Libelf``, which +extends Spack's ``Package`` class. for example, here is +``$SPACK_ROOT/var/spack/packages/libelf/package.py``: .. code-block:: python :linenos: @@ -301,8 +318,9 @@ package: def install(): ... -The **directory name** (``libelf``) is what users need to provide on -the command line. e.g., if you type any of these: +The **directory name** (``libelf``) determines the package name that +users should provide on the command line. e.g., if you type any of +these: .. code-block:: sh @@ -311,8 +329,8 @@ the command line. e.g., if you type any of these: Spack sees the package name in the spec and looks for ``libelf/package.py`` in ``var/spack/packages``. Likewise, if you say -``spack install docbook-xml``, then Spack looks for -``docbook-xml/package.py``. +``spack install py-numpy``, then Spack looks for +``py-numpy/package.py``. Spack uses the directory name as the package name in order to give packagers more freedom in naming their packages. Package names can @@ -342,8 +360,7 @@ some examples: ================= ================= In general, you won't have to remember this naming convention because -`spack-create`_ and `spack-edit`_ will generate boilerplate for you, -and you can just fill in the blanks. +`spack-create`_ and `spack-edit`_ handle the details for you. Adding new versions @@ -381,9 +398,8 @@ For the URL above, you might have to add an explicit URL because the version can't simply be substituted in the original ``url`` to construct the new one for ``8.2.1``. -Wehn you supply a custom URL for a version, Spack uses that URL -*verbatim* when fetching the version, and will *not* perform -extrapolation. +When you supply a custom URL for a version, Spack uses that URL +*verbatim* and does not perform extrapolation. Checksums ~~~~~~~~~~~~~~~~~ @@ -392,10 +408,11 @@ Spack uses a checksum to ensure that the downloaded package version is not corrupted or compromised. This is especially important when fetching from insecure sources, like unencrypted http. By default, a package will *not* be installed if it doesn't pass a checksum test -(though users can overried this with ``spack install --no-checksum``). +(though you can override this with ``spack install --no-checksum``). Spack can currently support checksums using the MD5, SHA-1, SHA-224, -SHA-256, SHA-384, and SHA-512 algorithms. +SHA-256, SHA-384, and SHA-512 algorithms. It determines the algorithm +to use based on the hash length. ``spack md5`` ^^^^^^^^^^^^^^^^^^^^^^ @@ -442,7 +459,7 @@ example for ``libelf``: How many would you like to checksum? (default is 5, q to abort) This does the same thing that ``spack create`` does, but it allows you -to go back and add new vesrions easily as you need them (e.g., as +to go back and add new versions easily as you need them (e.g., as they're released). It fetches the tarballs you ask for and prints out a list of ``version`` commands ready to copy/paste into your package file: @@ -459,54 +476,57 @@ By default, Spack will search for new tarball downloads by scraping the parent directory of the tarball you gave it. So, if your tarball is at ``http://example.com/downloads/foo-1.0.tar.gz``, Spack will look in ``http://example.com/downloads/`` for links to additional versions. -If you need to search another path for download links, see the -reference documentation on `attribute_list_url`_ and -`attributee_list_depth`_. +If you need to search another path for download links, you can supply +some extra attributes that control how your package finds new +versions. See the documentation on `attribute_list_url`_ and +`attribute_list_depth`_. .. note:: * This command assumes that Spack can extrapolate new URLs from an existing URL in the package, and that Spack can find similar URLs - on a webpage. If that's not possible, you'll need to manually add - ``version`` calls yourself. + on a webpage. If that's not possible, e.g. if the package's + developers don't name their tarballs consistently, you'll need to + manually add ``version`` calls yourself. * For ``spack checksum`` to work, Spack needs to be able to - ``import`` your pacakge in Python. That means it can't have any + ``import`` your package in Python. That means it can't have any syntax errors, or the ``import`` will fail. Use this once you've got your package in working order. .. _vcs-fetch: -Fetching from VCS Repositories +Fetching from VCS repositories -------------------------------------- -For some packages, source code is hosted in a Version Control System -(VCS) repository rather than as a tarball. Packages can be set up to -fetch from a repository instead of a tarball. Currently, Spack -supports fetching with `Git <git-fetch_>`_, `Mercurial (hg) -<hg-fetch_>`_, and `Subversion (SVN) <svn-fetch_>`_. +For some packages, source code is provided in a Version Control System +(VCS) repository rather than in a tarball. Spack can fetch packages +from VCS repositories. Currently, Spack supports fetching with `Git +<git-fetch_>`_, `Mercurial (hg) <hg-fetch_>`_, and `Subversion (SVN) +<svn-fetch_>`_. To fetch a package from a source repository, you add a ``version()`` call to your package with parameters indicating the repository URL and -any branch, tag, or revision to fetch. See below for the paramters +any branch, tag, or revision to fetch. See below for the parameters you'll need for each VCS system. Repositories and versions ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The package author is responsible for coming up with a sensible name -for each version. For example, if you're fetching from a tag like -``v1.0``, you might call that ``1.0``. If you're fetching a nameless -git commit or an older subversion revision, you might give the commit -an intuitive name, like ``dev`` for a development version, or -``some-fancy-new-feature`` if you want to be more specific. +for each version to be fetched from a repository. For example, if +you're fetching from a tag like ``v1.0``, you might call that ``1.0``. +If you're fetching a nameless git commit or an older subversion +revision, you might give the commit an intuitive name, like ``dev`` +for a development version, or ``some-fancy-new-feature`` if you want +to be more specific. In general, it's recommended to fetch tags or particular commits/revisions, NOT branches or the repository mainline, as branches move forward over time and you aren't guaranteed to get the same thing every time you fetch a particular version. Life isn't -simple, though, so this is not strictly enforced. +always simple, though, so this is not strictly enforced. In some future release, Spack may support extrapolating repository versions as it does for tarball URLs, but currently this is not @@ -623,7 +643,7 @@ Revisions revisions, you can use ``revision`` for branches, tags, and commits when you fetch with Mercurial. -As wtih git, you can fetch these versions using the ``spack install +As with git, you can fetch these versions using the ``spack install example@<version>`` command-line syntax. .. _svn-fetch: @@ -633,7 +653,7 @@ Subversion To fetch with subversion, use the ``svn`` and ``revision`` parameters: -Head +Fetching the head Simply add an ``svn`` parameter to ``version``: .. code-block:: python @@ -642,7 +662,7 @@ Head This is not recommended, as the head will move forward over time. -Revisions +Fetching a revision To fetch a particular revision, add a ``revision`` to the version call: @@ -746,11 +766,105 @@ from the URL and then applied to your source code. applies cleanly with ``-p1``, but if you're using a patch you didn't create yourself, ``level`` can be handy. +``patch()`` functions +~~~~~~~~~~~~~~~~~~~~~~~~ + +In addition to supplying patch files, you can write a custom function +to patch a package's source. For example, the ``py-pyside`` package +contains some custom code for tweaking the way the PySide build +handles ``RPATH``: + +.. _pyside-patch: -Finding Package Downloads +.. code-block:: python + :linenos: + + class PyPyside(Package): + ... + + def patch(self): + """Undo PySide RPATH handling and add Spack RPATH.""" + # Figure out the special RPATH + pypkg = self.spec['python'].package + rpath = self.rpath + rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'PySide')) + + # Add Spack's standard CMake args to the sub-builds. + # They're called BY setup.py so we have to patch it. + filter_file( + r'OPTION_CMAKE,', + r'OPTION_CMAKE, ' + ( + '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", ' + '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)), + 'setup.py') + + # PySide tries to patch ELF files to remove RPATHs + # Disable this and go with the one we set. + filter_file( + r'^\s*rpath_cmd\(pyside_path, srcpath\)', + r'#rpath_cmd(pyside_path, srcpath)', + 'pyside_postinstall.py') + +A ``patch`` function, if present, will be run after patch files are +applied and before ``install()`` is run. + +You could put this logic in ``install()``, but putting it in a patch +function gives you some benefits. First, spack ensures that the +``patch()`` function is run once per code checkout. That means that +if you run install, hit ctrl-C, and run install again, the code in the +patch function is only run once. Also, you can tell Spack to run only +the patching part of the build using the :ref:`spack-patch` command. + +Handling RPATHs ---------------------------- -We've already seen the ``homepage`` and ``url`` package attributes: +Spack installs each package in a way that ensures that all of its +dependencies are found when it runs. It does this using `RPATHs +<http://en.wikipedia.org/wiki/Rpath>`_. An RPATH is a search +path, stored in a binary (an executable or library), that tells the +dynamic loader where to find its dependencies at runtime. You may be +familiar with ```LD_LIBRARY_PATH`` +<http://tldp.org/HOWTO/Program-Library-HOWTO/shared-libraries.html>`_ +on Linux or ```DYLD_LIBRARY_PATH`` +<https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/dyld.1.html>` +on Mac OS X. RPATH is similar to these paths, in that it tells +the loader where to find libraries. Unlike them, it is embedded in +the binary and not set in each user's environment. + +RPATHs in Spack are handled in one of three ways: + + 1. For most packages, RPATHs are handled automatically using Spack's + :ref:`compiler wrappers <compiler-wrappers>`. These wrappers are + set in standard variables like ``CC``, ``CXX``, and ``FC``, so + most build systems (autotools and many gmake systems) pick them + up and use them. + 2. CMake also respects Spack's compiler wrappers, but many CMake + builds have logic to overwrite RPATHs when binaries are + installed. Spack provides the ``std_cmake_args`` variable, which + includes parameters necessary for CMake build use the right + installation RPATH. It can be used like this when ``cmake`` is + invoked: + + .. code-block:: python + + class MyPackage(Package): + ... + def install(self, spec, prefix): + cmake('..', *std_cmake_args) + make() + make('install') + + 3. If you need to modify the build to add your own RPATHs, you can + use the ``self.rpath`` property of your package, which will + return a list of all the RPATHs that Spack will use when it + links. You can see this how this is used in the :ref:`PySide + example <pyside-patch>` above. + + +Finding new versions +---------------------------- + +You've already seen the ``homepage`` and ``url`` package attributes: .. code-block:: python :linenos: @@ -786,7 +900,7 @@ url is: url = "http://www.mr511.de/software/libelf-0.8.13.tar.gz" -Spack spiders ``http://www.mr511.de/software/`` to find similar +Here, Spack spiders ``http://www.mr511.de/software/`` to find similar tarball links and ultimately to make a list of available versions of ``libelf``. @@ -813,7 +927,7 @@ the ``list_url``, because that is where links to old versions are: ~~~~~~~~~~~~~~~~~~~~~ ``libdwarf`` and many other packages have a listing of available -verisons on a single webpage, but not all do. For example, ``mpich`` +versions on a single webpage, but not all do. For example, ``mpich`` has a tarball URL that looks like this: url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz" @@ -840,7 +954,7 @@ when spidering the page. .. _attribute_parallel: -Parallel Builds +Parallel builds ------------------ By default, Spack will invoke ``make()`` with a ``-j <njobs>`` @@ -969,13 +1083,210 @@ command line to find installed packages or to install packages with particular constraints, and package authors can use specs to describe relationships between packages. +.. _setup-dependent-environment: + +``setup_dependent_environment()`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Spack provides a mechanism for dependencies to provide variables that +can be used in their dependents' build. Any package can declare a +``setup_dependent_environment()`` function, and this function will be +called before the ``install()`` method of any dependent packages. +This allows dependencies to set up environment variables and other +properties to be used by dependents. + +The function declaration should look like this: + +.. code-block:: python + + class Qt(Package): + ... + def setup_dependent_environment(self, module, spec, dep_spec): + """Dependencies of Qt find it using the QTDIR environment variable.""" + os.environ['QTDIR'] = self.prefix + +Here, the Qt package sets the ``QTDIR`` environment variable so that +packages that depend on a particular Qt installation will find it. + +The arguments to this function are: + + * **module**: the module of the dependent package, where global + properties can be assigned. + * **spec**: the spec of the *dependency package* (the one the function is called on). + * **dep_spec**: the spec of the dependent package (i.e. dep_spec depends on spec). + +A good example of using these is in the Python package: + +.. code-block:: python + + def setup_dependent_environment(self, module, spec, dep_spec): + # Python extension builds can have a global python executable function + module.python = Executable(join_path(spec.prefix.bin, 'python')) + + # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. + module.python_lib_dir = os.path.join(dep_spec.prefix, self.python_lib_dir) + module.python_include_dir = os.path.join(dep_spec.prefix, self.python_include_dir) + module.site_packages_dir = os.path.join(dep_spec.prefix, self.site_packages_dir) + + # Make the site packages directory if it does not exist already. + mkdirp(module.site_packages_dir) + + # Set PYTHONPATH to include site-packages dir for the + # extension and any other python extensions it depends on. + python_paths = [] + for d in dep_spec.traverse(): + if d.package.extends(self.spec): + python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) + os.environ['PYTHONPATH'] = ':'.join(python_paths) + +The first thing that happens here is that the ``python`` command is +inserted into module scope of the dependent. This allows most python +packages to have a very simple install method, like this: + +.. code-block:: python + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) + +Python's ``setup_dependent_environment`` method also sets up some +other variables, creates a directory, and sets up the ``PYTHONPATH`` +so that dependent packages can find their dependencies at build time. + + +.. _packaging_extensions: + +Extensions +------------------------- + +Spack's support for package extensions is documented extensively in +:ref:`extensions`. This section documents how to make your own +extendable packages and extensions. + +To support extensions, a package needs to set its ``extendable`` +property to ``True``, e.g.: + +.. code-block:: python + + class Python(Package): + ... + extendable = True + ... + +To make a package into an extension, simply add simply add an +``extends`` call in the package definition, and pass it the name of an +extendable package: + +.. code-block:: python + + class PyNumpy(Package): + ... + extends('python') + ... + +Now, the ``py-numpy`` package can be used as an argument to ``spack +activate``. When it is activated, all the files in its prefix will be +symbolically linked into the prefix of the python package. + +Sometimes, certain files in one package will conflict with those in +another, which means they cannot both be activated (symlinked) at the +same time. In this case, you can tell Spack to ignore those files +when it does the activation: + +.. code-block:: python + + class PyNose(Package): + ... + extends('python', ignore=r'bin/nosetests.*$') + ... + +The code above will prevent ``$prefix/bin/nosetests`` from being +linked in at activation time. + +.. note:: + + You can call *either* ``depends_on`` or ``extends`` on any one + package, but not both. For example you cannot both + ``depends_on('python')`` and ``extends(python)`` in the same + package. ``extends`` implies ``depends_on``. + + + +Activation & deactivation +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Spack's ``Package`` class has default ``activate`` and ``deactivate`` +implementations that handle symbolically linking extensions' prefixes +into the directory of the parent package. However, extendable +packages can override these methods to add custom activate/deactivate +logic of their own. For example, the ``activate`` and ``deactivate`` +methods in the Python class use the symbolic linking, but they also +handle details surrounding Python's ``.pth`` files, and other aspects +of Python packaging. + +Spack's extensions mechanism is designed to be extensible, so that +other packages (like Ruby, R, Perl, etc.) can provide their own +custom extension management logic, as they may not handle modules the +same way that Python does. + +Let's look at Python's activate function: + +.. code-block:: python + + def activate(self, ext_pkg, **kwargs): + kwargs.update(ignore=self.python_ignore(ext_pkg, kwargs)) + super(Python, self).activate(ext_pkg, **kwargs) + + exts = spack.install_layout.extension_map(self.spec) + exts[ext_pkg.name] = ext_pkg.spec + self.write_easy_install_pth(exts) + +This function is called on the *extendee* (Python). It first calls +``activate`` in the superclass, which handles symlinking the +extension package's prefix into this package's prefix. It then does +some special handling of the ``easy-install.pth`` file, part of +Python's setuptools. + +Deactivate behaves similarly to activate, but it unlinks files: + +.. code-block:: python + + def deactivate(self, ext_pkg, **kwargs): + kwargs.update(ignore=self.python_ignore(ext_pkg, kwargs)) + super(Python, self).deactivate(ext_pkg, **kwargs) + + exts = spack.install_layout.extension_map(self.spec) + if ext_pkg.name in exts: # Make deactivate idempotent. + del exts[ext_pkg.name] + self.write_easy_install_pth(exts) + +Both of these methods call some custom functions in the Python +package. See the source for Spack's Python package for details. + + +Activation arguments +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +You may have noticed that the ``activate`` function defined above +takes keyword arguments. These are the keyword arguments from +``extends()``, and they are passed to both activate and deactivate. + +This capability allows an extension to customize its own activation by +passing arguments to the extendee. Extendees can likewise implement +custom ``activate()`` and ``deactivate()`` functions to suit their +needs. + +The only keyword argument supported by default is the ``ignore`` +argument, which can take a regex, list of regexes, or a predicate to +determine which files *not* to symlink during activation. + + .. _virtual-dependencies: Virtual dependencies ----------------------------- In some cases, more than one package can satisfy another package's -dependency. One way this can happen is if a pacakge depends on a +dependency. One way this can happen is if a package depends on a particular *interface*, but there are multiple *implementations* of the interface, and the package could be built with any of them. A *very* common interface in HPC is the `Message Passing Interface (MPI) @@ -988,7 +1299,7 @@ MPI has several different implementations (e.g., `MPICH applications can be built with any one of them. Complicating matters, MPI does not have a standardized ABI, so a package built with one implementation cannot simply be relinked with another implementation. -Many pacakage managers handle interfaces like this by requiring many +Many package managers handle interfaces like this by requiring many similar package files, e.g., ``foo``, ``foo-mvapich``, ``foo-mpich``, but Spack avoids this explosion of package files by providing support for *virtual dependencies*. @@ -1014,7 +1325,7 @@ supplying a ``depends_on`` call in the package definition. For example: depends_on("adept-utils") depends_on("callpath") -Here, ``callpath`` and ``adept-utils`` are concrete pacakges, but +Here, ``callpath`` and ``adept-utils`` are concrete packages, but there is no actual package file for ``mpi``, so we say it is a *virtual* package. The syntax of ``depends_on``, is the same for both. If we look inside the package file of an MPI implementation, @@ -1038,7 +1349,7 @@ to ``provides`` to add constraints. This allows Spack to support the notion of *versioned interfaces*. The MPI standard has gone through many revisions, each with new functions added, and each revision of the standard has a version number. Some packages may require a recent -implementation that supports MPI-3 fuctions, but some MPI versions may +implementation that supports MPI-3 functions, but some MPI versions may only provide up to MPI-2. Others may need MPI 2.1 or higher. You can indicate this by adding a version constraint to the spec passed to ``provides``: @@ -1070,7 +1381,7 @@ constraints on the *providing* package, or the *provider*. The provider only provides the declared virtual spec when *it* matches the constraints in the when clause. Here, when ``mpich`` is at version 3 or higher, it provides MPI up to version 3. When ``mpich`` -is at version 1 or higher, it provides the MPI virtual pacakge at +is at version 1 or higher, it provides the MPI virtual package at version 1. The ``when`` qualifier ensures that Spack selects a suitably high @@ -1190,6 +1501,7 @@ explicitly. Concretization policies are discussed in more detail in :ref:`site-configuration`. Sites using Spack can customize them to match the preferences of their own users. +.. _spack-spec: ``spack spec`` ~~~~~~~~~~~~~~~~~~~~ @@ -1232,7 +1544,7 @@ software should be installed. Spack provides wrapper functions for ``configure`` and ``make`` so that you can call them in a similar way to how you'd call a shell -comamnd. In reality, these are Python functions. Spack provides +command. In reality, these are Python functions. Spack provides these functions to make writing packages more natural. See the section on :ref:`shell wrappers <shell-wrappers>`. @@ -1287,11 +1599,11 @@ information. .. _install-environment: -The Install environment +The install environment -------------------------- In general, you should not have to do much differently in your install -method than you would when installing a pacakge on the command line. +method than you would when installing a package on the command line. In fact, you may need to do *less* than you would on the command line. Spack tries to set environment variables and modify compiler calls so @@ -1314,7 +1626,7 @@ purposes: #. Make build systems use Spack's compiler wrappers for their builds. #. Allow build systems to find dependencies more easily -The Compiler enviroment variables that Spack sets are: +The Compiler environment variables that Spack sets are: ============ =============================== Variable Purpose @@ -1344,9 +1656,10 @@ entering ``install()`` so that packages can locate dependencies easily: ======================= ============================= - ``PATH`` Set to point to ``/bin`` directories of dpeendencies + ``PATH`` Set to point to ``/bin`` directories of dependencies ``CMAKE_PREFIX_PATH`` Path to dependency prefixes for CMake ``PKG_CONFIG_PATH`` Path to any pkgconfig directories for dependencies + ``PYTHONPATH`` Path to site-packages dir of any python dependencies ======================= ============================= ``PATH`` is set up to point to dependencies ``/bin`` directories so @@ -1366,6 +1679,12 @@ dependencies using the GNU ``pkg-config`` tool. It is similar to ``CMAKE_PREFIX_PATH`` in that it allows a build to automatically discover its dependencies. +If you want to see the environment that a package will build with, or +if you want to run commands in that environment to test them out, you +can use the :ref:```spack env`` <spack-env>` command, documented +below. + +.. _compiler-wrappers: Compiler interceptors ~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1423,7 +1742,7 @@ the command line. Forking ``install()`` ~~~~~~~~~~~~~~~~~~~~~ -To give packagers free reign over their install environemnt, Spack +To give packagers free reign over their install environment, Spack forks a new process each time it invokes a package's ``install()`` method. This allows packages to have their own completely sandboxed build environment, without impacting other jobs that the main Spack @@ -1431,7 +1750,6 @@ process runs. Packages are free to change the environment or to modify Spack internals, because each ``install()`` call has its own dedicated process. - .. _prefix-objects: Prefix objects @@ -1552,7 +1870,7 @@ dependency version. You can use ``satisfies()`` to test for particular dependencies, e.g. ``foo.satisfies('^openmpi@1.2')`` or ``foo.satisfies('^mpich')``, -or you can use Python's builtin ``in`` operator: +or you can use Python's built-in ``in`` operator: .. code-block:: python @@ -1581,7 +1899,7 @@ Accessing Dependencies ~~~~~~~~~~~~~~~~~~~~~~~~~~ You may need to get at some file or binary that's in the prefix of one -of your dependencies. You can do that by subscripting the spec: +of your dependencies. You can do that by sub-scripting the spec: .. code-block:: python @@ -1901,9 +2219,9 @@ File functions Create an empty file at ``path``. -.. _pacakge-lifecycle: +.. _package-lifecycle: -Package Workflow Commands +Packaging workflow commands --------------------------------- When you are building packages, you will likely not get things @@ -1930,7 +2248,9 @@ A typical package workflow might look like this: ... repeat clean/install until install works ... Below are some commands that will allow you some finer-grained -controll over the install process. +control over the install process. + +.. _spack-fetch: ``spack fetch`` ~~~~~~~~~~~~~~~~~ @@ -1944,6 +2264,8 @@ directory will be located under ``$SPACK_HOME/var/spack``. When run after the archive has already been downloaded, ``spack fetch`` is idempotent and will not download the archive again. +.. _spack-stage: + ``spack stage`` ~~~~~~~~~~~~~~~~~ @@ -1952,6 +2274,8 @@ the downloaded archive in its temporary directory, where it will be built by ``spack install``. Similar to ``fetch``, if the archive has already been expanded, ``stage`` is idempotent. +.. _spack-patch: + ``spack patch`` ~~~~~~~~~~~~~~~~~ @@ -1963,43 +2287,45 @@ this step if they have been. If Spack discovers that patches didn't apply cleanly on some previous run, then it will restage the entire package before patching. +.. _spack-restage: -``spack clean`` +``spack restage`` ~~~~~~~~~~~~~~~~~ +Restores the source code to pristine state, as it was before building. -There are several variations of ``spack clean``. With no arguments, -``spack clean`` runs ``make clean`` in the expanded archive directory. -This is useful if an attempted build failed, and something needs to be -changed to get a package to build. If a particular package does not -have a ``make clean`` target, this will do nothing. +Does this in one of two ways: -``spack clean -w / --work`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Deletes the entire build directory and re-expands it from the downloaded -archive. This is useful if a package does not support a proper ``make clean`` -target. + 1. If the source was fetched as a tarball, deletes the entire build + directory and re-expands the tarball. + + 2. If the source was checked out from a repository, this deletes the + build directory and checks it out again. -``spack clean -d / --dist`` +.. _spack-clean: + +``spack clean`` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Deletes the build directory *and* the downloaded archive. If -``fetch``, ``stage``, or ``install`` are run again after this, the -process will start from scratch, and the archive archive will be -downloaded again. Useful if somehow a bad archive is downloaded -accidentally and needs to be cleaned out of the staging area. +Cleans up temporary files for a particular package, by deleting the +expanded/checked out source code *and* any downloaded archive. If +``fetch``, ``stage``, or ``install`` are run again after this, Spack's +build process will start from scratch. + + +.. _spack-purge: ``spack purge`` ~~~~~~~~~~~~~~~~~ - -Cleans up *everything* in the build directory. You can use this to -recover disk space if temporary files from interrupted or failed -installs accumulate in the staging area. +Cleans up all of Spack's temporary files. Use this to recover disk +space if temporary files from interrupted or failed installs +accumulate in the staging area. This is equivalent to running ``spack +clean`` for every package you have fetched or staged. Keeping the stage directory on success ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ By default, ``spack install`` will delete the staging area once a -pacakge has been successfully built and installed. Use +package has been successfully built and installed. Use ``--keep-stage`` to leave the build directory intact: .. code-block:: sh @@ -2032,7 +2358,86 @@ to get rid of the install prefix before you build again: spack uninstall -f <spec> -Interactive Shell Support +Graphing dependencies +-------------------------- + +.. _spack-graph: + +``spack graph`` +~~~~~~~~~~~~~~~~~~~ + +Spack provides the ``spack graph`` command for graphing dependencies. +The command by default generates an ASCII rendering of a spec's +dependency graph. For example:: + + $ spack graph mpileaks + o mpileaks + |\ + | |\ + | o | callpath + |/| | + | |\| + | |\ \ + | | |\ \ + | | | | o adept-utils + | |_|_|/| + |/| | | | + o | | | | mpi + / / / / + | | o | dyninst + | |/| | + |/|/| | + | | |/ + | o | libdwarf + |/ / + o | libelf + / + o boost + +At the top is the root package in the DAG, with dependency edges +emerging from it. On a color terminal, the edges are colored by which +dependency they lead to. + +You can also use ``spack graph`` to generate graphs in the widely used +`Dot <http://www.graphviz.org/doc/info/lang.html>`_ format. For +example:: + + $ spack graph --dot mpileaks + digraph G { + label = "Spack Dependencies" + labelloc = "b" + rankdir = "LR" + ranksep = "5" + + "boost" [label="boost"] + "callpath" [label="callpath"] + "libdwarf" [label="libdwarf"] + "mpileaks" [label="mpileaks"] + "mpi" [label="mpi"] + "adept-utils" [label="adept-utils"] + "dyninst" [label="dyninst"] + "libelf" [label="libelf"] + + "callpath" -> "dyninst" + "callpath" -> "adept-utils" + "callpath" -> "mpi" + "callpath" -> "libelf" + "callpath" -> "libdwarf" + "libdwarf" -> "libelf" + "mpileaks" -> "adept-utils" + "mpileaks" -> "callpath" + "mpileaks" -> "mpi" + "adept-utils" -> "boost" + "adept-utils" -> "mpi" + "dyninst" -> "boost" + "dyninst" -> "libelf" + "dyninst" -> "libdwarf" + } + +This graph can be provided as input to other graphing tools, such as +those in `Graphviz <http://www.graphviz.org>`_. + +Interactive shell support -------------------------- Spack provides some limited shell support to make life easier for @@ -2048,6 +2453,7 @@ For ``csh`` and ``tcsh`` run: ``spack cd`` will then be available. +.. _spack-cd: ``spack cd`` ~~~~~~~~~~~~~~~~~ @@ -2068,7 +2474,7 @@ build it: /Users/gamblin2/src/spack/var/spack/stage/libelf@0.8.13%gcc@4.8.3=linux-ppc64/libelf-0.8.13 ``spack cd`` here changed he current working directory to the -directory containing theexpanded ``libelf`` source code. There are a +directory containing the expanded ``libelf`` source code. There are a number of other places you can cd to in the spack directory hierarchy: .. command-output:: spack cd -h @@ -2078,6 +2484,35 @@ directory, install directory, package directory) and others change to core spack locations. For example, ``spack cd -m`` will take you to the main python source directory of your spack install. +.. _spack-env: + +``spack env`` +~~~~~~~~~~~~~~~~~~~~~~ + +``spack env`` functions much like the standard unix ``env`` command, +but it takes a spec as an argument. You can use it to see the +environment variables that will be set when a particular build runs, +for example: + +.. code-block:: sh + + $ spack env mpileaks@1.1%intel + +This will display the entire environment that will be set when the +``mpileaks@1.1%intel`` build runs. + +To run commands in a package's build environment, you can simply provided them after the spec argument to ``spack env``: + +.. code-block:: sh + + $ spack cd mpileaks@1.1%intel + $ spack env mpileaks@1.1%intel ./configure + +This will cd to the build directory and then run ``configure`` in the +package's build environment. + + +.. _spack-location: ``spack location`` ~~~~~~~~~~~~~~~~~~~~~~ diff --git a/lib/spack/docs/site_configuration.rst b/lib/spack/docs/site_configuration.rst index 4936e3052c..44071bbfc6 100644 --- a/lib/spack/docs/site_configuration.rst +++ b/lib/spack/docs/site_configuration.rst @@ -1,208 +1,15 @@ .. _site-configuration: -Site-specific configuration +Site configuration =================================== -.. _mirrors: - -Mirrors ----------------------------- - -Some sites may not have access to the internet for fetching packages. -These sites will need a local repository of tarballs from which they -can get their files. Spack has support for this with *mirrors*. A -mirror is a URL that points to a directory, either on the local -filesystem or on some server, containing tarballs for all of Spack's -packages. - -Here's an example of a mirror's directory structure:: - - mirror/ - cmake/ - cmake-2.8.10.2.tar.gz - dyninst/ - DyninstAPI-8.1.1.tgz - DyninstAPI-8.1.2.tgz - libdwarf/ - libdwarf-20130126.tar.gz - libdwarf-20130207.tar.gz - libdwarf-20130729.tar.gz - libelf/ - libelf-0.8.12.tar.gz - libelf-0.8.13.tar.gz - libunwind/ - libunwind-1.1.tar.gz - mpich/ - mpich-3.0.4.tar.gz - mvapich2/ - mvapich2-1.9.tgz - -The structure is very simple. There is a top-level directory. The -second level directories are named after packages, and the third level -contains tarballs for each package, named as they were in the -package's fetch URL. - -``spack mirror`` -~~~~~~~~~~~~~~~~~~~~~~~ - -Mirrors are managed with the ``spack mirror`` command. The help for -``spack mirror`` looks like this:: - - $ spack mirror -h - usage: spack mirror [-h] SUBCOMMAND ... - - positional arguments: - SUBCOMMAND - create Create a directory to be used as a spack mirror, and fill - it with package archives. - add Add a mirror to Spack. - remove Remove a mirror by name. - list Print out available mirrors to the console. - - optional arguments: - -h, --help show this help message and exit - -The ``create`` command actually builds a mirror by fetching all of its -packages from the internet and checksumming them. - -The other three commands are for managing mirror configuration. They -control the URL(s) from which Spack downloads its packages. - - -``spack mirror create`` -~~~~~~~~~~~~~~~~~~~~~~~ - -You can create a mirror using the ``spack mirror create`` command, assuming -you're on a machine where you can access the internet. - -The command will iterate through all of Spack's packages and download -the safe ones into a directory structure like the one above. Here is -what it looks like: - - -.. code-block:: bash - - $ spack mirror create libelf libdwarf - ==> Created new mirror in spack-mirror-2014-06-24 - ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.13.tar.gz - ########################################################## 81.6% - ==> Checksum passed for libelf@0.8.13 - ==> Added spack-mirror-2014-06-24/libelf/libelf-0.8.13.tar.gz to mirror - ==> Trying to fetch from http://www.mr511.de/software/libelf-0.8.12.tar.gz - ###################################################################### 98.6% - ==> Checksum passed for libelf@0.8.12 - ==> Added spack-mirror-2014-06-24/libelf/libelf-0.8.12.tar.gz to mirror - ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130207.tar.gz - ###################################################################### 97.3% - ==> Checksum passed for libdwarf@20130207 - ==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130207.tar.gz to mirror - ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130126.tar.gz - ######################################################## 78.9% - ==> Checksum passed for libdwarf@20130126 - ==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130126.tar.gz to mirror - ==> Trying to fetch from http://www.prevanders.net/libdwarf-20130729.tar.gz - ############################################################# 84.7% - ==> Checksum passed for libdwarf@20130729 - ==> Added spack-mirror-2014-06-24/libdwarf/libdwarf-20130729.tar.gz to mirror - -Once this is done, you can tar up the ``spack-mirror-2014-06-24`` directory and -copy it over to the machine you want it hosted on. - -Custom package sets -^^^^^^^^^^^^^^^^^^^^^^^^ - -Normally, ``spack mirror create`` downloads all the archives it has -checksums for. If you want to only create a mirror for a subset of -packages, you can do that by supplying a list of package specs on the -command line after ``spack mirror create``. For example, this -command:: - - $ spack mirror create libelf@0.8.12: boost@1.44: - -Will create a mirror for libelf versions greater than or equal to -0.8.12 and boost versions greater than or equal to 1.44. - -Mirror files -^^^^^^^^^^^^^^^^^^^^^^^^ - -If you have a *very* large number of packages you want to mirror, you -can supply a file with specs in it, one per line:: - - $ cat specs.txt - libdwarf - libelf@0.8.12: - boost@1.44: - boost@1.39.0 - ... - $ spack mirror create -f specs.txt - ... - -This is useful if there is a specific suite of software managed by -your site. - - -``spack mirror add`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Once you have a mirrror, you need to let spack know about it. This is -relatively simple. First, figure out the URL for the mirror. If it's -a file, you can use a file URL like this one:: - - file:///Users/gamblin2/spack-mirror-2014-06-24 - -That points to the directory on the local filesystem. If it were on a -web server, you could use a URL like this one: - - https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24 - -Spack will use the URL as the root for all of the packages it fetches. -You can tell your Spack installation to use that mirror like this: - -.. code-block:: bash - - $ spack mirror add local_filesystem file:///Users/gamblin2/spack-mirror-2014-06-24 - -Each mirror has a name so that you can refer to it again later. - -``spack mirror list`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -If you want to see all the mirrors Spack knows about you can run ``spack mirror list``:: - - $ spack mirror list - local_filesystem file:///Users/gamblin2/spack-mirror-2014-06-24 - -``spack mirror remove`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -And, if you want to remove a mirror, just remove it by name:: - - $ spack mirror remove local_filesystem - $ spack mirror list - ==> No mirrors configured. - -Mirror precedence -~~~~~~~~~~~~~~~~~~~~~~~~~ - -Adding a mirror really just adds a section in ``~/.spackconfig``:: - - [mirror "local_filesystem"] - url = file:///Users/gamblin2/spack-mirror-2014-06-24 - [mirror "remote_server"] - url = https://example.com/some/web-hosted/directory/spack-mirror-2014-06-24 - -If you want to change the order in which mirrors are searched for -packages, you can edit this file and reorder the sections. Spack will -search the topmost mirror first and the bottom-most mirror last. - - .. _temp-space: Temporary space ---------------------------- .. warning:: Temporary space configuration will be moved to configuration files. - The intructions here are old and refer to ``__init__.py`` + The instructions here are old and refer to ``__init__.py`` By default, Spack will try to do all of its building in temporary space. There are two main reasons for this. First, Spack is designed @@ -286,7 +93,7 @@ the virtual spec to specs for possible implementations, and later, so there is no need to fully concretize the spec when returning it. -The ``DefaultConcretizer`` is intendend to provide sensible defaults +The ``DefaultConcretizer`` is intended to provide sensible defaults for each policy, but there are certain choices that it can't know about. For example, one site might prefer ``OpenMPI`` over ``MPICH``, or another might prefer an old version of some packages. These types @@ -327,3 +134,53 @@ Set concretizer to *your own* class instead of the default: concretizer = MyConcretizer() The next time you run Spack, your changes should take effect. + + +Profiling +~~~~~~~~~~~~~~~~~~~~~ + +Spack has some limited built-in support for profiling, and can report +statistics using standard Python timing tools. To use this feature, +supply ``-p`` to Spack on the command line, before any subcommands. + +.. _spack-p: + +``spack -p`` +^^^^^^^^^^^^^^^^^^ + +``spack -p`` output looks like this: + +.. code-block:: sh + + $ spack -p graph dyninst + o dyninst + |\ + | |\ + | o | libdwarf + |/ / + o | libelf + / + o boost + + 307670 function calls (305943 primitive calls) in 0.127 seconds + + Ordered by: internal time + + ncalls tottime percall cumtime percall filename:lineno(function) + 853 0.021 0.000 0.066 0.000 inspect.py:472(getmodule) + 51197 0.011 0.000 0.018 0.000 inspect.py:51(ismodule) + 73961 0.010 0.000 0.010 0.000 {isinstance} + 1762 0.006 0.000 0.053 0.000 inspect.py:440(getsourcefile) + 32075 0.006 0.000 0.006 0.000 {hasattr} + 1760 0.004 0.000 0.004 0.000 {posix.stat} + 2240 0.004 0.000 0.004 0.000 {posix.lstat} + 2602 0.004 0.000 0.011 0.000 inspect.py:398(getfile) + 771 0.004 0.000 0.077 0.000 inspect.py:518(findsource) + 2656 0.004 0.000 0.004 0.000 {method 'match' of '_sre.SRE_Pattern' objects} + 30772 0.003 0.000 0.003 0.000 {method 'get' of 'dict' objects} + ... + +The bottom of the output shows the top most time consuming functions, +slowest on top. The profiling support is from Python's built-in tool, +`cProfile +<https://docs.python.org/2/library/profile.html#module-cProfile>`_. diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py index 0578415653..576aeb16bd 100644 --- a/lib/spack/llnl/util/filesystem.py +++ b/lib/spack/llnl/util/filesystem.py @@ -23,7 +23,7 @@ # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## __all__ = ['set_install_permissions', 'install', 'expand_user', 'working_dir', - 'touch', 'mkdirp', 'force_remove', 'join_path', 'ancestor', + 'touch', 'touchp', 'mkdirp', 'force_remove', 'join_path', 'ancestor', 'can_access', 'filter_file', 'change_sed_delimiter', 'is_exe'] import os @@ -204,6 +204,12 @@ def touch(path): os.utime(path, None) +def touchp(path): + """Like touch, but creates any parent directories needed for the file.""" + mkdirp(os.path.dirname(path)) + touch(path) + + def join_path(prefix, *args): path = str(prefix) for elt in args: diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py index db15da0506..332367f537 100644 --- a/lib/spack/llnl/util/lang.py +++ b/lib/spack/llnl/util/lang.py @@ -291,6 +291,37 @@ def check_kwargs(kwargs, fun): % (next(kwargs.iterkeys()), fun.