Adding Nek5000 to Spack (#6153)

* Start adding Nek5000 package

* Add tools to install: genmap, prenek, postnek

* Address comments by @davydden

* Use install_tree (thanks @junghans) and polish

* Update url

* Fix flake formatting errors

* Change F77 and CC compilers

Apparently spack compilers can't be called outside spack and we
have an underscore test in our Nek5000/core/makenek.inc file which
calls F77 compiler.

* Add support for visit and profiling options

* Fix a typo

* Fix a typo

* Remove the C check

* Add visit variant

* Update the install of int_tp tool

* Let MAXNEL to be set during installation

2 files changed, 154 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/nek5000/package.py b/var/spack/repos/builtin/packages/nek5000/package.py
new file mode 100644
index 0000000000..4755d28575
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nek5000/package.py
@@ -0,0 +1,153 @@
+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/spack/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+import numbers
+
+
+def is_integral(x):
+    """Any integer value"""
+    try:
+        return isinstance(int(x), numbers.Integral) and \
+            not isinstance(x, bool) and int(x) > 0
+    except ValueError:
+        return False
+
+
+class Nek5000(Package):
+    """A fast and scalable high-order solver for computational fluid
+       dynamics"""
+
+    homepage = "https://nek5000.mcs.anl.gov/"
+    url      = "https://github.com/Nek5000/Nek5000"
+
+    tags = ['cfd', 'flow', 'hpc', 'solver', 'navier-stokes',
+            'spectral-elements', 'fluid']
+
+    version('17.0.0-beta2', git='https://github.com/Nek5000/Nek5000.git',
+        commit='b95f46c59f017fff2fc19b66aa65a881085a7572')
+    version('develop',      git='https://github.com/Nek5000/Nek5000.git',
+        branch='master')
+
+    # MPI, Profiling and Visit variants
+    variant('mpi',       default=True, description='Build with MPI.')
+    variant('profiling', default=True, description='Build with profiling data.')
+    variant('visit',     default=False, description='Build with Visit.')
+
+    # Variant for MAXNEL, we need to read this from user
+    variant(
+        'MAXNEL',
+        default=150000,
+        description='Maximum number of elements for Nek5000 tools.',
+        values=is_integral
+    )
+
+    # Variants for Nek tools
+    variant('genbox',   default=True, description='Build genbox tool.')
+    variant('int_tp',   default=True, description='Build int_tp tool.')
+    variant('n2to3',    default=True, description='Build n2to3 tool.')
+    variant('postnek',  default=True, description='Build postnek tool.')
+    variant('reatore2', default=True, description='Build reatore2 tool.')
+    variant('genmap',   default=True, description='Build genmap tool.')
+    variant('nekmerge', default=True, description='Build nekmerge tool.')
+    variant('prenek',   default=True, description='Build prenek tool.')
+
+    # Dependencies
+    depends_on('mpi', when="+mpi")
+    depends_on('visit', when="+visit")
+
+    @run_before('install')
+    def fortran_check(self):
+        if not self.compiler.fc:
+            msg = 'Cannot build Nek5000 without a Fortran compiler.'
+            raise RuntimeError(msg)
+
+    def install(self, spec, prefix):
+        toolsDir   = 'tools'
+        binDir     = 'bin'
+
+        F77 = self.compiler.fc
+        CC  = self.compiler.cc
+
+        # Build the tools, maketools copy them to Nek5000/bin by default.
+        # We will then install Nek5000/bin under prefix after that.
+        with working_dir(toolsDir):
+            # Update the maketools script to use correct compilers
+            if self.version == Version('17.0.0-beta2'):  # Old release
+                filter_file(r'^F77\s*=.*', 'F77=\"' + F77 + '\"', 'maketools')
+            else:
+                filter_file(r'^FC\s*=.*', 'FC=\"' + F77 + '\"', 'maketools')
+            filter_file(r'^CC\s*=.*', 'CC=\"' + CC  + '\"',   'maketools')
+
+            maxnel = self.spec.variants['MAXNEL'].value
+            filter_file(r'^#MAXNEL\s*=.*', 'MAXNEL=' + maxnel, 'maketools')
+
+            makeTools = Executable('./maketools')
+
+            # Build the tools
+            if '+genbox' in spec:
+                makeTools('genbox')
+            if '+int_tp' in spec and self.version == Version('17.0.0-beta2'):
+                makeTools('int_tp')
+            if '+n2to3' in spec:
+                makeTools('n2to3')
+            if '+postnek' in spec:
+                makeTools('postnek')
+            if '+reatore2' in spec:
+                makeTools('reatore2')
+            if '+genmap' in spec:
+                makeTools('genmap')
+            if '+nekmerge' in spec:
+                makeTools('nekmerge')
+            if '+prenek' in spec:
+                makeTools('prenek')
+
+        with working_dir(binDir):
+            if '+mpi' in spec:
+                F77 = spec['mpi'].mpif77
+                CC  = spec['mpi'].mpicc
+            else:
+                filter_file(r'^#MPI=0', 'MPI=0', 'makenek')
+
+            if '+profiling' not in spec:
+                filter_file(r'^#PROFILING=0', 'PROFILING=0', 'makenek')
+
+            if '+visit' in spec:
+                filter_file(r'^#VISIT=1', 'VISIT=1', 'makenek')
+                filter_file(r'^#VISIT_INSTALL=.*', 'VISIT_INSTALL=\"' +
+                            spec['visit'].prefix.bin + '\"', 'makenek')
+
+            # Update the makenek to use correct compilers and
+            # Nek5000 source.
+            filter_file(r'^F77\s*=.*', 'F77=\"' + F77 + '\"', 'makenek')
+            filter_file(r'^CC\s*=.*', 'CC=\"'  + CC  + '\"',  'makenek')
+            filter_file(r'SOURCE_ROOT\s*=\"\$H.*',  'SOURCE_ROOT=\"' +
+                        prefix.bin.Nek5000 + '\"',  'makenek')
+
+        # Install Nek5000/bin in prefix/bin
+        install_tree(binDir, prefix.bin)
+
+        # Copy Nek5000 source to prefix/bin
+        install_tree('../Nek5000', prefix.bin.Nek5000)
diff --git a/var/spack/repos/builtin/packages/nekbone/package.py b/var/spack/repos/builtin/packages/nekbone/package.py
index 4531012110..053b80413d 100644
--- a/var/spack/repos/builtin/packages/nekbone/package.py
+++ b/var/spack/repos/builtin/packages/nekbone/package.py
@@ -32,6 +32,7 @@ class Nekbone(Package):
        the spectral element method."""
 
     homepage = "https://github.com/Nek5000/Nekbone"
+    url = "https://github.com/Nek5000/Nekbone/tarball/v17.0"
 
     tags = ['proxy-app', 'ecp-proxy-app']