new package: openmm (#16002)

* new package: openmm

* dependency adjustments

* 1. modify dependencies
2. openmm dynamically compiles cuda kernels during runtime,
   attempt to set up an environment that will work.

* Update var/spack/repos/builtin/packages/openmm/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

1 files changed, 48 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/openmm/package.py b/var/spack/repos/builtin/packages/openmm/package.py
new file mode 100644
index 0000000000..2867af4538
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openmm/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2020 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)
+
+import os
+
+
+class Openmm(CMakePackage, CudaPackage):
+    """A high performance toolkit for molecular simulation. Use it as
+    a library, or as an application. We include extensive language
+    bindings for Python, C, C++, and even Fortran. The code is open
+    source and actively maintained on Github, licensed under MIT and
+    LGPL. Part of the Omnia suite of tools for predictive biomolecular
+    simulation. """
+
+    homepage = "http://openmm.org/"
+    url      = "https://github.com/openmm/openmm/archive/7.4.1.tar.gz"
+
+    version('7.4.1', sha256='e8102b68133e6dcf7fcf29bc76a11ea54f30af71d8a7705aec0aee957ebe3a6d')
+
+    install_targets = ['install', 'PythonInstall']
+
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('cmake@3.1:', type='build')
+    depends_on('doxygen', type='build')
+    depends_on('swig', type='build')
+    depends_on('fftw')
+    depends_on('py-cython', type='build')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('cuda', when='+cuda', type=('build', 'link', 'run'))
+    extends('python')
+
+    def patch(self):
+        install_string = "set(PYTHON_SETUP_COMMAND \"install " \
+                         "--prefix={0}\")".format(self.prefix)
+
+        filter_file(r'set\(PYTHON_SETUP_COMMAND \"install.*',
+                    install_string,
+                    'wrappers/python/CMakeLists.txt')
+
+    def setup_run_environment(self, env):
+        spec = self.spec
+        if '+cuda' in spec:
+            env.set('OPENMM_CUDA_COMPILER',
+                    self.spec['cuda'].prefix.bin.nvcc)
+            env.prepend_path('PATH',
+                             os.path.dirname(self.compiler.cc))