megadock: new package at 4.0.3 (#10537)

* megadock: new package at 4.0.3

* megadock: remove CudaPackage redundancies

* megadock: move env vars to build targets, use cuda_arch variant

* megadock: flake8 fixes, more flexible mathlib

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

+# 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 Megadock(MakefilePackage, CudaPackage):
+    """an ultra-high-performance protein-protein docking for
+       heterogeneous supercomputers"""
+
+    homepage = "http://www.bi.cs.titech.ac.jp/megadock/"
+    url      = "http://www.bi.cs.titech.ac.jp/megadock/archives/megadock-4.0.3.tgz"
+
+    version('4.0.3', sha256='c1409a411555f4f7b4eeeda81caf622d8a28259a599ea1d2181069c55f257664')
+
+    variant('mpi', description='Enable MPI', default=False)
+
+    depends_on('fftw')
+    depends_on('mpi', when='+mpi')
+
+    def edit(self, spec, prefix):
+        # point cuda samples relative to cuda installation
+        filter_file('/opt/cuda/6.5/samples', '$(CUDA_INSTALL_PATH)/samples',
+                    'Makefile', string=True)
+
+        # need to link calcrg to compiler's math impl
+        # libm seems to be present in most compilers
+        mathlib = '-lm'
+
+        # prefer libimf with intel
+        if '%intel' in spec:
+            mathlib = '-limf'
+
+        filter_file('-o calcrg', '%s -o calcrg' % mathlib,
+                    'Makefile', string=True)
+
+        # makefile has a weird var for cuda_arch, use conditionally
+        if '+cuda' in spec:
+            arch = spec.variants['cuda_arch'].value
+            archflag = ''
+
+            if arch[0] != 'none':
+                archflag = '-arch=%s' % arch[0]
+
+            filter_file('-arch=$(SM_VERSIONS)', archflag,
+                        'Makefile', string=True)
+
+    @property
+    def build_targets(self):
+        spec = self.spec
+
+        targets = [
+            'USE_GPU=%s' % ('1' if '+cuda' in spec else '0'),
+            'USE_MPI=%s' % ('1' if '+mpi' in spec else '0'),
+            'OMPFLAG=%s' % self.compiler.openmp_flag,
+            'CPPCOMPILER=c++',
+            'FFTW_INSTALL_PATH=%s' % self.spec['fftw'].prefix,
+        ]
+
+        if '+cuda' in spec:
+            targets.append('CUDA_INSTALL_PATH=%s' % self.spec['cuda'].prefix)
+
+        if '+mpi' in spec:
+            targets.append('MPICOMPILER=%s' % self.spec['mpi'].mpicxx)
+
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        for suffix in ['', '-gpu', '-dp', '-gpu-dp']:
+            fn = 'megadock' + suffix
+            if os.path.isfile(fn):
+                install(fn, prefix.bin)