qmcpack: new package (#4907)

This adds QMCPACK along with patches to Quantum Espresso for using Quantum Espresso in QMCPACK workflows.

3 files changed, 253 insertions, 8 deletions

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index a39fd859c1..669311a148 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -104,7 +104,9 @@ class Espresso(Package):
         options = ['-prefix={0}'.format(prefix_path)]
 
         if '+mpi' in spec:
-            options.append('--enable-parallel')
+            options.append('--enable-parallel=yes')
+        else:
+            options.append('--enable-parallel=no')
 
         if '+openmp' in spec:
             options.append('--enable-openmp')
diff --git a/var/spack/repos/builtin/packages/intel-mkl/package.py b/var/spack/repos/builtin/packages/intel-mkl/package.py
index 23d1e920ca..9a3b9b9550 100644
--- a/var/spack/repos/builtin/packages/intel-mkl/package.py
+++ b/var/spack/repos/builtin/packages/intel-mkl/package.py
@@ -180,11 +180,15 @@ class IntelMkl(IntelPackage):
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # set up MKLROOT for everyone using MKL package
-        mkl_root = self.prefix.mkl.lib if sys.platform == 'darwin' else \
-            self.prefix.compilers_and_libraries.linux.mkl.lib.intel64
+        if sys.platform == 'darwin':
+            mkl_lib = self.prefix.mkl.lib
+            mkl_root = self.prefix.mkl
+        else:
+            mkl_lib = self.prefix.compilers_and_libraries.linux.mkl.lib.intel64
+            mkl_root = self.prefix.compilers_and_libraries.linux.mkl
 
-        spack_env.set('MKLROOT', self.prefix)
-        spack_env.append_path('SPACK_COMPILER_EXTRA_RPATHS', mkl_root)
+        spack_env.set('MKLROOT', mkl_root)
+        spack_env.append_path('SPACK_COMPILER_EXTRA_RPATHS', mkl_lib)
 
     def setup_environment(self, spack_env, run_env):
         """Adds environment variables to the generated module file.
@@ -205,6 +209,11 @@ class IntelMkl(IntelPackage):
         # this problem.
         mklvars = os.path.join(self.prefix.mkl.bin, 'mklvars.sh')
 
