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| author | Mario Melara <maamelara@gmail.com> | 2017-11-12 23:24:18 -0700 |
|---|---|---|
| committer | Todd Gamblin <tgamblin@llnl.gov> | 2017-11-12 23:24:18 -0700 |
| commit | 2f1cbb5caa6a46d55952612a75c5d374bff31b0d (patch) | |
| tree | 5b794b1e045491b2725a00e5cdb2531eae910b6d /lib | |
| parent | 9db7eaade8a4f929e0ec543686888e2b911b90d3 (diff) | |
| download | spack-2f1cbb5caa6a46d55952612a75c5d374bff31b0d.tar.gz spack-2f1cbb5caa6a46d55952612a75c5d374bff31b0d.tar.bz2 spack-2f1cbb5caa6a46d55952612a75c5d374bff31b0d.tar.xz spack-2f1cbb5caa6a46d55952612a75c5d374bff31b0d.zip | |
Add build systems tutorial for SC17 (#6125)
* First draft for SC17 build systems portion
Added tutorial_buildsystems.rst file as well as example files under
the tutorial/ directory.
* Remove floating `
* Add requested changes, and examples of subclasses
Added in the requested changes to the documentation. Also added in
information about the subclasses and the defaults that they provide.
Also fixed some phrasing issues, formatting and punctuation.
* Flake8 fixes and new files for classes
Made flake8 fixes to pass tests and also added files to demonstrate code
in the classes.
* Minor edits
Edits in formatting and made some sentence changes
* Flake8 fixes
More flake8 fixes
* Flake8 fix
* Change section order on tutorial and minor edits
Placed the section at the appropriate section for the tutorial and then
added some minor edits that were requested.
* Add requested changes and more details
Added more details to Cmake, Makefile and Python Packages.
* Fixed formatting and minor edits
* Fix doc build error
Diffstat (limited to 'lib')
18 files changed, 2539 insertions, 3 deletions
diff --git a/lib/spack/docs/tutorial.rst b/lib/spack/docs/tutorial.rst index 47dc17a407..6974fe5e1a 100644 --- a/lib/spack/docs/tutorial.rst +++ b/lib/spack/docs/tutorial.rst @@ -39,7 +39,10 @@ correspond to sections in the slides above. 1. :ref:`basics-tutorial` 2. :ref:`configs-tutorial` 3. :ref:`packaging-tutorial` - 4. :ref:`modules-tutorial` + 4. :ref:`build-systems-tutorial` + 5. :ref:`advanced-packaging-tutorial` + 6. :ref:`modules-tutorial` + 7. :ref:`modules-tutorial` Full contents: @@ -47,5 +50,6 @@ Full contents: tutorial_basics tutorial_configuration tutorial_packaging + tutorial_buildsystems tutorial_advanced_packaging tutorial_modules diff --git a/lib/spack/docs/tutorial/examples/1.package.py b/lib/spack/docs/tutorial/examples/1.package.py index 359a457567..308779d016 100644 --- a/lib/spack/docs/tutorial/examples/1.package.py +++ b/lib/spack/docs/tutorial/examples/1.package.py @@ -30,8 +30,7 @@ class Mpileaks(Package): MPI_Datatypes.""" homepage = "https://github.com/hpc/mpileaks" - url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" - + url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" # NOQA version('1.0', '8838c574b39202a57d7c2d68692718aa') # FIXME: Add dependencies if required. diff --git a/lib/spack/docs/tutorial/examples/Autotools/0.package.py b/lib/spack/docs/tutorial/examples/Autotools/0.package.py new file mode 100644 index 0000000000..44a157b36a --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Autotools/0.package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class Mpileaks(AutoToolsPackage): + """Tool to detect and report leaked MPI objects like MPI_Requests and + MPI_Datatypes.""" + + homepage = "https://github.com/hpc/mpileaks" + url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" + + version('1.0', '8838c574b39202a57d7c2d68692718aa') + + depends_on("mpi") + depends_on("adept-utils") + depends_on("callpath") + + def install(self, spec, prefix): + configure("--prefix=" + prefix, + "--with-adept-utils=" + spec['adept-utils'].prefix, + "--with-callpath=" + spec['callpath'].prefix) + make() + make("install") diff --git a/lib/spack/docs/tutorial/examples/Autotools/1.package.py b/lib/spack/docs/tutorial/examples/Autotools/1.package.py new file mode 100644 index 0000000000..fba2720329 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Autotools/1.package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class Mpileaks(AutoToolsPackage): + """Tool to detect and report leaked MPI objects like MPI_Requests and + MPI_Datatypes.""" + + homepage = "https://github.com/hpc/mpileaks" + url = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz" + + version('1.0', '8838c574b39202a57d7c2d68692718aa') + + depends_on("mpi") + depends_on("adept-utils") + depends_on("callpath") + + def configure_args(self): + args = ["--with-adept-utils=" + spec['adept-utils'].prefix, + "--with-callpath=" + spec['callpath'].prefix] + return args diff --git a/lib/spack/docs/tutorial/examples/Autotools/autotools_class.py b/lib/spack/docs/tutorial/examples/Autotools/autotools_class.py new file mode 100644 index 0000000000..90ff8540bd --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Autotools/autotools_class.py @@ -0,0 +1,460 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 inspect +import os +import os.path +import shutil +import stat +from subprocess import PIPE +from subprocess import check_call + +import llnl.util.tty as tty +from llnl.util.filesystem import working_dir, join_path, force_remove +from spack.package import PackageBase, run_after, run_before +from spack.util.executable import Executable + + +class AutotoolsPackage(PackageBase): + """Specialized class for packages built using GNU Autotools. + + This class provides four phases that can be overridden: + + 1. :py:meth:`~.AutotoolsPackage.autoreconf` + 2. :py:meth:`~.AutotoolsPackage.configure` + 3. :py:meth:`~.AutotoolsPackage.build` + 4. :py:meth:`~.AutotoolsPackage.install` + + They all have sensible defaults and for many packages the only thing + necessary will be to override the helper method + :py:meth:`~.AutotoolsPackage.configure_args`. + For a finer tuning you may also override: + + +-----------------------------------------------+--------------------+ + | **Method** | **Purpose** | + +===============================================+====================+ + | :py:attr:`~.AutotoolsPackage.build_targets` | Specify ``make`` | + | | targets for the | + | | build phase | + +-----------------------------------------------+--------------------+ + | :py:attr:`~.AutotoolsPackage.install_targets` | Specify ``make`` | + | | targets for the | + | | install phase | + +-----------------------------------------------+--------------------+ + | :py:meth:`~.AutotoolsPackage.check` | Run build time | + | | tests if required | + +-----------------------------------------------+--------------------+ + + """ + #: Phases of a GNU Autotools package + phases = ['autoreconf', 'configure', 'build', 'install'] + #: This attribute is used in UI queries that need to know the build + #: system base class + build_system_class = 'AutotoolsPackage' + #: Whether or not to update ``config.guess`` on old architectures + patch_config_guess = True + + #: Targets for ``make`` during the :py:meth:`~.AutotoolsPackage.build` + #: phase + build_targets = [] + #: Targets for ``make`` during the :py:meth:`~.AutotoolsPackage.install` + #: phase + install_targets = ['install'] + + #: Callback names for build-time test + build_time_test_callbacks = ['check'] + + #: Callback names for install-time test + install_time_test_callbacks = ['installcheck'] + + #: Set to true to force the autoreconf step even if configure is present + force_autoreconf = False + #: Options to be passed to autoreconf when using the default implementation + autoreconf_extra_args = [] + + @run_after('autoreconf') + def _do_patch_config_guess(self): + """Some packages ship with an older config.guess and need to have + this updated when installed on a newer architecture. In particular, + config.guess fails for PPC64LE for version prior to a 2013-06-10 + build date (automake 1.13.4).""" + + if not self.patch_config_guess or not self.spec.satisfies( + 'target=ppc64le' + ): + return + my_config_guess = None + config_guess = None + if os.path.exists('config.guess'): + # First search the top-level source directory + my_config_guess = 'config.guess' + else: + # Then search in all sub directories. + # We would like to use AC_CONFIG_AUX_DIR, but not all packages + # ship with their configure.in or configure.ac. + d = '.' + dirs = [os.path.join(d, o) for o in os.listdir(d) + if os.path.isdir(os.path.join(d, o))] + for dirname in dirs: + path = os.path.join(dirname, 'config.guess') + if os.path.exists(path): + my_config_guess = path + + if my_config_guess is not None: + try: + check_call([my_config_guess], stdout=PIPE, stderr=PIPE) + # The package's config.guess already runs OK, so just use it + return + except Exception: + pass + else: + return + + # Look for a spack-installed automake package + if 'automake' in self.spec: + automake_path = os.path.join(self.spec['automake'].prefix, 'share', + 'automake-' + + str(self.spec['automake'].version)) + path = os.path.join(automake_path, 'config.guess') + if os.path.exists(path): + config_guess = path + # Look for the system's config.guess + if config_guess is None and os.path.exists('/usr/share'): + automake_dir = [s for s in os.listdir('/usr/share') if + "automake" in s] + if automake_dir: + automake_path = os.path.join('/usr/share', automake_dir[0]) + path = os.path.join(automake_path, 'config.guess') + if os.path.exists(path): + config_guess = path + if config_guess is not None: + try: + check_call([config_guess], stdout=PIPE, stderr=PIPE) + mod = os.stat(my_config_guess).st_mode & 0o777 | stat.S_IWUSR + os.chmod(my_config_guess, mod) + shutil.copyfile(config_guess, my_config_guess) + return + except Exception: + pass + + raise RuntimeError('Failed to find suitable config.guess') + + @property + def configure_directory(self): + """Returns the directory where 'configure' resides. + + :return: directory where to find configure + """ + return