text: # 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)
  
  from spack import *
  import os
  import shutil
  
  
  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}/Amber18.tar.bz2".format(os.getcwd())
      maintainers = ['hseara']
  
      version('18', sha256='2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277')
      version('16', sha256='3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d')
  
      resources = [
          # [version amber, version ambertools , sha256sum]
          ('18', '19', '0c86937904854b64e4831e047851f504ec45b42e593db4ded92c1bee5973e699'),
          ('16', '16', '7b876afe566e9dd7eb6a5aa952a955649044360f15c1f5d4d91ba7f41f3105fa'),
      ]
      for ver, ambertools_ver, checksum in resources:
          resource(when='@{0}'.format(ver),
                   name='AmberTools',
                   url='file://{0}/AmberTools{1}.tar.bz2'.format(os.getcwd(),
                                                                 ambertools_ver),
                   sha256=checksum,
                   destination='',
                   placement='ambertools_tmpdir',
                   )
  
      patches = [
          ('18', '1', '3cefac9a24ece99176d5d2d58fea2722de3e235be5138a128428b9260fe922ad'),
          ('18', '2', '3a0707a9a59dcbffa765dcf87b68001450095c51b96ec39d21260ba548a2f66a'),
          ('18', '3', '24c2e06f71ae553a408caa3f722254db2cbf1ca4db274542302184e3d6ca7015'),
          ('18', '4', '51de613e8fda20cc92979265cf7179288df8c1af4202f02794ad7327fda2657b'),
          ('18', '5', 'c70354bfa312603e4819efce11a242ddcc3830895453d9424f0c83f7ae98bc5b'),
          ('18', '6', '3450433a8697b27e43172043be68d31515a7c7c00b2b248f84043dd70a2f59a8'),
          ('18', '7', '10ba41422b7a3eb5b32bc6453231100544cf620c764ab8332c629a3b9fc749d4'),
          ('18', '8', '73968dc0fd99bcbd5eae2223bd54f414879c062ac933948ba6b8b67383dc6a53'),
          ('18', '9', 'e7d72fa31560f1e8ea572b8c73259d9fe512f56fbeb1b58ae014c43b9b5b6290'),
          ('18', '10', '1bee419a3b0b686a729aa12515b0f96a9a8f43478ca2c01ea1661cc1698c6266'),
          ('18', '11', '926557f0c137ea8dbf99a0487b25e131b12dfd39977d3e515f01f49187e6a09c'),
          ('18', '12', '7e2645d539d257f7064808308048622818c9083dedfa4ac0a958cd15181231ac'),
          ('18', '13', '95d2e33d0d05b8f9b6d8091d1c804271ec3a69e9aef792cc3b1ab8a2165eca3e'),
          ('18', '14', 'a1adfb072f60ffcb67adb589df7c5578629441bee4ccb89ab635a6e8d7a35277'),
          ('18', '15', '4deb3df329c05729561dcc7310e49059eaddc504c4210ad31fad11dc70f61742'),
          ('18', '16', 'cf02f9b949127363bad1aa700ab662a3c7cf9ce0e2e4750e066d2204b9500a99'),
          ('18', '17', '480300f949e0dd6402051810a9714adb388cf96e454a55346c76954cdd69413d'),
          ('16', '1.txt', 'c7ef2303bb35131a48e2256c5a3c7b391efa73e2acf757d7e39760efb6320ed4'),
          ('16', '2', 'a4db183f7c337a67f5d6b5015e3ae0af0d0edaa56894f0e9e3469c99708fed1c'),
          ('16', '3', '5b279531c42445c6f58281dd94588460218d2258ec9013c8447f3e2b7b81bf02'),
          ('16', '4', '035bddd63bc9d5fd6de26beab31887e5c14c3caa4958d2424d72f3c49832bd42'),
          ('16', '5', '02d8a1fcb6baa466de4e3683afa48076394acd805f490fbbe50ab19040675136'),
          ('16', '6', '69a3e64d75255d9179c98a2b3a63fe76d5be08c9fc41f27ac197663c97915113'),
          ('16', '7', '0d674c907758e90a168345e6b35b7a0de79c2ead390ab372465a354fcab67d17'),
          ('16', '8', 'd722c0db46af905a5bd13b60e3130c4ddfb0c9da86df0a33253e5f8d53068946'),
          ('16', '9', 'b563e744fbc50c1240d23df369750879df2cec69fba933704b97a73a66d9c4f1'),
          ('16', '10', '99affc65740080b7a1ab87c5c9119bf5be7cf47b2b2d8fc13407d35bd2ba6238'),
          ('16', '11', '86b89dbcae80ef48720fd3c7da88cffbdabfd4021af5a827339b56a33ddae27a'),
          ('16', '12', 'c8d61d1efbd44086f88d74ad9e07dfdc3737dc7053c7d2503131ba0918973a03'),
          ('16', '13', '5ce28e6e0118a4780ad72fc096e617c874cde7d140e15f87451babb25aaf2d8f'),
          ('16', '14', '93703e734e76da30a5e050189a66d5a4d6bec5885752503c4c798e2f44049080'),
          ('16', '15', 'a156ec246cd06688043cefde24de0d715fd46b08f5c0235015c2c5c3c6e37488'),
      ]
      for ver, num, checksum in patches:
          patch_url_str = 'https://ambermd.org/bugfixes/{0}.0/update.{1}'
          patch(patch_url_str.format(ver, num),
                sha256=checksum, level=0, when='@{0}'.format(ver))
  