-        if os.path.isfile(mklvars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                mklvars, 'intel64'))
+        if sys.platform == 'darwin':
+            if os.path.isfile(mklvars):
+                run_env.extend(EnvironmentModifications.from_sourcing_file(
+                    mklvars))
+        else:
+            if os.path.isfile(mklvars):
+                run_env.extend(EnvironmentModifications.from_sourcing_file(
+                    mklvars, 'intel64'))
diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py
new file mode 100644
index 0000000000..8d96c4b99f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qmcpack/package.py
@@ -0,0 +1,234 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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/llnl/spack
+# Please also see the LICENSE file 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 *
+
+
+class Qmcpack(CMakePackage):
+    """QMCPACK, is a modern high-performance open-source Quantum Monte
+       Carlo (QMC) simulation code."""
+
+    # Package information
+    homepage = "http://www.qmcpack.org/"
+    url      = "https://github.com/QMCPACK/qmcpack.git"
+
+    # This download method is untrusted, and is not recommended
+    # by the Spack manual. However, it is easier to maintain
+    # because github hashes can occasionally change
+    version('3.2.0', git=url, tag='v3.2.0')
+    version('3.1.1', git=url, tag='v3.1.1')
+    version('3.1.0', git=url, tag='v3.1.0')
+    version('3.0.0', git=url, tag='v3.0.0')
+    version('develop', git=url)
+
+    # These defaults match those in the QMCPACK manual
+    variant('debug', default=False, description='Build debug version')
+    variant('mpi', default=True, description='Build with MPI support')
+    variant('cuda', default=False,
+            description='Enable CUDA and GPU acceleration')
+    variant('complex', default=False,
+            description='Build the complex (general twist/k-point) version')
+    variant('mixed', default=False,
+            description='Build the mixed precision (mixture of single and '
+                        'double precision) version for gpu and cpu')
+    variant('soa', default=False,
+            description='Build with Structure-of-Array instead of '
+                        'Array-of-Structure code. Only for CPU code'
+                        'and only in mixed precision')
+    variant('timers', default=False,
+             description='Build with support for timers')
+    variant('da', default=False,
+            description='Install with support for basic data analysis tools')
+    variant('gui', default=False,
+            description='Install with Matplotlib (long installation time)')
+
+    # cuda variant implies mixed precision variant by default, but there is
+    # no way to express this in variant syntax, need something like
+    # variant('+mixed', default=True, when='+cuda', description="...")
+
+    # conflicts
+    conflicts('+soa', when='+cuda')
+    conflicts('^openblas+ilp64')
+    conflicts('^intel-mkl+ilp64')
+
+    # Dependencies match those in the QMCPACK manual
+    depends_on('cmake@3.4.3:', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('libxml2')
+    depends_on('hdf5')
+    depends_on('hdf5+mpi', when='+mpi')
+    depends_on('hdf5~mpi', when='~mpi')
+    depends_on('boost')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('fftw')
+    depends_on('fftw+mpi', when='+mpi')
+    depends_on('fftw~mpi', when='~mpi')
+    depends_on('cuda', when='+cuda')
+
+    # qmcpack data analysis tools
+    # basic command line tool based on Python and NumPy
+    # blas and lapack patching fails often and so are disabled at this time
+    depends_on('py-numpy~blas~lapack', type='run', when='+da')
+
+    # GUI is optional fpr data anlysis
+    # py-matplotlib leads to a long complex DAG for dependencies
+    depends_on('py-matplotlib', type='run', when='+gui')
+
+    # B-spline basis calculation require a patched version of
+    # Quantum Espresso 5.3.0 (see QMCPACK manual)
+    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_espresso-5.3.0.diff'
+    patch_checksum = '0d8d7ba805313ddd4c02ee32c96d2f12e7091e9e82e22671d3ad5a24247860c4'
+    depends_on('espresso@5.3.0~elpa',
+               patches=patch(patch_url, sha256=patch_checksum),
+               when='+mpi')
+
+    depends_on('espresso@5.3.0~elpa~scalapack~mpi',
+               patches=patch(patch_url, sha256=patch_checksum),
+               when='~mpi')
+
+    def patch(self):
+        # FindLibxml2QMC.cmake doesn't check the environment by default
+        # for libxml2, so we fix that.
+        filter_file(r'$ENV{LIBXML2_HOME}/lib',
