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authorJustin S <3630356+codeandkey@users.noreply.github.com>2019-06-18 21:01:03 -0500
committerPeter Scheibel <scheibel1@llnl.gov>2019-06-18 19:01:03 -0700
commit2287dd6165ca0150f243fdee9cbfa8ca92785e37 (patch)
treeea486af5173717cf87a79dce67dd6861c63f5670 /var
parentda800c21bd0af0c1868cf9cb5913cf9127559d4a (diff)
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New package: amber (starting at v16) (#11619)
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/amber/package.py79
1 files changed, 79 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/amber/package.py b/var/spack/repos/builtin/packages/amber/package.py
new file mode 100644
index 0000000000..94e3f23d1e
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+++ b/var/spack/repos/builtin/packages/amber/package.py
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+# 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)