__name__)) +def match_predicate(*args): + """Utility function for making string matching predicates. + + Each arg can be a: + - regex + - list or tuple of regexes + - predicate that takes a string. + + This returns a predicate that is true if: + - any arg regex matches + - any regex in a list or tuple of regexes matches. + - any predicate in args matches. + """ + def match(string): + for arg in args: + if isinstance(arg, basestring): + if re.search(arg, string): + return True + elif isinstance(arg, list) or isinstance(arg, tuple): + if any(re.search(i, string) for i in arg): + return True + elif callable(arg): + if arg(string): + return True + else: + raise ValueError("args to match_predicate must be regex, " + "list of regexes, or callable.") + return False + return match + + class RequiredAttributeError(ValueError): def __init__(self, message): super(RequiredAttributeError, self).__init__(message) diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py new file mode 100644 index 0000000000..4d778eca1e --- /dev/null +++ b/lib/spack/llnl/util/link_tree.py @@ -0,0 +1,197 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://scalability-llnl.github.io/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +"""LinkTree class for setting up trees of symbolic links.""" +__all__ = ['LinkTree'] + +import os +import shutil +from llnl.util.filesystem import * + +empty_file_name = '.spack-empty' + + +def traverse_tree(source_root, dest_root, rel_path='', **kwargs): + """Traverse two filesystem trees simultaneously. + + Walks the LinkTree directory in pre or post order. Yields each + file in the source directory with a matching path from the dest + directory, along with whether the file is a directory. + e.g., for this tree:: + + root/ + a/ + file1 + file2 + b/ + file3 + + When called on dest, this yields:: + + ('root', 'dest') + ('root/a', 'dest/a') + ('root/a/file1', 'dest/a/file1') + ('root/a/file2', 'dest/a/file2') + ('root/b', 'dest/b') + ('root/b/file3', 'dest/b/file3') + + Optional args: + + order=[pre|post] -- Whether to do pre- or post-order traveral. + + ignore=<predicate> -- Predicate indicating which files to ignore. + + follow_nonexisting -- Whether to descend into directories in + src that do not exit in dest. Default True. + + follow_links -- Whether to descend into symlinks in src. + + """ + follow_nonexisting = kwargs.get('follow_nonexisting', True) + follow_links = kwargs.get('follow_link', False) + + # Yield in pre or post order? + order = kwargs.get('order', 'pre') + if order not in ('pre', 'post'): + raise ValueError("Order must be 'pre' or 'post'.") + + # List of relative paths to ignore under the src root. + ignore = kwargs.get('ignore', lambda filename: False) + + # Don't descend into ignored directories + if ignore(rel_path): + return + + source_path = os.path.join(source_root, rel_path) + dest_path = os.path.join(dest_root, rel_path) + + # preorder yields directories before children + if order == 'pre': + yield (source_path, dest_path) + + for f in os.listdir(source_path): + source_child = os.path.join(source_path, f) + dest_child = os.path.join(dest_path, f) + rel_child = os.path.join(rel_path, f) + + # Treat as a directory + if os.path.isdir(source_child) and ( + follow_links or not os.path.islink(source_child)): + + # When follow_nonexisting isn't set, don't descend into dirs + # in source that do not exist in dest + if follow_nonexisting or os.path.exists(dest_child): + tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs) + for t in tuples: yield t + + # Treat as a file. + elif not ignore(os.path.join(rel_path, f)): + yield (source_child, dest_child) + + if order == 'post': + yield (source_path, dest_path) + + + +class LinkTree(object): + """Class to create trees of symbolic links from a source directory. + + LinkTree objects are constructed with a source root. Their + methods allow you to create and delete trees of symbolic links + back to the source tree in specific destination directories. + Trees comprise symlinks only to files; directries are never + symlinked to, to prevent the source directory from ever being + modified. + + """ + def __init__(self, source_root): + if not os.path.exists(source_root): + raise IOError("No such file or directory: '%s'", source_root) + + self._root = source_root + + + def find_conflict(self, dest_root, **kwargs): + """Returns the first file in dest that conflicts with src""" + kwargs['follow_nonexisting'] = False + for src, dest in traverse_tree(self._root, dest_root, **kwargs): + if os.path.isdir(src): + if os.path.exists(dest) and not os.path.isdir(dest): + return dest + elif os.path.exists(dest): + return dest + return None + + + def merge(self, dest_root, **kwargs): + """Link all files in src into dest, creating directories if necessary.""" + kwargs['order'] = 'pre' + for src, dest in traverse_tree(self._root, dest_root, **kwargs): + if os.path.isdir(src): + if not os.path.exists(dest): + mkdirp(dest) + continue + + if not os.path.isdir(dest): + raise ValueError("File blocks directory: %s" % dest) + + # mark empty directories so they aren't removed on unmerge. + if not os.listdir(dest): + marker = os.path.join(dest, empty_file_name) + touch(marker) + + else: + assert(not os.path.exists(dest)) + os.symlink(src, dest) + + + def unmerge(self, dest_root, **kwargs): + """Unlink all files in dest that exist in src. + + Unlinks directories in dest if they are empty. + + """ + kwargs['order'] = 'post' + for src, dest in traverse_tree(self._root, dest_root, **kwargs): + if os.path.isdir(src): + # Skip non-existing links. + if not os.path.exists(dest): + continue + + if not os.path.isdir(dest): + raise ValueError("File blocks directory: %s" % dest) + + # remove directory if it is empty. + if not os.listdir(dest): + shutil.rmtree(dest, ignore_errors=True) + + # remove empty dir marker if present. + marker = os.path.join(dest, empty_file_name) + if os.path.exists(marker): + os.remove(marker) + + elif os.path.exists(dest): + if not os.path.islink(dest): + raise ValueError("%s is not a link tree!" % dest) + os.remove(dest) diff --git a/lib/spack/llnl/util/tty/colify.py b/lib/spack/llnl/util/tty/colify.py index 6b2909990c..66c52c3968 100644 --- a/lib/spack/llnl/util/tty/colify.py +++ b/lib/spack/llnl/util/tty/colify.py @@ -169,6 +169,15 @@ def colify(elts, **options): if not elts: return (0, ()) + # environment size is of the form "<rows>x<cols>" + env_size = os.environ.get('COLIFY_SIZE') + if env_size: + try: + r, c = env_size.split('x') + console_rows, console_cols = int(r), int(c) + tty = True + except: pass + # Use only one column if not a tty. if not tty: if tty is False or not output.isatty(): diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index 6697e00e40..eb891e3d57 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -78,7 +78,7 @@ concretizer = DefaultConcretizer() # Version information from spack.version import Version -spack_version = Version("0.8") +spack_version = Version("0.8.15") # # Executables used by Spack @@ -138,7 +138,7 @@ sys_type = None # should live. This file is overloaded for spack core vs. for packages. # __all__ = ['Package', 'Version', 'when', 'ver'] -from spack.package import Package +from spack.package import Package, ExtensionConflictError from spack.version import Version, ver from spack.multimethod import when diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py index 45353ec640..59b25d96e7 100644 --- a/lib/spack/spack/build_environment.py +++ b/lib/spack/spack/build_environment.py @@ -28,6 +28,7 @@ Skimming this module is a nice way to get acquainted with the types of calls you can make from within the install() function. """ import os +import sys import shutil import multiprocessing import platform @@ -183,6 +184,10 @@ def set_module_variables_for_package(pkg): if platform.mac_ver()[0]: m.std_cmake_args.append('-DCMAKE_FIND_FRAMEWORK=LAST') + # Set up CMake rpath + m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE') + m.std_cmake_args.append('-DCMAKE_INSTALL_RPATH=%s' % ":".join(get_rpaths(pkg))) + # Emulate some shell commands for convenience m.pwd = os.getcwd m.cd = os.chdir @@ -202,8 +207,78 @@ def set_module_variables_for_package(pkg): m.prefix = pkg.prefix +def get_rpaths(pkg): + """Get a list of all the rpaths for a package.""" + rpaths = [pkg.prefix.lib, pkg.prefix.lib64] + rpaths.extend(d.prefix.lib for d in pkg.spec.traverse(root=False) + if os.path.isdir(d.prefix.lib)) + rpaths.extend(d.prefix.lib64 for d in pkg.spec.traverse(root=False) + if os.path.isdir(d.prefix.lib64)) + return rpaths + + def setup_package(pkg): """Execute all environment setup routines.""" set_compiler_environment_variables(pkg) set_build_environment_variables(pkg) set_module_variables_for_package(pkg) + + # Allow dependencies to set up environment as well. + for dep_spec in pkg.spec.traverse(root=False): + dep_spec.package.setup_dependent_environment( + pkg.module, dep_spec, pkg.spec) + + +def fork(pkg, function): + """Fork a child process to do part of a spack build. + + Arguments: + + pkg -- pkg whose environemnt we should set up the + forked process for. + function -- arg-less function to run in the child process. + + Usage: + def child_fun(): + # do stuff + build_env.fork(pkg, child_fun) + + Forked processes are run with the build environemnt set up by + spack.build_environment. This allows package authors to have + full control over the environment, etc. without offecting + other builds that might be executed in the same spack call. + + If something goes wrong, the child process is expected toprint + the error and the parent process will exit with error as + well. If things go well, the child exits and the parent + carries on. + """ + try: + pid = os.fork() + except OSError, e: + raise InstallError("Unable to fork build process: %s" % e) + + if pid == 0: + # Give the child process the package's build environemnt. + setup_package(pkg) + + try: + # call the forked function. + function() + + # Use os._exit here to avoid raising a SystemExit exception, + # which interferes with unit tests. + os._exit(0) + except: + # Child doesn't raise or return to main spack code. + # Just runs default exception handler and exits. + sys.excepthook(*sys.exc_info()) + os._exit(1) + + else: + # Parent process just waits for the child to complete. If the + # child exited badly, assume it already printed an appropriate + # message. Just make the parent exit with an error code. + pid, returncode = os.waitpid(pid, 0) + if returncode != 0: + sys.exit(1) diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py index 537db536dd..b96ac5af51 100644 --- a/lib/spack/spack/cmd/__init__.py +++ b/lib/spack/spack/cmd/__init__.py @@ -121,3 +121,18 @@ def elide_list(line_list, max_num=10): return line_list[:max_num-1] + ['...'] + line_list[-1:] else: return line_list + + +def disambiguate_spec(spec): + matching_specs = spack.db.get_installed(spec) + if not matching_specs: + tty.die("Spec '%s' matches no installed packages." % spec) + + elif len(matching_specs) > 1: + args = ["%s matches multiple packages." % spec, + "Matching packages:"] + args += [" " + str(s) for s in matching_specs] + args += ["Use a more specific spec."] + tty.die(*args) + + return matching_specs[0] diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py new file mode 100644 index 0000000000..4070baaa70 --- /dev/null +++ b/lib/spack/spack/cmd/activate.py @@ -0,0 +1,58 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://scalability-llnl.github.io/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from external import argparse +import llnl.util.tty as tty +import spack +import spack.cmd + +description = "Activate a package extension." + +def setup_parser(subparser): + subparser.add_argument( + '-f', '--force', action='store_true', + help="Activate without first activating dependencies.") + subparser.add_argument( + 'spec', nargs=argparse.REMAINDER, help="spec of package extension to activate.") + + +def activate(parser, args): + # TODO: shouldn't have to concretize here. Fix DAG issues. + specs = spack.cmd.parse_specs(args.spec, concretize=True) + if len(specs) != 1: + tty.die("activate requires one spec. %d given." % len(specs)) + + # TODO: remove this hack when DAG info is stored in dir layout. + # This ensures the ext spec is always normalized properly. + spack.db.get(specs[0]) + + spec = spack.cmd.disambiguate_spec(specs[0]) + + if not spec.package.is_extension: + tty.die("%s is not an extension." % spec.name) + + if spec.package.activated: + tty.die("Package %s is already activated." % specs[0].short_spec) + + spec.package.do_activate() diff --git a/lib/spack/spack/cmd/clean.py b/lib/spack/spack/cmd/clean.py index 79dd91c5bf..c20136ebe5 100644 --- a/lib/spack/spack/cmd/clean.py +++ b/lib/spack/spack/cmd/clean.py @@ -1,5 +1,5 @@ ############################################################################## -# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC. # Produced at the Lawrence Livermore National Laboratory. # # This file is part of Spack. @@ -28,39 +28,19 @@ import llnl.util.tty as tty import spack import spack.cmd -import spack.stage as stage -description = "Remove staged files for packages" +description = "Remove build stage and source tarball for packages." def setup_parser(subparser): - subparser.add_argument('-c', "--clean", action="store_true", dest='clean', - help="run make clean in the build directory (default)") - subparser.add_argument('-w', "--work", action="store_true", dest='work', - help="delete the build directory and re-expand it from its archive.") - subparser.add_argument('-d', "--dist", action="store_true", dest='dist', - help="delete the downloaded archive.") subparser.add_argument('packages', nargs=argparse.REMAINDER, help="specs of packages to clean") def clean(parser, args): if not args.packages: - tty.die("spack clean requires at least one package argument") + tty.die("spack clean requires at least one package spec.") specs = spack.cmd.parse_specs(args.packages, concretize=True) for spec in specs: package = spack.db.get(spec) - if args.dist: - package.do_clean_dist() - tty.msg("Cleaned %s" % package.name) - - elif args.work: - package.do_clean_work() - tty.msg("Restaged %s" % package.name) - - else: - try: - package.do_clean() - except subprocess.CalledProcessError, e: - tty.warn("Warning: 'make clean' didn't work. Consider 'spack clean --work'.") - tty.msg("Made clean for %s" % package.name) + package.do_clean() diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py new file mode 100644 index 0000000000..c9a4d4b2f6 --- /dev/null +++ b/lib/spack/spack/cmd/deactivate.py @@ -0,0 +1,104 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://scalability-llnl.github.io/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from external import argparse +import llnl.util.tty as tty + +import spack +import spack.cmd +from spack.graph import topological_sort + +description = "Deactivate a package extension." + +def setup_parser(subparser): + subparser.add_argument( + '-f', '--force', action='store_true', + help="Run deactivation even if spec is NOT currently activated.") + subparser.add_argument( + '-a', '--all', action='store_true', + help="Deactivate all extensions of an extendable pacakge, or " + "deactivate an extension AND its dependencies.") + subparser.add_argument( + 'spec', nargs=argparse.REMAINDER, help="spec of package extension to deactivate.") + + +def deactivate(parser, args): + # TODO: shouldn't have to concretize here. Fix DAG issues. + specs = spack.cmd.parse_specs(args.spec, concretize=True) + if len(specs) != 1: + tty.die("deactivate requires one spec. %d given." % len(specs)) + + # TODO: remove this hack when DAG info is stored properly. + # This ensures the ext spec is always normalized properly. + spack.db.get(specs[0]) + + spec = spack.cmd.disambiguate_spec(specs[0]) + pkg = spec.package + + if args.all: + if pkg.extendable: + tty.msg("Deactivating all extensions of %s" % pkg.spec.short_spec) + ext_pkgs = spack.db.installed_extensions_for(spec) + + for ext_pkg in ext_pkgs: + ext_pkg.spec.normalize() + if ext_pkg.activated: + ext_pkg.do_deactivate(force=True) + + elif pkg.is_extension: + # TODO: store DAG info properly (see above) + spec.normalize() + + if not args.force and not spec.package.activated: + tty.die("%s is not activated." % pkg.spec.short_spec) + + tty.msg("Deactivating %s and all dependencies." % pkg.spec.short_spec) + + topo_order = topological_sort(spec) + index = spec.index() + + for name in topo_order: + espec = index[name] + epkg = espec.package + + # TODO: store DAG info properly (see above) + epkg.spec.normalize() + + if epkg.extends(pkg.extendee_spec): + if epkg.activated or args.force: + + epkg.do_deactivate(force=args.force) + + else: + tty.die("spack deactivate --all requires an extendable package or an extension.") + + else: + if not pkg.is_extension: + tty.die("spack deactivate requires an extension.", + "Did you mean 'spack deactivate --all'?") + + if not args.force and not spec.package.activated: + tty.die("Package %s is not activated." % specs[0].short_spec) + + spec.package.do_deactivate(force=args.force) diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py new file mode 100644 index 0000000000..fc8e6842c3 --- /dev/null +++ b/lib/spack/spack/cmd/extensions.py @@ -0,0 +1,98 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://scalability-llnl.github.io/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import sys +from external import argparse + +import llnl.util.tty as tty +from llnl.util.tty.colify import colify + +import spack +import spack.cmd +import spack.cmd.find + +description = "List extensions for package." + +def setup_parser(subparser): + format_group = subparser.add_mutually_exclusive_group() + format_group.add_argument( + '-l', '--long', action='store_const', dest='mode', const='long', + help='Show dependency hashes as well as versions.') + format_group.add_argument( + '-p', '--paths', action='store_const', dest='mode', const='paths', + help='Show paths to extension install directories') + format_group.add_argument( + '-d', '--deps', action='store_const', dest='mode', const='deps', + help='Show full dependency DAG of extensions') + + subparser.add_argument( + 'spec', nargs=argparse.REMAINDER, help='Spec of package to list extensions for') + + +def extensions(parser, args): + if not args.spec: + tty.die("extensions requires a package spec.") + + # Checks + spec = spack.cmd.parse_specs(args.spec) + if len(spec) > 1: + tty.die("Can only list extensions for one package.") + + if not spec[0].package.extendable: + tty.die("%s is not an extendable package." % spec[0].name) + + spec = spack.cmd.disambiguate_spec(spec[0]) + + if not spec.package.extendable: + tty.die("%s does not have extensions." % spec.short_spec) + + if not args.mode: + args.mode = 'short' + + # List package names of extensions + extensions = spack.db.extensions_for(spec) + if not extensions: + tty.msg("%s has no extensions." % spec.cshort_spec) + return + tty.msg(spec.cshort_spec) + tty.msg("%d extensions:" % len(extensions)) + colify(ext.name for ext in extensions) + + # List specs of installed extensions. + installed = [s.spec for s in spack.db.installed_extensions_for(spec)] + print + if not installed: + tty.msg("None installed.") + return + tty.msg("%d installed:" % len(installed)) + spack.cmd.find.display_specs(installed, mode=args.mode) + + # List specs of activated extensions. + activated = spack.install_layout.extension_map(spec) + print + if not activated: + tty.msg("None activated.") + return + tty.msg("%d currently activated:" % len(activated)) + spack.cmd.find.display_specs(activated.values(), mode=args.mode) diff --git a/lib/spack/spack/cmd/find.py b/lib/spack/spack/cmd/find.py index 1de3413d42..70b10edb4e 100644 --- a/lib/spack/spack/cmd/find.py +++ b/lib/spack/spack/cmd/find.py @@ -41,13 +41,13 @@ description ="Find installed spack packages" def setup_parser(subparser): format_group = subparser.add_mutually_exclusive_group() format_group.add_argument( - '-l', '--long', action='store_true', dest='long', + '-l', '--long', action='store_const', dest='mode', const='long', help='Show dependency hashes as well as versions.') format_group.add_argument( - '-p', '--paths', action='store_true', dest='paths', + '-p', '--paths', action='store_const', dest='mode', const='paths', help='Show paths to package install directories') format_group.add_argument( - '-d', '--deps', action='store_true', dest='full_deps', + '-d', '--deps', action='store_const', dest='mode', const='deps', help='Show full dependency DAG of installed packages') subparser.add_argument( @@ -55,26 +55,8 @@ def setup_parser(subparser): help='optional specs to filter results') -def find(parser, args): - # Filter out specs that don't exist. - query_specs = spack.cmd.parse_specs(args.query_specs) - query_specs, nonexisting = partition_list( - query_specs, lambda s: spack.db.exists(s.name)) - - if nonexisting: - msg = "No such package%s: " % ('s' if len(nonexisting) > 1 else '') - msg += ", ".join(s.name for s in nonexisting) - tty.msg(msg) - - if not query_specs: - return - - # Get all the specs the user asked for - if not query_specs: - specs = set(spack.db.installed_package_specs()) - else: - results = [set(spack.db.get_installed(qs)) for qs in query_specs] - specs = set.union(*results) +def display_specs(specs, **kwargs): + mode = kwargs.get('mode', 'short') # Make a dict with specs keyed by architecture and compiler. index = index_by(specs, ('architecture', 'compiler')) @@ -92,7 +74,7 @@ def find(parser, args): specs.sort() abbreviated = [s.format('$_$@$+', color=True) for s in specs] - if args.paths: + if mode == 'paths': # Print one spec per line along with prefix path width = max(len(s) for s in abbreviated) width += 2 @@ -101,11 +83,47 @@ def find(parser, args): for abbrv, spec in zip(abbreviated, specs): print format % (abbrv, spec.prefix) - elif args.full_deps: + elif mode == 'deps': for spec in specs: - print spec.tree(indent=4, format='$_$@$+', color=True), - else: + print spec.tree(indent=4, format='$_$@$+$#', color=True), + + elif mode in ('short', 'long'): fmt = '$-_$@$+' - if args.long: + if mode == 'long': fmt += '$#' colify(s.format(fmt, color=True) for s in specs) + + else: + raise ValueError( + "Invalid mode for display_specs: %s. Must be one of (paths, deps, short)." % mode) + + + +def find(parser, args): + # Filter out specs that don't exist. + query_specs = spack.cmd.parse_specs(args.query_specs) + query_specs, nonexisting = partition_list( + query_specs, lambda s: spack.db.exists(s.name)) + + if nonexisting: + msg = "No such package%s: " % ('s' if len(nonexisting) > 1 else '') + msg += ", ".join(s.name for s in nonexisting) + tty.msg(msg) + + if not query_specs: + return + + # Get all the specs the user asked for + if not query_specs: + specs = set(spack.db.installed_package_specs()) + else: + results = [set(spack.db.get_installed(qs)) for qs in query_specs] + specs = set.union(*results) + + if not args.mode: + args.mode = 'short' + + if sys.stdout.isatty(): + tty.msg("%d installed packages." % len(specs)) + display_specs(specs, mode=args.mode) + diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py index 509c336b69..709e894b7f 100644 --- a/lib/spack/spack/cmd/location.py +++ b/lib/spack/spack/cmd/location.py @@ -23,6 +23,7 @@ # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import os +import sys from external import argparse import llnl.util.tty as tty @@ -77,37 +78,30 @@ def location(parser, args): tty.die("You must supply a spec.") if len(specs) != 1: tty.die("Too many specs. Supply only one.") - spec = specs[0] if args.install_dir: # install_dir command matches against installed specs. - matching_specs = spack.db.get_installed(spec) - if not matching_specs: - tty.die("Spec '%s' matches no installed packages." % spec) + spec = spack.cmd.disambiguate_spec(specs[0]) + print spec.prefix - elif len(matching_specs) > 1: - args = ["%s matches multiple packages." % spec, - "Matching packages:"] - args += [" " + str(s) for s in matching_specs] - args += ["Use a more specific spec."] - tty.die(*args) + else: + spec = specs[0] - print matching_specs[0].prefix + if args.package_dir: + # This one just needs the spec name. + print join_path(spack.db.root, spec.name) - elif args.package_dir: - # This one just needs the spec name. - print join_path(spack.db.root, spec.name) + else: + # These versions need concretized specs. + spec.concretize() + pkg = spack.db.get(spec) + + if args.stage_dir: + print pkg.stage.path + + else: # args.build_dir is the default. + if not pkg.stage.source_path: + tty.die("Build directory does not exist yet. Run this to create it:", + "spack stage " + " ".join(args.spec)) + print pkg.stage.source_path - else: - # These versions need concretized specs. - spec.concretize() - pkg = spack.db.get(spec) - - if args.stage_dir: - print pkg.stage.path - - else: # args.build_dir is the default. - if not pkg.stage.source_path: - tty.die("Build directory does not exist yet. Run this to create it:", - "spack stage " + " ".join(args.spec)) - print pkg.stage.source_path diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py index 87c528881e..f048482845 100644 --- a/lib/spack/spack/cmd/package-list.py +++ b/lib/spack/spack/cmd/package-list.py @@ -23,6 +23,7 @@ # Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## import re +import cgi from StringIO import StringIO import llnl.util.tty as tty from llnl.util.tty.colify import * @@ -49,6 +50,8 @@ def print_rst_package_list(): """Print out information on all packages in restructured text.""" pkgs = sorted(spack.db.all_packages(), key=lambda s:s.name.lower()) + print ".. _package-list:" + print print "Package List" print "==================" @@ -70,9 +73,9 @@ def print_rst_package_list(): print print pkg.name print "-" * len(pkg.name) - print "Links" - print " * `Homepage <%s>`__" % pkg.homepage - print " * `%s/package.py <%s>`__" % (pkg.name, github_url(pkg)) + print "Links:" + print " * `%s <%s>`__" % (cgi.escape(pkg.homepage), pkg.homepage) + print " * `%s/package.py <%s>`__" % (pkg.name, github_url(pkg)) print if pkg.versions: print "Versions:" @@ -82,7 +85,7 @@ def print_rst_package_list(): print " " + ", ".join("`%s`_" % d if d != "mpi" else d for d in pkg.dependencies) print - print "Description" + print "Description:" print pkg.format_doc(indent=2) print print "-----" diff --git a/lib/spack/spack/cmd/restage.py b/lib/spack/spack/cmd/restage.py new file mode 100644 index 0000000000..e735a12c32 --- /dev/null +++ b/lib/spack/spack/cmd/restage.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2014, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://scalability-llnl.github.io/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from external import argparse + +import llnl.util.tty as tty + +import spack +import spack.cmd + +description = "Revert checked out package source code." + +def setup_parser(subparser): + subparser.add_argument('packages', nargs=argparse.REMAINDER, + help="specs of packages to restage") + + +def restage(parser, args): + if not args.packages: + tty.die("spack restage requires at least one package spec.") + + specs = spack.cmd.parse_specs(args.packages, concretize=True) + for spec in specs: + package = spack.db.get(spec) + package.do_restage() diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py index e787c460ad..6ded455390 100644 --- a/lib/spack/spack/cmd/uninstall.py +++ b/lib/spack/spack/cmd/uninstall.py @@ -65,8 +65,8 @@ def uninstall(parser, args): " b) use a more specific spec."] tty.die(*args) - if len(matching_specs) == 0: + if args.force: continue tty.die("%s does not match any installed packages." % spec) for s in matching_specs: diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py index 42cac0c9d2..b2cf5dc801 100644 --- a/lib/spack/spack/directory_layout.py +++ b/lib/spack/spack/directory_layout.py @@ -27,9 +27,11 @@ import os import exceptions import hashlib import shutil +import tempfile from contextlib import closing import llnl.util.tty as tty +from llnl.util.lang import memoized from llnl.util.filesystem import join_path, mkdirp import spack @@ -53,6 +55,19 @@ class DirectoryLayout(object): self.root = root + @property + def hidden_file_paths(self): + """Return a list of hidden files used by the directory layout. + + Paths are relative to the root of an install directory. + + If the directory layout uses no hidden files to maintain + state, this should return an empty container, e.g. [] or (,). + + """ + raise NotImplementedError() + + def all_specs(self): """To be implemented by subclasses to traverse all specs for which there is a directory within the root. @@ -71,6 +86,42 @@ class DirectoryLayout(object): raise NotImplementedError() + def extension_map(self, spec): + """Get a dict of currently installed extension packages for a spec. + + Dict maps { name : extension_spec } + Modifying dict does not affect internals of this layout. + """ + raise NotImplementedError() + + + def check_extension_conflict(self, spec, ext_spec): + """Ensure that ext_spec can be activated in spec. + + If not, raise ExtensionAlreadyInstalledError or + ExtensionConflictError. + """ + raise NotImplementedError() + + + def check_activated(self, spec, ext_spec): + """Ensure that ext_spec can be removed from spec. + + If not, raise NoSuchExtensionError. + """ + raise NotImplementedError() + + + def add_extension(self, spec, ext_spec): + """Add to the list of currently installed extensions.""" + raise NotImplementedError() + + + def remove_extension(self, spec, ext_spec): + """Remove from the list of currently installed extensions.""" + raise NotImplementedError() + + def path_for_spec(self, spec): """Return an absolute path from the root to a directory for the spec.""" _check_concrete(spec) @@ -81,12 +132,17 @@ class DirectoryLayout(object): def remove_path_for_spec(self, spec): - """Removes a prefix and any empty parent directories from the root.""" + """Removes a prefix and any empty parent directories from the root. + Raised RemoveFailedError if something goes wrong. + """ path = self.path_for_spec(spec) assert(path.startswith(self.root)) if os.path.exists(path): - shutil.rmtree(path, True) + try: + shutil.rmtree(path) + except exceptions.OSError, e: + raise RemoveFailedError(spec, path, e) path = os.path.dirname(path) while path != self.root: @@ -134,9 +190,18 @@ class SpecHashDirectoryLayout(DirectoryLayout): """Prefix size is number of characters in the SHA-1 prefix to use to make each hash unique. """ - spec_file_name = kwargs.get('spec_file_name', '.spec') + spec_file_name = kwargs.get('spec_file_name', '.spec') + extension_file_name = kwargs.get('extension_file_name', '.extensions') super(SpecHashDirectoryLayout, self).__init__(root) self.spec_file_name = spec_file_name + self.extension_file_name = extension_file_name + + # Cache of already written/read extension maps. + self._extension_maps = {} + + @property + def hidden_file_paths(self): + return ('.spec', '.extensions') def relative_path_for_spec(self, spec): @@ -159,6 +224,9 @@ class SpecHashDirectoryLayout(DirectoryLayout): if all(spack.db.exists(s.name) for s in spec.traverse()): copy = spec.copy() + + # TODO: It takes a lot of time to normalize every spec on read. + # TODO: Storing graph info with spec files would fix this. copy.normalize() if copy.concrete: return copy # These are specs spack still understands. @@ -212,17 +280,116 @@ class SpecHashDirectoryLayout(DirectoryLayout): self.write_spec(spec, spec_file_path) + @memoized def all_specs(self): if not os.path.isdir(self.root): - return + return [] + specs = [] for path in traverse_dirs_at_depth(self.root, 3): arch, compiler, last_dir = path spec_file_path = join_path( self.root, arch, compiler, last_dir, self.spec_file_name) if os.path.exists(spec_file_path): spec = self.read_spec(spec_file_path) - yield spec + specs.append(spec) + return specs + + + def extension_file_path(self, spec): + """Gets full path to an installed package's extension file""" + _check_concrete(spec) + return join_path(self.path_for_spec(spec), self.extension_file_name) + + + def _extension_map(self, spec): + """Get a dict<name -> spec> for all extensions currnetly + installed for this package.""" + _check_concrete(spec) + + if not spec in self._extension_maps: + path = self.extension_file_path(spec) + if not os.path.exists(path): + self._extension_maps[spec] = {} + + else: + exts = {} + with closing(open(path)) as ext_file: + for line in ext_file: + try: + spec = Spec(line.strip()) + exts[spec.name] = spec + except spack.error.SpackError, e: + # TODO: do something better here -- should be + # resilient to corrupt files. + raise InvalidExtensionSpecError(str(e)) + self._extension_maps[spec] = exts + + return self._extension_maps[spec] + + + def extension_map(self, spec): + """Defensive copying version of _extension_map() for external API.""" + return self._extension_map(spec).copy() + + + def check_extension_conflict(self, spec, ext_spec): + exts = self._extension_map(spec) + if ext_spec.name in exts: + installed_spec = exts[ext_spec.name] + if ext_spec == installed_spec: + raise ExtensionAlreadyInstalledError(spec, ext_spec) + else: + raise ExtensionConflictError(spec, ext_spec, installed_spec) + + + def check_activated(self, spec, ext_spec): + exts = self._extension_map(spec) + if (not ext_spec.name in exts) or (ext_spec != exts[ext_spec.name]): + raise NoSuchExtensionError(spec, ext_spec) + + + def _write_extensions(self, spec, extensions): + path = self.extension_file_path(spec) + + # Create a temp file in the same directory as the actual file. + dirname, basename = os.path.split(path) + tmp = tempfile.NamedTemporaryFile( + prefix=basename, dir=dirname, delete=False) + + # Write temp file. + with closing(tmp): + for extension in sorted(extensions.values()): + tmp.write("%s\n" % extension) + + # Atomic update by moving tmpfile on top of old one. + os.rename(tmp.name, path) + + + def add_extension(self, spec, ext_spec): + _check_concrete(spec) + _check_concrete(ext_spec) + + # Check whether it's already installed or if it's a conflict. + exts = self._extension_map(spec) + self.check_extension_conflict(spec, ext_spec) + + # do the actual adding. + exts[ext_spec.name] = ext_spec + self._write_extensions(spec, exts) + + + def remove_extension(self, spec, ext_spec): + _check_concrete(spec) + _check_concrete(ext_spec) + + # Make sure it's installed before removing. + exts = self._extension_map(spec) + self.check_activated(spec, ext_spec) + + # do the actual removing. + del exts[ext_spec.name] + self._write_extensions(spec, exts) class DirectoryLayoutError(SpackError): @@ -239,6 +406,15 @@ class SpecHashCollisionError(DirectoryLayoutError): % installed_spec, new_spec) +class RemoveFailedError(DirectoryLayoutError): + """Raised when a DirectoryLayout cannot remove an install prefix.""" + def __init__(self, installed_spec, prefix, error): + super(RemoveFailedError, self).__init__( + 'Could not remove prefix %s for %s : %s' + % prefix, installed_spec.short_spec, error) + self.cause = error + + class InconsistentInstallDirectoryError(DirectoryLayoutError): """Raised when a package seems to be installed to the wrong place.""" def __init__(self, message): @@ -250,3 +426,34 @@ class InstallDirectoryAlreadyExistsError(DirectoryLayoutError): def __init__(self, path): super(InstallDirectoryAlreadyExistsError, self).__init__( "Install path %s already exists!") + + +class InvalidExtensionSpecError(DirectoryLayoutError): + """Raised when an extension file has a bad spec in it.""" + def __init__(self, message): + super(InvalidExtensionSpecError, self).__init__(message) + + +class ExtensionAlreadyInstalledError(DirectoryLayoutError): + """Raised when an extension is added to a package that already has it.""" + def __init__(self, spec, ext_spec): + super(ExtensionAlreadyInstalledError, self).__init__( + "%s is already installed in %s" % (ext_spec.short_spec, spec.short_spec)) + + +class ExtensionConflictError(DirectoryLayoutError): + """Raised when an extension is added to a package that already has it.""" + def __init__(self, spec, ext_spec, conflict): + super(ExtensionConflictError, self).__init__( + "%s cannot be installed in %s because it conflicts with %s."% ( + ext_spec.short_spec, spec.short_spec, conflict.short_spec)) + + +class NoSuchExtensionError(DirectoryLayoutError): + """Raised when an extension isn't there on deactivate.""" + def __init__(self, spec, ext_spec): + super(NoSuchExtensionError, self).__init__( + "%s cannot be removed from %s because it's not activated."% ( + ext_spec.short_spec, spec.short_spec)) + + diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index a71f3a1531..48313e2b37 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -41,6 +41,7 @@ in order to build it. They need to define the following methods: Archive a source directory, e.g. for creating a mirror. """ import os +import sys import re import shutil from functools import wraps @@ -141,13 +142,19 @@ class URLFetchStrategy(FetchStrategy): tty.msg("Trying to fetch from %s" % self.url) + curl_args = ['-O', # save file to disk + '-f', # fail on >400 errors + '-D', '-', # print out HTML headers + '-L', self.url,] + + if sys.stdout.isatty(): + curl_args.append('-#') # status bar when using a tty + else: + curl_args.append('-sS') # just errors when not. + # Run curl but grab the mime type from the http headers - headers = spack.curl('-#', # status bar - '-O', # save file to disk - '-f', # fail on >400 errors - '-D', '-', # print out HTML headers - '-L', self.url, - return_output=True, fail_on_error=False) + headers = spack.curl( + *curl_args, return_output=True, fail_on_error=False) if spack.curl.returncode != 0: # clean up archive on failure. diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py index 98b7f2323f..1c44e8abaa 100644 --- a/lib/spack/spack/hooks/__init__.py +++ b/lib/spack/spack/hooks/__init__.py @@ -31,7 +31,9 @@ Currently the following hooks are supported: + * pre_install() * post_install() + * pre_uninstall() * post_uninstall() This can be used to implement support for things like module @@ -70,5 +72,8 @@ class HookRunner(object): # # Define some functions that can be called to fire off hooks. # -post_install = HookRunner('post_install') +pre_install = HookRunner('pre_install') +post_install = HookRunner('post_install') + +pre_uninstall = HookRunner('pre_uninstall') post_uninstall = HookRunner('post_uninstall') diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py new file mode 100644 index 0000000000..cf87a78c8c --- /dev/null +++ b/lib/spack/spack/hooks/extensions.py @@ -0,0 +1,36 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://scalability-llnl.github.io/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## + +import spack + + +def pre_uninstall(pkg): + # Need to do this b/c uninstall does not automatically do it. + # TODO: store full graph info in stored .spec file. + pkg.spec.normalize() + + if pkg.is_extension: + if pkg.activated: + pkg.do_deactivate(force=True) diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py index 114c7b6a35..306c8085aa 100644 --- a/lib/spack/spack/mirror.py +++ b/lib/spack/spack/mirror.py @@ -146,7 +146,7 @@ def create(path, specs, **kwargs): stage = None try: # create a subdirectory for the current package@version - archive_path = join_path(path, mirror_archive_path(spec)) + archive_path = os.path.abspath(join_path(path, mirror_archive_path(spec))) subdir = os.path.dirname(archive_path) mkdirp(subdir) diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py index 755e9ea900..7d2ca97a62 100644 --- a/lib/spack/spack/modules.py +++ b/lib/spack/spack/modules.py @@ -49,6 +49,7 @@ import os import re import textwrap import shutil +from glob import glob from contextlib import closing import llnl.util.tty as tty @@ -123,6 +124,13 @@ class EnvModule(object): if os.path.isdir(directory): add_path(var, directory) + # Add python path unless it's an actual python installation + # TODO: is there a better way to do this? + if self.spec.name != 'python': + site_packages = glob(join_path(self.spec.prefix.lib, "python*/site-packages")) + if site_packages: + add_path('PYTHONPATH', site_packages[0]) + # short description is just the package + version # TODO: maybe packages can optionally provide it. self.short_description = self.spec.format("$_ $@") diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 1dfd3d1c83..75e6142a9d 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -45,6 +45,7 @@ import textwrap from StringIO