self.stage.source_path + + @property + def configure_abs_path(self): + # Absolute path to configure + configure_abs_path = join_path( + os.path.abspath(self.configure_directory), 'configure' + ) + return configure_abs_path + + @property + def build_directory(self): + """Override to provide another place to build the package""" + return self.configure_directory + + def default_flag_handler(self, spack_env, flag_val): + # Relies on being the first thing that can affect the spack_env + # EnvironmentModification after it is instantiated or no other + # method trying to affect these variables. Currently both are true + # flag_val is a tuple (flag, value_list). + spack_env.set(flag_val[0].upper(), + ' '.join(flag_val[1])) + return [] + + @run_before('autoreconf') + def delete_configure_to_force_update(self): + if self.force_autoreconf: + force_remove(self.configure_abs_path) + + def autoreconf(self, spec, prefix): + """Not needed usually, configure should be already there""" + # If configure exists nothing needs to be done + if os.path.exists(self.configure_abs_path): + return + # Else try to regenerate it + autotools = ['m4', 'autoconf', 'automake', 'libtool'] + missing = [x for x in autotools if x not in spec] + if missing: + msg = 'Cannot generate configure: missing dependencies {0}' + raise RuntimeError(msg.format(missing)) + tty.msg('Configure script not found: trying to generate it') + tty.warn('*********************************************************') + tty.warn('* If the default procedure fails, consider implementing *') + tty.warn('* a custom AUTORECONF phase in the package *') + tty.warn('*********************************************************') + with working_dir(self.configure_directory): + m = inspect.getmodule(self) + # This part should be redundant in principle, but + # won't hurt + m.libtoolize() + m.aclocal() + # This line is what is needed most of the time + # --install, --verbose, --force + autoreconf_args = ['-ivf'] + if 'pkg-config' in spec: + autoreconf_args += [ + '-I', + join_path(spec['pkg-config'].prefix, 'share', 'aclocal'), + ] + autoreconf_args += self.autoreconf_extra_args + m.autoreconf(*autoreconf_args) + + @run_after('autoreconf') + def set_configure_or_die(self): + """Checks the presence of a ``configure`` file after the + autoreconf phase. If it is found sets a module attribute + appropriately, otherwise raises an error. + + :raises RuntimeError: if a configure script is not found in + :py:meth:`~AutotoolsPackage.configure_directory` + """ + # Check if a configure script is there. If not raise a RuntimeError. + if not os.path.exists(self.configure_abs_path): + msg = 'configure script not found in {0}' + raise RuntimeError(msg.format(self.configure_directory)) + + # Monkey-patch the configure script in the corresponding module + inspect.getmodule(self).configure = Executable( + self.configure_abs_path + ) + + def configure_args(self): + """Produces a list containing all the arguments that must be passed to + configure, except ``--prefix`` which will be pre-pended to the list. + + :return: list of arguments for configure + """ + return [] + + def configure(self, spec, prefix): + """Runs configure with the arguments specified in + :py:meth:`~.AutotoolsPackage.configure_args` + and an appropriately set prefix. + """ + options = ['--prefix={0}'.format(prefix)] + self.configure_args() + + with working_dir(self.build_directory, create=True): + inspect.getmodule(self).configure(*options) + + def build(self, spec, prefix): + """Makes the build targets specified by + :py:attr:``~.AutotoolsPackage.build_targets`` + """ + with working_dir(self.build_directory): + inspect.getmodule(self).make(*self.build_targets) + + def install(self, spec, prefix): + """Makes the install targets specified by + :py:attr:``~.AutotoolsPackage.install_targets`` + """ + with working_dir(self.build_directory): + inspect.getmodule(self).make(*self.install_targets) + + run_after('build')(PackageBase._run_default_build_time_test_callbacks) + + def check(self): + """Searches the Makefile for targets ``test`` and ``check`` + and runs them if found. + """ + with working_dir(self.build_directory): + self._if_make_target_execute('test') + self._if_make_target_execute('check') + + def _activate_or_not( + self, + name, + activation_word, + deactivation_word, + activation_value=None + ): + """This function contains the current implementation details of + :py:meth:`~.AutotoolsPackage.with_or_without` and + :py:meth:`~.AutotoolsPackage.enable_or_disable`. + + Args: + name (str): name of the variant that is being processed + activation_word (str): the default activation word ('with' in the + case of ``with_or_without``) + deactivation_word (str): the default deactivation word ('without' + in the case of ``with_or_without``) + activation_value (callable): callable that accepts a single + value. This value is either one of the allowed values for a + multi-valued variant or the name of a bool-valued variant. + Returns the parameter to be used when the value is activated. + + The special value 'prefix' can also be assigned and will return + ``spec[name].prefix`` as activation parameter. + + Examples: + + Given a package with: + + .. code-block:: python + + variant('foo', values=('x', 'y'), description='') + variant('bar', default=True, description='') + + calling this function like: + + .. code-block:: python + + _activate_or_not( + 'foo', 'with', 'without', activation_value='prefix' + ) + _activate_or_not('bar', 'with', 'without') + + will generate the following configuration options: + + .. code-block:: console + + --with-x=<prefix-to-x> --without-y --with-bar + + for ``<spec-name> foo=x +bar`` + + Returns: + list of strings that corresponds to the activation/deactivation + of the variant that has been processed + + Raises: + KeyError: if name is not among known variants + """ + spec = self.spec + args = [] + + if activation_value == 'prefix': + activation_value = lambda x: spec[x].prefix + + # Defensively look that the name passed as argument is among + # variants + if name not in self.variants: + msg = '"{0}" is not a variant of "{1}"' + raise KeyError(msg.format(name, self.name)) + + # Create a list of pairs. Each pair includes a configuration + # option and whether or not that option is activated + if set(self.variants[name].values) == set((True, False)): + # BoolValuedVariant carry information about a single option. + # Nonetheless, for uniformity of treatment we'll package them + # in an iterable of one element. + condition = '+{name}'.format(name=name) + options = [(name, condition in spec)] + else: + condition = '{name}={value}' + options = [ + (value, condition.format(name=name, value=value) in spec) + for value in self.variants[name].values + ] + + # For each allowed value in the list of values + for option_value, activated in options: + # Search for an override in the package for this value + override_name = '{0}_or_{1}_{2}'.format( + activation_word, deactivation_word, option_value + ) + line_generator = getattr(self, override_name, None) + # If not available use a sensible default + if line_generator is None: + def _default_generator(is_activated): + if is_activated: + line = '--{0}-{1}'.format( + activation_word, option_value + ) + if activation_value is not None and activation_value(option_value): # NOQA=ignore=E501 + line += '={0}'.format( + activation_value(option_value) + ) + return line + return '--{0}-{1}'.format(deactivation_word, option_value) + line_generator = _default_generator + args.append(line_generator(activated)) + return args + + def with_or_without(self, name, activation_value=None): + """Inspects a variant and returns the arguments that activate + or deactivate the selected feature(s) for the configure options. + + This function works on all type of variants. For bool-valued variants + it will return by default ``--with-{name}`` or ``--without-{name}``. + For other kinds of variants it will cycle over the allowed values and + return either ``--with-{value}`` or ``--without-{value}``. + + If activation_value is given, then for each possible value of the + variant, the option ``--with-{value}=activation_value(value)`` or + ``--without-{value}`` will be added depending on whether or not + ``variant=value`` is in the spec. + + Args: + name (str): name of a valid multi-valued variant + activation_value (callable): callable that accepts a single + value and returns the parameter to be used leading to an entry + of the type ``--with-{name}={parameter}``. + + The special value 'prefix' can also be assigned and will return + ``spec[name].prefix`` as activation parameter. + + Returns: + list of arguments to configure + """ + return self._activate_or_not(name, 'with', 'without', activation_value) + + def enable_or_disable(self, name, activation_value=None): + """Same as :py:meth:`~.AutotoolsPackage.with_or_without` but substitute + ``with`` with ``enable`` and ``without`` with ``disable``. + + Args: + name (str): name of a valid multi-valued variant + activation_value (callable): if present accepts a single value + and returns the parameter to be used leading to an entry of the + type ``--enable-{name}={parameter}`` + + The special value 'prefix' can also be assigned and will return + ``spec[name].prefix`` as activation parameter. + + Returns: + list of arguments to configure + """ + return self._activate_or_not( + name, 'enable', 'disable', activation_value + ) + + run_after('install')(PackageBase._run_default_install_time_test_callbacks) + + def installcheck(self): + """Searches the Makefile for an ``installcheck`` target + and runs it if found. + """ + with working_dir(self.build_directory): + self._if_make_target_execute('installcheck') + + # Check that self.prefix is there after installation + run_after('install')(PackageBase.sanity_check_prefix) diff --git a/lib/spack/docs/tutorial/examples/Cmake/0.package.py