New package: amber (starting at v16) (#11619)

var/spack/repos/builtin/packages/amber/package.py

@@ -0,0 +1,79 @@
+# Copyright 2013-2019 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 *
+import os
+
+
+class Amber(Package, CudaPackage):
+    """Amber is a suite of biomolecular simulation programs.
+
+       Note: A manual download is required for Amber.
+       Spack will search your current directory for the download file.
+       Alternatively, add this file to a mirror so that Spack can find it.
+       For instructions on how to set up a mirror, see
+       http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "http://ambermd.org/"
+    url      = "file://{0}/Amber16.tar.bz2".format(os.getcwd())
+
+    version('16', sha256='3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d')
+
+    variant('mpi', description='Build MPI executables', default=True)
+
+    resource(
+        name='AmberTools',
+        sha256='7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa',
+        url='file://{0}/AmberTools16.tar.bz2'.format(os.getcwd()),
+        destination='.',
+    )
+
+    depends_on('mpi', when='+mpi')
+    depends_on('cuda@7.5.18', when='+cuda')
+
+    depends_on('netcdf-fortran')
+    depends_on('python+tkinter@2.7:2.8', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-matplotlib@:2.9', type=('build', 'run'))
+    depends_on('zlib')
+
+    def setup_environment(self, spack_env, run_env):
+        sp_dir = join_path(self.prefix, 'python2.7/site-packages')
+
+        run_env.set('AMBERHOME', self.prefix)
+        run_env.prepend_path('PYTHONPATH', sp_dir)
+
+    def install(self, spec, prefix):
+        # install AmberTools where it should be
+        install_tree('amber16', '.')
+
+        base_args = [
+            '-noX11',
+            '--no-updates',
+            '--skip-python',
+            '--with-netcdf', self.spec['netcdf-fortran'].prefix
+        ]
+
+        configure_env = {
+            'AMBERHOME': self.stage.source_path,
+            'CUDA_HOME': self.spec['cuda'].prefix,
+        }
+
+        conf = Executable('./configure')
+
+        conf(*(base_args + ['gnu']), extra_env=configure_env)
+        make('install', extra_env=configure_env)
+
+        if '+mpi' in spec:
+            conf(*(base_args + ['-mpi', 'gnu']), extra_env=configure_env)
+            make('install', extra_env=configure_env)
+
+        if '+cuda' in spec:
+            conf(*(base_args + ['-cuda', 'gnu']), extra_env=configure_env)
+            make('install', extra_env=configure_env)
+
+        # just install everything that was built
+        install_tree('.', prefix)