import StringIO import llnl.util.tty as tty +from llnl.util.link_tree import LinkTree from llnl.util.filesystem import * from llnl.util.lang import * @@ -286,10 +287,9 @@ class Package(object): .. code-block:: python - p.do_clean() # runs make clean - p.do_clean_work() # removes the build directory and + p.do_clean() # removes the stage directory entirely + p.do_restage() # removes the build directory and # re-expands the archive. - p.do_clean_dist() # removes the stage directory entirely The convention used here is that a do_* function is intended to be called internally by Spack commands (in spack.cmd). These aren't for package @@ -320,12 +320,21 @@ class Package(object): """Patches to apply to newly expanded source, if any.""" patches = {} + """Specs of package this one extends, or None. + + Currently, ppackages can extend at most one other package. + """ + extendees = {} + # # These are default values for instance variables. # """By default we build in parallel. Subclasses can override this.""" parallel = True + """Most packages are NOT extendable. Set to True if you want extensions.""" + extendable = False + def __init__(self, spec): # this determines how the package should be built. @@ -395,6 +404,9 @@ class Package(object): self._fetch_time = 0.0 self._total_time = 0.0 + if self.is_extension: + spack.db.get(self.extendee_spec)._check_extendable() + @property def version(self): @@ -481,6 +493,47 @@ class Package(object): self._fetcher = f + @property + def extendee_spec(self): + """Spec of the extendee of this package, or None if it is not an extension.""" + if not self.extendees: + return None + name = next(iter(self.extendees)) + if not name in self.spec: + spec, kwargs = self.extendees[name] + return spec + + # Need to do this to get the concrete version of the spec + return self.spec[name] + + + @property + def extendee_args(self): + """Spec of the extendee of this package, or None if it is not an extension.""" + if not self.extendees: + return None + name = next(iter(self.extendees)) + return self.extendees[name][1] + + + @property + def is_extension(self): + return len(self.extendees) > 0 + + + def extends(self, spec): + return (spec.name in self.extendees and + spec.satisfies(self.extendees[spec.name][0])) + + + @property + def activated(self): + if not self.is_extension: + raise ValueError("is_extension called on package that is not an extension.") + exts = spack.install_layout.extension_map(self.extendee_spec) + return (self.name in exts) and (exts[self.name] == self.spec) + + def preorder_traversal(self, visited=None, **kwargs): """This does a preorder traversal of the package's dependence DAG.""" virtual = kwargs.get("virtual", False) @@ -741,34 +794,27 @@ class Package(object): tty.msg("Installing %s" % self.name) if not ignore_deps: - self.do_install_dependencies() + self.do_install_dependencies(**kwargs) start_time = time.time() if not fake_install: self.do_patch() - # Fork a child process to do the build. This allows each - # package authors to have full control over their environment, - # etc. without offecting other builds that might be executed - # in the same spack call. - try: - pid = os.fork() - except OSError, e: - raise InstallError("Unable to fork build process: %s" % e) + # create the install directory. The install layout + # handles this in case so that it can use whatever + # package naming scheme it likes. + spack.install_layout.make_path_for_spec(self.spec) - if pid == 0: + def real_work(): try: tty.msg("Building %s." % self.name) - # create the install directory. The install layout - # handles this in case so that it can use whatever - # package naming scheme it likes. - spack.install_layout.make_path_for_spec(self.spec) + # Run the pre-install hook in the child process after + # the directory is created. + spack.hooks.pre_install(self) # Set up process's build environment before running install. self.stage.chdir_to_source() - build_env.setup_package(self) - if fake_install: self.do_fake_install() else: @@ -776,10 +822,7 @@ class Package(object): self.install(self.spec, self.prefix) # Ensure that something was actually installed. - if not os.listdir(self.prefix): - raise InstallError( - "Install failed for %s. Nothing was installed!" - % self.name) + self._sanity_check_install() # On successful install, remove the stage. if not keep_stage: @@ -790,14 +833,10 @@ class Package(object): build_time = self._total_time - self._fetch_time tty.msg("Successfully installed %s." % self.name, - "Fetch: %.2f sec. Build: %.2f sec. Total: %.2f sec." - % (self._fetch_time, build_time, self._total_time)) + "Fetch: %s. Build: %s. Total: %s." + % (_hms(self._fetch_time), _hms(build_time), _hms(self._total_time))) print_pkg(self.prefix) - # Use os._exit here to avoid raising a SystemExit exception, - # which interferes with unit tests. - os._exit(0) - except: if not keep_prefix: # If anything goes wrong, remove the install prefix @@ -807,28 +846,26 @@ class Package(object): "Spack will think this package is installed." + "Manually remove this directory to fix:", self.prefix) + raise - # Child doesn't raise or return to main spack code. - # Just runs default exception handler and exits. - sys.excepthook(*sys.exc_info()) - os._exit(1) - - # Parent process just waits for the child to complete. If the - # child exited badly, assume it already printed an appropriate - # message. Just make the parent exit with an error code. - pid, returncode = os.waitpid(pid, 0) - if returncode != 0: - sys.exit(1) - + build_env.fork(self, real_work) # Once everything else is done, run post install hooks spack.hooks.post_install(self) - def do_install_dependencies(self): + def _sanity_check_install(self): + installed = set(os.listdir(self.prefix)) + installed.difference_update(spack.install_layout.hidden_file_paths) + if not installed: + raise InstallError( + "Install failed for %s. Nothing was installed!" % self.name) + + + def do_install_dependencies(self, **kwargs): # Pass along paths of dependencies here for dep in self.spec.dependencies.values(): - dep.package.do_install() + dep.package.do_install(**kwargs) @property @@ -840,6 +877,32 @@ class Package(object): fromlist=[self.__class__.__name__]) + def setup_dependent_environment(self, module, spec, dependent_spec): + """Called before the install() method of dependents. + + Default implementation does nothing, but this can be + overridden by an extendable package to set up the install + environment for its extensions. This is useful if there are + some common steps to installing all extensions for a + certain package. + + Some examples: + + 1. Installing python modules generally requires PYTHONPATH to + point to the lib/pythonX.Y/site-packages directory in the + module's install prefix. This could set that variable. + + 2. Extensions often need to invoke the 'python' interpreter + from the Python installation being extended. This routine can + put a 'python' Execuable object in the module scope for the + extension package to simplify extension installs. + + 3. A lot of Qt extensions need QTDIR set. This can be used to do that. + + """ + pass + + def install(self, spec, prefix): """Package implementations override this with their own build configuration.""" raise InstallError("Package %s provides no install method!" % self.name) @@ -859,6 +922,10 @@ class Package(object): "The following installed packages depend on it: %s" % ' '.join(formatted_deps)) + # Pre-uninstall hook runs first. + spack.hooks.pre_uninstall(self) + + # Uninstalling in Spack only requires removing the prefix. self.remove_prefix() tty.msg("Successfully uninstalled %s." % self.spec.short_spec) @@ -866,26 +933,127 @@ class Package(object): spack.hooks.post_uninstall(self) - def do_clean(self): - if self.stage.expanded_archive_path: - self.stage.chdir_to_source() - self.clean() + def _check_extendable(self): + if not self.extendable: + raise ValueError("Package %s is not extendable!" % self.name) + + + def _sanity_check_extension(self): + if not self.is_extension: + raise ActivationError("This package is not an extension.") + extendee_package = self.extendee_spec.package + extendee_package._check_extendable() + + if not extendee_package.installed: + raise ActivationError("Can only (de)activate extensions for installed packages.") + if not self.installed: + raise ActivationError("Extensions must first be installed.") + if not self.extendee_spec.name in self.extendees: + raise ActivationError("%s does not extend %s!" % (self.name, self.extendee.name)) - def clean(self): - """By default just runs make clean. Override if this isn't good.""" - # TODO: should we really call make clean, ro just blow away the directory? - make = build_env.MakeExecutable('make', self.parallel) - make('clean') + def do_activate(self, **kwargs): + """Called on an etension to invoke the extendee's activate method. - def do_clean_work(self): - """By default just blows away the stage directory and re-stages.""" + Commands should call this routine, and should not call + activate() directly. + """ + self._sanity_check_extension() + force = kwargs.get('force', False) + + # TODO: get rid of this normalize - DAG handling. + self.spec.normalize() + + spack.install_layout.check_extension_conflict(self.extendee_spec, self.spec) + + if not force: + for spec in self.spec.traverse(root=False): + if spec.package.extends(self.extendee_spec): + # TODO: fix this normalize() requirement -- revisit DAG handling. + spec.package.spec.normalize() + if not spec.package.activated: + spec.package.do_activate(**kwargs) + + self.extendee_spec.package.activate(self, **self.extendee_args) + + spack.install_layout.add_extension(self.extendee_spec, self.spec) + tty.msg("Activated extension %s for %s." + % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@"))) + + + def activate(self, extension, **kwargs): + """Symlinks all files from the extension into extendee's install dir. + + Package authors can override this method to support other + extension mechanisms. Spack internals (commands, hooks, etc.) + should call do_activate() method so that proper checks are + always executed. + + """ + def ignore(filename): + return (filename in spack.install_layout.hidden_file_paths or + kwargs.get('ignore', lambda f: False)(filename)) + + tree = LinkTree(extension.prefix) + conflict = tree.find_conflict(self.prefix, ignore=ignore) + if conflict: + raise ExtensionConflictError(conflict) + tree.merge(self.prefix, ignore=ignore) + + + def do_deactivate(self, **kwargs): + """Called on the extension to invoke extendee's deactivate() method.""" + self._sanity_check_extension() + force = kwargs.get('force', False) + + # Allow a force deactivate to happen. This can unlink + # spurious files if something was corrupted. + if not force: + spack.install_layout.check_activated(self.extendee_spec, self.spec) + + activated = spack.install_layout.extension_map(self.extendee_spec) + for name, aspec in activated.items(): + if aspec != self.spec and self.spec in aspec: + raise ActivationError( + "Cannot deactivate %s beacuse %s is activated and depends on it." + % (self.spec.short_spec, aspec.short_spec)) + + self.extendee_spec.package.deactivate(self, **self.extendee_args) + + # redundant activation check -- makes SURE the spec is not + # still activated even if something was wrong above. + if self.activated: + spack.install_layout.remove_extension(self.extendee_spec, self.spec) + + tty.msg("Deactivated extension %s for %s." + % (self.spec.short_spec, self.extendee_spec.format("$_$@$+$%@"))) + + + def deactivate(self, extension, **kwargs): + """Unlinks all files from extension out of this package's install dir. + + Package authors can override this method to support other + extension mechanisms. Spack internals (commands, hooks, etc.) + should call do_deactivate() method so that proper checks are + always executed. + + """ + def ignore(filename): + return (filename in spack.install_layout.hidden_file_paths or + kwargs.get('ignore', lambda f: False)(filename)) + + tree = LinkTree(extension.prefix) + tree.unmerge(self.prefix, ignore=ignore) + + + def do_restage(self): + """Reverts expanded/checked out source to a pristine state.""" self.stage.restage() - def do_clean_dist(self): - """Removes the stage directory where this package was built.""" + def do_clean(self): + """Removes the package's build stage and source tarball.""" if os.path.exists(self.stage.path): self.stage.destroy() @@ -1002,15 +1170,23 @@ def validate_package_url(url_string): def print_pkg(message): """Outputs a message with a package icon.""" - mac_ver = py_platform.mac_ver()[0] - if mac_ver and Version(mac_ver) >= Version('10.7'): - print u"\U0001F4E6" + tty.indent, - else: - from llnl.util.tty.color import cwrite - cwrite('@*g{[+]} ') + from llnl.util.tty.color import cwrite + cwrite('@*g{[+]} ') print message +def _hms(seconds): + """Convert time in seconds to hours, minutes, seconds.""" + m, s = divmod(seconds, 60) + h, m = divmod(m, 60) + + parts = [] + if h: parts.append("%dh" % h) + if m: parts.append("%dm" % m) + if s: parts.append("%.2fs" % s) + return ' '.join(parts) + + class FetchError(spack.error.SpackError): """Raised when something goes wrong during fetch.""" def __init__(self, message, long_msg=None): @@ -1057,3 +1233,17 @@ class NoURLError(PackageError): def __init__(self, cls): super(NoURLError, self).__init__( "Package %s has no version with a URL." % cls.__name__) + + +class ExtensionError(PackageError): pass + + +class ExtensionConflictError(ExtensionError): + def __init__(self, path): + super(ExtensionConflictError, self).__init__( + "Extension blocked by file: %s" % path) + + +class ActivationError(ExtensionError): + def __init__(self, msg, long_msg=None): + super(ActivationError, self).__init__(msg, long_msg) diff --git a/lib/spack/spack/packages.py b/lib/spack/spack/packages.py index db43d3909a..43c4c191c1 100644 --- a/lib/spack/spack/packages.py +++ b/lib/spack/spack/packages.py @@ -77,6 +77,8 @@ class PackageDB(object): copy = spec.copy() self.instances[copy] = package_class(copy) except Exception, e: + if spack.debug: + sys.excepthook(*sys.exc_info()) raise FailedConstructorError(spec.name, e) return self.instances[spec] @@ -110,6 +112,24 @@ class PackageDB(object): return providers + @_autospec + def extensions_for(self, extendee_spec): + return [p for p in self.all_packages() if p.extends(extendee_spec)] + + + @_autospec + def installed_extensions_for(self, extendee_spec): + for s in self.installed_package_specs(): + try: + if s.package.extends(extendee_spec): + yield s.package + except UnknownPackageError, e: + # Skip packages we know nothing about + continue + # TODO: add some conditional way to do this instead of + # catching exceptions. + + def dirname_for_package_name(self, pkg_name): """Get the directory name for a particular package. This is the directory that contains its package.py file.""" @@ -172,6 +192,7 @@ class PackageDB(object): yield self.get(name) + @memoized def exists(self, pkg_name): """Whether a package with the supplied name exists .""" return os.path.exists(self.filename_for_package_name(pkg_name)) diff --git a/lib/spack/spack/relations.py b/lib/spack/spack/relations.py index b1f4348945..a0c7723473 100644 --- a/lib/spack/spack/relations.py +++ b/lib/spack/spack/relations.py @@ -68,7 +68,7 @@ provides spack install mpileaks ^mvapich spack install mpileaks ^mpich """ -__all__ = [ 'depends_on', 'provides', 'patch', 'version' ] +__all__ = [ 'depends_on', 'extends', 'provides', 'patch', 'version' ] import re import inspect @@ -107,8 +107,9 @@ def depends_on(*specs): """Adds a dependencies local variable in the locals of the calling class, based on args. """ pkg = get_calling_package_name() + clocals = caller_locals() + dependencies = clocals.setdefault('dependencies', {}) - dependencies = caller_locals().setdefault('dependencies', {}) for string in specs: for spec in spack.spec.parse(string): if pkg == spec.name: @@ -116,6 +117,34 @@ def depends_on(*specs): dependencies[spec.name] = spec +def extends(spec, **kwargs): + """Same as depends_on, but dependency is symlinked into parent prefix. + + This is for Python and other language modules where the module + needs to be installed into the prefix of the Python installation. + Spack handles this by installing modules into their own prefix, + but allowing ONE module version to be symlinked into a parent + Python install at a time. + + keyword arguments can be passed to extends() so that extension + packages can pass parameters to the extendee's extension + mechanism. + + """ + pkg = get_calling_package_name() + clocals = caller_locals() + dependencies = clocals.setdefault('dependencies', {}) + extendees = clocals.setdefault('extendees', {}) + if extendees: + raise RelationError("Packages can extend at most one other package.") + + spec = Spec(spec) + if pkg == spec.name: + raise CircularReferenceError('extends', pkg) + dependencies[spec.name] = spec + extendees[spec.name] = (spec, kwargs) + + def provides(*specs, **kwargs): """Allows packages to provide a virtual dependency. If a package provides 'mpi', other packages can declare that they depend on "mpi", and spack diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 2f4fe9ca24..dffdccaddb 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -553,6 +553,13 @@ class Spec(object): @property + def cshort_spec(self): + """Returns a version of the spec with the dependencies hashed + instead of completely enumerated.""" + return self.format('$_$@$%@$+$=$#', color=True) + + + @property def prefix(self): return Prefix(spack.install_layout.path_for_spec(self)) diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index 0eda667abc..c53e6774fc 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -51,7 +51,8 @@ test_names = ['versions', 'hg_fetch', 'mirror', 'url_extrapolate', - 'cc'] + 'cc', + 'link_tree'] def list_tests(): diff --git a/lib/spack/spack/test/git_fetch.py b/lib/spack/spack/test/git_fetch.py index f6d9bfcf05..04422adb57 100644 --- a/lib/spack/spack/test/git_fetch.py +++ b/lib/spack/spack/test/git_fetch.py @@ -61,7 +61,7 @@ class GitFetchTest(MockPackagesTest): if self.repo.stage is not None: self.repo.stage.destroy() - self.pkg.do_clean_dist() + self.pkg.do_clean() def assert_rev(self, rev): @@ -93,7 +93,7 @@ class GitFetchTest(MockPackagesTest): untracked_file = 'foobarbaz' touch(untracked_file) self.assertTrue(os.path.isfile(untracked_file)) - self.pkg.do_clean_work() + self.pkg.do_restage() self.assertFalse(os.path.isfile(untracked_file)) self.assertTrue(os.path.isdir(self.pkg.stage.source_path)) diff --git a/lib/spack/spack/test/hg_fetch.py b/lib/spack/spack/test/hg_fetch.py index 97c5b665e7..e1ab2cffe6 100644 --- a/lib/spack/spack/test/hg_fetch.py +++ b/lib/spack/spack/test/hg_fetch.py @@ -60,7 +60,7 @@ class HgFetchTest(MockPackagesTest): if self.repo.stage is not None: self.repo.stage.destroy() - self.pkg.do_clean_dist() + self.pkg.do_clean() def try_fetch(self, rev, test_file, args): @@ -87,7 +87,7 @@ class HgFetchTest(MockPackagesTest): untracked = 'foobarbaz' touch(untracked) self.assertTrue(os.path.isfile(untracked)) - self.pkg.do_clean_work() + self.pkg.do_restage() self.assertFalse(os.path.isfile(untracked)) self.assertTrue(os.path.isdir(self.pkg.stage.source_path)) diff --git a/lib/spack/spack/test/link_tree.py b/lib/spack/spack/test/link_tree.py new file mode 100644 index 0000000000..bc7c2c6b5e --- /dev/null +++ b/lib/spack/spack/test/link_tree.py @@ -0,0 +1,153 @@ +############################################################################## +# Copyright (c) 2013, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://scalability-llnl.github.io/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License (as published by +# the Free Software Foundation) version 2.1 dated February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import os +import unittest +import shutil +import tempfile +from contextlib import closing + +from llnl.util.filesystem import * +from llnl.util.link_tree import LinkTree + +from spack.stage import Stage + + +class LinkTreeTest(unittest.TestCase): + """Tests Spack's LinkTree class.""" + + def setUp(self): + self.stage = Stage('link-tree-test') + + with working_dir(self.stage.path): + touchp('source/1') + touchp('source/a/b/2') + touchp('source/a/b/3') + touchp('source/c/4') + touchp('source/c/d/5') + touchp('source/c/d/6') + touchp('source/c/d/e/7') + + source_path = os.path.join(self.stage.path, 'source') + self.link_tree = LinkTree(source_path) + + + def tearDown(self): + if self.stage: + self.stage.destroy() + + + def check_file_link(self, filename): + self.assertTrue(os.path.isfile(filename)) + self.assertTrue(os.path.islink(filename)) + + + def check_dir(self, filename): + self.assertTrue(os.path.isdir(filename)) + + + def test_merge_to_new_directory(self): + with working_dir(self.stage.path): + self.link_tree.merge('dest') + + self.check_file_link('dest/1') + self.check_file_link('dest/a/b/2') + self.check_file_link('dest/a/b/3') + self.check_file_link('dest/c/4') + self.check_file_link('dest/c/d/5') + self.check_file_link('dest/c/d/6') + self.check_file_link('dest/c/d/e/7') + + self.link_tree.unmerge('dest') + + self.assertFalse(os.path.exists('dest')) + + + def