Update LBANN generator and bug fix (#9906)

* Added a package for the MDAnalysis toolkit.

* Added Ninja as the generator for LBANN, Hydrogen, and Aluminum.  Also
fixed a bug in how the Conduit variant is included in LBANN.  Added
new versions for Hydrogen and LBANN.

* Updated lbann package so that the CMAKE parameters are set when the
variant is on and off.

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

@@ -34,6 +34,9 @@ class Aluminum(CMakePackage):
     depends_on('nccl', when='+nccl')
     depends_on('hwloc')
 
+    generator = 'Ninja'
+    depends_on('ninja', type='build')
+
     def cmake_args(self):
         spec = self.spec
         args = [

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

@@ -13,10 +13,11 @@ class Hydrogen(CMakePackage):
        and optimization library. Based on the Elemental library."""
 
     homepage = "http://libelemental.org"
-    url      = "https://github.com/LLNL/Elemental/archive/0.99.tar.gz"
+    url      = "https://github.com/LLNL/Elemental/archive/v1.0.1.tar.gz"
     git      = "https://github.com/LLNL/Elemental.git"
 
     version('develop', branch='hydrogen')
+    version('1.0.1', sha256='27cf76e1ef1d58bd8f9b1e34081a14a682b7ff082fb5d1da56713e5e0040e528')
     version('1.0', sha256='d8a97de3133f2c6b6bb4b80d32b4a4cc25eb25e0df4f0cec0f8cb19bf34ece98')
     version('0.99', 'b678433ab1d498da47acf3dc5e056c23')
 
@@ -93,6 +94,9 @@ class Hydrogen(CMakePackage):
     conflicts('@0:0.98', msg="Hydrogen did not exist before v0.99. " +
               "Did you mean to use Elemental instead?")
 
+    generator = 'Ninja'
+    depends_on('ninja', type='build')
+
     @property
     def libs(self):
         shared = True if '+shared' in self.spec else False

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

@@ -18,6 +18,7 @@ class Lbann(CMakePackage):
     git      = "https://github.com/LLNL/lbann.git"
 
     version('develop', branch='develop')
+    version('0.96', sha256='97af78e9d3c405e963361d0db96ee5425ee0766fa52b43c75b8a5670d48e4b4a')
     version('0.95', sha256='d310b986948b5ee2bedec36383a7fe79403721c8dc2663a280676b4e431f83c2')
     version('0.94', sha256='567e99b488ebe6294933c98a212281bffd5220fc13a0a5cd8441f9a3761ceccf')
     version('0.93', '1913a25a53d4025fa04c16f14afdaa55')
@@ -34,8 +35,9 @@ class Lbann(CMakePackage):
     variant('build_type', default='Release',
             description='The build type to build',
             values=('Debug', 'Release'))
-    variant('al', default=True, description='Builds with support for Aluminum Library')
+    variant('al', default=False, description='Builds with support for Aluminum Library')
     variant('conduit', default=False, description='Builds with support for Conduit Library')
+    variant('vtune', default=False, description='Builds with support for Intel VTune')
 
     # It seems that there is a need for one statement per version bounds
     depends_on('hydrogen +openmp_blas +shared +int64', when='@:0.90,0.95: ~al')
@@ -82,12 +84,15 @@ class Lbann(CMakePackage):
                '~pthreads_pf ~python ~qt ~stitching ~superres ~ts ~video'
                '~videostab ~videoio ~vtk', when='+opencv')
 
-    depends_on('protobuf@3.0.2:')
+    depends_on('protobuf@3.0.2: build_type=Release')
     depends_on('cnpy')
     depends_on('nccl', when='+gpu +nccl')
 
     depends_on('conduit@master +hdf5', when='+conduit')
 
+    generator = 'Ninja'
+    depends_on('ninja', type='build')
+
     @property
     def common_config_args(self):
         spec = self.spec
@@ -110,10 +115,16 @@ def cmake_args(self):
         args = self.common_config_args
         args.extend([
             '-DLBANN_WITH_TOPO_AWARE:BOOL=%s' % ('+gpu +nccl' in spec),
+            '-DLBANN_WITH_ALUMINUM:BOOL=%s' % ('+al' in spec),
+            '-DLBANN_WITH_CONDUIT:BOOL=%s' % ('+conduit' in spec),
+            '-DLBANN_WITH_CUDA:BOOL=%s' % ('+gpu' in spec),
+            '-DLBANN_WITH_CUDNN:BOOL=%s' % ('+gpu' in spec),
+            '-DLBANN_WITH_NCCL:BOOL=%s' % ('+gpu +nccl' in spec),
+            '-DLBANN_WITH_SOFTMAX_CUDA:BOOL=%s' % ('+gpu' in spec),
             '-DLBANN_SEQUENTIAL_INITIALIZATION:BOOL=%s' %
             ('+seq_init' in spec),
             '-DLBANN_WITH_TBINF=OFF',
-            '-DLBANN_WITH_VTUNE=OFF',
+            '-DLBANN_WITH_VTUNE:BOOL=%s' % ('+vtune' in spec),
             '-DLBANN_DATATYPE={0}'.format(spec.variants['dtype'].value),
             '-DLBANN_VERBOSE=0'])
 
@@ -126,14 +137,15 @@ def cmake_args(self):
                 '-DElemental_DIR={0}/CMake/elemental'.format(
                     spec['elemental'].prefix)])
 
+        if '+vtune' in spec:
+            args.extend(['-DVTUNE_DIR={0}'.format(spec['vtune'].prefix)])
+
         if '+al' in spec:
-            args.extend(['-DLBANN_WITH_ALUMINUM:BOOL=%s' % ('+al' in spec),
+            args.extend(['-DAluminum_DIR={0}'.format(spec['aluminum'].prefix)])
-                         '-DAluminum_DIR={0}'.format(spec['aluminum'].prefix)])
 
         if '+conduit' in spec:
-            args.extend(['-DLBANN_CONDUIT_DIR:BOOL=%s' % ('+conduit' in spec),
+            args.extend(['-DLBANN_CONDUIT_DIR={0}'.format(
-                         '-DLBANN_CONDUIT_DIR={0}'.format(
+                spec['conduit'].prefix)])
-                             spec['conduit'].prefix)])
 
         # Add support for OpenMP
         if (self.spec.satisfies('%clang')):
@@ -153,19 +165,15 @@ def cmake_args(self):
 
         if '+gpu' in spec:
             args.extend([
-                '-DLBANN_WITH_CUDA:BOOL=%s' % ('+gpu' in spec),
-                '-DLBANN_WITH_SOFTMAX_CUDA:BOOL=%s' % ('+gpu' in spec),
                 '-DCUDA_TOOLKIT_ROOT_DIR={0}'.format(
                     spec['cuda'].prefix)])
             args.extend([
-                '-DLBANN_WITH_CUDNN:BOOL=%s' % ('+gpu' in spec),
                 '-DcuDNN_DIR={0}'.format(
                     spec['cudnn'].prefix)])
             args.extend(['-DCUB_DIR={0}'.format(
                 spec['cub'].prefix)])
             if '+nccl' in spec:
                 args.extend([
-                    '-DLBANN_WITH_NCCL:BOOL=%s' % ('+gpu +nccl' in spec),
                     '-DNCCL_DIR={0}'.format(
                         spec['nccl'].prefix)])