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

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')