diff options
| -rw-r--r-- | lib/spack/spack/spec.py | 6 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/abinit/package.py | 134 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/hdf5/package.py | 87 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/libxc/package.py | 27 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/netcdf-fortran/package.py | 13 |
5 files changed, 180 insertions, 87 deletions
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 534bc6c2d3..adddb87428 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -901,16 +901,12 @@ class SpecBuildInterface(ObjectWrapper): ) is_virtual = Spec.is_virtual(name) - self._query_to_package = QueryState( + self.last_query = QueryState( name=name, extra_parameters=query_parameters, isvirtual=is_virtual ) - @property - def last_query(self): - return self._query_to_package - @key_ordering class Spec(object): diff --git a/var/spack/repos/builtin/packages/abinit/package.py b/var/spack/repos/builtin/packages/abinit/package.py index 1798059ee7..fe1c7ec778 100644 --- a/var/spack/repos/builtin/packages/abinit/package.py +++ b/var/spack/repos/builtin/packages/abinit/package.py @@ -28,13 +28,15 @@ from spack import * -class Abinit(Package): +class Abinit(AutotoolsPackage): """ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave - or wavelet basis. ABINIT also includes options to optimize the geometry - according to the DFT forces and stresses, or to perform molecular dynamics + or wavelet basis. + + ABINIT also includes options to optimize the geometry according to the + DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be @@ -44,11 +46,12 @@ class Abinit(Package): programs are provided. """ - homepage = "http://www.abinit.org" - url = "http://ftp.abinit.org/abinit-8.0.8b.tar.gz" + homepage = 'http://www.abinit.org' + url = 'http://ftp.abinit.org/abinit-8.0.8b.tar.gz' + version('8.2.2', '5f25250e06fdc0815c224ffd29858860') # Versions before 8.0.8b are not supported. - version("8.0.8b", "abc9e303bfa7f9f43f95598f87d84d5d") + version('8.0.8b', 'abc9e303bfa7f9f43f95598f87d84d5d') variant('mpi', default=True, description='Builds with MPI support. Requires MPI2+') @@ -57,7 +60,7 @@ class Abinit(Package): variant('scalapack', default=False, description='Enables scalapack support. Requires MPI') # variant('elpa', default=False, - # description='Uses elpa instead of scalapack. Requires MPI') + # description='Uses elpa instead of scalapack. Requires MPI') # TODO: To be tested. # It was working before the last `git pull` but now all tests crash. @@ -71,111 +74,108 @@ class Abinit(Package): # Add dependencies # currently one cannot forward options to virtual packages, see #1712. - # depends_on("blas", when="~openmp") - # depends_on("blas+openmp", when="+openmp") + # depends_on('blas', when='~openmp') + # depends_on('blas+openmp', when='+openmp') depends_on('blas') - depends_on("lapack") + depends_on('lapack') # Require MPI2+ - depends_on("mpi@2:", when="+mpi") + depends_on('mpi@2:', when='+mpi') - depends_on("scalapack", when="+scalapack+mpi") - # depends_on("elpa", when="+elpa+mpi~openmp") - # depends_on("elpa+openmp", when="+elpa+mpi+openmp") + depends_on('scalapack', when='+scalapack+mpi') - depends_on("fftw+float", when="~openmp") - depends_on("fftw+float+openmp", when="+openmp") + # depends_on('elpa~openmp', when='+elpa+mpi~openmp') + # depends_on('elpa+openmp', when='+elpa+mpi+openmp') - depends_on("netcdf-fortran", when="+hdf5") - depends_on("hdf5+mpi", when='+mpi+hdf5') # required for NetCDF-4 support + depends_on('fftw+float', when='~openmp') + depends_on('fftw+float+openmp', when='+openmp') + + depends_on('netcdf-fortran', when='+hdf5') + depends_on('hdf5+mpi', when='+mpi+hdf5') # required for NetCDF-4 support # pin libxc version - depends_on("libxc@2.2.1") + depends_on("libxc@2.2.2") - def validate(self, spec): - """ - Checks if incompatible variants have been activated at the same time + # Cannot ask for +scalapack if it does not depend on MPI + conflicts('+scalapack', when='~mpi') - :param spec: spec of the package - :raises RuntimeError: in case of inconsistencies - """ - error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active' + # Elpa is a substitute for scalapack and needs mpi + # conflicts('+elpa', when='~mpi') + # conflicts('+elpa', when='+scalapack') - if '+scalapack' in spec and '~mpi' in spec: - raise RuntimeError(error.format(variant='scalapack')) + def configure_args(self): - if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec): - raise RuntimeError(error.format(variant='elpa')) + spec = self.spec - def install(self, spec, prefix): - self.validate(spec) - - options = ['--prefix=%s' % prefix] + options = [] oapp = options.append if '+mpi' in spec: # MPI version: # let the configure script auto-detect MPI support from mpi_prefix - oapp("--with-mpi-prefix=%s" % spec["mpi"].prefix) - oapp("--enable-mpi=yes") - oapp("--enable-mpi-io=yes") + oapp('--with-mpi-prefix={0}'.format(spec['mpi'].prefix)) + oapp('--enable-mpi=yes') + oapp('--enable-mpi-io=yes') # Activate OpenMP in Abinit Fortran code. if '+openmp' in spec: oapp('--enable-openmp=yes') - # BLAS/LAPACK + # BLAS/LAPACK/SCALAPACK-ELPA + linalg = spec['lapack'].libs + spec['blas'].libs if '+scalapack' in spec: - oapp("--with-linalg-flavor=custom+scalapack") - linalg = (spec['scalapack'].libs + - spec['lapack'].libs + spec['blas'].libs) + oapp('--with-linalg-flavor=custom+scalapack') + linalg = spec['scalapack'].libs + linalg # elif '+elpa' in spec: else: - oapp("--with-linalg-flavor=custom") - linalg = spec['lapack'].libs + spec['blas'].libs + oapp('--with-linalg-flavor=custom') - oapp("--with-linalg-libs=%s" % linalg.ld_flags) + oapp('--with-linalg-libs={0}'.format(linalg.ld_flags)) # FFTW3: use sequential or threaded version if +openmp - fftflavor, fftlibs = "fftw3", "-lfftw3 -lfftw3f" + fftflavor, fftlibs = 'fftw3', '-lfftw3 -lfftw3f' if '+openmp' in spec: - fftflavor = "fftw3-threads" - fftlibs = "-lfftw3_omp -lfftw3 -lfftw3f" + fftflavor = 'fftw3-threads' + fftlibs = '-lfftw3_omp -lfftw3 -lfftw3f' options.extend([ - "--with-fft-flavor=%s" % fftflavor, - "--with-fft-incs=-I%s" % spec["fftw"].prefix.include, - "--with-fft-libs=-L%s %s" % (spec["fftw"].prefix.lib, fftlibs), + '--with-fft-flavor=%s' % fftflavor, + '--with-fft-incs=-I%s' % spec['fftw'].prefix.include, + '--with-fft-libs=-L%s %s' % (spec['fftw'].prefix.lib, fftlibs), ]) - oapp("--with-dft-flavor=atompaw+libxc") + oapp('--with-dft-flavor=atompaw+libxc') # LibXC library + libxc = spec['libxc:fortran'] options.extend([ - "with_libxc_incs=-I%s" % spec["libxc"].prefix.include, - "with_libxc_libs=-L%s -lxcf90 -lxc" % spec["libxc"].prefix.lib, + 'with_libxc_incs={0}'.format(libxc.cppflags), + 'with_libxc_libs={0}'.format(libxc.libs.ld_flags + ' -lm') ]) # Netcdf4/HDF5 - if "+hdf5" in spec: - oapp("--with-trio-flavor=netcdf") + if '+hdf5' in spec: + oapp('--with-trio-flavor=netcdf') # Since version 8, Abinit started to use netcdf4 + hdf5 and we have - # to link with -lhdf5_hl -lhdf5 - hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib + # to link with the high level HDF5 library + hdf5 = spec['hdf5:hl'] + netcdff = spec['netcdf-fortran:shared'] options.extend([ - "--with-netcdf-incs=-I%s" % ( - spec["netcdf-fortran"].prefix.include), - "--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % ( - spec["netcdf-fortran"].prefix.lib, hdf_libs), + '--with-netcdf-incs={0}'.format(netcdff.cppflags), + '--with-netcdf-libs={0}'.format( + netcdff.libs.ld_flags + ' ' + hdf5.libs.ld_flags + ), ]) else: # In Spack we do our best to avoid building any internally provided # dependencies, such as netcdf3 in this case. - oapp("--with-trio-flavor=none") + oapp('--with-trio-flavor=none') - configure(*options) - make() + return options - # make("check") - # make("tests_in") - make("install") + def check(self): + """This method is called after the build phase if tests have been + explicitly activated by user. + """ + make('check') + make('tests_in') diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 15139db645..27ec1b3bc4 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -70,23 +70,82 @@ class Hdf5(AutotoolsPackage): depends_on('szip', when='+szip') depends_on('zlib@1.1.2:') - @run_before('configure') - def validate(self): - """ - Checks if incompatible variants have been activated at the same time + # According to ./configure --help thread-safe capabilities are: + # "Not compatible with the high-level library, Fortran, or C++ wrappers." + # (taken from