test_merge_to_existing_directory(self): + with working_dir(self.stage.path): + + touchp('dest/x') + touchp('dest/a/b/y') + + self.link_tree.merge('dest') + + self.check_file_link('dest/1') + self.check_file_link('dest/a/b/2') + self.check_file_link('dest/a/b/3') + self.check_file_link('dest/c/4') + self.check_file_link('dest/c/d/5') + self.check_file_link('dest/c/d/6') + self.check_file_link('dest/c/d/e/7') + + self.assertTrue(os.path.isfile('dest/x')) + self.assertTrue(os.path.isfile('dest/a/b/y')) + + self.link_tree.unmerge('dest') + + self.assertTrue(os.path.isfile('dest/x')) + self.assertTrue(os.path.isfile('dest/a/b/y')) + + self.assertFalse(os.path.isfile('dest/1')) + self.assertFalse(os.path.isfile('dest/a/b/2')) + self.assertFalse(os.path.isfile('dest/a/b/3')) + self.assertFalse(os.path.isfile('dest/c/4')) + self.assertFalse(os.path.isfile('dest/c/d/5')) + self.assertFalse(os.path.isfile('dest/c/d/6')) + self.assertFalse(os.path.isfile('dest/c/d/e/7')) + + + def test_merge_with_empty_directories(self): + with working_dir(self.stage.path): + mkdirp('dest/f/g') + mkdirp('dest/a/b/h') + + self.link_tree.merge('dest') + self.link_tree.unmerge('dest') + + self.assertFalse(os.path.exists('dest/1')) + self.assertFalse(os.path.exists('dest/a/b/2')) + self.assertFalse(os.path.exists('dest/a/b/3')) + self.assertFalse(os.path.exists('dest/c/4')) + self.assertFalse(os.path.exists('dest/c/d/5')) + self.assertFalse(os.path.exists('dest/c/d/6')) + self.assertFalse(os.path.exists('dest/c/d/e/7')) + + self.assertTrue(os.path.isdir('dest/a/b/h')) + self.assertTrue(os.path.isdir('dest/f/g')) + + + def test_ignore(self): + with working_dir(self.stage.path): + touchp('source/.spec') + touchp('dest/.spec') + + self.link_tree.merge('dest', ignore=lambda x: x == '.spec') + self.link_tree.unmerge('dest', ignore=lambda x: x == '.spec') + + self.assertFalse(os.path.exists('dest/1')) + self.assertFalse(os.path.exists('dest/a')) + self.assertFalse(os.path.exists('dest/c')) + + self.assertTrue(os.path.isfile('source/.spec')) + self.assertTrue(os.path.isfile('dest/.spec')) diff --git a/lib/spack/spack/test/svn_fetch.py b/lib/spack/spack/test/svn_fetch.py index a48a86dcc3..0159fb087f 100644 --- a/lib/spack/spack/test/svn_fetch.py +++ b/lib/spack/spack/test/svn_fetch.py @@ -60,7 +60,7 @@ class SvnFetchTest(MockPackagesTest): if self.repo.stage is not None: self.repo.stage.destroy() - self.pkg.do_clean_dist() + self.pkg.do_clean() def assert_rev(self, rev): @@ -99,7 +99,7 @@ class SvnFetchTest(MockPackagesTest): untracked = 'foobarbaz' touch(untracked) self.assertTrue(os.path.isfile(untracked)) - self.pkg.do_clean_work() + self.pkg.do_restage() self.assertFalse(os.path.isfile(untracked)) self.assertTrue(os.path.isdir(self.pkg.stage.source_path)) diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index 91b1dc4630..b2bcbaf6c7 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -165,8 +165,8 @@ fi # # Set up modules and dotkit search paths in the user environment # -_sp_share_dir="$(dirname $_sp_source_file)" -_sp_prefix="$(dirname $(dirname $_sp_share_dir))" +_sp_share_dir=$(cd "$(dirname $_sp_source_file)" && pwd) +_sp_prefix=$(cd "$(dirname $(dirname $_sp_share_dir))" && pwd) # TODO: fix SYS_TYPE to something non-LLNL-specific _spack_pathadd DK_NODE "$_sp_share_dir/dotkit/$SYS_TYPE" diff --git a/var/spack/packages/ImageMagick/package.py b/var/spack/packages/ImageMagick/package.py index 657b9255a3..753ea80ca6 100644 --- a/var/spack/packages/ImageMagick/package.py +++ b/var/spack/packages/ImageMagick/package.py @@ -3,18 +3,32 @@ from spack import * class Imagemagick(Package): """ImageMagick is a image processing library""" homepage = "http://www.imagemagic.org" - url = "http://www.imagemagick.org/download/ImageMagick-6.8.9-10.tar.gz" - version('6.9.0-0', '2cf094cb86ec518fa5bc669ce2d21613') - version('6.8.9-10', 'aa050bf9785e571c956c111377bbf57c') - version('6.8.9-9', 'e63fed3e3550851328352c708f800676') + #------------------------------------------------------------------------- + # ImageMagick does not keep around anything but *-10 versions, so + # this URL may change. If you want the bleeding edge, you can + # uncomment it and see if it works but you may need to try to + # fetch a newer version (-6, -7, -8, -9, etc.) or you can stick + # wtih the older, stable, archived -10 versions below. + # + # TODO: would be nice if spack had a way to recommend avoiding a + # TODO: bleeding edge version, but not comment it out. + # ------------------------------------------------------------------------- + # version('6.9.0-6', 'c1bce7396c22995b8bdb56b7797b4a1b', + # url="http://www.imagemagick.org/download/ImageMagick-6.9.0-6.tar.bz2") + + #------------------------------------------------------------------------- + # *-10 versions are archived, so these versions should fetch reliably. + # ------------------------------------------------------------------------- + version('6.8.9-10', 'aa050bf9785e571c956c111377bbf57c', + url="http://sourceforge.net/projects/imagemagick/files/old-sources/6.x/6.8/ImageMagick-6.8.9-10.tar.gz/download") depends_on('libtool') depends_on('jpeg') depends_on('libpng') depends_on('freetype') depends_on('fontconfig') -# depends_on('libtiff') + depends_on('libtiff') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/packages/Mitos/package.py b/var/spack/packages/Mitos/package.py new file mode 100644 index 0000000000..272360a55c --- /dev/null +++ b/var/spack/packages/Mitos/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Mitos(Package): + """Mitos is a library and a tool for collecting sampled memory + performance data to view with MemAxes""" + + homepage = "https://github.com/scalability-llnl/Mitos" + url = "https://github.com/scalability-llnl/Mitos" + + version('0.7', git='https://github.com/scalability-llnl/Mitos.git', tag='v0.7') + + depends_on('dyninst') + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', *std_cmake_args) + make() + make("install") diff --git a/var/spack/packages/R/package.py b/var/spack/packages/R/package.py new file mode 100644 index 0000000000..2e6f65a742 --- /dev/null +++ b/var/spack/packages/R/package.py @@ -0,0 +1,33 @@ +from spack import * + +class R(Package): + """R is 'GNU S', a freely available language and environment for + statistical computing and graphics which provides a wide va + riety of statistical and graphical techniques: linear and + nonlinear modelling, statistical tests, time series analysis, + classification, clustering, etc. Please consult the R project + homepage for further information.""" + homepage = "http://www.example.com" + url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz" + + version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74') + + depends_on("readline") + depends_on("ncurses") + depends_on("icu") + depends_on("glib") + depends_on("zlib") + depends_on("libtiff") + depends_on("jpeg") + depends_on("cairo") + depends_on("pango") + depends_on("freetype") + depends_on("tcl") + depends_on("tk") + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix, + "--enable-R-shlib", + "--enable-BLAS-shlib") + make() + make("install") diff --git a/var/spack/packages/bison/package.py b/var/spack/packages/bison/package.py new file mode 100644 index 0000000000..7c526fb958 --- /dev/null +++ b/var/spack/packages/bison/package.py @@ -0,0 +1,17 @@ +from spack import * + +class Bison(Package): + """Bison is a general-purpose parser generator that converts + an annotated context-free grammar into a deterministic LR or + generalized LR (GLR) parser employing LALR(1) parser tables.""" + + homepage = "http://www.gnu.org/software/bison/" + url = "http://ftp.gnu.org/gnu/bison/bison-3.0.tar.gz" + + version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/clang/package.py b/var/spack/packages/clang/package.py index b0097bd126..4f10385dbd 100644 --- a/var/spack/packages/clang/package.py +++ b/var/spack/packages/clang/package.py @@ -29,11 +29,10 @@ class Clang(Package): Objective C and Objective C++ front-end for the LLVM compiler. """ homepage = "http://clang.llvm.org" - url = "http://llvm.org/releases/3.4.2/cfe-3.4.2.src.tar.gz" + list_url = "http://llvm.org/releases/download.html" depends_on("llvm") - - version('3.4.2', '87945973b7c73038871c5f849a818588') + version('3.4.2', '87945973b7c73038871c5f849a818588', url='http://llvm.org/releases/3.4.2/cfe-3.4.2.src.tar.xz') def install(self, spec, prefix): env['CXXFLAGS'] = self.compiler.cxx11_flag diff --git a/var/spack/packages/dbus/package.py b/var/spack/packages/dbus/package.py index 5fee103f03..f7f394498c 100644 --- a/var/spack/packages/dbus/package.py +++ b/var/spack/packages/dbus/package.py @@ -23,3 +23,7 @@ class Dbus(Package): configure("--prefix=%s" % prefix) make() make("install") + + # dbus needs a machine id generated after install + dbus_uuidgen = Executable(join_path(prefix.bin, 'dbus-uuidgen')) + dbus_uuidgen('--ensure') diff --git a/var/spack/packages/dri2proto/package.py b/var/spack/packages/dri2proto/package.py new file mode 100644 index 0000000000..11dfa568e2 --- /dev/null +++ b/var/spack/packages/dri2proto/package.py @@ -0,0 +1,14 @@ +from spack import * + +class Dri2proto(Package): + """DRI2 Protocol Headers.""" + homepage = "http://http://cgit.freedesktop.org/xorg/proto/dri2proto/" + url = "http://xorg.freedesktop.org/releases/individual/proto/dri2proto-2.8.tar.gz" + + version('2.8', '19ea18f63d8ae8053c9fa84b60365b77') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/dyninst/package.py b/var/spack/packages/dyninst/package.py index 2e6f3e010a..f3d661f9a9 100644 --- a/var/spack/packages/dyninst/package.py +++ b/var/spack/packages/dyninst/package.py @@ -31,8 +31,9 @@ class Dyninst(Package): url = "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.1.2/DyninstAPI-8.1.2.tgz" list_url = "http://www.dyninst.org/downloads/dyninst-8.x" - version('8.2.1', 'abf60b7faabe7a2e4b54395757be39c7', - url="http://www.paradyn.org/release8.2/DyninstAPI-8.2.1.tgz") +# Doesn't build right with boost@1.55.0 +# version('8.2.1', 'abf60b7faabe7a2e4b54395757be39c7', +# url="http://www.paradyn.org/release8.2/DyninstAPI-8.2.1.tgz") version('8.1.2', 'bf03b33375afa66fe0efa46ce3f4b17a', url="http://www.paradyn.org/release8.1.2/DyninstAPI-8.1.2.tgz") version('8.1.1', 'd1a04e995b7aa70960cd1d1fac8bd6ac', @@ -40,7 +41,7 @@ class Dyninst(Package): depends_on("libelf") depends_on("libdwarf") - depends_on("boost@1.42:1.43") + depends_on("boost@1.42:") # new version uses cmake def install(self, spec, prefix): diff --git a/var/spack/packages/flex/package.py b/var/spack/packages/flex/package.py new file mode 100644 index 0000000000..b065904912 --- /dev/null +++ b/var/spack/packages/flex/package.py @@ -0,0 +1,15 @@ +from spack import * + +class Flex(Package): + """Flex is a tool for generating scanners.""" + + homepage = "http://flex.sourceforge.net/" + url = "http://download.sourceforge.net/flex/flex-2.5.39.tar.gz" + + version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/geos/package.py b/var/spack/packages/geos/package.py new file mode 100644 index 0000000000..4a2657e32f --- /dev/null +++ b/var/spack/packages/geos/package.py @@ -0,0 +1,31 @@ +from spack import * + +class Geos(Package): + """GEOS (Geometry Engine - Open Source) is a C++ port of the Java + Topology Suite (JTS). As such, it aims to contain the complete + functionality of JTS in C++. This includes all the OpenGIS + Simple Features for SQL spatial predicate functions and spatial + operators, as well as specific JTS enhanced topology functions.""" + + homepage = "http://trac.osgeo.org/geos/" + url = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2" + + version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae') + version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e') + version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488') + version('3.3.9', '4794c20f07721d5011c93efc6ccb8e4e') + version('3.3.8', '75be476d0831a2d14958fed76ca266de') + version('3.3.7', '95ab996d22672b067d92c7dee2170460') + version('3.3.6', '6fadfb941541875f4976f75fb0bbc800') + version('3.3.5', '2ba61afb7fe2c5ddf642d82d7b16e75b') + version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1') + version('3.3.3', '8454e653d7ecca475153cc88fd1daa26') + + extends('python') + depends_on('swig') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix, + "--enable-python") + make() + make("install") diff --git a/var/spack/packages/gperf/package.py b/var/spack/packages/gperf/package.py new file mode 100644 index 0000000000..32551b67b4 --- /dev/null +++ b/var/spack/packages/gperf/package.py @@ -0,0 +1,19 @@ +from spack import * + +class Gperf(Package): + """GNU gperf is a perfect hash function generator. For a given + list of strings, it produces a hash function and hash table, in + form of C or C++ code, for looking up a value depending on the + input string. The hash function is perfect, which means that the + hash table has no collisions, and the hash table lookup needs a + single string comparison only.""" + + homepage = "https://www.gnu.org/software/gperf/" + url = "http://ftp.gnu.org/pub/gnu/gperf/gperf-3.0.4.tar.gz" + + version('3.0.4', 'c1f1db32fb6598d6a93e6e88796a8632') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/packages/hdf5/package.py b/var/spack/packages/hdf5/package.py index 615c2a7fe4..992dd8ec70 100644 --- a/var/spack/packages/hdf5/package.py +++ b/var/spack/packages/hdf5/package.py @@ -18,12 +18,14 @@ class Hdf5(Package): # TODO: currently hard-coded to use OpenMPI def install(self, spec, prefix): + configure( "--prefix=%s" % prefix, "--with-zlib=%s" % spec['zlib'].prefix, "--enable-parallel", - "CC=%s" % spec['openmpi'].prefix.bin + "/mpicc", - "CXX=%s" % spec['openmpi'].prefix.bin + "/mpic++") + "--enable-shared", + "CC=%s" % spec['mpich'].prefix.bin + "/mpicc", + "CXX=%s" % spec['mpich'].prefix.bin + "/mpic++") make() make("install") diff --git a/var/spack/packages/icu4c/package.py b/var/spack/packages/icu4c/package.py new file mode 100644 index 0000000000..55b44463b2 --- /dev/null +++ b/var/spack/packages/icu4c/package.py @@ -0,0 +1,17 @@ +from spack import * + +class Icu4c(Package): + """ICU is a mature, widely used set of C/C++ and Java libraries + providing Unicode and Globalization support for software applications.""" + + homepage = "http://site.icu-project.org/" + url = "http://downloads.sourceforge.net/project/icu/ICU4C/54.1/icu4c-54_1-src.tgz" + + version('54_1', 'e844caed8f2ca24c088505b0d6271bc0') + + def install(self, spec, prefix): + cd("source") + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/libdrm/package.py b/var/spack/packages/libdrm/package.py new file mode 100644 index 0000000000..00736b7811 --- /dev/null +++ b/var/spack/packages/libdrm/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Libdrm(Package): + """A userspace library for accessing the DRM, direct + rendering manager, on Linux, BSD and other operating + systems that support the ioctl interface.""" + + homepage = "http://dri.freedesktop.org/libdrm/" # no real website... + url = "http://dri.freedesktop.org/libdrm/libdrm-2.4.59.tar.gz" + + version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6') + version('2.4.33', '86e4e3debe7087d5404461e0032231c8') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/libdwarf/package.py b/var/spack/packages/libdwarf/package.py index c4d71ebc01..099a974e93 100644 --- a/var/spack/packages/libdwarf/package.py +++ b/var/spack/packages/libdwarf/package.py @@ -53,13 +53,6 @@ class Libdwarf(Package): parallel = False - def clean(self): - for dir in dwarf_dirs: - with working_dir(dir): - if os.path.exists('Makefile'): - make('clean') - - def install(self, spec, prefix): # dwarf build does not set arguments for ar properly make.add_default_arg('ARFLAGS=rcs') diff --git a/var/spack/packages/libgcrypt/package.py b/var/spack/packages/libgcrypt/package.py new file mode 100644 index 0000000000..1d0a57f317 --- /dev/null +++ b/var/spack/packages/libgcrypt/package.py @@ -0,0 +1,19 @@ +from spack import * + +class Libgcrypt(Package): + """Libgcrypt is a general purpose cryptographic library based on + the code from GnuPG. It provides functions for all cryptographic + building blocks: symmetric ciphers, hash algorithms, MACs, public + key algorithms, large integer functions, random numbers and a lot + of supporting functions. """ + homepage = "http://www.gnu.org/software/libgcrypt/" + url = "ftp://ftp.gnupg.org/gcrypt/libgcrypt/libgcrypt-1.6.2.tar.bz2" + + version('1.6.2', 'b54395a93cb1e57619943c082da09d5f') + + depends_on("libgpg-error") + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/packages/libgpg-error/package.py b/var/spack/packages/libgpg-error/package.py new file mode 100644 index 0000000000..6c1d1a10a7 --- /dev/null +++ b/var/spack/packages/libgpg-error/package.py @@ -0,0 +1,17 @@ +from spack import * + +class LibgpgError(Package): + """Libgpg-error is a small library that defines common error + values for all GnuPG components. Among these are GPG, GPGSM, + GPGME, GPG-Agent, libgcrypt, Libksba, DirMngr, Pinentry, + SmartCard Daemon and possibly more in the future. """ + + homepage = "https://www.gnupg.org/related_software/libgpg-error" + url = "ftp://ftp.gnupg.org/gcrypt/libgpg-error/libgpg-error-1.18.tar.bz2" + + version('1.18', '12312802d2065774b787cbfc22cc04e9') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/packages/libpng/package.py b/var/spack/packages/libpng/package.py index c148a3d58c..e02b08663e 100644 --- a/var/spack/packages/libpng/package.py +++ b/var/spack/packages/libpng/package.py @@ -5,9 +5,9 @@ class Libpng(Package): homepage = "http://www.libpng.org/pub/png/libpng.html" url = "http://download.sourceforge.net/libpng/libpng-1.6.16.tar.gz" - version('1.6.14', '2101b3de1d5f348925990f9aa8405660') - version('1.6.15', '829a256f3de9307731d4f52dc071916d') version('1.6.16', '1a4ad377919ab15b54f6cb6a3ae2622d') + version('1.6.15', '829a256f3de9307731d4f52dc071916d') + version('1.6.14', '2101b3de1d5f348925990f9aa8405660') def install(self, spec, prefix): configure("--prefix=%s" % prefix) diff --git a/var/spack/packages/libxcb/package.py b/var/spack/packages/libxcb/package.py new file mode 100644 index 0000000000..521cd0d475 --- /dev/null +++ b/var/spack/packages/libxcb/package.py @@ -0,0 +1,21 @@ +from spack import * + +class Libxcb(Package): + """The X protocol C-language Binding (XCB) is a replacement + for Xlib featuring a small footprint, latency hiding, direct + access to the protocol, improved threading support, and + extensibility.""" + + homepage = "http://xcb.freedesktop.org/" + url = "http://xcb.freedesktop.org/dist/libxcb-1.11.tar.gz" + + version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb') + + depends_on("python") + depends_on("xcb-proto") + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/libxml2/package.py b/var/spack/packages/libxml2/package.py index 5eaed36d94..72199d8def 100644 --- a/var/spack/packages/libxml2/package.py +++ b/var/spack/packages/libxml2/package.py @@ -9,6 +9,9 @@ class Libxml2(Package): version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788') + depends_on('zlib') + depends_on('xz') + def install(self, spec, prefix): configure("--prefix=%s" % prefix, "--without-python") diff --git a/var/spack/packages/libxshmfence/package.py b/var/spack/packages/libxshmfence/package.py new file mode 100644 index 0000000000..3aa2448b46 --- /dev/null +++ b/var/spack/packages/libxshmfence/package.py @@ -0,0 +1,16 @@ +from spack import * + +class Libxshmfence(Package): + """This is a tiny library that exposes a event API on top of Linux + futexes.""" + + homepage = "http://keithp.com/blogs/dri3_extension/" # not really... + url = "http://xorg.freedesktop.org/archive/individual/lib/libxshmfence-1.2.tar.gz" + + version('1.2', 'f0b30c0fc568b22ec524859ee28556f1') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/libxslt/package.py b/var/spack/packages/libxslt/package.py new file mode 100644 index 0000000000..f97332d020 --- /dev/null +++ b/var/spack/packages/libxslt/package.py @@ -0,0 +1,24 @@ +from spack import * + +class Libxslt(Package): + """Libxslt is the XSLT C library developed for the GNOME + project. XSLT itself is a an XML language to define + transformation for XML. Libxslt is based on libxml2 the XML C + library developed for the GNOME project. It also implements + most of the EXSLT set of processor-portable extensions + functions and some of Saxon's evaluate and expressions + extensions.""" + homepage = "http://www.xmlsoft.org/XSLT/index.html" + url = "http://xmlsoft.org/sources/libxslt-1.1.28.tar.gz" + + version('1.1.28', '9667bf6f9310b957254fdcf6596600b7') + + depends_on("libxml2") + depends_on("xz") + depends_on("zlib") + depends_on("libgcrypt") + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/packages/llvm/package.py b/var/spack/packages/llvm/package.py index c7a10df55a..9d2be690bb 100644 --- a/var/spack/packages/llvm/package.py +++ b/var/spack/packages/llvm/package.py @@ -32,9 +32,13 @@ class