espresso: fixed compilation for 6.1 (elpa) and added support for hdf5 (…

…spack#4483)

* espresso: fixed compilation for 6.1 (elpa) and added support for hdf5

* espresso: addressed items in @davydden review

* espresso: fixed behavior for espresso@:5.4.0

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

@@ -53,8 +53,11 @@ def url_for_version(self, version):
     # override default implementation which returns static lib
     @property
     def libs(self):
+
+        libname = 'libelpa_openmp' if '+openmp' in self.spec else 'libelpa'
+
         return find_libraries(
-            ['libelpa'], root=self.prefix, shared=True, recurse=True
+            libname, root=self.prefix, shared=True, recurse=True
         )
 
     build_directory = 'spack-build'

var/spack/repos/builtin/packages/espresso/dspev_drv_elpa.patch

@@ -0,0 +1,42 @@
+diff -ruN LAXlib-orig/dspev_drv.f90 LAXlib/dspev_drv.f90
+--- a/LAXlib/dspev_drv.f90	2017-06-12 15:00:46.157372185 +0200
++++ b/LAXlib/dspev_drv.f90	2017-06-12 15:01:19.937371580 +0200
+@@ -708,11 +708,11 @@
+
+ #if defined(__ELPA_2016)
+      ! -> ELPA 2016.11.001_pre
+-     ierr = elpa_get_communicators(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
+-     success = solve_evp_real_1stage(n,  n,   s, lds,    w,  vv, lds,SIZE(s,2),nb  ,mpi_comm_rows, mpi_comm_cols, ortho_comm)
++     !ierr = elpa_get_communicators(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
++     !success = solve_evp_real_1stage(n,  n,   s, lds,    w,  vv, lds,SIZE(s,2),nb  ,mpi_comm_rows, mpi_comm_cols, ortho_comm)
+      ! -> ELPA 2016.05.003
+-     !ierr = get_elpa_row_col_comms(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
+-     !success = solve_evp_real_1stage(n,  n,   s, lds,    w,  vv, lds,SIZE(s,2),nb  ,mpi_comm_rows, mpi_comm_cols)
++     ierr = get_elpa_row_col_comms(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
++     success = solve_evp_real_1stage(n,  n,   s, lds,    w,  vv, lds,SIZE(s,2),nb  ,mpi_comm_rows, mpi_comm_cols)
+ #elif defined(__ELPA_2015)
+      ierr = get_elpa_row_col_comms(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
+      ierr = solve_evp_real(n,  n,   s, lds,    w,  vv, lds,SIZE(s,2),nb  ,mpi_comm_rows, mpi_comm_cols)
+diff -ruN LAXlib-orig/zhpev_drv.f90 LAXlib/zhpev_drv.f90
+--- a/LAXlib/zhpev_drv.f90	2017-06-12 15:00:46.157372185 +0200
++++ b/LAXlib/zhpev_drv.f90	2017-06-12 15:02:09.309370696 +0200
+@@ -1519,13 +1519,13 @@
+
+ #if defined(__ELPA_2016)
+      ! -> ELPA 2016.11.001_pre
+-     ierr = elpa_get_communicators(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
+-     success = solve_evp_complex_1stage_double(n, n, h, size(h,1), w,  v, size(h,1), size(h,2), nb, &
+-                           mpi_comm_rows, mpi_comm_cols, ortho_comm)
++     !ierr = elpa_get_communicators(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
++     !success = solve_evp_complex_1stage_double(n, n, h, size(h,1), w,  v, size(h,1), size(h,2), nb, &
++     !                      mpi_comm_rows, mpi_comm_cols, ortho_comm)
+      ! -> ELPA 2016.05.003
+-     !ierr = get_elpa_row_col_comms(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
+-     !success = solve_evp_complex(n, n, h, size(h,1), w,  v, size(h,1), size(h,2), nb, &
+-     !                      mpi_comm_rows, mpi_comm_cols)
++     ierr = get_elpa_row_col_comms(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
++     success = solve_evp_complex(n, n, h, size(h,1), w,  v, size(h,1), size(h,2), nb, &
++                           mpi_comm_rows, mpi_comm_cols)
+ #elif defined(__ELPA_2015)
+      ierr = get_elpa_row_col_comms(ortho_comm, my_prow, my_pcol,mpi_comm_rows, mpi_comm_cols)
+      ierr = solve_evp_complex(n, n, h, size(h,1), w,  v, size(h,1), size(h,2), nb, &

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

@@ -22,16 +22,17 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+import glob
+import os.path
+
 from spack import *
-import os
-from glob import glob
 
 
 class Espresso(Package):
-    """QE is an integrated suite of Open-Source computer codes for
-    electronic-structure calculations and materials modeling at
-    the nanoscale. It is based on density-functional theory, plane
-    waves, and pseudopotentials.
+    """Quantum-ESPRESSO is an integrated suite of Open-Source computer codes
+    for electronic-structure calculations and materials modeling at the
+    nanoscale. It is based on density-functional theory, plane waves, and
+    pseudopotentials.
     """
 
     homepage = 'http://quantum-espresso.org'
@@ -55,34 +56,43 @@ class Espresso(Package):
     variant('scalapack', default=True, description='Enables scalapack support')
     variant('elpa', default=True, description='Uses elpa as an eigenvalue solver')
 