hdf5@1.10.0patch1) + conflicts('+threadsafe', when='+cxx') + conflicts('+threadsafe', when='+fortran') - :param spec: spec of the package - :raises RuntimeError: in case of inconsistencies + @property + def libs(self): + """Hdf5 can be queried for the following parameters: + + - "hl": high-level interface + - "cxx": C++ APIs + - "fortran": fortran APIs + + :return: list of matching libraries """ + query_parameters = self.spec.last_query.extra_parameters + + shared = '+shared' in self.spec + + # This map contains a translation from query_parameters + # to the libraries needed + query2libraries = { + tuple(): ['libhdf5'], + ('cxx', 'fortran', 'hl'): [ + 'libhdf5hl_fortran', + 'libhdf5_hl_cpp', + 'libhdf5_hl', + 'libhdf5_fortran', + 'libhdf5', + ], + ('cxx', 'hl'): [ + 'libhdf5_hl_cpp', + 'libhdf5_hl', + 'libhdf5', + ], + ('fortran', 'hl'): [ + 'libhdf5hl_fortran', + 'libhdf5_hl', + 'libhdf5_fortran', + 'libhdf5', + ], + ('hl',): [ + 'libhdf5_hl', + 'libhdf5', + ], + ('cxx', 'fortran'): [ + 'libhdf5_fortran', + 'libhdf5_cpp', + 'libhdf5', + ], + ('cxx',): [ + 'libhdf5_cpp', + 'libhdf5', + ], + ('fortran',): [ + 'libhdf5_fortran', + 'libhdf5', + ] + } + + # Turn the query into the appropriate key + key = tuple(sorted(query_parameters)) + libraries = query2libraries[key] + + return find_libraries( + libraries, root=self.prefix, shared=shared, recurse=True + ) + + @run_before('configure') + def fortran_check(self): spec = self.spec if '+fortran' in spec and not self.compiler.fc: msg = 'cannot build a fortran variant without a fortran compiler' raise RuntimeError(msg) - if '+threadsafe' in spec and ('+cxx' in spec or '+fortran' in spec): - msg = 'cannot use variant +threadsafe with either +cxx or +fortran' - raise RuntimeError(msg) - def configure_args(self): spec = self.spec # Handle compilation after spec validation @@ -156,11 +215,9 @@ class Hdf5(AutotoolsPackage): return ["--with-zlib=%s" % spec['zlib'].prefix] + extra_args - def configure(self, spec, prefix): - # Run the default autotools package configure - super(Hdf5, self).configure(spec, prefix) - - if '@:1.8.14' in spec: + @run_after('configure') + def patch_postdeps(self): + if '@:1.8.14' in self.spec: # On Ubuntu14, HDF5 1.8.12 (and maybe other versions) # mysteriously end up with "-l -l" in the postdeps in the # libtool script. Patch this by removing the spurious -l's. diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py index d773395e6c..ab9f75eac4 100644 --- a/var/spack/repos/builtin/packages/libxc/package.py +++ b/var/spack/repos/builtin/packages/libxc/package.py @@ -36,6 +36,33 @@ class Libxc(Package): version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec') version('2.2.1', '38dc3a067524baf4f8521d5bb1cd0b8f') + @property + def libs(self): + """Libxc can be queried for the following parameters: + + - "static": returns the static library version of libxc + (by default the shared version is returned) + + :return: list of matching libraries + """ + query_parameters = self.spec.last_query.extra_parameters + + libraries = ['libxc'] + + # Libxc installs both shared and static libraries. + # If a client ask for static explicitly then return + # the static libraries + shared = False if 'static' in query_parameters else True + + # Libxc has a fortran90 interface: give clients the + # possibility to query for it + if 'fortran' in query_parameters: + libraries = ['libxcf90'] + libraries + + return find_libraries( + libraries, root=self.prefix, shared=shared, recurse=True + ) + def install(self, spec, prefix): # Optimizations for the Intel compiler, suggested by CP2K optflags = '-O2' diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py index a2556d8783..3f6a5bbf04 100644 --- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py +++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py @@ -35,3 +35,16 @@ class NetcdfFortran(AutotoolsPackage): version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e') depends_on('netcdf') + + @property + def libs(self): + libraries = ['libnetcdff'] + + # This package installs both shared and static libraries. Permit + # clients to query which one they want. + query_parameters = self.spec.last_query.extra_parameters + shared = 'shared' in query_parameters + + return find_libraries( + libraries, root=self.prefix, shared=shared, recurse=True + ) |