Llvm(Package): it is the full name of the project. """ homepage = "http://llvm.org/" - url = "http://llvm.org/releases/3.4.2/llvm-3.4.2.src.tar.gz" + list_url = "http://llvm.org/releases/download.html" - version('3.4.2', 'a20669f75967440de949ac3b1bad439c') + version('3.5.1', '2d3d8004f38852aa679e5945b8ce0b14', url='http://llvm.org/releases/3.5.1/llvm-3.5.1.src.tar.xz') + version('3.4.2', 'a20669f75967440de949ac3b1bad439c', url='http://llvm.org/releases/3.4.2/llvm-3.4.2.src.tar.gz') + version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') + version('2.9', '793138412d2af2c7c7f54615f8943771', url='http://llvm.org/releases/2.9/llvm-2.9.tgz') + version('2.8', '220d361b4d17051ff4bb21c64abe05ba', url='http://llvm.org/releases/2.8/llvm-2.8.tgz') def install(self, spec, prefix): env['CXXFLAGS'] = self.compiler.cxx11_flag diff --git a/var/spack/packages/memaxes/package.py b/var/spack/packages/memaxes/package.py new file mode 100644 index 0000000000..afa62009a6 --- /dev/null +++ b/var/spack/packages/memaxes/package.py @@ -0,0 +1,20 @@ +from spack import * + +class Memaxes(Package): + """MemAxes is a visualizer for sampled memory trace data.""" + + homepage = "https://github.com/scalability-llnl/MemAxes" + + version('0.5', 'b0f561d48aa7301e028d074bc4b5751b', + url='https://github.com/scalability-llnl/MemAxes/archive/v0.5.tar.gz') + + depends_on("cmake@2.8.9:") + depends_on("qt@5:") + depends_on("vtk") + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', *std_cmake_args) + make() + make("install") + diff --git a/var/spack/packages/mesa/package.py b/var/spack/packages/mesa/package.py new file mode 100644 index 0000000000..2dba878a77 --- /dev/null +++ b/var/spack/packages/mesa/package.py @@ -0,0 +1,33 @@ +from spack import * + +class Mesa(Package): + """Mesa is an open-source implementation of the OpenGL + specification - a system for rendering interactive 3D graphics.""" + + homepage = "http://www.mesa3d.org" + url = "ftp://ftp.freedesktop.org/pub/mesa/older-versions/8.x/8.0.5/MesaLib-8.0.5.tar.gz" + # url = "ftp://ftp.freedesktop.org/pub/mesa/10.4.4/MesaLib-10.4.4.tar.gz" + + # version('10.4.4', '8d863a3c209bf5116b2babfccccc68ce') + version('8.0.5', 'cda5d101f43b8784fa60bdeaca4056f2') + + # mesa 7.x, 8.x, 9.x + depends_on("libdrm@2.4.33") + depends_on("llvm@3.0") + + # patch("llvm-fixes.patch") # using newer llvm + + # mesa 10.x + # depends_on("py-mako") + # depends_on("flex") + # depends_on("bison") + # depends_on("dri2proto") + # depends_on("libxcb") + # depends_on("libxshmfence") + + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/netcdf/package.py b/var/spack/packages/netcdf/package.py new file mode 100644 index 0000000000..34284ea725 --- /dev/null +++ b/var/spack/packages/netcdf/package.py @@ -0,0 +1,28 @@ +from spack import * + +class Netcdf(Package): + """NetCDF is a set of software libraries and self-describing, machine-independent + data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + + homepage = "http://www.unidata.ucar.edu/software/netcdf/" + url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz" + + version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae') + + # Dependencies: + # >HDF5 + depends_on("hdf5") + + def install(self, spec, prefix): + configure( + "--prefix=%s" % prefix, + "--disable-dap", # Disable DAP. + "--disable-shared", # Don't build shared libraries (use static libs). + "CPPFLAGS=-I%s/include" % spec['hdf5'].prefix, # Link HDF5's include dir. + "LDFLAGS=-L%s/lib" % spec['hdf5'].prefix) # Link HDF5's lib dir. + + make("install") + + # Check the newly installed netcdf package. Currently disabled. + # make("check") diff --git a/var/spack/packages/py-basemap/package.py b/var/spack/packages/py-basemap/package.py new file mode 100644 index 0000000000..45f1085ba1 --- /dev/null +++ b/var/spack/packages/py-basemap/package.py @@ -0,0 +1,20 @@ +from spack import * +import os + +class PyBasemap(Package): + """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python.""" + homepage = "http://matplotlib.org/basemap/" + url = "https://downloads.sourceforge.net/project/matplotlib/matplotlib-toolkits/basemap-1.0.7/basemap-1.0.7.tar.gz" + + version('1.0.7', '48c0557ced9e2c6e440b28b3caff2de8') + + extends('python') + depends_on('py-setuptools') + depends_on('py-numpy') + depends_on('py-matplotlib') + depends_on('py-pil') + depends_on("geos") + + def install(self, spec, prefix): + env['GEOS_DIR'] = spec['geos'].prefix + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-biopython/package.py b/var/spack/packages/py-biopython/package.py new file mode 100644 index 0000000000..8ecaf48626 --- /dev/null +++ b/var/spack/packages/py-biopython/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyBiopython(Package): + """It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.""" + homepage = "http://biopython.org/wiki/Main_Page" + url = "http://biopython.org/DIST/biopython-1.65.tar.gz" + + version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67') + + extends('python') + depends_on('py-mx') + depends_on('py-numpy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-cython/package.py b/var/spack/packages/py-cython/package.py new file mode 100644 index 0000000000..af67a15526 --- /dev/null +++ b/var/spack/packages/py-cython/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyCython(Package): + """The Cython compiler for writing C extensions for the Python language.""" + homepage = "https://pypi.python.org/pypi/cython" + url = "https://pypi.python.org/packages/source/C/Cython/Cython-0.21.2.tar.gz" + + version('0.21.2', 'd21adb870c75680dc857cd05d41046a4') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-dateutil/package.py b/var/spack/packages/py-dateutil/package.py new file mode 100644 index 0000000000..3bd2f2ca13 --- /dev/null +++ b/var/spack/packages/py-dateutil/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyDateutil(Package): + """Extensions to the standard Python datetime module.""" + homepage = "https://pypi.python.org/pypi/dateutil" + url = "https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.4.0.tar.gz" + + version('2.4.0', '75714163bb96bedd07685cdb2071b8bc') + + extends('python') + depends_on('py-setuptools') + depends_on('py-six') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-epydoc/package.py b/var/spack/packages/py-epydoc/package.py new file mode 100644 index 0000000000..af05510504 --- /dev/null +++ b/var/spack/packages/py-epydoc/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyEpydoc(Package): + """Epydoc is a tool for generating API documentation documentation for Python modules, based on their docstrings.""" + homepage = "https://pypi.python.org/pypi/epydoc" + url = "https://pypi.python.org/packages/source/e/epydoc/epydoc-3.0.1.tar.gz" + + version('3.0.1', '36407974bd5da2af00bf90ca27feeb44') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-gnuplot/package.py b/var/spack/packages/py-gnuplot/package.py new file mode 100644 index 0000000000..ede4472c03 --- /dev/null +++ b/var/spack/packages/py-gnuplot/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyGnuplot(Package): + """Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplot plotting program.""" + homepage = "http://gnuplot-py.sourceforge.net/" + url = "http://downloads.sourceforge.net/project/gnuplot-py/Gnuplot-py/1.8/gnuplot-py-1.8.tar.gz" + + version('1.8', 'abd6f571e7aec68ae7db90a5217cd5b1') + + extends('python') + depends_on('py-numpy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-h5py/package.py b/var/spack/packages/py-h5py/package.py new file mode 100644 index 0000000000..f72b3ac06e --- /dev/null +++ b/var/spack/packages/py-h5py/package.py @@ -0,0 +1,18 @@ +from spack import * +import re + +class PyH5py(Package): + """The h5py package provides both a high- and low-level interface to the HDF5 library from Python.""" + homepage = "https://pypi.python.org/pypi/h5py" + url = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz" + + version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758') + + extends('python', ignore=lambda f: re.match(r'cy*', f)) + depends_on('hdf5') + depends_on('py-numpy') + depends_on('py-cython') + + def install(self, spec, prefix): + python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix) + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-ipython/package.py b/var/spack/packages/py-ipython/package.py new file mode 100644 index 0000000000..907ea9edcd --- /dev/null +++ b/var/spack/packages/py-ipython/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyIpython(Package): + """IPython provides a rich toolkit to help you make the most out of using Python interactively.""" + homepage = "https://pypi.python.org/pypi/ipython" + url = "https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz" + + version('2.3.1', '2b7085525dac11190bfb45bb8ec8dcbf') + + extends('python') + depends_on('py-pygments') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-libxml2/package.py b/var/spack/packages/py-libxml2/package.py new file mode 100644 index 0000000000..59005428e4 --- /dev/null +++ b/var/spack/packages/py-libxml2/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyLibxml2(Package): + """A Python wrapper around libxml2.""" + homepage = "https://xmlsoft.org/python.html" + url = "ftp://xmlsoft.org/libxml2/python/libxml2-python-2.6.21.tar.gz" + + version('2.6.21', '229dd2b3d110a77defeeaa73af83f7f3') + + extends('python') + depends_on('libxml2') + depends_on('libxslt') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-mako/package.py b/var/spack/packages/py-mako/package.py new file mode 100644 index 0000000000..3e91ffd8e5 --- /dev/null +++ b/var/spack/packages/py-mako/package.py @@ -0,0 +1,16 @@ +from spack import * + +class PyMako(Package): + """A super-fast templating language that borrows the best + ideas from the existing templating languages.""" + + homepage = "https://pypi.python.org/pypi/mako" + url = "https://pypi.python.org/packages/source/M/Mako/Mako-1.0.1.tar.gz" + + version('1.0.1', '9f0aafd177b039ef67b90ea350497a54') + + depends_on('py-setuptools') + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-matplotlib/package.py b/var/spack/packages/py-matplotlib/package.py new file mode 100644 index 0000000000..04037f004e --- /dev/null +++ b/var/spack/packages/py-matplotlib/package.py @@ -0,0 +1,46 @@ +from spack import * +import os + +class PyMatplotlib(Package): + """Python plotting package.""" + homepage = "https://pypi.python.org/pypi/matplotlib" + url = "https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.4.2.tar.gz" + + version('1.4.2', '7d22efb6cce475025733c50487bd8898') + + extends('python', ignore=r'bin/nosetests.*$') + + depends_on('py-pyside') + depends_on('py-ipython') + depends_on('py-pyparsing') + depends_on('py-six') + depends_on('py-dateutil') + depends_on('py-pytz') + depends_on('py-nose') + depends_on('py-numpy') + + depends_on('qt') + depends_on('bzip2') + depends_on('tcl') + depends_on('tk') + depends_on('qhull') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) + + if str(self.version) == '1.4.2': + # hack to fix configuration file + config_file = None + for p,d,f in os.walk(prefix.lib): + for file in f: + if file.find('matplotlibrc') != -1: + config_file = join_path(p, 'matplotlibrc') + print config_file + if config_file == None: + raise InstallError('could not find config file') + filter_file(r'backend : pyside', + 'backend : Qt4Agg', + config_file) + filter_file(r'#backend.qt4 : PyQt4', + 'backend.qt4 : PySide', + config_file) diff --git a/var/spack/packages/py-mpi4py/package.py b/var/spack/packages/py-mpi4py/package.py new file mode 100644 index 0000000000..8001689a18 --- /dev/null +++ b/var/spack/packages/py-mpi4py/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyMpi4py(Package): + """This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.""" + homepage = "https://pypi.python.org/pypi/mpi4py" + url = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz" + + version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c') + extends('python') + depends_on('py-setuptools') + depends_on('mpi') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-mx/package.py b/var/spack/packages/py-mx/package.py new file mode 100644 index 0000000000..717ee0562b --- /dev/null +++ b/var/spack/packages/py-mx/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyMx(Package): + """The eGenix.com mx Base Distribution for Python is a collection of professional quality software tools which enhance Python's usability in many important areas such as fast text searching, date/time processing and high speed data types.""" + homepage = "http://www.egenix.com/products/python/mxBase/" + url = "https://downloads.egenix.com/python/egenix-mx-base-3.2.8.tar.gz" + + version('3.2.8', '9d9d3a25f9dc051a15e97f452413423b') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-nose/package.py b/var/spack/packages/py-nose/package.py new file mode 100644 index 0000000000..155019289d --- /dev/null +++ b/var/spack/packages/py-nose/package.py @@ -0,0 +1,16 @@ +from spack import * + +class PyNose(Package): + """nose extends the test loading and running features of unittest, + making it easier to write, find and run tests.""" + + homepage = "https://pypi.python.org/pypi/nose" + url = "https://pypi.python.org/packages/source/n/nose/nose-1.3.4.tar.gz" + + version('1.3.4', '6ed7169887580ddc9a8e16048d38274d') + + extends('python', ignore=r'bin/nosetests.*$') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-numpy/package.py b/var/spack/packages/py-numpy/package.py new file mode 100644 index 0000000000..e6cb6a464f --- /dev/null +++ b/var/spack/packages/py-numpy/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyNumpy(Package): + """array processing for numbers, strings, records, and objects.""" + homepage = "https://pypi.python.org/pypi/numpy" + url = "https://pypi.python.org/packages/source/n/numpy/numpy-1.9.1.tar.gz" + + version('1.9.1', '78842b73560ec378142665e712ae4ad9') + + extends('python') + depends_on('py-nose') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-pexpect/package.py b/var/spack/packages/py-pexpect/package.py new file mode 100644 index 0000000000..ff5fac84e0 --- /dev/null +++ b/var/spack/packages/py-pexpect/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyPexpect(Package): + """Pexpect allows easy control of interactive console applications.""" + homepage = "https://pypi.python.org/pypi/pexpect" + url = "https://pypi.python.org/packages/source/p/pexpect/pexpect-3.3.tar.gz" + + version('3.3', '0de72541d3f1374b795472fed841dce8') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-pil/package.py b/var/spack/packages/py-pil/package.py new file mode 100644 index 0000000000..743b761981 --- /dev/null +++ b/var/spack/packages/py-pil/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyPil(Package): + """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities.""" + + homepage = "http://www.pythonware.com/products/pil/" + url = "http://effbot.org/media/downloads/Imaging-1.1.7.tar.gz" + + version('1.1.7', 'fc14a54e1ce02a0225be8854bfba478e') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-pmw/package.py b/var/spack/packages/py-pmw/package.py new file mode 100644 index 0000000000..56131811e9 --- /dev/null +++ b/var/spack/packages/py-pmw/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyPmw(Package): + """Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts.""" + homepage = "https://pypi.python.org/pypi/Pmw" + url = "https://pypi.python.org/packages/source/P/Pmw/Pmw-2.0.0.tar.gz" + + version('2.0.0', 'c7c3f26c4f5abaa99807edefee578fc0') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-pychecker/package.py b/var/spack/packages/py-pychecker/package.py new file mode 100644 index 0000000000..bda5a746aa --- /dev/null +++ b/var/spack/packages/py-pychecker/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyPychecker(Package): + """""" + homepage = "http://pychecker.sourceforge.net/" + url = "http://sourceforge.net/projects/pychecker/files/pychecker/0.8.19/pychecker-0.8.19.tar.gz" + + version('0.8.19', 'c37182863dfb09209d6ba4f38fce9d2b') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-pygments/package.py b/var/spack/packages/py-pygments/package.py new file mode 100644 index 0000000000..990eebde65 --- /dev/null +++ b/var/spack/packages/py-pygments/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PyPygments(Package): + """Pygments is a syntax highlighting package written in Python.""" + homepage = "https://pypi.python.org/pypi/pygments" + url = "https://pypi.python.org/packages/source/P/Pygments/Pygments-2.0.1.tar.gz" + + version('2.0.1', 'e0daf4c14a4fe5b630da765904de4d6c') + + extends('python') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-pylint/package.py b/var/spack/packages/py-pylint/package.py new file mode 100644 index 0000000000..7a6ee7dbbc --- /dev/null +++ b/var/spack/packages/py-pylint/package.py @@ -0,0 +1,16 @@ +from spack import * +import re + +class PyPylint(Package): + """array processing for numbers, strings, records, and objects.""" + homepage = "https://pypi.python.org/pypi/pylint" + url = "https://pypi.python.org/packages/source/p/pylint/pylint-1.4.1.tar.gz" + + version('1.4.1', 'df7c679bdcce5019389038847e4de622') + + extends('python') + depends_on('py-nose') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-pyparsing/package.py b/var/spack/packages/py-pyparsing/package.py new file mode 100644 index 0000000000..a6e50ad139 --- /dev/null +++ b/var/spack/packages/py-pyparsing/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyPyparsing(Package): + """A Python Parsing Module.""" + homepage = "https://pypi.python.org/pypi/pyparsing" + url = "https://pypi.python.org/packages/source/p/pyparsing/pyparsing-2.0.3.tar.gz" + + version('2.0.3', '0fe479be09fc2cf005f753d3acc35939') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-pyqt/package.py b/var/spack/packages/py-pyqt/package.py new file mode 100644 index 0000000000..8edca105bb --- /dev/null +++ b/var/spack/packages/py-pyqt/package.py @@ -0,0 +1,24 @@ +from spack import * + +class PyPyqt(Package): + """PyQt is a set of Python v2 and v3 bindings for Digia's Qt + application framework and runs on all platforms supported by Qt + including Windows, MacOS/X and Linux.""" + homepage = "http://www.riverbankcomputing.com/software/pyqt/intro" + url = "http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3/PyQt-x11-gpl-4.11.3.tar.gz" + + version('4.11.3', '997c3e443165a89a559e0d96b061bf70') + + extends('python') + depends_on('py-sip') + + # TODO: allow qt5 when conditional deps are supported. + # TODO: Fix version matching so that @4 works like @:4 + depends_on('qt@:4') + + def install(self, spec, prefix): + python('configure.py', + '--confirm-license', + '--destdir=%s' % site_packages_dir) + make() + make('install') diff --git a/var/spack/packages/py-pyside/package.py b/var/spack/packages/py-pyside/package.py new file mode 100644 index 0000000000..bb5da44d02 --- /dev/null +++ b/var/spack/packages/py-pyside/package.py @@ -0,0 +1,45 @@ +from spack import * +import os + +class PyPyside(Package): + """array processing for numbers, strings, records, and objects.""" + homepage = "https://pypi.python.org/pypi/pyside" + url = "https://pypi.python.org/packages/source/P/PySide/PySide-1.2.2.tar.gz" + + version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d') + + # TODO: make build dependency + # depends_on("cmake") + + extends('python') + depends_on('py-setuptools') + depends_on('qt@:4') + + def patch(self): + """Undo PySide RPATH handling and add Spack RPATH.""" + # Figure out the special RPATH + pypkg = self.spec['python'].package + rpath = self.rpath + rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'PySide')) + + # Add Spack's standard CMake args to the sub-builds. + # They're called BY setup.py so we have to patch it. + filter_file( + r'OPTION_CMAKE,', + r'OPTION_CMAKE, ' + ( + '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", ' + '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)), + 'setup.py') + + # PySide tries to patch ELF files to remove RPATHs + # Disable this and go with the one we set. + filter_file( + r'^\s*rpath_cmd\(pyside_path, srcpath\)', + r'#rpath_cmd(pyside_path, srcpath)', + 'pyside_postinstall.py') + + + def install(self, spec, prefix): + python('setup.py', 'install', + '--prefix=%s' % prefix, + '--jobs=%s' % make_jobs) diff --git a/var/spack/packages/py-pytz/package.py b/var/spack/packages/py-pytz/package.py new file mode 100644 index 0000000000..80bcfe82ca --- /dev/null +++ b/var/spack/packages/py-pytz/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyPytz(Package): + """World timezone definitions, modern and historical.""" + homepage = "https://pypi.python.org/pypi/pytz" + url = "https://pypi.python.org/packages/source/p/pytz/pytz-2014.10.tar.gz" + + version('2014.10', 'eb1cb941a20c5b751352c52486aa1dd7') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-rpy2/package.py b/var/spack/packages/py-rpy2/package.py new file mode 100644 index 0000000000..dd0c0672af --- /dev/null +++ b/var/spack/packages/py-rpy2/package.py @@ -0,0 +1,16 @@ +from spack import * + +class