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sirius (new versions, fixes), q-e-sirius (new package), nlcglib (new package) (#17844)

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* sirius, update versions, fixes, add missing options

- sirius/spfft: depend on fftw-api
- cleanup +shared option
- sirius add option for memory pool
- sirius add version 6.5.3 and 6.5.4
- sirius: add spfft dependency for @master, @develop

* add nlcglib package

Robust wave function optimization for SIRIUS.

* add q-e-sirius package

based on q-e package

* Update var/spack/repos/builtin/packages/q-e-sirius/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* nlcglib: pass nvcc_wrapper to cmake

* Add 6.5.6

* Make flake8 happy

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
This commit is contained in:
Simon Pintarelli 2020-08-04 19:03:04 +02:00 committed by GitHub
parent 3a02d1a847
commit c3a38e0b14
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3 changed files with 399 additions and 4 deletions
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64
var/spack/repos/builtin/packages/nlcglib/package.py Normal file
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@ -0,0 +1,64 @@
# 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 *
class Nlcglib(CMakePackage, CudaPackage):
"""Nonlinear CG methods for wave-function optimization in DFT."""
homepage = "https://github.com/simonpintarelli/nlcglib"
git = "https://github.com/simonpintarelli/nlcglib.git"
url = "https://github.com/simonpintarelli/nlcglib/archive/v0.9.tar.gz"
maintainers = ['simonpintarelli']
version('master', branch='master')
version('develop', branch='develop')
version('0.9', sha256='8d5bc6b85ee714fb3d6480f767e7f43e5e7d569116cf60e48f533a7f50a37a08')
variant('wrapper', default=False,
description='Use nvcc-wrapper for CUDA build')
variant('openmp', default=False)
variant('build_type', default='Release',
description='CMake build type',
values=('Debug', 'Release', 'RelWithDebInfo'))
depends_on('lapack')
depends_on('kokkos +cuda~cuda_relocatable_device_code+cuda_lambda')
depends_on('kokkos-nvcc-wrapper', when='+wrapper')
depends_on('kokkos +cuda~cuda_relocatable_device_code+cuda_lambda+wrapper', when='+wrapper')
depends_on("cmake@3.15:", type='build')
depends_on('kokkos+cuda~cuda_relocatable_device_code+cuda_lambda+openmp+wrapper', when='+openmp+wrapper')
def cmake_args(self):
options = []
if '+openmp' in self.spec:
options.append('-DUSE_OPENMP=On')
else:
options.append('-DUSE_OPENMP=Off')
if self.spec['blas'].name in ['intel-mkl', 'intel-parallel-studio']:
options.append('-DLAPACK_VENDOR=MKL')
elif self.spec['blas'].name in ['openblas']:
options.append('-DLAPACK_VENDOR=OpenBLAS')
else:
raise Exception('blas/lapack must be either openblas or mkl.')
options.append('-DBUILD_TESTS=OFF')
if '+wrapper' in self.spec:
options.append('-DCMAKE_CXX_COMPILER=%s' %
self.spec['kokkos-nvcc-wrapper'].kokkos_cxx)
if '+cuda' in self.spec:
cuda_arch = self.spec.variants['cuda_arch'].value
if cuda_arch[0] != 'none':
options += [
'-DCMAKE_CUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0])
]
return options