b/lib/spack/docs/tutorial/examples/Cmake/0.package.py new file mode 100644 index 0000000000..724b3fdf94 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Cmake/0.package.py @@ -0,0 +1,60 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 +############################################################################## +# +# This is a template package file for Spack. We've put "FIXME" +# next to all the things you'll want to change. Once you've handled +# them, you can save this file and test your package like this: +# +# spack install callpath +# +# You can edit this file again by typing: +# +# spack edit callpath +# +# See the Spack documentation for more information on packaging. +# If you submit this package back to Spack as a pull request, +# please first remove this boilerplate and all FIXME comments. +# +from spack import * + + +class Callpath(CMakePackage): + """FIXME: Put a proper description of your package here.""" + + # FIXME: Add a proper url for your package's homepage here. + homepage = "http://www.example.com" + url = "https://github.com/llnl/callpath/archive/v1.0.1.tar.gz" + + version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a') + + # FIXME: Add dependencies if required. + # depends_on('foo') + + def cmake_args(self): + # FIXME: Add arguments other than + # FIXME: CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE + # FIXME: If not needed delete this function + args = [] + return args diff --git a/lib/spack/docs/tutorial/examples/Cmake/1.package.py b/lib/spack/docs/tutorial/examples/Cmake/1.package.py new file mode 100644 index 0000000000..dcb44260d2 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Cmake/1.package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class Callpath(CMakePackage): + """Library for representing callpaths consistently in + distributed-memory performance tools.""" + + homepage = "https://github.com/llnl/callpath" + url = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz" + + version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a') + + depends_on("elf", type="link") + depends_on("libdwarf") + depends_on("dyninst") + depends_on("adept-utils") + depends_on("mpi") + depends_on("cmake@2.8:", type="build") diff --git a/lib/spack/docs/tutorial/examples/Cmake/2.package.py b/lib/spack/docs/tutorial/examples/Cmake/2.package.py new file mode 100644 index 0000000000..126a841ce9 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Cmake/2.package.py @@ -0,0 +1,52 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class Callpath(CMakePackage): + """Library for representing callpaths consistently in + distributed-memory performance tools.""" + + homepage = "https://github.com/llnl/callpath" + url = "https://github.com/llnl/callpath/archive/v1.0.3.tar.gz" + + version('1.0.3', 'c89089b3f1c1ba47b09b8508a574294a') + + depends_on("elf", type="link") + depends_on("libdwarf") + depends_on("dyninst") + depends_on("adept-utils") + depends_on("mpi") + depends_on("cmake@2.8:", type="build") + + def cmake_args(self): + args = ["-DCALLPATH_WALKER=dyninst"] + + if self.spec.satisfies("^dyninst@9.3.0:"): + std.flag = self.compiler.cxx_flag + args.append("-DCMAKE_CXX_FLAGS='{0}' -fpermissive'".format( + std_flag)) + + return args diff --git a/lib/spack/docs/tutorial/examples/Cmake/cmake_class.py b/lib/spack/docs/tutorial/examples/Cmake/cmake_class.py new file mode 100644 index 0000000000..5b0f5526c9 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Cmake/cmake_class.py @@ -0,0 +1,224 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 inspect +import os +import platform + +import spack.build_environment +from llnl.util.filesystem import working_dir, join_path +from spack.util.environment import filter_system_paths +from spack.directives import depends_on, variant +from spack.package import PackageBase, InstallError, run_after + + +class CMakePackage(PackageBase): + """Specialized class for packages built using CMake + + For more information on the CMake build system, see: + https://cmake.org/cmake/help/latest/ + + This class provides three phases that can be overridden: + + 1. :py:meth:`~.CMakePackage.cmake` + 2. :py:meth:`~.CMakePackage.build` + 3. :py:meth:`~.CMakePackage.install` + + They all have sensible defaults and for many packages the only thing + necessary will be to override :py:meth:`~.CMakePackage.cmake_args`. + For a finer tuning you may also override: + + +-----------------------------------------------+--------------------+ + | **Method** | **Purpose** | + +===============================================+====================+ + | :py:meth:`~.CMakePackage.root_cmakelists_dir` | Location of the | + | | root CMakeLists.txt| + +-----------------------------------------------+--------------------+ + | :py:meth:`~.CMakePackage.build_directory` | Directory where to | + | | build the package | + +-----------------------------------------------+--------------------+ + + + """ + #: Phases of a CMake package + phases = ['cmake', 'build', 'install'] + #: This attribute is used in UI queries that need to know the build + #: system base class + build_system_class = 'CMakePackage' + + build_targets = [] + install_targets = ['install'] + + build_time_test_callbacks = ['check'] + + #: The build system generator to use. + #: + #: See ``cmake --help`` for a list of valid generators. + #: Currently, "Unix Makefiles" and "Ninja" are the only generators + #: that Spack supports. Defaults to "Unix Makefiles". + #: + #: See https://cmake.org/cmake/help/latest/manual/cmake-generators.7.html + #: for more information. + generator = 'Unix Makefiles' + + # https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html + variant('build_type', default='RelWithDebInfo', + description='CMake build type', + values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel')) + + depends_on('cmake', type='build') + + @property + def root_cmakelists_dir(self): + """The relative path to the directory containing CMakeLists.txt + + This path is relative to the root of the extracted tarball, + not to the ``build_directory``. Defaults to the current directory. + + :return: directory containing CMakeLists.txt + """ + return self.stage.source_path + + @property + def std_cmake_args(self): + """Standard cmake arguments provided as a property for + convenience of package writers + + :return: standard cmake arguments + """ + # standard CMake arguments + return CMakePackage._std_args(self) + + @staticmethod + def _std_args(pkg): + """Computes the standard cmake arguments for a generic package""" + try: + generator = pkg.generator + except AttributeError: + generator = 'Unix Makefiles' + + # Make sure a valid generator was chosen + valid_generators = ['Unix Makefiles', 'Ninja'] + if generator not in valid_generators: + msg = "Invalid CMake generator: '{0}'\n".format(generator) + msg += "CMakePackage currently supports the following " + msg += "generators: '{0}'".format("', '".join(valid_generators)) + raise InstallError(msg) + + try: + build_type = pkg.spec.variants['build_type'].value + except KeyError: + build_type = 'RelWithDebInfo' + + args = [ + '-G', generator, + '-DCMAKE_INSTALL_PREFIX:PATH={0}'.format(pkg.prefix), + '-DCMAKE_BUILD_TYPE:STRING={0}'.format(build_type), + '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' + ] + + if platform.mac_ver()[0]: + args.append('-DCMAKE_FIND_FRAMEWORK:STRING=LAST') + + # Set up CMake rpath + args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE') + rpaths = ':'.join(spack.build_environment.get_rpaths(pkg)) + args.append('-DCMAKE_INSTALL_RPATH:STRING={0}'.format(rpaths)) + # CMake's find_package() looks in CMAKE_PREFIX_PATH first, help CMake + # to find immediate link dependencies in right places: + deps = [d.prefix for d in + pkg.spec.dependencies(deptype=('build', 'link'))] + deps = filter_system_paths(deps) + args.append('-DCMAKE_PREFIX_PATH:STRING={0}'.format(';'.join(deps))) + return args + + @property + def build_directory(self): + """Returns the directory to use when building the package + + :return: directory where to build the package + """ + return join_path(self.stage.source_path, 'spack-build') + + def default_flag_handler(self, spack_env, flag_val): + # Relies on being the first thing that can affect the spack_env + # EnvironmentModification after it is instantiated or no other + # method trying to affect these variables. Currently both are true + # flag_val is a tuple (flag, value_list) + spack_env.set(flag_val[0].upper(), + ' '.join(flag_val[1])) + return [] + + def cmake_args(self): + """Produces a list containing all the arguments that must be passed to + cmake, except: + + * CMAKE_INSTALL_PREFIX + * CMAKE_BUILD_TYPE + + which will be set automatically. + + :return: list of arguments for cmake + """ + return [] + + def cmake(self, spec, prefix): + """Runs ``cmake`` in the build directory""" + options = [os.path.abspath(self.root_cmakelists_dir)] + options += self.std_cmake_args + options += self.cmake_args() + with working_dir(self.build_directory, create=True): + inspect.getmodule(self).cmake(*options) + + def build(self, spec, prefix): + """Make the build targets""" + with working_dir(self.build_directory): + if self.generator == 'Unix Makefiles': + inspect.getmodule(self).make(*self.build_targets) + elif self.generator == 'Ninja': + inspect.getmodule(self).ninja(*self.build_targets) + + def install(self, spec, prefix): + """Make the install targets""" + with working_dir(self.build_directory): + if self.generator == 'Unix Makefiles': + inspect.getmodule(self).make(*self.install_targets) + elif self.generator == 'Ninja': + inspect.getmodule(self).ninja(*self.install_targets) + + run_after('build')(PackageBase._run_default_build_time_test_callbacks) + + def check(self): + """Searches the CMake-generated Makefile for the target ``test`` + and runs it if found. + """ + with working_dir(self.build_directory): + if self.generator == 'Unix Makefiles': + self._if_make_target_execute('test') + elif self.generator == 'Ninja': + self._if_ninja_target_execute('test') + + # Check that self.prefix is there after installation + run_after('install')(PackageBase.sanity_check_prefix) diff --git a/lib/spack/docs/tutorial/examples/Makefile/0.package.py b/lib/spack/docs/tutorial/examples/Makefile/0.package.py new file mode 100644 index 0000000000..641b6ccb8f --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Makefile/0.package.py @@ -0,0 +1,45 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class Bowtie(MakefilePackage): + """FIXME: Put a proper description of your package here.""" + + # FIXME: Add a proper url for your package's homepage here. + homepage = "http://www.example.com" + url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip" + + version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf') + + # FIXME: Add dependencies if required. + # depends_on('foo') + + def edit(self, spec, prefix): + # FIXME: Edit the Makefile if necessary + # FIXME: If not needed delete this function + # makefile = FileFilter('Makefile') + # makefile.filter('CC = .