amber: Improved package.py and added version 18 (#13945)

* amber: Improved package.py and added version 18

- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()

* dealii: Added 'threads' variant that controls the TBB dependency (#13931)

* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB

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

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

* amber: Improved package.py and added version 18

- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()

* amber: Adding missing flex and bison dependencies

* Removed cray variant; flex and bison now build only

* amber: Improved package.py and added version 18

- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()

* amber: Adding missing flex and bison dependencies

* Removed cray variant; flex and bison now build only

* dealii: Fixed flake8 issues

* amber: corrected typo

* amber: Removed unused variant python

2 files changed, 159 insertions, 50 deletions

diff --git a/var/spack/repos/builtin/packages/amber/package.py b/var/spack/repos/builtin/packages/amber/package.py
index 93af77bbbc..e33f04c3a1 100644
--- a/var/spack/repos/builtin/packages/amber/package.py
+++ b/var/spack/repos/builtin/packages/amber/package.py
@@ -5,6 +5,7 @@
 
 from spack import *
 import os
+import shutil
 
 
 class Amber(Package, CudaPackage):
@@ -17,63 +18,171 @@ class Amber(Package, CudaPackage):
        http://spack.readthedocs.io/en/latest/mirrors.html"""
 
     homepage = "http://ambermd.org/"
-    url      = "file://{0}/Amber16.tar.bz2".format(os.getcwd())
+    url      = "file://{0}/Amber18.tar.bz2".format(os.getcwd())
+    maintainers = ['hseara']
 
+    version('18', sha256='2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277')
     version('16', sha256='3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d')
 
-    variant('mpi', description='Build MPI executables', default=True)
+    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)
 
-    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')
+    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')
 
-    def setup_run_environment(self, env):
-        sp_dir = join_path(self.prefix, 'python2.7/site-packages')
-
-        env.set('AMBERHOME', self.prefix)
-        env.prepend_path('PYTHONPATH', sp_dir)
+    # Cuda dependencies
+    depends_on('cuda@:10.1.243', 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):
-        # 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,
-        }
-
+        # 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')
-
-        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)
+        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)
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 3dc407fa11..f44b25e539 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -97,7 +97,7 @@ class Dealii(CMakePackage, CudaPackage):
                         patch('boost_1.68.0.patch',
                               level=1,
                               when='@1.68.0'),
-                       ],
+                        ],
                when='~python')
     depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams+python',
                patches=[patch('boost_1.65.1_singleton.patch',
@@ -106,7 +106,7 @@ class Dealii(CMakePackage, CudaPackage):
                         patch('boost_1.68.0.patch',
                               level=1,
                               when='@1.68.0'),
-                       ],
+                        ],
                when='+python')
     # bzip2 is not needed since 9.0
     depends_on('bzip2', when='@:8.99')