      variant('mpi', description='Build MPI executables',
              default=True)
      variant('openmp', description='Use OpenMP pragmas to parallelize',
              default=False)
      variant('x11', description='Build programs that require X11',
              default=False)
      variant('update', description='Update the sources prior compilation',
              default=False)
  
      depends_on('zlib')
      depends_on('flex', type='build')
      depends_on('bison', type='build')
      depends_on('netcdf-fortran')
      # Potential issues with openmpi 4
      # (http://archive.ambermd.org/201908/0105.html)
      depends_on('mpi', when='+mpi')
  
      # Cuda dependencies
      depends_on('cuda@:10.2.89', when='@18:+cuda')
      depends_on('cuda@7.5.18', when='@:16+cuda')
  
      # conflicts
      conflicts('+x11', when='platform=cray',
                msg='x11 amber applications not available for cray')
      conflicts('+openmp', when='%clang',
                msg='openmp optimizations not available for the clang compiler')
      conflicts('+openmp', when='%pgi',
                msg='openmp optimizations not available for the pgi compiler')
  
      def setup_build_environment(self, env):
          amber_src = self.stage.source_path
          env.set('AMBERHOME', amber_src)
          # CUDA
          if self.spec.satisfies('+cuda'):
              env.set('CUDA_HOME', self.spec['cuda'].prefix)
  
      def install(self, spec, prefix):
          # The resource command does not allow us to expand the package in the
          # root stage folder as required, as it already contains files. Here we
          # install AmberTools where it should be, which results in 3 copies of
          # the  ambertools (~9 GB). This has to be improved in the future.
          install_tree('ambertools_tmpdir', '.')
          shutil.rmtree(join_path(self.stage.source_path, 'ambertools_tmpdir'))
  
          # Select compiler style
          if self.spec.satisfies('%cce'):
              compiler = 'cray'
          elif self.spec.satisfies('%gcc'):
              compiler = 'gnu'
          elif self.spec.satisfies('%intel'):
              compiler = 'intel'
          elif self.spec.satisfies('%pgi'):
              compiler = 'pgi'
          elif self.spec.satisfies('%clang'):
              compiler = 'clang'
          else:
              raise InstallError('Unknown compiler, exiting!!!')
  
          # Base configuration
          conf = Executable('./configure')
          base_args = ['--skip-python',
                       '--with-netcdf', self.spec['netcdf-fortran'].prefix,
                       ]
          if self.spec.satisfies('~x11'):
              base_args += ['-noX11']
  
          # Update the sources: Apply all upstream patches
          if self.spec.satisfies('+update'):
              update = Executable('./update_amber')
              update(*(['--update']))
          else:
              base_args += ['--no-updates']
  
          # Single core
          conf(*(base_args + [compiler]))
          make('install')
  
          # CUDA
          if self.spec.satisfies('+cuda'):
              conf(*(base_args + ['-cuda', compiler]))
              make('install')
  
          # MPI
          if self.spec.satisfies('+mpi'):
              conf(*(base_args + ['-mpi', compiler]))
              make('install')
  
          # Openmp
          if self.spec.satisfies('+openmp'):
              make('clean')
              conf(*(base_args + ['-openmp', compiler]))
              make('openmp')
  
          # CUDA + MPI
          if self.spec.satisfies('+cuda') and self.spec.satisfies('+mpi'):
              make('clean')
              conf(*(base_args + ['-cuda', '-mpi', compiler]))
              make('install')
  
          # just install everything that was built
          install_tree('.', prefix)
  
      def setup_run_environment(self, env):
          env.set('AMBER_PREFIX', self.prefix)
          env.set('AMBERHOME', self.prefix)
          # CUDA
          if self.spec.satisfies('+cuda'):
              env.prepend_path('LD_LIBRARY_PATH', self.spec['cuda'].prefix.lib)
  