*', 'CC = cc') + return diff --git a/lib/spack/docs/tutorial/examples/Makefile/1.package.py b/lib/spack/docs/tutorial/examples/Makefile/1.package.py new file mode 100644 index 0000000000..709bc71afa --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Makefile/1.package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class Bowtie(MakefilePackage): + """Bowtie is an ultrafast, memory efficient short read aligner + for short DNA sequences (reads) from next-gen sequencers.""" + + homepage = "https://sourceforge.net/projects/bowtie-bio/" + url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip" + + version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf') + + variant("tbb", default=False, description="Use Intel thread building block") + + depends_on("tbb", when="+tbb") + + def edit(self, spec, prefix): + # FIXME: Edit the Makefile if necessary + # FIXME: If not needed delete this function + # makefile = FileFilter('Makefile') + # makefile.filter('CC = .*', 'CC = cc') + return diff --git a/lib/spack/docs/tutorial/examples/Makefile/2.package.py b/lib/spack/docs/tutorial/examples/Makefile/2.package.py new file mode 100644 index 0000000000..10aba473e3 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Makefile/2.package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class Bowtie(MakefilePackage): + """Bowtie is an ultrafast, memory efficient short read aligner + for short DNA sequences (reads) from next-gen sequencers.""" + + homepage = "https://sourceforge.net/projects/bowtie-bio/" + url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip" + + version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf') + + variant("tbb", default=False, description="Use Intel thread building block") + + depends_on("tbb", when="+tbb") + + def edit(self, spec, prefix): + makefile = FileFilter("Makefile") + makefile.filter('CC= .*', 'CC = ' + env['CC']) + makefile.filter('CXX = .*', 'CXX = ' + env['CXX']) diff --git a/lib/spack/docs/tutorial/examples/Makefile/3.package.py b/lib/spack/docs/tutorial/examples/Makefile/3.package.py new file mode 100644 index 0000000000..269ab2c454 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Makefile/3.package.py @@ -0,0 +1,53 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class Bowtie(MakefilePackage): + """Bowtie is an ultrafast, memory efficient short read aligner + for short DNA sequences (reads) from next-gen sequencers.""" + + homepage = "https://sourceforge.net/projects/bowtie-bio/" + url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip" + + version('1.2.1.1', 'ec06265730c5f587cd58bcfef6697ddf') + + variant("tbb", default=False, description="Use Intel thread building block") + + depends_on("tbb", when="+tbb") + + def edit(self, spec, prefix): + makefile = FileFilter("Makefile") + makefile.filter('CC= .*', 'CC = ' + env['CC']) + makefile.filter('CXX = .*', 'CXX = ' + env['CXX']) + + def build(self, spec, prefix): + if "+tbb" in spec: + make() + else: + make("NO_TBB=1") + + def install(self, spec, prefix): + make('prefix={0}'.format(self.prefix), 'install') diff --git a/lib/spack/docs/tutorial/examples/Makefile/makefile_class.py b/lib/spack/docs/tutorial/examples/Makefile/makefile_class.py new file mode 100644 index 0000000000..5ffb88f43d --- /dev/null +++ b/lib/spack/docs/tutorial/examples/Makefile/makefile_class.py @@ -0,0 +1,129 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 inspect + +import llnl.util.tty as tty +from llnl.util.filesystem import working_dir +from spack.package import PackageBase, run_after + + +class MakefilePackage(PackageBase): + """Specialized class for packages that are built using editable Makefiles + + This class provides three phases that can be overridden: + + 1. :py:meth:`~.MakefilePackage.edit` + 2. :py:meth:`~.MakefilePackage.build` + 3. :py:meth:`~.MakefilePackage.install` + + It is usually necessary to override the :py:meth:`~.MakefilePackage.edit` + phase, while :py:meth:`~.MakefilePackage.build` and + :py:meth:`~.MakefilePackage.install` have sensible defaults. + For a finer tuning you may override: + + +-----------------------------------------------+--------------------+ + | **Method** | **Purpose** | + +===============================================+====================+ + | :py:attr:`~.MakefilePackage.build_targets` | Specify ``make`` | + | | targets for the | + | | build phase | + +-----------------------------------------------+--------------------+ + | :py:attr:`~.MakefilePackage.install_targets` | Specify ``make`` | + | | targets for the | + | | install phase | + +-----------------------------------------------+--------------------+ + | :py:meth:`~.MakefilePackage.build_directory` | Directory where the| + | | Makefile is located| + +-----------------------------------------------+--------------------+ + """ + #: Phases of a package that is built with an hand-written Makefile + phases = ['edit', 'build', 'install'] + #: This attribute is used in UI queries that need to know the build + #: system base class + build_system_class = 'MakefilePackage' + + #: Targets for ``make`` during the :py:meth:`~.MakefilePackage.build` + #: phase + build_targets = [] + #: Targets for ``make`` during the :py:meth:`~.MakefilePackage.install` + #: phase + install_targets = ['install'] + + #: Callback names for build-time test + build_time_test_callbacks = ['check'] + + #: Callback names for install-time test + install_time_test_callbacks = ['installcheck'] + + @property + def build_directory(self): + """Returns the directory containing the main Makefile + + :return: build directory + """ + return self.stage.source_path + + def edit(self, spec, prefix): + """Edits the Makefile before calling make. This phase cannot + be defaulted. + """ + tty.msg('Using default implementation: skipping edit phase.') + + def build(self, spec, prefix): + """Calls make, passing :py:attr:`~.MakefilePackage.build_targets` + as targets. + """ + with working_dir(self.build_directory): + inspect.getmodule(self).make(*self.build_targets) + + def install(self, spec, prefix): + """Calls make, passing :py:attr:`~.MakefilePackage.install_targets` + as targets. + """ + with working_dir(self.build_directory): + inspect.getmodule(self).make(*self.install_targets) + + run_after('build')(PackageBase._run_default_build_time_test_callbacks) + + def check(self): + """Searches the Makefile for targets ``test`` and ``check`` + and runs them if found. + """ + with working_dir(self.build_directory): + self._if_make_target_execute('test') + self._if_make_target_execute('check') + + run_after('install')(PackageBase._run_default_install_time_test_callbacks) + + def installcheck(self): + """Searches the Makefile for an ``installcheck`` target + and runs it if found. + """ + with working_dir(self.build_directory): + self._if_make_target_execute('installcheck') + + # Check that self.prefix is there after installation + run_after('install')(PackageBase.sanity_check_prefix) diff --git a/lib/spack/docs/tutorial/examples/PyPackage/0.package.py b/lib/spack/docs/tutorial/examples/PyPackage/0.package.py new file mode 100644 index 0000000000..48114075a7 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/PyPackage/0.package.py @@ -0,0 +1,60 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 +############################################################################## +# +# This is a template package file for Spack. We've put "FIXME" +# next to all the things you'll want to change. Once you've handled +# them, you can save this file and test your package like this: +# +# spack install py-pandas +# +# You can edit this file again by typing: +# +# spack edit py-pandas +# +# See the Spack documentation for more information on packaging. +# If you submit this package back to Spack as a pull request, +# please first remove this boilerplate and all FIXME comments. +# +from spack import * + + +class PyPandas(PythonPackage): + """FIXME: Put a proper description of your package here.""" + + # FIXME: Add a proper url for your package's homepage here. + homepage = "http://www.example.com" + url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz" + + version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3') + + # FIXME: Add dependencies if required. + # depends_on('py-setuptools', type='build') + # depends_on('py-foo', type=('build', 'run')) + + def build_args(self, spec, prefix): + # FIXME: Add arguments other than --prefix + # FIXME: If not needed delete this function + args = [] + return args diff --git a/lib/spack/docs/tutorial/examples/PyPackage/1.package.py b/lib/spack/docs/tutorial/examples/PyPackage/1.package.py new file mode 100644 index 0000000000..a9cbff00e2 