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author | Adam J. Stewart <ajstewart426@gmail.com> | 2018-11-14 23:30:44 -0600 |
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committer | GitHub <noreply@github.com> | 2018-11-14 23:30:44 -0600 |
commit | 2723db9f73e3a711336c92caf5506502073213c6 (patch) | |
tree | ad4409ac6873a08605002873323571f8410eee68 /var | |
parent | b9c50249cfd57f70227368e69bf56ab2fc784723 (diff) | |
download | spack-2723db9f73e3a711336c92caf5506502073213c6.tar.gz spack-2723db9f73e3a711336c92caf5506502073213c6.tar.bz2 spack-2723db9f73e3a711336c92caf5506502073213c6.tar.xz spack-2723db9f73e3a711336c92caf5506502073213c6.zip |
Add GMT, CitcomS, and fstrack packages (#9768)
* Add initial packages for citcoms and dependencies
* Ignore Pythia imports
* Add py-merlin package
* Add GMT package
* Fixes to get GMT working
* Get hc package building
* Get CitcomS 3.2.0 working
* Add fstrack package
* Fix hash
Diffstat (limited to 'var')
-rw-r--r-- | var/spack/repos/builtin/packages/citcoms/package.py | 78 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/exchanger/package.py | 21 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/fstrack/package.py | 54 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/gmt/package.py | 79 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/gmt/type.patch | 17 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/hc/package.py | 38 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/py-merlin/package.py | 21 | ||||
-rw-r--r-- | var/spack/repos/builtin/packages/py-pythia/package.py | 20 |
8 files changed, 328 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/citcoms/package.py b/var/spack/repos/builtin/packages/citcoms/package.py new file mode 100644 index 0000000000..0c5cbcd507 --- /dev/null +++ b/var/spack/repos/builtin/packages/citcoms/package.py @@ -0,0 +1,78 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Citcoms(AutotoolsPackage): + """CitcomS is a finite element code designed to solve compressible + thermochemical convection problems relevant to Earth's mantle.""" + + homepage = "https://geodynamics.org/cig/software/citcoms/" + url = "https://github.com/geodynamics/citcoms/releases/download/v3.3.1/CitcomS-3.3.1.tar.gz" + + version('3.3.1', sha256='e3520e0a933e4699d31e86fe309b8c154ea6ecb0f42a1cf6f25e8d13d825a4b3') + version('3.2.0', sha256='773a14d91ecbb4a4d1e04317635fab79819d83c57b47f19380ff30b9b19cb07a') + + variant('pyre', default=False, description='build Pyre modules') + variant('exchanger', default=False, description='use Exchanger') + variant('ggrd', default=False, description='use GGRD file support') + variant('cuda', default=False, description='use CUDA') + variant('hdf5', default=False, description='add HDF5 support') + + # Required dependencies + depends_on('mpi') + depends_on('zlib') + + # Optional dependencies + depends_on('exchanger', when='+exchanger') + depends_on('py-pythia', type=('build', 'run'), when='+pyre') + depends_on('hc', when='+ggrd') + depends_on('cuda', when='+cuda') + depends_on('hdf5+mpi', when='+hdf5') + + conflicts('+pyre', when='@3.3:', msg='Pyre support was removed from 3.3+') + conflicts('+exchanger', when='@3.3:', msg='Exchanger support was removed from 3.3+') + + def setup_environment(self, spack_env, run_env): + if '+ggrd' in self.spec: + spack_env.set('HC_HOME', self.spec['hc'].prefix) + + def configure_args(self): + args = ['CC={0}'.format(self.spec['mpi'].mpicc)] + + # Flags only valid in 3.2 + if self.spec.satisfies('@:3.2'): + if '+pyre' in self.spec: + args.append('--with-pyre') + else: + args.append('--without-pyre') + + if '+exchanger' in self.spec: + args.append('--with-exchanger') + else: + args.append('--without-exchanger') + + if '+ggrd' in self.spec: + args.append('--with-ggrd') + else: + args.append('--without-ggrd') + + if '+cuda' in self.spec: + args.append('--with-cuda') + else: + args.append('--without-cuda') + + if '+hdf5' in self.spec: + args.extend([ + '--with-hdf5', + # https://github.com/geodynamics/citcoms/issues/2 + 'CPPFLAGS=-DH5_USE_16_API', + 'CFLAGS=-DH5_USE_16_API' + ]) + else: + args.append('--without-hdf5') + + return args diff --git a/var/spack/repos/builtin/packages/exchanger/package.py b/var/spack/repos/builtin/packages/exchanger/package.py new file mode 100644 index 0000000000..66bc6b9bcf --- /dev/null +++ b/var/spack/repos/builtin/packages/exchanger/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Exchanger(AutotoolsPackage): + """Exchanger is a package containing several C++ base classes. These + classes, when customized for a solver, can provide communication channels + between solvers. This packaged is used by CitcomS for solver coupling.""" + + homepage = "https://geodynamics.org/cig/software/exchanger/" + url = "https://geodynamics.org/cig/software/exchanger/Exchanger-1.0.1.tar.gz" + + version('1.0.1', sha256='1e6c8311db96582bcf2c9aee16a863a5730c1aa54cb3aa7d0249239c6e0b68ee') + + depends_on('python', type=('build', 'run')) + depends_on('py-merlin', type='build') + depends_on('py-pythia@0.8.1.0:0.8.1.