ppOpen-APPL/FEM: New package. (#15911)

* ppOpen-APPL/FEM: New package.

* typo fix.
Update patch.

var/spack/repos/builtin/packages/ppopen-appl-fem/gcc_struct_atomic.patch

@@ -0,0 +1,69 @@
+diff --git a/ppohFEM/src/solver/matrix/hecmw_mat_ass.f90 b/ppohFEM/src/solver/matrix/hecmw_mat_ass.f90
+index dda6a62..6010d6d 100644
+--- a/ppohFEM/src/solver/matrix/hecmw_mat_ass.f90
++++ b/ppohFEM/src/solver/matrix/hecmw_mat_ass.f90
+@@ -322,7 +322,7 @@ module hecmw_matrix_ass
+    subroutine hecmw_mat_ass_bc(hecMAT, inode, idof, RHS, conMAT)
+       type (hecmwST_matrix)     :: hecMAT
+       integer(kind=kint) :: inode, idof
+-      real(kind=kreal) :: RHS
++      real(kind=kreal) :: RHS, tmp
+       type (hecmwST_matrix),optional     :: conMAT
+       integer(kind=kint) :: NDOF, in, i, ii, iii, ndof2, k, iS, iE, iiS, iiE, ik
+ 
+@@ -338,13 +338,13 @@ module hecmw_matrix_ass
+ 
+       DO i = NDOF-1,0,-1
+         IF( i .NE. NDOF-idof ) THEN
++          tmp = hecMAT%D(ndof2*inode-ii)*RHS
+ !$omp atomic
+-          hecMAT%B(NDOF*inode-i) = hecMAT%B(NDOF*inode-i)        &
+-                                 - hecMAT%D(ndof2*inode-ii)*RHS
++          hecMAT%B(NDOF*inode-i) = hecMAT%B(NDOF*inode-i) - tmp
+           if(present(conMAT)) then
++            tmp = conMAT%D(ndof2*inode-ii)*RHS
+ !$omp atomic
+-            conMAT%B(NDOF*inode-i) = conMAT%B(NDOF*inode-i)        &
+-                                   - conMAT%D(ndof2*inode-ii)*RHS
++            conMAT%B(NDOF*inode-i) = conMAT%B(NDOF*inode-i) - tmp
+           endif
+         ENDIF
+         ii = ii - NDOF
+@@ -393,14 +393,14 @@ module hecmw_matrix_ass
+           if (hecMAT%itemU(ik) .eq. inode) then
+             iii = ndof2 - idof
+             DO i = NDOF-1,0,-1
++              tmp = hecMAT%AU(ndof2*ik-iii)*RHS
+ !$omp atomic
+-              hecMAT%B(NDOF*in-i) = hecMAT%B(NDOF*in-i)      &
+-                                  - hecMAT%AU(ndof2*ik-iii)*RHS
++              hecMAT%B(NDOF*in-i) = hecMAT%B(NDOF*in-i) - tmp
+               hecMAT%AU(ndof2*ik-iii)= 0.d0
+               if(present(conMAT)) then
++                tmp = conMAT%AU(ndof2*ik-iii)*RHS
+ !$omp atomic
+-                conMAT%B(NDOF*in-i) = conMAT%B(NDOF*in-i)      &
+-                                    - conMAT%AU(ndof2*ik-iii)*RHS
++                conMAT%B(NDOF*in-i) = conMAT%B(NDOF*in-i) - tmp
+                 conMAT%AU(ndof2*ik-iii)= 0.d0
+               endif
+               iii = iii - NDOF
+@@ -432,14 +432,14 @@ module hecmw_matrix_ass
+             iii  = ndof2 - idof
+ 
+             DO i = NDOF-1, 0, -1
++              tmp = hecMAT%AL(ndof2*ik-iii)*RHS
+ !$omp atomic
+-              hecMAT%B(NDOF*in-i) = hecMAT%B(NDOF*in-i)      &
+-                                  - hecMAT%AL(ndof2*ik-iii)*RHS
++              hecMAT%B(NDOF*in-i) = hecMAT%B(NDOF*in-i) - tmp
+               hecMAT%AL(ndof2*ik-iii) = 0.d0
+               if(present(conMAT)) then
++                tmp = conMAT%AL(ndof2*ik-iii)*RHS
+ !$omp atomic
+-                conMAT%B(NDOF*in-i) = conMAT%B(NDOF*in-i)      &
+-                                    - conMAT%AL(ndof2*ik-iii)*RHS
++                conMAT%B(NDOF*in-i) = conMAT%B(NDOF*in-i) - tmp
+                 conMAT%AL(ndof2*ik-iii) = 0.d0
+               endif
+               iii = iii - NDOF

var/spack/repos/builtin/packages/ppopen-appl-fem/package.py

@@ -0,0 +1,63 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+import os
+
+
+class PpopenApplFem(MakefilePackage):
+    """
+    ppOpen-APPL/FEM (ppohFEM) is a middleware to allow a Finite Element
+    Method (FEM) analysis code developer to devote himself to development of
+    the application software by offering a function commonly used in FEM.
+    """
+
+    homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/"
+    url = "file://{0}/ppohFEM_1.0.1.tar.gz".format(os.getcwd())
+
+    version('1.0.1', sha256='eea8837fa3eda284759b7ebf27c27cea8cbf9cf65cf37c62941700e1321aeb07')
+
+    depends_on('mpi')
+    depends_on('metis')
+
+    # gcc does not support OpenMP atomic to same structure reference.
+    # For example a%b = a%b - a%c
+    # To avoid this, the patch is replace as follows:
+    #   tmp = a%c
+    #   !%omp atomic
+    #   a%b = a%b - a%c
+    patch('gcc_struct_atomic.patch', when='%gcc')
+    parallel = False
+
+    def edit(self, spec, prefix):
+        fflags = ['-O3', '-I.', self.compiler.openmp_flag]
+        if spec.satisfies('%gcc'):
+            fflags.extend(['-cpp', '-ffree-line-length-none'])
+        makefile_in = FileFilter('Makefile.in')
+        makefile_in.filter(
+            r'^PREFIX *=.*$',
+            'PREFIX = {0}'.format(prefix)
+        )
+        makefile_in.filter(
+            r'^F90OPTFLAGS *=.*$',
+            'F90OPTFLAGS = {0}'.format(' '.join(fflags))
+        )
+        makefile_in.filter(
+            r'^METISDIR *=.*$',
+            'METISDIR = {0}'.format(spec['metis'].prefix)
+        )
+        makefile_in.filter('mpicc', spec['mpi'].mpicc)
+        makefile_in.filter('mpif90', spec['mpi'].mpifc)
+
+    def install(self, spec, prefix):
+        for d in ['ppohFEM', 'app_flow', 'app_heat', 'app_struct']:
+            with working_dir(d):
+                for install_dir in ['bin', 'lib', 'include']:
+                    if os.path.isdir(install_dir):
+                        install_tree(
+                            install_dir,
+                            join_path(prefix, install_dir)
+                        )