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/PyPackage/1.package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 spack import * + + +class PyPandas(PythonPackage): + """pandas is a Python package providing fast, flexible, and expressive + data structures designed to make working with relational or + labeled data both easy and intuitive. It aims to be the + fundamental high-level building block for doing practical, real + world data analysis in Python. Additionally, it has the broader + goal of becoming the most powerful and flexible open source data + analysis / manipulation tool available in any language. + """ + homepage = "http://pandas.pydata.org/" + url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz" + + version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3') + version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') + version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8') + version('0.16.0', 'bfe311f05dc0c351f8955fbd1e296e73') + + depends_on('py-dateutil', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-cython', type='build') + depends_on('py-pytz', type=('build', 'run')) + depends_on('py-numexpr', type=('build', 'run')) + depends_on('py-bottleneck', type=('build', 'run')) diff --git a/lib/spack/docs/tutorial/examples/PyPackage/python_package_class.py b/lib/spack/docs/tutorial/examples/PyPackage/python_package_class.py new file mode 100644 index 0000000000..190620d7a2 --- /dev/null +++ b/lib/spack/docs/tutorial/examples/PyPackage/python_package_class.py @@ -0,0 +1,399 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files 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 Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, 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 Lesser 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 inspect +import os + +from spack.directives import depends_on, extends +from spack.package import PackageBase, run_after + +from llnl.util.filesystem import working_dir + + +class PythonPackage(PackageBase): + """Specialized class for packages that are built using Python + setup.py files + + This class provides the following phases that can be overridden: + + * build + * build_py + * build_ext + * build_clib + * build_scripts + * clean + * install + * install_lib + * install_headers + * install_scripts + * install_data + * sdist + * register + * bdist + * bdist_dumb + * bdist_rpm + * bdist_wininst + * upload + * check + + These are all standard setup.py commands and can be found by running: + + .. code-block:: console + + $ python setup.py --help-commands + + By default, only the 'build' and 'install' phases are run, but if you + need to run more phases, simply modify your ``phases`` list like so: + + .. code-block:: python + + phases = ['build_ext', 'install', 'bdist'] + + Each phase provides a function <phase> that runs: + + .. code-block:: console + + $ python setup.py --no-user-cfg <phase> + + Each phase also has a <phase_args> function that can pass arguments to + this call. All of these functions are empty except for the ``install_args`` + function, which passes ``--prefix=/path/to/installation/directory``. + + If you need to run a phase which is not a standard setup.py command, + you'll need to define a function for it like so: + + .. code-block:: python + + def configure(self, spec, prefix): + self.setup_py('configure') + """ + # Default phases + phases = ['build', 'install'] + + # Name of modules that the Python package provides + # This is used to test whether or not the installation succeeded + # These names generally come from running: + # + # >>> import setuptools + # >>> setuptools.find_packages() + # + # in the source tarball directory + import_modules = [] + + # To be used in UI queries that require to know which + # build-system class we are using + build_system_class = 'PythonPackage' + + #: Callback names for build-time test + build_time_test_callbacks = ['test'] + + #: Callback names for install-time test + install_time_test_callbacks = ['import_module_test'] + + extends('python') + + depends_on('python', type=('build', 'run')) + + def setup_file(self): + """Returns the name of the setup file to use.""" + return 'setup.py' + + @property + def build_directory(self): + """The directory containing the ``setup.py`` file.""" + return self.stage.source_path + + def python(self, *args, **kwargs): + inspect.getmodule(self).python(*args, **kwargs) + + def setup_py(self, *args, **kwargs): + setup = self.setup_file() + + with working_dir(self.build_directory): + self.python(setup, '--no-user-cfg', *args, **kwargs) + + def _setup_command_available(self, command): + """Determines whether or not a setup.py command exists. + + Args: + command (str): The command to look for + + Returns: + bool: True if the command is found, else False + """ + kwargs = { + 'output': os.devnull, + 'error': os.devnull, + 'fail_on_error': False + } + + python = inspect.getmodule(self).python + setup = self.setup_file() + + python(setup, '--no-user-cfg', command, '--help', **kwargs) + return python.returncode == 0 + + # The following phases and their descriptions come from: + # $ python setup.py --help-commands + + # Standard commands + + def build(self, spec, prefix): + """Build everything needed to install.""" + args = self.build_args(spec, prefix) + + self.setup_py('build', *args) + + def build_args(self, spec, prefix): + """Arguments to pass to build.""" + return [] + + def build_py(self, spec, prefix): + '''"Build" pure Python modules (copy to build directory).''' + args = self.build_py_args(spec, prefix) + + self.setup_py('build_py', *args) + + def build_py_args(self, spec, prefix): + """Arguments to pass to build_py.""" + return [] + + def build_ext(self, spec, prefix): + """Build C/C++ extensions (compile/link to build directory).""" + args = self.build_ext_args(spec, prefix) + + self.setup_py('build_ext', *args) + + def build_ext_args(self, spec, prefix): + """Arguments to pass to build_ext.""" + return [] + + def build_clib(self, spec, prefix): + """Build C/C++ libraries used by Python extensions.""" + args = self.build_clib_args(spec, prefix) + + self.setup_py('build_clib', *args) + + def build_clib_args(self, spec, prefix): + """Arguments to pass to build_clib.""" + return [] + + def build_scripts(self, spec, prefix): + '''"Build" scripts (copy and fixup #! line).''' + args = self.build_scripts_args(spec, prefix) + + self.setup_py('build_scripts', *args) + + def clean(self, spec, prefix): + """Clean up temporary files from 'build' command.""" + args = self.clean_args(spec, prefix) + + self.setup_py('clean', *args) + + def clean_args(self, spec, prefix): + """Arguments to pass to clean.""" + return [] + + def install(self, spec, prefix): + """Install everything from build directory.""" + args = self.install_args(spec, prefix) + + self.setup_py('install', *args) + + def install_args(self, spec, prefix): + """Arguments to pass to install.""" + args = ['--prefix={0}'.format(prefix)] + + # This option causes python packages (including setuptools) NOT + # to create eggs or easy-install.pth files. Instead, they + # install naturally into $prefix/pythonX.Y/site-packages. + # + # Eggs add an extra level of indirection to sys.path, slowing + # down large HPC runs. They are also deprecated in favor of + # wheels, which use a normal layout when installed. + # + # Spack manages the package directory on its own by symlinking + # extensions into the site-packages directory, so we don't really + # need the .pth files or egg directories, anyway. + if ('py-setuptools' == spec.name or # this is setuptools, or + 'py-setuptools' in spec._dependencies): # it's an immediate dep + args += ['--single-version-externally-managed', '--root=/'] + + return args + + def install_lib(self, spec, prefix): + """Install all Python modules (extensions and pure Python).""" + args = self.install_lib_args(spec, prefix) + + self.setup_py('install_lib', *args) + + def install_lib_args(self, spec, prefix): + """Arguments to pass to install_lib.""" + return [] + + def install_headers(self, spec, prefix): + """Install C/C++ header files.""" + args = self.install_headers_args(spec, prefix) + + self.setup_py('install_headers', *args) + + def install_headers_args(self, spec, prefix): + """Arguments to pass to install_headers.""" + return [] + + def install_scripts(self, spec, prefix): + """Install scripts (Python or otherwise).""" + args = self.install_scripts_args(spec, prefix) + + self.setup_py('install_scripts', *args) + + def install_scripts_args(self, spec, prefix): + """Arguments to pass to install_scripts.""" + return [] + + def install_data(self, spec, prefix): + """Install data files.""" + args = self.install_data_args(spec, prefix) + + self.setup_py('install_data', *args) + + def install_data_args(self, spec, prefix): + """Arguments to pass to install_data.""" + return [] + + def sdist(self, spec, prefix): + """Create a source distribution (tarball, zip file, etc.).""" + args = self.sdist_args(spec, prefix) + + self.setup_py('sdist', *args) + + def sdist_args(self, spec, prefix): + """Arguments to pass to sdist.""" + return [] + + def register(self, spec, prefix): + """Register the distribution with the Python package index.""" + args = self.register_args(spec, prefix) + + self.setup_py('register', *args) + + def register_args(self, spec, prefix): + """Arguments to pass to register.""" + return [] + + def bdist(self, spec, prefix): + """Create a built (binary) distribution.""" + args = self.bdist_args(spec, prefix) + + self.setup_py('bdist', *args) + + def bdist_args(self, spec, prefix): + """Arguments to pass to bdist.""" + return [] + + def bdist_dumb(self, spec, prefix): + '''Create a "dumb" built distribution.''' + args = self.bdist_dumb_args(spec, prefix) + + self.setup_py('bdist_dumb', *args) + + def bdist_dumb_args(self, spec, prefix): + """Arguments to pass to bdist_dumb.""" + return [] + + def