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/fstrack/package.py b/var/spack/repos/builtin/packages/fstrack/package.py new file mode 100644 index 0000000000..7fd338547d --- /dev/null +++ b/var/spack/repos/builtin/packages/fstrack/package.py @@ -0,0 +1,54 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Fstrack(MakefilePackage): + """Package with tools to analyze symmetry components of elastic tensors, + predict synthetic waveforms and compute automated shear wave splitting + along ray paths, and to track finite strain and predict LPO from mantle + flow given on GMT/netcdf grds.""" + + homepage = "http://www-udc.ig.utexas.edu/external/becker/data.html#fstrack" + url = "http://www-udc.ig.utexas.edu/external/becker/software/fstrack-0.5.3.092918.tgz" + + version('0.5.3.092918', sha256='34b31687fdfa207b9659425238b805eaacf0b0209e7e3343c1a3cb4c9e62345d') + + variant('flow', default=True, description='Build the flow tracker') + + depends_on('gmt@4.0:4.999', when='+flow') + depends_on('netcdf', when='+flow') + + parallel = False + + def setup_environment(self, spack_env, run_env): + # Compilers + spack_env.set('F90', spack_fc) + + # Compiler flags (assumes GCC) + spack_env.set('CFLAGS', '-O2') + spack_env.set('FFLAGS', '-ffixed-line-length-132 -x f77-cpp-input -O2') + spack_env.set('FFLAGS_DEBUG', '-g -x f77-cpp-input') + spack_env.set('F90FLAGS', '-O2 -x f95-cpp-input') + spack_env.set('F90FLAGS_DEBUG', '-g -x f95-cpp-input') + spack_env.set('LDFLAGS', '-lm') + + if '+flow' in self.spec: + spack_env.set('GMTHOME', self.spec['gmt'].prefix) + spack_env.set('NETCDFDIR', self.spec['netcdf'].prefix) + + def build(self, spec, prefix): + with working_dir('eispack'): + make() + + with working_dir('d-rex'): + make() + + with working_dir('fstrack'): + if '+flow' in spec: + make('really_all') + else: + make() diff --git a/var/spack/repos/builtin/packages/gmt/package.py b/var/spack/repos/builtin/packages/gmt/package.py new file mode 100644 index 0000000000..f60b9660ce --- /dev/null +++ b/var/spack/repos/builtin/packages/gmt/package.py @@ -0,0 +1,79 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Gmt(Package): + """GMT (Generic Mapping Tools) is an open source collection of about 80 + command-line tools for manipulating geographic and Cartesian data sets + (including filtering, trend fitting, gridding, projecting, etc.) and + producing PostScript illustrations ranging from simple x-y plots via + contour maps to artificially illuminated surfaces and 3D perspective views. + """ + + homepage = "http://gmt.soest.hawaii.edu/" + url = "https://github.com/GenericMappingTools/gmt/archive/5.4.4.tar.gz" + + version('5.4.4', sha256='b593dfb101e6507c467619f3d2190a9f78b09d49fe2c27799750b8c4c0cd2da0') + version('4.5.9', sha256='9b13be96ccf4bbd38c14359c05dfa7eeeb4b5f06d6f4be9c33d6c3ea276afc86', + url='ftp://ftp.soest.hawaii.edu/gmt/legacy/gmt-4.5.9.tar.bz2') + + variant('pcre', default=False, description='Enable the PCRE interface') + variant('gdal', default=False, description='Enable the GDAL interface') + variant('fftw', default=True, description='Fast FFTs') + variant('lapack', default=True, description='Fast matrix inversion') + variant('blas', default=True, description='Fast matrix multiplications') + + # http://gmt.soest.hawaii.edu/projects/gmt/wiki/BuildingGMT + + # Required dependencies + depends_on('ghostscript') + depends_on('subversion') + depends_on('cmake@2.8.5:', type='build', when='@5:') + depends_on('netcdf@4:') + depends_on('curl', when='@5.4:') + + # Optional dependencies + depends_on('pcre', when='+pcre') + depends_on('gdal', when='+gdal') + depends_on('fftw', when='+fftw') + depends_on('lapack', when='+lapack') + depends_on('blas', when='+blas') + depends_on('graphicsmagick', type='test') + + patch('type.patch', when='@4.5.9') + + @when('@5:') + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', *std_cmake_args) + + make() + make('install') + + @when('@:4') + def