diff options
| -rw-r--r-- | lib/spack/docs/packaging_guide.rst | 98 | ||||
| -rw-r--r-- | lib/spack/spack/__init__.py | 7 | ||||
| -rw-r--r-- | lib/spack/spack/compilers/gcc.py | 3 | ||||
| -rw-r--r-- | lib/spack/spack/package.py | 55 | ||||
| -rw-r--r-- | lib/spack/spack/url.py | 2 | ||||
| -rw-r--r-- | lib/spack/spack/util/compression.py | 7 | ||||
| -rwxr-xr-x | share/spack/setup-env.sh | 2 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/curl/package.py | 1 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/libelf/package.py | 3 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/netlib-scalapack/package.py | 11 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/openblas/package.py | 7 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/papi/package.py | 1 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/superlu-dist/package.py | 63 |
13 files changed, 221 insertions, 39 deletions
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 169899212d..519c0da232 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -1559,11 +1559,11 @@ you ask for a particular spec. A user may have certain preferences for how packages should be concretized on their system. For example, one user may prefer packages built with OpenMPI and the Intel compiler. Another user may prefer -packages be built with MVAPICH and GCC. +packages be built with MVAPICH and GCC. Spack can be configured to prefer certain compilers, package versions, depends_on, and variants during concretization. -The preferred configuration can be controlled via the +The preferred configuration can be controlled via the ``~/.spack/packages.yaml`` file for user configuations, or the ``etc/spack/packages.yaml`` site configuration. @@ -1582,32 +1582,32 @@ Here's an example packages.yaml file that sets preferred packages: compiler: [gcc@4.4.7, gcc@4.6:, intel, clang, pgi] providers: mpi: [mvapich, mpich, openmpi] - + At a high level, this example is specifying how packages should be -concretized. The dyninst package should prefer using gcc 4.9 and +concretized. The dyninst package should prefer using gcc 4.9 and be built with debug options. The gperftools package should prefer version 2.2 over 2.4. Every package on the system should prefer mvapich for -its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9). -These options are used to fill in implicit defaults. Any of them can be overwritten +its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9). +These options are used to fill in implicit defaults. Any of them can be overwritten on the command line if explicitly requested. -Each packages.yaml file begins with the string ``packages:`` and +Each packages.yaml file begins with the string ``packages:`` and package names are specified on the next level. The special string ``all`` -applies settings to each package. Underneath each package name is -one or more components: ``compiler``, ``variants``, ``version``, -or ``providers``. Each component has an ordered list of spec +applies settings to each package. Underneath each package name is +one or more components: ``compiler``, ``variants``, ``version``, +or ``providers``. Each component has an ordered list of spec ``constraints``, with earlier entries in the list being preferred over later entries. -Sometimes a package installation may have constraints that forbid +Sometimes a package installation may have constraints that forbid the first concretization rule, in which case Spack will use the first legal concretization rule. Going back to the example, if a user -requests gperftools 2.3 or later, then Spack will install version 2.4 +requests gperftools 2.3 or later, then Spack will install version 2.4 as the 2.4 version of gperftools is preferred over 2.3. -An explicit concretization rule in the preferred section will always -take preference over unlisted concretizations. In the above example, +An explicit concretization rule in the preferred section will always +take preference over unlisted concretizations. In the above example, xlc isn't listed in the compiler list. Every listed compiler from gcc to pgi will thus be preferred over the xlc compiler. @@ -1844,6 +1844,20 @@ dedicated process. .. _prefix-objects: + +Failing the build +---------------------- + +Sometimes you don't want a package to successfully install unless some +condition is true. You can explicitly cause the build to fail from +``install()`` by raising an ``InstallError``, for example: + +.. code-block:: python + + if spec.architecture.startswith('darwin'): + raise InstallError('This package does not build on Mac OS X!') + + Prefix objects ---------------------- @@ -2160,6 +2174,62 @@ package, this allows us to avoid race conditions in the library's build system. +.. _sanity-checks: + +Sanity checking an intallation +-------------------------------- + +By