317
var/spack/repos/builtin/packages/q-e-sirius/package.py Normal file
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# 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)
# adapted from official quantum espresso package
import glob
import os.path
from spack import *
class QESirius(Package):
"""SIRIUS enabled fork of QuantumESPRESSO. """
homepage = 'https://github.com/electronic-structure/q-e-sirius/'
url = 'https://github.com/electronic-structure/q-e-sirius/archive/v6.5-rc4-sirius.tar.gz'
git = 'https://github.com/electronic-structure/q-e-sirius.git'
maintainers = ['simonpintarelli']
version('develop', branch='ristretto')
version('6.5-rc2-sirius', sha256='460b678406eec36e4ee828c027929cf8720c3965a85c20084c53398b123c9ae9')
version('6.5-rc3-sirius', sha256='1bfb8c1bba815b5ab2d733f51a8f9aa7b079f2859e6f14e4dcda708ebf172b02')
version('6.5-rc4-sirius', sha256='be5529d65e4b301d6a6d1235e8d88277171c1732768bf1cf0c7fdeae154c79f1')
variant('mpi', default=True, description='Builds with mpi support')
variant('openmp', default=True, description='Enables openMP support')
variant('scalapack', default=True, description='Enables scalapack support')
variant('elpa', default=False, 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='none', description='Builds with HDF5 support',
values=('parallel', 'serial', 'none'), multi=False
)
# Enables building Electron-phonon Wannier 'epw.x' executable
# http://epw.org.uk/Main/About
variant('epw', default=False,
description='Builds Electron-phonon Wannier executable')
# Apply upstream patches by default. Variant useful for 3rd party
# patches which are incompatible with upstream patches
desc = 'Apply recommended upstream patches. May need to be set '
desc += 'to False for third party patches or plugins'
variant('patch', default=True, description=desc)
# QMCPACK converter patch
# https://github.com/QMCPACK/qmcpack/tree/develop/external_codes/quantum_espresso
variant('qmcpack', default=False,
description='Build QE-to-QMCPACK wave function converter')
# Dependencies
depends_on('blas')
depends_on('lapack')
depends_on('fftw-api@3')
depends_on('sirius+fortran')
depends_on('mpi', when='+mpi')
depends_on('scalapack', when='+scalapack+mpi')
depends_on('elpa+openmp', when='+elpa+openmp')
depends_on('elpa~openmp', when='+elpa~openmp')
# Versions of HDF5 prior to 1.8.16 lead to QE runtime errors
depends_on('hdf5@1.8.16:+fortran+hl+mpi', when='hdf5=parallel')
depends_on('hdf5@1.8.16:+fortran+hl~mpi', when='hdf5=serial')
depends_on('hdf5', when='+qmcpack')
# TODO: enable building EPW when ~mpi
depends_on('mpi', when='+epw')
# CONFLICTS SECTION
# Omitted for now due to concretizer bug
# MKL with 64-bit integers not supported.
# conflicts(
# '^mkl+ilp64',
# msg='Quantum ESPRESSO does not support MKL 64-bit integer variant'
# )
# We can't ask for scalapack or elpa if we don't want MPI
conflicts(
'+scalapack',
when='~mpi',
msg='scalapack is a parallel library and needs MPI support'
)
conflicts(
'+elpa',
when='~mpi',
msg='elpa is a parallel library and needs MPI support'
)
# HDF5 support introduced in 6.1.0, but the configure had some limitations.
# In recent tests (Oct 2019), GCC and Intel work with the HDF5 Spack
# package for the default variant. This is only for hdf5=parallel variant.
# Support, for hdf5=serial was introduced in 6.4.1 but required a patch
# for the serial (no MPI) case. This patch was to work around an issue
# that only manifested itself inside the Spack environment.
conflicts(
'hdf5=parallel',
when='@:6.0',
msg='parallel HDF5 support only in QE 6.1.0 and later'
)
conflicts(
'hdf5=serial',
when='@:6.4.0',
msg='serial HDF5 support only in QE 6.4.1 and later'
)
conflicts(
'hdf5=parallel',
when='~mpi',
msg='parallel HDF5 requires MPI support'
)
# 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')
# Some QMCPACK converters are incompatible with upstream patches.
# HDF5 is a hard requirement. Need to do two HDF5 cases explicitly
# since Spack lacks support for expressing NOT operation.
conflicts(
'@6.4+patch',
when='+qmcpack',
msg='QE-to-QMCPACK wave function converter requires '
'deactivatation of upstream patches'
)
conflicts(
'@6.3:6.4.0 hdf5=serial',
when='+qmcpack',
msg='QE-to-QMCPACK wave function converter only '
'supported with parallel HDF5'
)
conflicts(
'hdf5=none',
when='+qmcpack',
msg='QE-to-QMCPACK wave function converter requires HDF5'
)
# The first version of Q-E to feature integrated EPW is 6.0.0,
# as per http://epw.org.uk/Main/DownloadAndInstall .
# Complain if trying to install a version older than this.
conflicts('+epw', when='@:5',
msg='EPW only available from version 6.0.0 and on')
# Below goes some constraints as shown in the link above.
# Constraints may be relaxed as successful reports
# of different compiler+mpi combinations arrive
# TODO: enable building EPW when ~mpi
conflicts('+epw', when='~mpi', msg='EPW needs MPI')
# EPW doesn't gets along well with OpenMPI 2.x.x
conflicts('+epw', when='^openmpi@2.0.0:2.999.999',
msg='OpenMPI version incompatible with EPW')