bdist_rpm(self, spec, prefix): + """Create an RPM distribution.""" + args = self.bdist_rpm(spec, prefix) + + self.setup_py('bdist_rpm', *args) + + def bdist_rpm_args(self, spec, prefix): + """Arguments to pass to bdist_rpm.""" + return [] + + def bdist_wininst(self, spec, prefix): + """Create an executable installer for MS Windows.""" + args = self.bdist_wininst_args(spec, prefix) + + self.setup_py('bdist_wininst', *args) + + def bdist_wininst_args(self, spec, prefix): + """Arguments to pass to bdist_wininst.""" + return [] + + def upload(self, spec, prefix): + """Upload binary package to PyPI.""" + args = self.upload_args(spec, prefix) + + self.setup_py('upload', *args) + + def upload_args(self, spec, prefix): + """Arguments to pass to upload.""" + return [] + + def check(self, spec, prefix): + """Perform some checks on the package.""" + args = self.check_args(spec, prefix) + + self.setup_py('check', *args) + + def check_args(self, spec, prefix): + """Arguments to pass to check.""" + return [] + + # Testing + + def test(self): + """Run unit tests after in-place build. + + These tests are only run if the package actually has a 'test' command. + """ + if self._setup_command_available('test'): + args = self.test_args(self.spec, self.prefix) + + self.setup_py('test', *args) + + def test_args(self, spec, prefix): + """Arguments to pass to test.""" + return [] + + run_after('build')(PackageBase._run_default_build_time_test_callbacks) + + def import_module_test(self): + """Attempts to import the module that was just installed. + + This test is only run if the package overrides + :py:attr:`import_modules` with a list of module names.""" + + # Make sure we are importing the installed modules, + # not the ones in the current directory + with working_dir('..'): + for module in self.import_modules: + self.python('-c', 'import {0}'.format(module)) + + run_after('install')(PackageBase._run_default_install_time_test_callbacks) + + # Check that self.prefix is there after installation + run_after('install')(PackageBase.sanity_check_prefix) diff --git a/lib/spack/docs/tutorial_buildsystems.rst b/lib/spack/docs/tutorial_buildsystems.rst new file mode 100644 index 0000000000..cdc8aeed7c --- /dev/null +++ b/lib/spack/docs/tutorial_buildsystems.rst @@ -0,0 +1,778 @@ +.. _build-systems-tutorial: + +============================== +Spack Package Build Systems +============================== + +You may begin to notice after writing a couple of package template files a +pattern emerge for some packages. For example, you may find yourself writing +an :code:`install()` method that invokes: :code:`configure`, :code:`cmake`, +:code:`make`, :code:`make install`. You may also find yourself writing +:code:`"prefix=" + prefix` as an argument to configure or cmake. Rather than +having you repeat these lines for all packages, Spack has classes that can +take care of these patterns. In addition, these package files allow for finer +grained control of these build systems. In this section, we will describe +each build system and give examples on how these can be manipulated to +install a package. + +----------------------- +Package class Hierarchy +----------------------- +.. graphviz:: + + digraph { + {Package, MakefilePackage, AutotoolsPackage, CMakePackage, PythonPackage, RPackage} -> PackageBaseClass + } + +The above diagram gives a high level view of the class hierarchy and how each +package relates. Each subclass inherits from the :code:`PackageBaseClass` +super class. The bulk of the work is done in this super class which includes +fetching, extracting to a staging directory and installing. Each subclass +then adds additional build-system-specific functionality. In the following +sections, we will go over examples of how to utilize each subclass and to see +how powerful these abstractions are when packaging. + +----------------- +Package +----------------- + +We've already seen examples of a :code:`Package` class in our walkthrough for writing +package files, so we won't be spending much time with them here. Briefly, +the Package class allows for abitrary control over the build process, whereas +subclasses rely on certain patterns (e.g. :code:`configure` :code:`make` +:code:`make install`) to be useful. :code:`Package` classes are particularly useful +for packages that have a non-conventional way of being built since the packager +can utilize some of Spack's helper functions to customize the building and +installing of a package. + +------------------- +Autotools +------------------- + +As we have seen earlier, packages using :code:`Autotools` use :code:`configure`, +:code:`make` and :code:`make install` commands to execute the build and +install process. In our :code:`Package` class, your typical build incantation will +consist of the following: + +.. code-block:: python + + def install(self, spec, prefix): + configure("--prefix=" + prefix) + make() + make("install") + +You'll see that this looks similar to what we wrote in our packaging tutorial. + +The :code:`Autotools` subclass aims to simplify writing package files and provides +convenience methods to manipulate each of the different phases for a :code:`Autotools` +build system. + +:code:`Autotools` packages consist of four phases: + +1. :code:`autoreconf()` +2. :code:`configure()` +3. :code:`build()` +4. :code:`install()` + + +Each of these phases have sensible defaults. Let's take a quick look at some +the internals of the :code:`Autotools` class: + +.. code-block:: console + + $ spack edit --build-system autotools + + +This will open the :code:`AutotoolsPackage` file in your text editor. + +.. note:: + The examples showing code for these classes is abridged to avoid having + long examples. We only show what is relevant to the packager. + + +.. literalinclude:: tutorial/examples/Autotools/autotools_class.py + :language: python + :emphasize-lines: 42,45,62 + :lines: 40-95,259-267 + :linenos: + + +Important to note are the highlighted lines. These properties allow the +packager to set what build targets and install targets they want for their +package. If, for example, we wanted to add as our build target :code:`foo` +then we can append to our :code:`build_targets` property: + +.. code-block:: python + + build_targets = ["foo"] + +Which is similiar to invoking make in our Package + +.. code-block:: python + + make("foo") + +This is useful if we have packages that ignore environment variables and need +a command-line argument. + +Another thing to take note of is in the :code:`configure()` method. +Here we see that the :code:`prefix` argument is already included since it is a +common pattern amongst packages using :code:`Autotools`. We then only have to +override :code:`configure_args()`, which will then return it's output to +to :code:`configure()`. Then, :code:`configure()` will append the common +arguments + +Let's look at the :code:`mpileaks` package.py file that we worked on earlier: + +.. code-block:: console + + $ spack edit mpileaks + +Notice that mpileaks is a :code:`Package` class but uses the :code:`Autotools` +build system. Although this package is acceptable let's make this into an +:code:`AutotoolsPackage` class and simplify it further. + +.. literalinclude:: tutorial/examples/Autotools/0.package.py + :language: python + :emphasize-lines: 28 + :linenos: + +We first inherit from the :code:`AutotoolsPackage` class. + + +Although we could keep the :code:`install()` method, most of it can be handled +by the :code:`AutotoolsPackage` base class. In fact, the only thing that needs +to be overridden is :code:`configure_args()`. + +.. literalinclude:: tutorial/examples/Autotools/1.package.py + :language: python + :emphasize-lines: 42,43 + :linenos: + +Since Spack takes care of setting the prefix for us we can exclude that as +an argument to :code:`configure`. Our packages look simpler, and the packager +does not need to worry about whether they have properly included :code:`configure` +and :code:`make`. + +This version of the :code:`mpileaks` package installs the same as the previous, +but the :code:`AutotoolsPackage` class lets us do it with a cleaner looking +package file. + +----------------- +Makefile +----------------- + +Packages that utilize :code:`GNU Make` or a :code:`Makefile` usually require you +to edit a :code:`Makefile` to set up platform and compiler specific variables. +These packages are handled by the :code:`Makefile` subclass which provides +convenience methods to help write these types of packages. + +A :code:`MakefilePackage` class has three phases that can be overridden. These include: + + 1. :code:`edit()` + 2. :code:`build()` + 3. :code:`install()` + +Packagers then have the ability to control how a :code:`Makefile` is edited, and +what targets to include for the build phase or install phase. + +Let's also take a look inside the :code:`MakefilePackage` class: + +.. code-block:: console + + $ spack edit --build-system makefile + +Take note of the following: + + +.. literalinclude:: tutorial/examples/Makefile/makefile_class.py + :language: python + :lines: 33-79,89-107 + :emphasize-lines: 48,54,61 + :linenos: + +Similar to :code:`Autotools`, :code:`MakefilePackage` class has properties +that can be set by the packager. We can also override the different +methods highlighted. + + +Let's try to recreate the Bowtie_ package: + +.