cp2k: update to 4.1 + update of dependencies (#3561)

* libint: updated version, ported to AutotoolsPackage

* elpa: updated version, ported to AutotoolsPackage

* wannier90: updated version, ported to MakefilePackage

* pexsi: updated version, ported to MakefilePackage

* cp2k: updated version, removed wannier 90 from dependencies if cp2k@4.1

* plumed: updated version

Modifications:

* modules has been turned into a single variant, as different versions
  have different modules available
* added dictionaries for patches

* netlib-scalapack: ported to CMakePackage

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

@@ -26,24 +26,15 @@
 from spack import *
 
 
-class Elpa(Package):
-    """
-    Eigenvalue solvers for Petaflop-Applications (ELPA)
-    """
+class Elpa(AutotoolsPackage):
+    """Eigenvalue solvers for Petaflop-Applications (ELPA)"""
 
     homepage = 'http://elpa.mpcdf.mpg.de/'
     url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
 
-    version(
-        '2016.05.003',
-        '88a9f3f3bfb63e16509dd1be089dcf2c',
-        url='http://elpa.mpcdf.mpg.de/html/Releases/2016.05.003/elpa-2016.05.003.tar.gz'
-    )
-    version(
-        '2015.11.001',
-        'de0f35b7ee7c971fd0dca35c900b87e6',
-        url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
-    )
+    version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376')
+    version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c')
+    version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6')
 
     variant('openmp', default=False, description='Activates OpenMP support')
 
@@ -52,30 +43,26 @@ class Elpa(Package):
     depends_on('lapack')
     depends_on('scalapack')
 
-    def install(self, spec, prefix):
+    def url_for_version(self, version):
+        t = 'http://elpa.mpcdf.mpg.de/html/Releases/{0}/elpa-{0}.tar.gz'
+        if version < Version('2016.05.003'):
+            t = 'http://elpa.mpcdf.mpg.de/elpa-{0}.tar.gz'
+        return t.format(str(version))
 
-        options = [
-            'CC={0}'.format(self.spec['mpi'].mpicc),
-            'FC={0}'.format(self.spec['mpi'].mpifc),
-            'CXX={0}'.format(self.spec['mpi'].mpicxx),
-            'FCFLAGS={0}'.format(
-                spec['lapack'].libs.joined()
-            ),
-            'LDFLAGS={0}'.format(
-                spec['lapack'].libs.joined()
-            ),
-            'SCALAPACK_FCFLAGS={0}'.format(
-                spec['scalapack'].libs.joined()
-            ),
-            'SCALAPACK_LDFLAGS={0}'.format(
-                spec['scalapack'].libs.joined()
-            ),
-            '--prefix={0}'.format(self.prefix)
-        ]
+    def setup_environment(self, spack_env, run_env):
 
-        if '+openmp' in spec:
+        spec = self.spec
+
+        spack_env.set('CC', spec['mpi'].mpicc)
+        spack_env.set('FC', spec['mpi'].mpifc)
+        spack_env.set('CXX', spec['mpi'].mpicxx)
+
+        spack_env.set('LDFLAGS', spec['lapack'].libs.search_flags)
+        spack_env.set('LIBS', spec['lapack'].libs.link_flags)
+        spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
+
+    def configure_args(self):
+        options = []
+        if '+openmp' in self.spec:
             options.append("--enable-openmp")
-
-        configure(*options)
-        make()
-        make("install")
+        return options