PyRpy2(Package): + """rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.""" + homepage = "https://pypi.python.org/pypi/rpy2" + url = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz" + + version('2.5.4', '115a20ac30883f096da2bdfcab55196d') + + extends('python') + depends_on('py-setuptools') + + depends_on('R') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-scientificpython/package.py b/var/spack/packages/py-scientificpython/package.py new file mode 100644 index 0000000000..020d830703 --- /dev/null +++ b/var/spack/packages/py-scientificpython/package.py @@ -0,0 +1,17 @@ +from spack import * + +class PyScientificpython(Package): + """ScientificPython is a collection of Python modules for + scientific computing. It contains support for geometry, + mathematical functions, statistics, physical units, IO, + visualization, and parallelization.""" + + homepage = "https://sourcesup.renater.fr/projects/scientific-py/" + url = "https://sourcesup.renater.fr/frs/download.php/4411/ScientificPython-2.8.1.tar.gz" + + version('2.8.1', '73ee0df19c7b58cdf2954261f0763c77') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-scikit-learn/package.py b/var/spack/packages/py-scikit-learn/package.py new file mode 100644 index 0000000000..c59c05a619 --- /dev/null +++ b/var/spack/packages/py-scikit-learn/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PyScikitLearn(Package): + """""" + homepage = "https://pypi.python.org/pypi/scikit-learn" + url = "https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.15.2.tar.gz" + + version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-scipy/package.py b/var/spack/packages/py-scipy/package.py new file mode 100644 index 0000000000..b5325b919f --- /dev/null +++ b/var/spack/packages/py-scipy/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyScipy(Package): + """Scientific Library for Python.""" + homepage = "https://pypi.python.org/pypi/scipy" + url = "https://pypi.python.org/packages/source/s/scipy/scipy-0.15.0.tar.gz" + + version('0.15.0', '639112f077f0aeb6d80718dc5019dc7a') + + extends('python') + depends_on('py-nose') + depends_on('py-numpy') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-setuptools/package.py b/var/spack/packages/py-setuptools/package.py new file mode 100644 index 0000000000..755288d55c --- /dev/null +++ b/var/spack/packages/py-setuptools/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PySetuptools(Package): + """Easily download, build, install, upgrade, and uninstall Python packages.""" + homepage = "https://pypi.python.org/pypi/setuptools" + url = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz" + + version('11.3.1', '01f69212e019a2420c1693fb43593930') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-shiboken/package.py b/var/spack/packages/py-shiboken/package.py new file mode 100644 index 0000000000..e4bf4ce07e --- /dev/null +++ b/var/spack/packages/py-shiboken/package.py @@ -0,0 +1,45 @@ +from spack import * +import os + +class PyShiboken(Package): + """Shiboken generates bindings for C++ libraries using CPython source code.""" + homepage = "https://shiboken.readthedocs.org/" + url = "https://pypi.python.org/packages/source/S/Shiboken/Shiboken-1.2.2.tar.gz" + + version('1.2.2', '345cfebda221f525842e079a6141e555') + + # TODO: make build dependency + # depends_on("cmake") + + extends('python') + depends_on("py-setuptools") + depends_on("libxml2") + depends_on("qt@:4.8") + + def patch(self): + """Undo Shiboken RPATH handling and add Spack RPATH.""" + # Add Spack's standard CMake args to the sub-builds. + # They're called BY setup.py so we have to patch it. + pypkg = self.spec['python'].package + rpath = self.rpath + rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'Shiboken')) + + filter_file( + r'OPTION_CMAKE,', + r'OPTION_CMAKE, ' + ( + '"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE", ' + '"-DCMAKE_INSTALL_RPATH=%s",' % ':'.join(rpath)), + 'setup.py') + + # Shiboken tries to patch ELF files to remove RPATHs + # Disable this and go with the one we set. + filter_file( + r'^\s*rpath_cmd\(shiboken_path, srcpath\)', + r'#rpath_cmd(shiboken_path, srcpath)', + 'shiboken_postinstall.py') + + + def install(self, spec, prefix): + python('setup.py', 'install', + '--prefix=%s' % prefix, + '--jobs=%s' % make_jobs) diff --git a/var/spack/packages/py-sip/package.py b/var/spack/packages/py-sip/package.py new file mode 100644 index 0000000000..6753bdd2a5 --- /dev/null +++ b/var/spack/packages/py-sip/package.py @@ -0,0 +1,20 @@ +from spack import * +import os + +class PySip(Package): + """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + homepage = "http://www.riverbankcomputing.com/software/sip/intro" + url = "http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.5/sip-4.16.5.tar.gz" + + version('4.16.5', '6d01ea966a53e4c7ae5c5e48c40e49e5') + + extends('python') + + def install(self, spec, prefix): + python('configure.py', + '--destdir=%s' % site_packages_dir, + '--bindir=%s' % spec.prefix.bin, + '--incdir=%s' % python_include_dir, + '--sipdir=%s' % os.path.join(spec.prefix.share, 'sip')) + make() + make('install') diff --git a/var/spack/packages/py-six/package.py b/var/spack/packages/py-six/package.py new file mode 100644 index 0000000000..05c5bd00a9 --- /dev/null +++ b/var/spack/packages/py-six/package.py @@ -0,0 +1,14 @@ +from spack import * + +class PySix(Package): + """Python 2 and 3 compatibility utilities.""" + homepage = "https://pypi.python.org/pypi/six" + url = "https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz" + + version('1.9.0', '476881ef4012262dfc8adc645ee786c4') + + extends('python') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-sympy/package.py b/var/spack/packages/py-sympy/package.py new file mode 100644 index 0000000000..c17e35b95f --- /dev/null +++ b/var/spack/packages/py-sympy/package.py @@ -0,0 +1,13 @@ +from spack import * + +class PySympy(Package): + """SymPy is a Python library for symbolic mathematics.""" + homepage = "https://pypi.python.org/pypi/sympy" + url = "https://pypi.python.org/packages/source/s/sympy/sympy-0.7.6.tar.gz" + + version('0.7.6', '3d04753974306d8a13830008e17babca') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/py-virtualenv/package.py b/var/spack/packages/py-virtualenv/package.py new file mode 100644 index 0000000000..2d10d440a6 --- /dev/null +++ b/var/spack/packages/py-virtualenv/package.py @@ -0,0 +1,15 @@ +from spack import * +import shutil + +class PyVirtualenv(Package): + """virtualenv is a tool to create isolated Python environments.""" + homepage = "http://virtualenv.readthedocs.org/projects/virtualenv/" + url = "https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.6.tar.gz" + + version('1.11.6', 'f61cdd983d2c4e6aeabb70b1060d6f49') + + extends('python') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/packages/python/package.py b/var/spack/packages/python/package.py index e6c3e28820..31a12ea653 100644 --- a/var/spack/packages/python/package.py +++ b/var/spack/packages/python/package.py @@ -1,10 +1,19 @@ +import os +import re +from contextlib import closing +from llnl.util.lang import match_predicate + from spack import * +import spack + class Python(Package): """The Python programming language.""" homepage = "http://www.python.org" url = "http://www.python.org/ftp/python/2.7.8/Python-2.7.8.tar.xz" + extendable = True + version('2.7.8', 'd235bdfa75b8396942e360a70487ee00') depends_on("openssl") @@ -23,3 +32,126 @@ class Python(Package): "--enable-shared") make() make("install") + + + # ======================================================================== + # Set up environment to make install easy for python extensions. + # ======================================================================== + + @property + def python_lib_dir(self): + return os.path.join('lib', 'python%d.%d' % self.version[:2]) + + + @property + def python_include_dir(self): + return os.path.join('include', 'python%d.%d' % self.version[:2]) + + + @property + def site_packages_dir(self): + return os.path.join(self.python_lib_dir, 'site-packages') + + + def setup_dependent_environment(self, module, spec, ext_spec): + """Called before python modules' install() methods. + + In most cases, extensions will only need to have one line:: + + python('setup.py', 'install', '--prefix=%s' % prefix) + """ + # Python extension builds can have a global python executable function + module.python = Executable(join_path(spec.prefix.bin, 'python')) + + # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs. + module.python_lib_dir = os.path.join(ext_spec.prefix, self.python_lib_dir) + module.python_include_dir = os.path.join(ext_spec.prefix, self.python_include_dir) + module.site_packages_dir = os.path.join(ext_spec.prefix, self.site_packages_dir) + + # Make the site packages directory if it does not exist already. + mkdirp(module.site_packages_dir) + + # Set PYTHONPATH to include site-packages dir for the + # extension and any other python extensions it depends on. + python_paths = [] + for d in ext_spec.traverse(): + if d.package.extends(self.spec): + python_paths.append(os.path.join(d.prefix, self.site_packages_dir)) + os.environ['PYTHONPATH'] = ':'.join(python_paths) + + + # ======================================================================== + # Handle specifics of activating and deactivating python modules. + # ======================================================================== + + def python_ignore(self, ext_pkg, args): + """Add some ignore files to activate/deactivate args.""" + ignore_arg = args.get('ignore', lambda f: False) + + # Always ignore easy-install.pth, as it needs to be merged. + patterns = [r'easy-install\.pth$'] + + # Ignore pieces of setuptools installed by other packages. + if ext_pkg.name != 'py-setuptools': + patterns.append(r'/site\.pyc?$') + patterns.append(r'setuptools\.pth') + patterns.append(r'bin/easy_install[^/]*$') + patterns.append(r'setuptools.*egg$') + + return match_predicate(ignore_arg, patterns) + + + def write_easy_install_pth(self, exts): + paths = [] + for ext in sorted(exts.values()): + ext_site_packages = os.path.join(ext.prefix, self.site_packages_dir) + easy_pth = "%s/easy-install.pth" % ext_site_packages + + if not os.path.isfile(easy_pth): + continue + + with closing(open(easy_pth)) as f: + for line in f: + line = line.rstrip() + + # Skip lines matching these criteria + if not line: continue + if re.search(r'^(import|#)', line): continue + if (ext.name != 'py-setuptools' and + re.search(r'setuptools.*egg$', line)): continue + + paths.append(line) + + site_packages = os.path.join(self.prefix, self.site_packages_dir) + main_pth = "%s/easy-install.pth" % site_packages + + if not paths: + if os.path.isfile(main_pth): + os.remove(main_pth) + + else: + with closing(open(main_pth, 'w')) as f: + f.write("import sys; sys.__plen = len(sys.path)\n") + for path in paths: + f.write("%s\n" % path) + f.write("import sys; new=sys.path[sys.__plen:]; del sys.path[sys.__plen:]; " + "p=getattr(sys,'__egginsert',0); sys.path[p:p]=new; sys.__egginsert = p+len(new)\n") + + + def activate(self, ext_pkg, **args): + args.update(ignore=self.python_ignore(ext_pkg, args)) + super(Python, self).activate(ext_pkg, **args) + + exts = spack.install_layout.extension_map(self.spec) + exts[ext_pkg.name] = ext_pkg.spec + self.write_easy_install_pth(exts) + + + def deactivate(self, ext_pkg, **args): + args.update(ignore=self.python_ignore(ext_pkg, args)) + super(Python, self).deactivate(ext_pkg, **args) + + exts = spack.install_layout.extension_map(self.spec) + if ext_pkg.name in exts: # Make deactivate idempotent. + del exts[ext_pkg.name] + self.write_easy_install_pth(exts) diff --git a/var/spack/packages/qhull/package.py b/var/spack/packages/qhull/package.py new file mode 100644 index 0000000000..9da4078a70 --- /dev/null +++ b/var/spack/packages/qhull/package.py @@ -0,0 +1,27 @@ +from spack import * + +class Qhull(Package): + """Qhull computes the convex hull, Delaunay triangulation, Voronoi + diagram, halfspace intersection about a point, furt hest-site + Delaunay triangulation, and furthest-site Voronoi diagram. The + source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull + implements the Quickhull algorithm for computing the convex + hull. It handles roundoff errors from floating point + arithmetic. It computes volumes, surface areas, and + approximations to the convex hull. + + Qhull does not support triangulation of non-convex surfaces, + mesh generation of non-convex objects, medium-sized inputs in + 9-D and higher, alpha shapes, weighted Voronoi diagrams, + Voronoi volumes, or constrained Delaunay triangulations.""" + + homepage = "http://www.qhull.org" + + version('1.0', 'd0f978c0d8dfb2e919caefa56ea2953c', + url="http://www.qhull.org/download/qhull-2012.1-src.tgz") + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', *std_cmake_args) + make() + make("install") diff --git a/var/spack/packages/qt/package.py b/var/spack/packages/qt/package.py index 01f9de7f3c..4a9a867511 100644 --- a/var/spack/packages/qt/package.py +++ b/var/spack/packages/qt/package.py @@ -1,9 +1,20 @@ +import os from spack import * +import os class Qt(Package): """Qt is a comprehensive cross-platform C++ application framework.""" homepage = "http://qt.io" + list_url = 'http://download.qt-project.org/official_releases/qt/' + list_depth = 2 + version('5.4.0', 'e8654e4b37dd98039ba20da7a53877e6', + url='http://download.qt-project.org/official_releases/qt/5.4/5.4.0/single/qt-everywhere-opensource-src-5.4.0.tar.gz') + version('5.3.2', 'febb001129927a70174467ecb508a682', + url='http://download.qt.io/archive/qt/5.3/5.3.2/single/qt-everywhere-opensource-src-5.3.2.tar.gz') + + version('5.2.1', 'a78408c887c04c34ce615da690e0b4c8', + url='http://download.qt.io/archive/qt/5.2/5.2.1/single/qt-everywhere-opensource-src-5.2.1.tar.gz') version('4.8.6', '2edbe4d6c2eff33ef91732602f3518eb', url="http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz") @@ -20,25 +31,77 @@ class Qt(Package): depends_on("libmng") depends_on("jpeg") + # Webkit + # depends_on("gperf") + # depends_on("flex") + # depends_on("bison") + # depends_on("ruby") + # depends_on("icu4c") + + # OpenGL hardware acceleration + depends_on("mesa") + depends_on("libxcb") + + + def setup_dependent_environment(self, module, spec, dep_spec): + """Dependencies of Qt find it using the QTDIR environment variable.""" + os.environ['QTDIR'] = self.prefix + + def patch(self): + if self.spec.satisfies('@4'): + qmake_conf = 'mkspecs/common/g++-base.conf' + elif self.spec.satisfies('@5'): + qmake_conf = 'qtbase/mkspecs/common/g++-base.conf' + else: + return + # Fix qmake compilers in the default mkspec - qmake_conf = 'mkspecs/common/g++-base.conf' - filter_file(r'^QMAKE_CC *=.*$', 'QMAKE_CC = cc', qmake_conf) - filter_file(r'^QMAKE_CXX *=.*$', 'QMAKE_CXX = c++', qmake_conf) + filter_file(r'^QMAKE_COMPILER *=.*$', 'QMAKE_COMPILER = cc', qmake_conf) + filter_file(r'^QMAKE_CC *=.*$', 'QMAKE_CC = cc', qmake_conf) + filter_file(r'^QMAKE_CXX *=.*$', 'QMAKE_CXX = c++', qmake_conf) + + + + @property + def common_config_args(self): + return [ + '-prefix', self.prefix, + '-v', + '-opensource', + '-opengl', + "-release", + '-shared', + '-confirm-license', + '-openssl-linked', + '-dbus-linked', + '-optimized-qmake', + '-no-openvg', + '-no-pch', + # NIS is deprecated in more recent glibc + "-no-nis"] + # Don't disable all the database drivers, but should + # really get them into spack at some point. + + + @when('@4') + def configure(self): + configure('-fast', + '-no-webkit', + *self.common_config_args) + + + @when('@5') + def configure(self): + configure('-no-eglfs', + '-no-directfb', + '-qt-xcb', + # If someone wants to get a webkit build working, be my guest! + '-skip', 'qtwebkit', + *self.common_config_args) def install(self, spec, prefix): - configure('-v', - '-confirm-license', - '-opensource', - '-prefix', prefix, - '-openssl-linked', - '-dbus-linked', - '-fast', - '-optimized-qmake', - '-no-pch', - '-no-phonon', - '-no-phonon-backend', - '-no-openvg') + self.configure() make() make("install") diff --git a/var/spack/packages/ruby/package.py b/var/spack/packages/ruby/package.py new file mode 100644 index 0000000000..718fd0a3be --- /dev/null +++ b/var/spack/packages/ruby/package.py @@ -0,0 +1,16 @@ +from spack import * + +class Ruby(Package): + """A dynamic, open source programming language with a focus on + simplicity and productivity.""" + + homepage = "https://www.ruby-lang.org/" + url = "http://cache.ruby-lang.org/pub/ruby/2.2/ruby-2.2.0.tar.gz" + + version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") diff --git a/var/spack/packages/tcl/package.py b/var/spack/packages/tcl/package.py new file mode 100644 index 0000000000..529adf7788 --- /dev/null +++ b/var/spack/packages/tcl/package.py @@ -0,0 +1,22 @@ +from spack import * + +class Tcl(Package): + """Tcl (Tool Command Language) is a very powerful but easy to + learn dynamic programming language, suitable for a very wide + range of uses, including web and desktop applications, + networking, administration, testing and many more. Open source + and business-friendly, Tcl is a mature yet evolving language + that is truly cross platform, easily deployed and highly + extensible.""" + homepage = "http://www.tcl.tk" + + version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f', + url="http://prdownloads.sourceforge.net/tcl/tcl8.6.3-src.tar.gz") + + depends_on('zlib') + + def install(self, spec, prefix): + with working_dir('unix'): + configure("--prefix=%s" % prefix) + make() + make("install") diff --git a/var/spack/packages/tk/package.py b/var/spack/packages/tk/package.py new file mode 100644 index 0000000000..96736f6f95 --- /dev/null +++ b/var/spack/packages/tk/package.py @@ -0,0 +1,22 @@ +from spack import * + +class Tk(Package): + """Tk is a graphical user interface toolkit that takes developing + desktop applications to a higher level than conventional + approaches. Tk is the standard GUI not only for Tcl, but for + many other dynamic languages, and can produce rich, native + applications that run unchanged across Windows, Mac OS X, Linux + and more.""" + homepage = "http://www.tcl.tk" + url = "http://prdownloads.sourceforge.net/tcl/tk8.6.3-src.tar.gz" + + version('src', '85ca4dbf4dcc19777fd456f6ee5d0221') + + depends_on("tcl") + + def install(self, spec, prefix): + with working_dir('unix'): + configure("--prefix=%s" % prefix, + "--with-tcl=%s" % spec['tcl'].prefix.lib) + make() + make("install") diff --git a/var/spack/packages/util-linux/package.py b/var/spack/packages/util-linux/package.py new file mode 100644 index 0000000000..cb7ceabf57 --- /dev/null +++ b/var/spack/packages/util-linux/package.py @@ -0,0 +1,20 @@ +from spack import * +import os + +class UtilLinux(Package): + """Util-linux is a suite of essential utilities for any Linux system.""" + + homepage = "http://freecode.com/projects/util-linux" + url = "https://www.kernel.org/pub/linux/utils/util-linux/v2.25/util-linux-2.25.tar.gz" + + version('2.25', 'f6d7fc6952ec69c4dc62c8d7c59c1d57') + + depends_on("python@2.7:") + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix, + "PKG_CONFIG_PATH=%s/pkgconfig" % spec['python'].prefix.lib, + "--disable-use-tty-group") + + make() + make("install") diff --git a/var/spack/packages/vtk/package.py b/var/spack/packages/vtk/package.py new file mode 100644 index 0000000000..4a27a8fedb --- /dev/null +++ b/var/spack/packages/vtk/package.py @@ -0,0 +1,40 @@ +from spack import * + +class Vtk(Package): + """The Visualization Toolkit (VTK) is an open-source, freely + available software system for 3D computer graphics, image + processing and visualization. """ + homepage = "http://www.vtk.org" + url = "http://www.vtk.org/files/release/6.1/VTK-6.1.0.tar.gz" + + version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d') + + depends_on("qt") + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake_args = [ + "..", + "-DBUILD_SHARED_LIBS=ON", + # Disable wrappers for other languages. + "-DVTK_WRAP_PYTHON=OFF", + "-DVTK_WRAP_JAVA=OFF", + "-DVTK_WRAP_TCL=OFF"] + cmake_args.extend(std_cmake_args) + + # Enable Qt support here. + cmake_args.extend([ + "-DQT_QMAKE_EXECUTABLE:PATH=%s/qmake" % spec['qt'].prefix.bin, + "-DVTK_Group_Qt:BOOL=ON", + # Ignore webkit because it's hard to build w/Qt + "-DVTK_Group_Qt=OFF", + "-DModule_vtkGUISupportQt:BOOL=ON", + "-DModule_vtkGUISupportQtOpenGL:BOOL=ON" + ]) + + if spec['qt'].satisfies('@5'): + cmake_args.append("-DVTK_QT_VERSION:STRING=5") + + cmake(*cmake_args) + make() + make("install") diff --git a/var/spack/packages/xcb-proto/package.py b/var/spack/packages/xcb-proto/package.py new file mode 100644 index 0000000000..17a94bd892 --- /dev/null +++ b/var/spack/packages/xcb-proto/package.py @@ -0,0 +1,15 @@ +from spack import * + +class XcbProto(Package): + """Protocol for libxcb""" + + homepage = "http://xcb.freedesktop.org/" + url = "http://xcb.freedesktop.org/dist/xcb-proto-1.11.tar.gz" + + version('1.11', 'c8c6cb72c84f58270f4db1f39607f66a') + + def install(self, spec, prefix): + configure("--prefix=%s" % prefix) + + make() + make("install") |