# EPW also doesn't gets along well with PGI 17.x + OpenMPI 1.10.7
conflicts('+epw', when='^openmpi@1.10.7%pgi@17.0:17.12',
msg='PGI+OpenMPI version combo incompatible with EPW')
# Spurious problems running in parallel the Makefile
# generated by the configure
parallel = False
def install(self, spec, prefix):
prefix_path = prefix.bin if '@:5.4.0' in spec else prefix
options = ['-prefix={0}'.format(prefix_path)]
sirius = spec['sirius']
options.append('LIBS={0}'.format(sirius.libs[0]))
options.append('LD_LIBS={0}'.format(sirius.libs[0]))
options.append('--disable-xml')
# QE autoconf compiler variables has some limitations:
# 1. There is no explicit MPICC variable so we must re-purpose
# CC for the case of MPI.
# 2. F90 variable is set to be consistent with MPIF90 wrapper
# 3. If an absolute path for F90 is set, the build system breaks.
#
# Thus, due to 2. and 3. the F90 variable is not explictly set
# because it would be mostly pointless and could lead to erroneous
# behaviour.
if '+mpi' in spec:
mpi = spec['mpi']
options.append('--enable-parallel=yes')
options.append('MPIF90={0}'.format(mpi.mpifc))
options.append('CC={0}'.format(mpi.mpicc))
else:
options.append('--enable-parallel=no')
options.append('CC={0}'.format(spack_cc))
options.append('F77={0}'.format(spack_f77))
options.append('F90={0}'.format(spack_fc))
header_dir = sirius.headers.directories[0]
f90flags = 'F90FLAGS=-cpp -I {0}/sirius'.format(header_dir)
if self.spec.satisfies('%gcc@10:'):
f90flags += '-fallow-argument-mismatch'
options.append(f90flags)
if '+openmp' in spec:
options.append('--enable-openmp')
# QE external BLAS, FFT, SCALAPACK detection is a bit tricky.
# More predictable to pass in the correct link line to QE.
# If external detection of BLAS, LAPACK and FFT fails, QE
# is supposed to revert to internal versions of these libraries
# instead -- but more likely it will pickup versions of these
# libraries found in its the system path, e.g. Red Hat or
# Ubuntu's FFTW3 package.
# FFT
# FFT detection gets derailed if you pass into the CPPFLAGS, instead
# you need to pass it in the FFTW_INCLUDE and FFT_LIBS directory.
# QE supports an internal FFTW2, but only an external FFTW3 interface.
if '^mkl' in spec:
# A seperate FFT library is not needed when linking against MKL
options.append(
'FFTW_INCLUDE={0}'.format(join_path(env['MKLROOT'],
'include/fftw')))
if '^fftw@3:' in spec:
fftw_prefix = spec['fftw'].prefix
options.append('FFTW_INCLUDE={0}'.format(fftw_prefix.include))
fftw_ld_flags = spec['fftw'].libs.ld_flags
options.append('FFT_LIBS={0}'.format(fftw_ld_flags))
# External BLAS and LAPACK requires the correct link line into
# BLAS_LIBS, do no use LAPACK_LIBS as the autoconf scripts indicate
# that this variable is largely ignored/obsolete.
# For many Spack packages, lapack.libs = blas.libs, hence it will
# appear twice in in link line but this is harmless
lapack_blas = spec['lapack'].libs + spec['blas'].libs
# qe-6.5 fails to detect MKL for FFT if BLAS_LIBS is set due to
# an unfortunate upsteam change in their autoconf/configure:
# - qe-6.5/install/m4/x_ac_qe_blas.m4 only sets 'have_blas'
# but no 'have_mkl' if BLAS_LIBS is set (which seems to be o.k.)
# - however, qe-6.5/install/m4/x_ac_qe_fft.m4 in 6.5 unfortunately
# relies on x_ac_qe_blas.m4 to detect MKL and set 'have_mkl'
# - qe-5.4 up to 6.4.1 had a different logic and worked fine with
# BLAS_LIBS being set
# However, MKL is correctly picked up by qe-6.5 for BLAS and FFT if
# MKLROOT is set (which SPACK does automatically for ^mkl)
if not ('quantum-espresso@6.5' in spec and '^mkl' in spec):
options.append('BLAS_LIBS={0}'.format(lapack_blas.ld_flags))
if '+scalapack' in spec:
scalapack_option = 'intel' if '^mkl' in spec else 'yes'
options.append('--with-scalapack={0}'.format(scalapack_option))
if '+elpa' in spec:
# Spec for elpa
elpa = spec['elpa']
# 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.join(
elpa.headers.directories[0],
'modules'
)
options.extend([
'--with-elpa-include={0}'.format(elpa_include),
'--with-elpa-lib={0}'.format(elpa.libs[0])
])
if spec.variants['hdf5'].value != 'none':
options.append('--with-hdf5={0}'.format(spec['hdf5'].prefix))
if spec.satisfies('@6.4.1,6.5'):
options.extend([
'--with-hdf5-include={0}'.format(
spec['hdf5'].headers.directories[0]
),
'--with-hdf5-libs={0}'.format(
spec['hdf5:hl,fortran'].libs.ld_flags
)
])
configure(*options)
# Filter file must be applied after configure executes
# QE 6.1.0 to QE 6.4 have `-L` missing in front of zlib library
# This issue is backported through an internal patch in 6.4.1, but
# can't be applied to the '+qmcpack' variant
if spec.variants['hdf5'].value != 'none':
if (spec.satisfies('@6.1.0:6.4.0') or
(spec.satisfies('@6.4.1') and '+qmcpack' in spec)):
make_inc = join_path(self.stage.source_path, 'make.inc')
zlib_libs = spec['zlib'].prefix.lib + ' -lz'
filter_file(
zlib_libs, format(spec['zlib'].libs.ld_flags), make_inc
)
if '+epw' in spec:
make('all', 'epw')
else:
make('all')
if 'platform=darwin' in spec:
mkdirp(prefix.bin)
for filename in glob.glob("bin/*.x"):
install(filename, prefix.bin)
else:
make('install')