+                    '${LIBXML2_HOME}/lib $ENV{LIBXML2_HOME}/lib',
+                    'CMake/FindLibxml2QMC.cmake')
+
+    def cmake_args(self):
+        args = []
+
+        if '+mpi' in self.spec:
+            mpi = self.spec['mpi']
+            args.append('-DCMAKE_C_COMPILER={0}'.format(mpi.mpicc))
+            args.append('-DCMAKE_CXX_COMPILER={0}'.format(mpi.mpicxx))
+            args.append('-DMPI_BASE_DIR:PATH={0}'.format(mpi.prefix))
+
+        # Currently FFTW_HOME and LIBXML2_HOME are used by CMake.
+        # Any CMake warnings about other variables are benign.
+        xml2_prefix = self.spec['libxml2'].prefix
+        args.append('-DLIBXML2_HOME={0}'.format(xml2_prefix))
+        args.append('-DLibxml2_INCLUDE_DIRS={0}'.format(xml2_prefix.include))
+        args.append('-DLibxml2_LIBRARY_DIRS={0}'.format(xml2_prefix.lib))
+
+        fftw_prefix = self.spec['fftw'].prefix
+        args.append('-DFFTW_HOME={0}'.format(fftw_prefix))
+        args.append('-DFFTW_INCLUDE_DIRS={0}'.format(fftw_prefix.include))
+        args.append('-DFFTW_LIBRARY_DIRS={0}'.format(fftw_prefix.lib))
+
+        args.append('-DBOOST_ROOT={0}'.format(self.spec['boost'].prefix))
+        args.append('-DHDF5_ROOT={0}'.format(self.spec['hdf5'].prefix))
+
+        # Default is MPI, serial version is convenient for cases, e.g. laptops
+        if '+mpi' in self.spec:
+            args.append('-DQMC_MPI=1')
+        elif '~mpi' in self.spec:
+            args.append('-DQMC_MPI=0')
+
+        # Default is real-valued single particle orbitals
+        if '+complex' in self.spec:
+            args.append('-DQMC_COMPLEX=1')
+        elif '~complex' in self.spec:
+            args.append('-DQMC_COMPLEX=0')
+
+        # When '-DQMC_CUDA=1', CMake automatically sets:
+        # '-DQMC_MIXED_PRECISION=1'
+        #
+        # There is a double-precision CUDA path, but it is not as well
+        # tested.
+
+        if '+cuda' in self.spec:
+            args.append('-DQMC_CUDA=1')
+        elif '~cuda' in self.spec:
+            args.append('-DQMC_CUDA=0')
+
+        # Mixed-precision versues double-precision CPU and GPU code
+        if '+mixed' in self.spec:
+            args.append('-DQMC_MIXED_PRECISION=1')
+        elif '~mixed' in self.spec:
+            args.append('-DQMC_MIXED_PRECISION=0')
+
+        # New Structure-of-Array (SOA) code, much faster than default
+        # Array-of-Structure (AOS) code.
+        # No support for local atomic orbital basis.
+        if '+soa' in self.spec:
+            args.append('-DENABLE_SOA=1')
+        elif '~soa' in self.spec:
+            args.append('-DENABLE_SOA=0')
+
+        # Manual Timers
+        if '+timers' in self.spec:
+            args.append('-DENABLE_TIMERS=1')
+        elif '~timers' in self.spec:
+            args.append('-DENABLE_TIMERS=0')
+
+    #     # Proper MKL detection not working.
+    #     # Include MKL flags
+    #     if 'intel-mkl' in self.spec:
+    #         args.append('-DBLA_VENDOR=Intel10_64lp_seq')
+    #         args.append('-DQMC_INCLUDE={0}'.format(join_path(env['MKLROOT'],'include')))
+        return args
+
+    # def setup_environment(self, spack_env, run_env):
+    #     # Add MKLROOT/lib to the CMAKE_PREFIX_PATH to enable CMake to find
+    #     # MKL libraries. MKLROOT environment variable must be defined for
+    #     # this to work properly.
+    #     if 'intel-mkl' in self.spec:
+    #         spack_env.append_path('CMAKE_PREFIX_PATH',format(join_path(env['MKLROOT'],'lib')))
+
+    def install(self, spec, prefix):
+        """Make the install targets"""
+
+        # QMCPACK 'make install' does nothing, which causes
+        # Spack to throw an error.
+        #
+        # This install method creates the top level directory
+        # and copies the bin subdirectory into the appropriate
+        # location. We do not copy include or lib at this time due
+        # to technical difficulties in qmcpack itself.
+
+        mkdirp(prefix)
+
+        # We assume cwd is self.stage.source_path
+
+        # install manual
+        install_tree('manual', prefix.manual)
+
+        # install nexus
+        install_tree('nexus', prefix.nexus)
+
+        with working_dir(self.build_directory):
+            mkdirp(prefix)
+
+            # install binaries
+            install_tree('bin', prefix.bin)
+
+    @run_after('build')
+    @on_package_attributes(run_tests=True)
+    def check(self):
+        """Run ctest after building binary.
+        It can take over 24 hours to run all the regression tests, here we
+        only run the unit tests and short tests."""
+        with working_dir(self.build_directory):
+            ctest('-L', 'unit')
+            ctest('-R', 'short')