default, Spack assumes that a build has failed if nothing is +written to the install prefix, and that it has succeeded if anything +(a file, a directory, etc.) is written to the install prefix after +``install()`` completes. + +Consider a simple autotools build like this: + +.. code-block:: python + + def install(self, spec, prefix): + configure("--prefix=" + prefix) + make() + make("install") + +If you are using using standard autotools or CMake, ``configure`` and +``make`` will not write anything to the install prefix. Only ``make +install`` writes the files, and only once the build is already +complete. Not all builds are like this. Many builds of scientific +software modify the install prefix *before* ``make install``. Builds +like this can falsely report that they were successfully installed if +an error occurs before the install is complete but after files have +been written to the ``prefix``. + + +``sanity_check_is_file`` and ``sanity_check_is_dir`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +You can optionally specify *sanity checks* to deal with this problem. +Add properties like this to your package: + +.. code-block:: python + + class MyPackage(Package): + ... + + sanity_check_is_file = ['include/libelf.h'] + sanity_check_is_dir = [lib] + + def install(self, spec, prefix): + configure("--prefix=" + prefix) + make() + make("install") + +Now, after ``install()`` runs, Spack will check whether +``$prefix/include/libelf.h`` exists and is a file, and whether +``$prefix/lib`` exists and is a directory. If the checks fail, then +the build will fail and the install prefix will be removed. If they +succeed, Spack considers the build succeeful and keeps the prefix in +place. + + .. _file-manipulation: File manipulation functions diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index 3051d3f742..aee11f061f 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -188,3 +188,10 @@ __all__ += spack.directives.__all__ import spack.util.executable from spack.util.executable import * __all__ += spack.util.executable.__all__ + +from spack.package import \ + install_dependency_symlinks, flatten_dependencies, DependencyConflictError, \ + InstallError, ExternalPackageError +__all__ += [ + 'install_dependency_symlinks', 'flatten_dependencies', 'DependencyConflictError', + 'InstallError', 'ExternalPackageError'] diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py index 495b638a3a..64214db32d 100644 --- a/lib/spack/spack/compilers/gcc.py +++ b/lib/spack/spack/compilers/gcc.py @@ -40,7 +40,8 @@ class Gcc(Compiler): fc_names = ['gfortran'] # MacPorts builds gcc versions with prefixes and -mp-X.Y suffixes. - suffixes = [r'-mp-\d\.\d'] + # Homebrew and Linuxes may build gcc with -X, -X.Y suffixes + suffixes = [r'-mp-\d\.\d', r'-\d\.\d', r'-\d'] # Named wrapper links within spack.build_env_path link_paths = {'cc' : 'gcc/gcc', diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 02fb3e5834..dafad0b184 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -318,16 +318,17 @@ class Package(object): """Most packages are NOT extendable. Set to True if you want extensions.""" extendable = False - """List of prefix-relative file paths. If these do not exist after - install, or if they exist but are not files, sanity checks fail. + """List of prefix-relative file paths (or a single path). If these do + not exist after install, or if they exist but are not files, + sanity checks fail. """ - sanity_check_files = [] + sanity_check_is_file = [] - """List of prefix-relative directory paths. If these do not exist - after install, or if they exist but are not directories, sanity - checks will fail. + """List of prefix-relative directory paths (or a single path). If + these do not exist after install, or if they exist but are not + directories, sanity checks will fail. """ - sanity_check_dirs = [] + sanity_check_is_dir = [] def __init__(self, spec): @@ -966,14 +967,17 @@ class Package(object): def sanity_check_prefix(self): """This function checks whether install succeeded.""" def check_paths(path_list, filetype, predicate): + if isinstance(path_list, basestring): + path_list = [path_list] + for path in path_list: abs_path = os.path.join(self.prefix, path) if not predicate(abs_path): raise InstallError("Install failed for %s. No such %s in prefix: %s" % (self.name, filetype, path)) - check_paths(self.sanity_check_files, 'file', os.path.isfile) - check_paths(self.sanity_check_dirs, 'directory', os.path.isdir) + check_paths(self.sanity_check_is_file, 'file', os.path.isfile) + check_paths(self.sanity_check_is_dir, 'directory', os.path.isdir) installed = set(os.listdir(self.prefix)) installed.difference_update(spack.install_layout.hidden_file_paths) @@ -1239,6 +1243,27 @@ class Package(object): return " ".join("-Wl,-rpath,%s" % p for p in