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qmcpack: new package (#4907)

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This adds QMCPACK along with patches to Quantum Espresso for using Quantum Espresso in QMCPACK workflows.
This commit is contained in:
William Scullin 2017-10-06 15:51:18 -05:00 committed by Todd Gamblin
parent d05f98d405
commit 3d8d3e8882
3 changed files with 253 additions and 8 deletions
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4
var/spack/repos/builtin/packages/espresso/package.py
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@ -104,7 +104,9 @@ def install(self, spec, prefix):
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')

23
var/spack/repos/builtin/packages/intel-mkl/package.py
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@ -180,11 +180,15 @@ def scalapack_libs(self):
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 @@ def setup_environment(self, spack_env, run_env):
# 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'))

234
var/spack/repos/builtin/packages/qmcpack/package.py Normal file
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@ -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')