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml + + +.. code-block:: console + + $ spack create -f https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip + ==> This looks like a URL for bowtie + ==> Found 1 version of bowtie: + + 1.2.1.1 https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip + + ==> How many would you like to checksum? (default is 1, q to abort) 1 + ==> Downloading... + ==> Fetching https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.1.1/bowtie-1.2.1.1-src.zip + ######################################################################## 100.0% + ==> Checksummed 1 version of bowtie + ==> This package looks like it uses the makefile build system + ==> Created template for bowtie package + ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/bowtie/package.py + +Once the fetching is completed, Spack will open up your text editor in the +usual fashion and create a template of a :code:`MakefilePackage` package.py. + +.. literalinclude:: tutorial/examples/Makefile/0.package.py + :language: python + :linenos: + +Spack was successfully able to detect that :code:`Bowtie` uses :code:`GNU Make`. +Let's add in the rest of our details for our package: + +.. literalinclude:: tutorial/examples/Makefile/1.package.py + :language: python + :emphasize-lines: 29,30,32,33,37,39 + :linenos: + +As we mentioned earlier, most packages using a :code:`Makefile` have hard-coded +variables that must be edited. These variables are fine if you happen to not +care about setup or types of compilers used but Spack is designed to work with +any compiler. The :code:`MakefilePackage` subclass makes it easy to edit +these :code:`Makefiles` by having an :code:`edit()` method that +can be overridden. + +Let's take a look at the default :code:`Makefile` that :code:`Bowtie` provides. +If we look inside, we see that :code:`CC` and :code:`CXX` point to our GNU +compiler: + +.. code-block:: console + + $ spack stage bowtie + +.. note:: + As usual make sure you have shell support activated with spack: + :code:`source /path/to/spack_root/spack/share/spack/setup-env.sh` + +.. code-block:: console + + $ spack cd -s bowtie + $ cd bowtie-1.2 + $ vim Makefile + + +.. code-block:: make + + CPP = g++ -w + CXX = $(CPP) + CC = gcc + LIBS = $(LDFLAGS) -lz + HEADERS = $(wildcard *.h) + +To fix this, we need to use the :code:`edit()` method to write our custom +:code:`Makefile`. + +.. literalinclude:: tutorial/examples/Makefile/2.package.py + :language: python + :emphasize-lines: 42,43,44 + :linenos: + +Here we use a :code:`FileFilter` object to edit our :code:`Makefile`. It takes +in a regular expression and then replaces :code:`CC` and :code:`CXX` to whatever +Spack sets :code:`CC` and :code:`CXX` environment variables to. This allows us to +build :code:`Bowtie` with whatever compiler we specify through Spack's +:code:`spec` syntax. + +Let's change the build and install phases of our package: + +.. literalinclude:: tutorial/examples/Makefile/3.package.py + :language: python + :emphasize-lines: 46, 52 + :linenos: + +Here demonstrate another strategy that we can use to manipulate our package +We can provide command-line arguments to :code:`make()`. Since :code:`Bowtie` +can use :code:`tbb` we can either add :code:`NO_TBB=1` as a argument to prevent +:code:`tbb` support or we can just invoke :code:`make` with no arguments. + +:code:`Bowtie` requires our :code:`install_target` to provide a path to +the install directory. We can do this by providing :code:`prefix=` as a command +line argument to :code:`make()`. + +Let's look at a couple of other examples and go through them: + +.. code-block:: console + + $ spack edit cbench + +Some packages allow environment variables to be set and will honor them. +Packages that use :code:`?=` for assignment in their :code:`Makefile` +can be set using environment variables. In our :code:`cbench` example we +set two environment variables in our :code:`edit()` method: + +.. code-block:: python + + def edit(self, spec, prefix): + # The location of the Cbench source tree + env['CBENCHHOME'] = self.stage.source_path + + # The location that will contain all your tests and your results + env['CBENCHTEST'] = prefix + + # ... more code + +As you may have noticed, we didn't really write anything to the :code:`Makefile` +but rather we set environment variables that will override variables set in +the :code:`Makefile`. + +Some packages include a configuration file that sets certain compiler variables, +platform specific variables, and the location of dependencies or libraries. +If the file is simple and only requires a couple of changes, we can overwrite +those entries with our :code:`FileFilter` object. If the configuration involves +complex changes, we can write a new configuration file from scratch. + +Let's look at an example of this in the :code:`elk` package: + +.. code-block:: console + + $ spack edit elk + +.. code-block:: python + + def edit(self, spec, prefix): + # Dictionary of configuration options + config = { + 'MAKE': 'make', + 'AR': 'ar' + } + + # Compiler-specific flags + flags = '' + if self.compiler.name == 'intel': + flags = '-O3 -ip -unroll -no-prec-div' + elif self.compiler.name == 'gcc': + flags = '-O3 -ffast-math -funroll-loops' + elif self.compiler.name == 'pgi': + flags = '-O3 -lpthread' + elif self.compiler.name == 'g95': + flags = '-O3 -fno-second-underscore' + elif self.compiler.name == 'nag': + flags = '-O4 -kind=byte -dusty -dcfuns' + elif self.compiler.name == 'xl': + flags = '-O3' + config['F90_OPTS'] = flags + config['F77_OPTS'] = flags + + # BLAS/LAPACK support + # Note: BLAS/LAPACK must be compiled with OpenMP support + # if the +openmp variant is chosen + blas = 'blas.a' + lapack = 'lapack.a' + if '+blas' in spec: + blas = spec['blas'].libs.joined() + if '+lapack' in spec: + lapack = spec['lapack'].libs.joined() + # lapack must come before blas + config['LIB_LPK'] = ' '.join([lapack, blas]) + + # FFT support + if '+fft' in spec: + config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib, + 'libfftw3.so') + config['SRC_FFT'] = 'zfftifc_fftw.f90' + else: + config['LIB_FFT'] = 'fftlib.a' + config['SRC_FFT'] = 'zfftifc.f90' + + # MPI support + if '+mpi' in spec: + config['F90'] = spec['mpi'].mpifc + config['F77'] = spec['mpi'].mpif77 + else: + config['F90'] = spack_fc + config['F77'] = spack_f77 + config['SRC_MPI'] = 'mpi_stub.f90' + + # OpenMP support + if '+openmp' in spec: + config['F90_OPTS'] += ' ' + self.compiler.openmp_flag + config['F77_OPTS'] += ' ' + self.compiler.openmp_flag + else: + config['SRC_OMP'] = 'omp_stub.f90' + + # Libxc support + if '+libxc' in spec: + config['LIB_libxc'] = ' '.join([ + join_path(spec['libxc'].prefix.lib, 'libxcf90.so'), + join_path(spec['libxc'].prefix.lib, 'libxc.so') + ]) + config['SRC_libxc'] = ' '.join([ + 'libxc_funcs.f90', + 'libxc.f90', + 'libxcifc.f90' + ]) + else: + config['SRC_libxc'] = 'libxcifc_stub.f90' + + # Write configuration options to include file + with open('make.inc', 'w') as inc: + for key in config: + inc.write('{0} = {1}\n'.format(key, config[key])) + +:code:`config` is just a dictionary that we can add key-value pairs to. By the +end of the :code:`edit()` method we write the contents of our dictionary to +:code:`make.inc`. + +--------------- +CMake +--------------- + +CMake_ is another common build system that has been gaining popularity. It works +in a similar manner to :code:`Autotools` but with differences in variable names, +the number of configuration options available, and the handling of shared libraries. +Typical build incantations look like this: + +.. _CMake: https://cmake.org + +.. code-block:: python + + def install(self, spec, prefix): + cmake("-DCMAKE_INSTALL_PREFIX:PATH=/path/to/install_dir ..") + make() + make("install") + +As you can see from the example above, it's very similar to invoking +:code:`configure` and :code:`make` in an :code:`Autotools` build system. However, +the variable names and options differ. Most options in CMake are prefixed +with a :code:`'-D'` flag to indicate a configuration setting. + +In the :code:`CMakePackage` class we can override the following phases: + +1. :code:`cmake()` +2. :code:`build()` +3. :code:`install()` + +The :code:`CMakePackage` class also provides sensible defaults so we only need to +override :code:`cmake_args()`. + +Let's look at these defaults in the :code:`CMakePackage` class: + +.. code-block:: console + + $ spack edit --build-system cmake + + +And go into a bit of detail on the highlighted sections: + + +.. literalinclude:: tutorial/examples/Cmake/cmake_class.py + :language: python + :lines: 37-92, 94-155, 174-211 + :emphasize-lines: 57,68,86,94,96,99,100,101,102,111,117,135,136 + :linenos: + +Some :code:`CMake` packages use different generators. Spack is able to support +Unix-Makefile_ generators as well as Ninja_ generators. + +.. _Unix-Makefile: https://cmake.org/cmake/help/v3.4/generator/Unix%20Makefiles.html +.. _Ninja: https://cmake.org/cmake/help/v3.4/generator/Ninja.html + +Default generator is :code:`Unix Makefile`. + +Next we setup the build type. In :code:`CMake` you can specify the build type +that you want. Options include: + +1. empty +2. Debug +3. Release +4. RelWithDebInfo +5. MinSizeRel + +With these options you can specify whether you want your executable to have +the debug version only, release version or the release with debug information. +Release executables tend to be more optimized than Debug. In Spack, we set +the default as RelWithDebInfo unless otherwise specified through a variant. + +Spack then automatically sets up the :code:`-DCMAKE_INSTALL_PREFIX` path, +appends the build type (RelDebInfo default), and then specifies a verbose +:code:`Makefile`. + +Next we add the :code:`rpaths` to :code:`-DCMAKE_INSTALL_RPATH:STRING`. + + +Finally we add to :code:`-DCMAKE_PREFIX_PATH:STRING` the locations of all our +dependencies so that :code:`CMake` can find them. + +In the end our :code:`cmake` line will look like this (example is :code:`xrootd`): + +.. code-block:: console + + $ cmake $HOME/spack/var/spack/stage/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/xrootd-4.6.0 -G Unix Makefiles -DCMAKE_INSTALL_PREFIX:PATH=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_FIND_FRAMEWORK:STRING=LAST -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE -DCMAKE_INSTALL_RPATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib:$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/xrootd-4.6.0-4ydm74kbrp4xmcgda5upn33co5pwddyk/lib64 -DCMAKE_PREFIX_PATH:STRING=$HOME/spack/opt/spack/darwin-sierra-x86_64/clang-9.0.0-apple/cmake-3.9.4-hally3vnbzydiwl3skxcxcbzsscaasx5 + + +Saves a lot of typing doesn't it? + + +Let's try to recreate callpath_: + +.. _callpath: https://github.com/LLNL/callpath.git + +.. code-block:: console + + $ spack create -f https://github.com/llnl/callpath/archive/v1.0.3.tar.gz + ==> This looks like a URL for callpath + ==> Found 4 versions of callpath: + + 1.0.3 https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz + 1.0.2 https://github.com/LLNL/callpath/archive/v1.0.2.tar.gz + 1.0.1 https://github.com/LLNL/callpath/archive/v1.0.1.tar.gz + 1.0 https://github.com/LLNL/callpath/archive/v1.0.tar.gz + + ==> How many would you like to checksum? (default is 1, q to abort) 1 + ==> Downloading... + ==> Fetching https://github.com/LLNL/callpath/archive/v1.0.3.tar.gz + ######################################################################## 100.0% + ==> Checksummed 1 version of callpath + ==> This package looks like it uses the cmake build system + ==> Created template for callpath package + ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/callpath/package.py + + +which then produces the following template: + +.. literalinclude:: tutorial/examples/Cmake/0.package.py + :language: python + :linenos: + +Again we fill in the details: + +.. literalinclude:: tutorial/examples/Cmake/1.package.py + :language: python + :linenos: + :emphasize-lines: 28,32,33,37,38,39,40,41,42 + +As mentioned earlier, Spack will use sensible defaults to prevent repeated code +and to make writing :code:`CMake` package files simpler. + +In callpath, we want to add options to :code:`CALLPATH_WALKER` as well as add +compiler flags. We add the following options like so: + +.. literalinclude:: tutorial/examples/Cmake/2.package.py + :language: python + :linenos: + :emphasize-lines: 45,49,50 + +Now we can control our build options using :code:`cmake_args()`. If defaults are +sufficient enough for the package, we can leave this method out. + +:code:`CMakePackage` classes allow for control of other features in the +build system. For example, you can specify the path to the "out of source" +build directory and also point to the root of the :code:`CMakeLists.txt` file if it +is placed in a non-standard location. + +A good example of a package that has its :code:`CMakeLists.txt` file located at a +different location is found in :code:`spades`. + +.. code-block:: console + + $ spack edit spade. + +.. code-block:: python + + root_cmakelists_dir = "src" + +Here :code:`root_cmakelists_dir` will tell Spack where to find the location +of :code:`CMakeLists.txt`. In this example, it is located a directory level below in +the :code:`src` directory. + +Some :code:`CMake` packages also require the :code:`install` phase to be +overridden. For example, let's take a look at :code:`sniffles`. + +.. code-block:: console + + $ spack edit sniffles + +In the :code:`install()` method, we have to manually install our targets +so we override the :code:`install()` method to do it for us: + +.. code-block:: python + + # the build process doesn't actually install anything, do it by hand + def install(self, spec, prefix): + mkdir(prefix.bin) + src = "bin/sniffles-core-{0}".format(spec.version.dotted) + binaries = ['sniffles', 'sniffles-debug'] + for b in binaries: + install(join_path(src, b), join_path(prefix.bin, b)) + + +-------------- +PythonPackage +-------------- + +Python extensions and modules are built differently from source than most +applications. Python uses a :code:`setup.py` script to install Python modules. +The script consists of a call to :code:`setup()` which provides the information +required to build a module to Distutils. If you're familiar with pip or +easy_install, setup.py does the same thing. + +These modules are usually installed using the following line: + +.. code-block:: console + + $ python setup.py install + +There are also a list of commands and phases that you can call. To see the full +list you can run: + +.. code-block:: console + + $ python setup.py --help-commands + Standard commands: + build build everything needed to install + build_py "build" pure Python modules (copy to build directory) + build_ext build C/C++ extensions (compile/link to build directory) + build_clib build C/C++ libraries used by Python extensions + build_scripts "build" scripts (copy and fixup #! line) + clean (no description available) + install install everything from build directory + install_lib install all Python modules (extensions and pure Python) + install_headers install C/C++ header files + install_scripts install scripts (Python or otherwise) + install_data install data files + sdist create a source distribution (tarball, zip file, etc.) + register register the distribution with the Python package index + bdist create a built (binary) distribution + bdist_dumb create a "dumb" built distribution + bdist_rpm create an RPM distribution + bdist_wininst create an executable installer for MS Windows + upload upload binary package to PyPI + check perform some checks on the package + + +To see the defaults that Spack has for each a methods, we will take a look +at the :code:`PythonPackage` class: + +.. code-block:: console + + $ spack edit --build-system python + +We see the following: + + +.. literalinclude:: tutorial/examples/PyPackage/python_package_class.py + :language: python + :lines: 35, 161-364 + :linenos: + +Each of these methods have sensible defaults or they can be overridden. + +We can write package files for Python packages using the :code:`Package` class, +but the class brings with it a lot of methods that are useless for Python packages. +Instead, Spack has a :code: `PythonPackage` subclass that allows packagers +of Python modules to be able to invoke :code:`setup.py` and use :code:`Distutils`, +which is much more familiar to a typical python user. + + +We will write a package file for Pandas_: + +.. _pandas: https://pandas.pydata.org + +.. code-block:: console + + $ spack create -f https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz + ==> This looks like a URL for pandas + ==> Warning: Spack was unable to fetch url list due to a certificate verification problem. You can try running spack -k, which will not check SSL certificates. Use this at your own risk. + ==> Found 1 version of pandas: + + 0.19.0 https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz + + ==> How many would you like to checksum? (default is 1, q to abort) 1 + ==> Downloading... + ==> Fetching https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz + ######################################################################## 100.0% + ==> Checksummed 1 version of pandas + ==> This package looks like it uses the python build system + ==> Changing package name from pandas to py-pandas + ==> Created template for py-pandas package + ==> Created package file: /Users/mamelara/spack/var/spack/repos/builtin/packages/py-pandas/package.py + +And we are left with the following template: + +.. literalinclude:: tutorial/examples/PyPackage/0.package.py + :language: python + :linenos: + +As you can see this is not any different than any package template that we have +written. We have the choice of providing build options or using the sensible +defaults + +Luckily for us, there is no need to provide build args. + +Next we need to find the dependencies of a package. Dependencies are usually +listed in :code:`setup.py`. You can find the dependencies by searching for +:code:`install_requires` keyword in that file. Here it is for :code:`Pandas`: + +.. code-block:: python + + # ... code + if sys.version_info[0] >= 3: + + setuptools_kwargs = { + 'zip_safe': False, + 'install_requires': ['python-dateutil >= 2', + 'pytz >= 2011k', + 'numpy >= %s' % min_numpy_ver], + 'setup_requires': ['numpy >= %s' % min_numpy_ver], + } + if not _have_setuptools: + sys.exit("need setuptools/distribute for Py3k" + "\n$ pip install distribute") + + # ... more code + +You can find a more comprehensive list at the Pandas documentation_. + +.. _documentation: https://pandas.pydata.org/pandas-docs/stable/install.html + + +By reading the documentation and :code:`setup.py` we found that :code:`Pandas` +depends on :code:`python-dateutil`, :code:`pytz`, and :code:`numpy`, :code:`numexpr`, +and finally :code:`bottleneck`. + +Here is the completed :code:`Pandas` script: + +.. literalinclude:: tutorial/examples/PyPackage/1.package.py + :language: python + :linenos: + +It is quite important to declare all the dependencies of a Python package. +Spack can "activate" Python packages to prevent the user from having to +load each dependency module explictly. If a dependency is missed, Spack will +be unable to properly activate the package and it will cause an issue. To +learn more about extensions go to :ref:`cmd-spack-extensions`. + +From this example, you can see that building Python modules is made easy +through the :code:`PythonPackage` class. + +------------------- +Other Build Systems +------------------- + +Although we won't get in depth with any of the other build systems that Spack +supports, it is worth mentioning that Spack does provide subclasses +for the following build systems: + +1. :code:`IntelPackage` +2. :code:`SconsPackage` +3. :code:`WafPackage` +4. :code:`RPackage` +5. :code:`PerlPackage` +6. :code:`QMake` + + +Each of these classes have their own abstractions to help assist in writing +package files. For whatever doesn't fit nicely into the other build-systems, +you can use the :code:`Package` class. + +Hopefully by now you can see how we aim to make packaging simple and +robust through these classes. If you want to learn more about these build +systems, check out :ref:`installation_procedure` in the Packaging Guide. |