Merge pull request #1381 from davydden/pkg/mkl_linux

MKL linux fixes

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

@@ -62,10 +62,10 @@ def install(self, spec, prefix):
             '--prefix=%s' % prefix,
             '--with-lapack-libs=%s' % to_lib_name(
                 spec['lapack'].lapack_shared_lib),
-            '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix,
+            '--with-lapack-lib-dirs=%s' % spec['lapack'].prefix.lib,
             '--with-blas-libs=%s' % to_lib_name(
                 spec['blas'].blas_shared_lib),
-            '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix
+            '--with-blas-lib-dirs=%s' % spec['blas'].prefix.lib
         ]
 
         if '+shared' in self.spec:

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

@@ -12,9 +12,9 @@ class Mkl(IntelInstaller):
     mirror, see http://software.llnl.gov/spack/mirrors.html.
 
     To set the threading layer at run time set MKL_THREADING_LAYER
-    variable to one of the following values: INTEL, SEQUENTIAL, PGI.
+    variable to one of the following values: INTEL (default), SEQUENTIAL, PGI.
     To set interface layer at run time, use set the MKL_INTERFACE_LAYER
-    variable to LP64 or ILP64.
+    variable to LP64 (default) or ILP64.
     """
 
     homepage = "https://software.intel.com/en-us/intel-mkl"
@@ -38,6 +38,13 @@ def install(self, spec, prefix):
         for f in os.listdir(mkl_dir):
             os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f))
 
+        # Unfortunately MKL libs are natively distrubted in prefix/lib/intel64.
+        # To make MKL play nice with Spack, symlink all files to prefix/lib:
+        mkl_lib_dir = os.path.join(prefix, "lib", "intel64")
+        for f in os.listdir(mkl_lib_dir):
+            os.symlink(os.path.join(mkl_lib_dir, f),
+                       os.path.join(self.prefix, "lib", f))
+
     def setup_dependent_package(self, module, dspec):
         # For now use Single Dynamic Library:
         # To set the threading layer at run time, use the
@@ -53,6 +60,7 @@ def setup_dependent_package(self, module, dspec):
         name = 'libmkl_rt.%s' % dso_suffix
         libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
 
+        # Now set blas/lapack libs:
         self.spec.blas_shared_lib   = join_path(libdir, name)
         self.spec.lapack_shared_lib = self.spec.blas_shared_lib
 

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

@@ -138,16 +138,23 @@ def install(self, spec, prefix):
             '-DTPL_ENABLE_LAPACK=ON',
             '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
                 spec['lapack'].lapack_shared_lib),
-            '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
+            '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix.lib,
             '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
             '-DTrilinos_ENABLE_CXX11:BOOL=ON',
             '-DTPL_ENABLE_Netcdf:BOOL=ON',
             '-DTPL_ENABLE_HYPRE:BOOL=%s' % (
-                'ON' if '+hypre' in spec else 'OFF'),
+                'ON' if '+hypre' in spec else 'OFF')
-            '-DTPL_ENABLE_HDF5:BOOL=%s' % (
-                'ON' if '+hdf5' in spec else 'OFF'),
         ])
 
+        if '+hdf5' in spec:
+            options.extend([
+                '-DTPL_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+        else:
+            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
+
         if '+boost' in spec:
             options.extend([
                 '-DTPL_ENABLE_Boost:BOOL=ON',