self.rpath) +def install_dependency_symlinks(pkg, spec, prefix): + """Execute a dummy install and flatten dependencies""" + flatten_dependencies(spec, prefix) + +def flatten_dependencies(spec, flat_dir): + """Make each dependency of spec present in dir via symlink.""" + for dep in spec.traverse(root=False): + name = dep.name + + dep_path = spack.install_layout.path_for_spec(dep) + dep_files = LinkTree(dep_path) + + os.mkdir(flat_dir+'/'+name) + + conflict = dep_files.find_conflict(flat_dir+'/'+name) + if conflict: + raise DependencyConflictError(conflict) + + dep_files.merge(flat_dir+'/'+name) + + def validate_package_url(url_string): """Determine whether spack can handle a particular URL or not.""" url = urlparse(url_string) @@ -1326,6 +1351,10 @@ class InstallError(spack.error.SpackError): super(InstallError, self).__init__(message, long_msg) +class ExternalPackageError(InstallError): + """Raised by install() when a package is only for external use.""" + + class PackageStillNeededError(InstallError): """Raised when package is still needed by another on uninstall.""" def __init__(self, spec, dependents): @@ -1376,3 +1405,11 @@ class ExtensionConflictError(ExtensionError): class ActivationError(ExtensionError): def __init__(self, msg, long_msg=None): super(ActivationError, self).__init__(msg, long_msg) + + +class DependencyConflictError(spack.error.SpackError): + """Raised when the dependencies cannot be flattened as asked for.""" + def __init__(self, conflict): + super(DependencyConflictError, self).__init__( + "%s conflicts with another file in the flattened directory." %( + conflict)) diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py index ad551a6ded..f51f05cad7 100644 --- a/lib/spack/spack/url.py +++ b/lib/spack/spack/url.py @@ -142,7 +142,7 @@ def split_url_extension(path): def downloaded_file_extension(path): """This returns the type of archive a URL refers to. This is - sometimes confusing becasue of URLs like: + sometimes confusing because of URLs like: (1) https://github.com/petdance/ack/tarball/1.93_02 diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py index ea1f233bce..5ae5867428 100644 --- a/lib/spack/spack/util/compression.py +++ b/lib/spack/spack/util/compression.py @@ -27,13 +27,12 @@ import os from itertools import product from spack.util.executable import which -# Supported archvie extensions. +# Supported archive extensions. PRE_EXTS = ["tar"] EXTS = ["gz", "bz2", "xz", "Z", "zip", "tgz"] -# Add EXTS last so that .tar.gz is matched *before* tar.gz -ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(PRE_EXTS, EXTS)] + EXTS - +# Add PRE_EXTS and EXTS last so that .tar.gz is matched *before* .tar or .gz +ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(PRE_EXTS, EXTS)] + PRE_EXTS + EXTS def allowed_archive(path): return any(path.endswith(t) for t in ALLOWED_ARCHIVE_TYPES) diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index 586a5b836b..764af68400 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -141,7 +141,7 @@ function _spack_pathadd { fi # Do the actual prepending here. - eval "_pa_oldvalue=\$${_pa_varname}" + eval "_pa_oldvalue=\${${_pa_varname}:-}" if [ -d "$_pa_new_path" ] && [[ ":$_pa_oldvalue:" != *":$_pa_new_path:"* ]]; then if [ -n "$_pa_oldvalue" ]; then diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py index 9e684445c7..ab6305fc08 100644 --- a/var/spack/repos/builtin/packages/curl/package.py +++ b/var/spack/repos/builtin/packages/curl/package.py @@ -7,6 +7,7 @@ class Curl(Package): homepage = "http://curl.haxx.se" url = "http://curl.haxx.se/download/curl-7.46.0.tar.bz2" + version('7.47.1', '9ea3123449439bbd960cd25cf98796fb') version('7.46.0', '9979f989a2a9930d10f1b3deeabc2148') version('7.45.0', '62c1a352b28558f25ba6209214beadc8') version('7.44.0', '6b952ca00e5473b16a11f05f06aa8dae') diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py index 0fcb56c164..9f16708af5 100644 --- a/var/spack/repos/builtin/packages/libelf/package.py +++ b/var/spack/repos/builtin/packages/libelf/package.py @@ -38,8 +38,7 @@ class Libelf(Package): provides('elf') - sanity_check_files = ['include/libelf.h'] - sanity_check_dirs = ['lib'] + sanity_check_is_file = 'include/libelf.h' def install(self, spec, prefix): configure("--prefix=" + prefix, diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py index 22d538560e..a5b6eedafb 100644 --- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py +++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py @@ -1,8 +1,9 @@ from spack import * +import sys class NetlibScalapack(Package): """ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines""" - + homepage = "http://www.netlib.org/scalapack/" url = "http://www.netlib.org/scalapack/scalapack-2.0.2.tgz" @@ -32,17 +33,17 @@ class