install(self, spec, prefix): + args = [ + '--prefix={0}'.format(prefix), + '--enable-netcdf={0}'.format(spec['netcdf'].prefix), + '--enable-shared', + '--without-x' + ] + + if '+gdal' in spec: + args.append('--enable-gdal') + else: + args.append('--disable-gdal') + + configure(*args) + + # Building in parallel results in dozens of errors like: + # *** No rule to make target `../libgmtps.so', needed by `pssegyz'. + make(parallel=False) + + # Installing in parallel results in dozens of errors like: + # /usr/bin/install: cannot create directory '...': File exists + make('install', parallel=False) diff --git a/var/spack/repos/builtin/packages/gmt/type.patch b/var/spack/repos/builtin/packages/gmt/type.patch new file mode 100644 index 0000000000..c672179f30 --- /dev/null +++ b/var/spack/repos/builtin/packages/gmt/type.patch @@ -0,0 +1,17 @@ +Without this patch, I see compilation errors like: + +gmtdigitize.c:83:2: error: unknown type name 'gid_t'; did you mean 'pid_t'? +gmtdigitize.c:84:2: error: unknown type name 'uid_t'; did you mean 'pid_t'? + +Suggestion comes from https://stackoverflow.com/a/32282782/5828163 +--- a/src/misc/gmtdigitize.c 2018-11-07 12:30:46.000000000 -0600 ++++ b/src/misc/gmtdigitize.c 2018-11-07 12:31:36.000000000 -0600 +@@ -38,6 +38,8 @@ + */ + + #include "gmt.h" ++#include <sys/types.h> ++#include <unistd.h> + + #ifndef WIN32 + #include <termios.h> diff --git a/var/spack/repos/builtin/packages/hc/package.py b/var/spack/repos/builtin/packages/hc/package.py new file mode 100644 index 0000000000..685079dc24 --- /dev/null +++ b/var/spack/repos/builtin/packages/hc/package.py @@ -0,0 +1,38 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Hc(MakefilePackage): + """HC is a global mantle circulation solver following Hager & O'Connell + (1981) which can compute velocities, tractions, and geoid for simple + density distributions and plate velocities.""" + + homepage = "https://geodynamics.org/cig/software/hc/" + url = "https://geodynamics.org/cig/software/hc/hc-1.0.7.tar.gz" + + version('1.0.7', sha256='7499ea76ac4739a9c0941bd57d124fb681fd387c8d716ebb358e6af3395103ed') + + depends_on('gmt@4.2.1:4.999') + depends_on('netcdf') + + # Build phase fails in parallel with the following error messages: + # /usr/bin/ld: cannot find -lrick + # /usr/bin/ld: cannot find -lhc + # /usr/bin/ld: cannot find -lggrd + parallel = False + + def setup_environment(self, spack_env, run_env): + spack_env.set('GMTHOME', self.spec['gmt'].prefix) + spack_env.set('NETCDFHOME', self.spec['netcdf'].prefix) + spack_env.set('HC_HOME', self.prefix) + spack_env.unset('ARCH') + + def install(self, spec, prefix): + # Most files are installed during the build stage. + # Manually install header files as well. + for header in find('.', '*.h'): + install(header, prefix.include) diff --git a/var/spack/repos/builtin/packages/py-merlin/package.py b/var/spack/repos/builtin/packages/py-merlin/package.py new file mode 100644 index 0000000000..4af5e7d803 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-merlin/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyMerlin(PythonPackage): + """A custom version of Phillip J. Eby's setuptools.""" + + homepage = "https://pypi.org/project/merlin/" + url = "https://pypi.io/packages/source/m/merlin/merlin-1.8.tar.gz" + + version('1.8', sha256='a1ba9c13c74daa1724dd3820f1c241d7594d487b11f35347606986028c1881fd') + + depends_on('python@:2', type=('build', 'run')) + + def test(self): + # Unit tests are missing from tarball + pass diff --git a/var/spack/repos/builtin/packages/py-pythia/package.py b/var/spack/repos/builtin/packages/py-pythia/package.py new file mode 100644 index 0000000000..c8fdf746db --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pythia/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythia(PythonPackage): + """Pythia refers to the Pyre framework and a collection of packages that + interact with it, such as an interface to the ACIS solid modelling package. + """ + + homepage = "https://geodynamics.org/cig/software/pythia/" + url = "https://geodynamics.org/cig/software/github/pythia/v0.8.1.18/pythia-0.8.1.18.tar.gz" + + version('0.8.1.18', sha256='f6025e6d70046dc71e375eded3d731506f8dd79e2e53b7e1436754439dcdef1e') + + depends_on('python@:2', type=('build', 'run')) + depends_on('py-merlin', type='build') |