+    # Support for HDF5 has been added starting in version 6.1.0 and is
+    # still experimental, therefore we default to False for the variant
+    variant('hdf5', default=False, description='Builds with HDF5 support')
+
     depends_on('blas')
     depends_on('lapack')
-
     depends_on('mpi', when='+mpi')
-    depends_on('fftw~mpi', when='~mpi')
-    depends_on('fftw+mpi', when='+mpi')
-    # TODO : + mpi needed to avoid false dependencies installation
     depends_on('scalapack', when='+scalapack+mpi')
-    depends_on('elpa@2016.11.001.pre', when='@6.1.0+elpa')
+
+    depends_on('fftw+mpi', when='+mpi')
+    depends_on('fftw~mpi', when='~mpi')
+    depends_on('elpa+openmp', when='+elpa+openmp')
+    depends_on('elpa~openmp', when='+elpa~openmp')
+    depends_on('hdf5', when='+hdf5')
+
+    patch('dspev_drv_elpa.patch', when='@6.1 ^elpa@2016.05.004')
+    patch('dspev_drv_elpa.patch', when='@6.1 ^elpa@2016.05.003')
+
+    # We can't ask for scalapack or elpa if we don't want MPI
+    conflicts('+scalapack', when='~mpi')
+    conflicts('+elpa', when='~mpi')
+
+    # Elpa is formally supported by @:5.4.0, but QE configure searches
+    # for it in the wrong folders (or tries to download it within
+    # the build directory). Instead of patching Elpa to provide the
+    # folder QE expects as a link, we issue a conflict here.
+    conflicts('+elpa', when='@:5.4.0')
+    conflicts('+hdf5', when='@:5.4.0')
 
     # Spurious problems running in parallel the Makefile
     # generated by the configure
     parallel = False
 
-    def check_variants(self, spec):
-        error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
-        if '+scalapack' in spec and '~mpi' in spec:
-            raise RuntimeError(error.format(variant='scalapack'))
-        if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
-            raise RuntimeError(error.format(variant='elpa'))
-
     def install(self, spec, prefix):
-        self.check_variants(spec)
 
-        options = [
-            '-prefix=%s' % (prefix.bin if spec.satisfies('@:5.4.0') else
-                            prefix)
-        ]
+        prefix_path = prefix.bin if '@:5.4.0' in spec else prefix
+        options = ['-prefix={0}'.format(prefix_path)]
 
         if '+mpi' in spec:
             options.append('--enable-parallel')
@@ -91,38 +101,53 @@ def install(self, spec, prefix):
             options.append('--enable-openmp')
 
         if '+scalapack' in spec:
-            options.append('--with-scalapack=yes')
+            scalapack_option = 'intel' if '^intel-mkl' in spec else 'yes'
+            options.append('--with-scalapack={0}'.format(scalapack_option))
 
         if '+elpa' in spec:
-            if spec.satisfies('@:5.4.0'):
-                options.append('--with-elpa=yes')
-            else:
-                options.extend([
-                    '--with-elpa-include={0}'.format(
-                        join_path(spec['elpa'].prefix,
-                                  'include',
-                                  'elpa-{0}'.format(str(spec['elpa'].version)),
-                                  'modules')
-                    ),
-                    '--with-elpa-lib={0}'.format(spec['elpa'].libs.joined())
-                ])
+
+            # Spec for elpa
+            elpa = spec['elpa']
+
+            # Find where the Fortran module resides
+            elpa_module = find(elpa.prefix, 'elpa.mod')
+
+            # Compute the include directory from there: versions
+            # of espresso prior to 6.1 requires -I in front of the directory
+            elpa_include = '' if '@6.1:' in spec else '-I'
+            elpa_include += os.path.dirname(elpa_module[0])
+
+            options.extend([
+                '--with-elpa-include={0}'.format(elpa_include),
+                '--with-elpa-lib={0}'.format(elpa.libs[0])
+            ])
+
+        if '+hdf5' in spec:
+            options.append('--with-hdf5={0}'.format(spec['hdf5'].prefix))
 
         # Add a list of directories to search
         search_list = []
         for dependency_spec in spec.dependencies():
-            search_list.extend([dependency_spec.prefix.lib,
-                                dependency_spec.prefix.lib64])
+            search_list.extend([
+                dependency_spec.prefix.lib,
+                dependency_spec.prefix.lib64
+            ])
 
         search_list = " ".join(search_list)
-        options.append('LIBDIRS=%s' % search_list)
-        options.append('F90=%s' % os.environ['FC'])
+
+        options.extend([
+            'LIBDIRS={0}'.format(search_list),
+            'F90={0}'.format(env['SPACK_FC']),
+            'CC={0}'.format(env['SPACK_CC'])
+        ])
 
         configure(*options)
+
         make('all')
 
-        if spec.satisfies('platform=darwin'):
+        if 'platform=darwin' in spec:
             mkdirp(prefix.bin)
-            for filename in glob("bin/*.x"):
+            for filename in glob.glob("bin/*.x"):
                 install(filename, prefix.bin)
         else:
             make('install')