NetlibScalapack(Package): "-DCMAKE_C_FLAGS=-fPIC", "-DCMAKE_Fortran_FLAGS=-fPIC" ]) - + options.extend(std_cmake_args) - + with working_dir('spack-build', create=True): cmake('..', *options) make() make("install") def setup_dependent_environment(self, module, spec, dependent_spec): - # TODO treat OS that are not Linux... - lib_suffix = '.so' if '+shared' in spec['scalapack'] else '.a' + lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so' + lib_suffix = lib_dsuffix if '+shared' in spec['scalapack'] else '.a' spec['scalapack'].fc_link = '-L%s -lscalapack' % spec['scalapack'].prefix.lib spec['scalapack'].cc_link = spec['scalapack'].fc_link diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 3c909360a4..781a1e2ec8 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,10 +1,12 @@ from spack import * +import sys class Openblas(Package): """OpenBLAS: An optimized BLAS library""" homepage = "http://www.openblas.net" url = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz" + version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc') version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') # virtual dependency @@ -15,13 +17,14 @@ class Openblas(Package): make('libs', 'netlib', 'shared', 'CC=cc', 'FC=f77') make('install', "PREFIX='%s'" % prefix) + lib_dsuffix = 'dylib' if sys.platform == 'darwin' else 'so' # Blas virtual package should provide blas.a and libblas.a with working_dir(prefix.lib): symlink('libopenblas.a', 'blas.a') symlink('libopenblas.a', 'libblas.a') - symlink('libopenblas.so', 'libblas.so') + symlink('libopenblas.%s' % lib_dsuffix, 'libblas.%s' % lib_dsuffix) # Lapack virtual package should provide liblapack.a with working_dir(prefix.lib): symlink('libopenblas.a', 'liblapack.a') - symlink('libopenblas.so', 'liblapack.so') + symlink('libopenblas.%s' % lib_dsuffix, 'liblapack.%s' % lib_dsuffix) diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index 910e0aa9f9..53d69e28d9 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -13,6 +13,7 @@ class Papi(Package): homepage = "http://icl.cs.utk.edu/papi/index.html" url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" + version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412') version('5.4.1', '9134a99219c79767a11463a76b0b01a2') version('5.3.0', '367961dd0ab426e5ae367c2713924ffb') diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py new file mode 100644 index 0000000000..c4c76909b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -0,0 +1,63 @@ +from spack import * + +class SuperluDist(Package): + """A general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.""" + homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" + url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz" + + version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae') + version('4.2', 'ae9fafae161f775fbac6eba11e530a65') + version('4.1', '4edee38cc29f687bd0c8eb361096a455') + version('4.0', 'c0b98b611df227ae050bc1635c6940e0') + + depends_on ('mpi') + depends_on ('blas') + depends_on ('lapack') + depends_on ('parmetis') + depends_on ('metis') + + def install(self, spec, prefix): + makefile_inc = [] + makefile_inc.extend([ + 'PLAT = _mac_x', + 'DSuperLUroot = %s' % self.stage.source_path, #self.stage.path, prefix + 'DSUPERLULIB = $(DSuperLUroot)/lib/libsuperlu_dist.a', + 'BLASDEF = -DUSE_VENDOR_BLAS', + 'BLASLIB = -L%s -llapack %s -lblas' % (spec['lapack'].prefix.lib, spec['blas'].prefix.lib), # FIXME: avoid hardcoding blas/lapack lib names + 'METISLIB = -L%s -lmetis' % spec['metis'].prefix.lib, + 'PARMETISLIB = -L%s -lparmetis' % spec['parmetis'].prefix.lib, + 'FLIBS =', + 'LIBS = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)', + 'ARCH = ar', + 'ARCHFLAGS = cr', + 'RANLIB = true', + 'CC = mpicc', # FIXME avoid hardcoding MPI compiler names + 'CFLAGS = -fPIC -std=c99 -O2 -I%s -I%s' %(spec['parmetis'].prefix.include, spec['metis'].prefix.include), + 'NOOPTS = -fPIC -std=c99', + 'FORTRAN = mpif77', + 'F90FLAGS = -O2', + 'LOADER = mpif77', + 'LOADOPTS =', + 'CDEFS = -DAdd_' + ]) + + #with working_dir('src'): + with open('make.inc', 'w') as fh: + fh.write('\n'.join(makefile_inc)) + + make("lib", parallel=False) + + # FIXME: + # cd "EXAMPLE" do + # system "make" + + # need to install by hand + headers_location = join_path(self.prefix.include,'superlu_dist') + mkdirp(headers_location) + # FIXME: fetch all headers in the folder automatically + for header in ['Cnames.h','cublas_utils.h','dcomplex.h','html_mainpage.h','machines.h','old_colamd.h','psymbfact.h','superlu_ddefs.h','superlu_defs.h','superlu_enum_consts.h','superlu_zdefs.h','supermatrix.h','util_dist.h']: + superludist_header = join_path(self.stage.source_path, 'SRC/',header) + install(superludist_header, headers_location) + + superludist_lib = join_path(self.stage.source_path, 'lib/libsuperlu_dist.a') + install(superludist_lib,self.prefix.lib) |