22
var/spack/repos/builtin/packages/sirius/package.py
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@ -16,9 +16,15 @@ class Sirius(CMakePackage, CudaPackage):
list_url = "https://github.com/electronic-structure/SIRIUS/releases"
git = "https://github.com/electronic-structure/SIRIUS.git"
maintainers = ['simonpintarelli', 'haampie', 'dev-zero']
version('develop', branch='develop')
version('master', branch='master')
version('6.5.6', sha256='c8120100bde4477545eae489ea7f9140d264a3f88696ec92728616d78f214cae')
version('6.5.5', sha256='0b23d3a8512682eea67aec57271031c65f465b61853a165015b38f7477651dd1')
version('6.5.4', sha256='5f731926b882a567d117afa5e0ed33291f1db887fce52f371ba51f014209b85d')
version('6.5.3', sha256='eae0c303f332425a8c792d4455dca62557931b28a5df8b4c242652d5ffddd580')
version('6.5.2', sha256='c18adc45b069ebae03f94eeeeed031ee99b3d8171fa6ee73c7c6fb1e42397fe7')
version('6.5.1', sha256='599dd0fa25a4e83db2a359257a125e855d4259188cf5b0065b8e7e66378eacf3')
version('6.5.0', sha256='5544f3abbb71dcd6aa08d18aceaf53c38373de4cbd0c3af44fbb39c20cfeb7cc')
@ -36,10 +42,12 @@ class Sirius(CMakePackage, CudaPackage):
variant('openmp', default=True, description="Build with OpenMP support")
variant('fortran', default=False, description="Build Fortran bindings")
variant('python', default=False, description="Build Python bindings")
variant('memory_pool', default=True, description="Build with memory pool")
variant('elpa', default=False, description="Use ELPA")
variant('vdwxc', default=False, description="Enable libvdwxc support")
variant('scalapack', default=False, description="Enable scalapack support")
variant('magma', default=False, description="Enable MAGMA support")
variant('nlcglib', default=False, description="enable robust wave function optimization")
variant('build_type', default='Release',
description='CMake build type',
values=('Debug', 'Release', 'RelWithDebInfo'))
@ -48,7 +56,7 @@ class Sirius(CMakePackage, CudaPackage):
depends_on('mpi')
depends_on('gsl')
depends_on('lapack')
depends_on('fftw') # SIRIUS does not care about MPI-support in FFTW
depends_on('fftw-api@3')
depends_on('libxc')
depends_on('spglib')
depends_on('hdf5+hl')
@ -64,15 +72,20 @@ class Sirius(CMakePackage, CudaPackage):
depends_on('magma', when='+magma')
depends_on('spfft', when='@6.4.0:')
depends_on('spfft', when='@master')
depends_on('spfft', when='@develop')
depends_on('spfft+cuda', when='@6.4.0:+cuda')
depends_on('spfft+cuda', when='@master+cuda')
depends_on('spfft+cuda', when='@develop+cuda')
depends_on('elpa+openmp', when='+elpa+openmp')
depends_on('elpa~openmp', when='+elpa~openmp')
depends_on('nlcglib', when='+nlcglib')
depends_on('libvdwxc+mpi', when='+vdwxc')
depends_on('scalapack', when='+scalapack')
depends_on('cuda', when='+cuda')
extends('python', when='+python')
conflicts('+shared', when='@6.3.0:') # option to build shared libraries has been removed
conflicts('+shared', when='@6.3.0:6.4.999')
# TODO:
# add support for CRAY_LIBSCI, ROCm, testing
@ -90,9 +103,8 @@ def libs(self):
return find_libraries(
libraries, root=self.prefix,
shared=False, recursive=True
shared='+shared' in self.spec, recursive=True
)
else:
if '+fortran' in self.spec:
libraries += ['libsirius_f']
@ -125,7 +137,9 @@ def _def(variant, flag=None):
_def('+openmp'),
_def('+elpa'),
_def('+magma'),
_def('+nlcglib'),
_def('+vdwxc'),
_def('+memory_pool'),
_def('+scalapack'),
_def('+fortran', 'CREATE_FORTRAN_BINDINGS'),
_def('+python', 'CREATE_PYTHON_MODULE'),