zhangyiss/spack
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Update/lammps package: new variants for refactoring of code modules (#29788)

Browse Source 
* lammps package: kokkos variant, add support for cray-fftw

* lammps package: added bugfix version 20210929.3

* lammps package: added packages molfile, plugin, user-brownian

* lammps package: package refactor at versions 20210702 and 20210728

* lammps package: fix for ml-iap variant

* lammps package: fix for conflicts of dielectric variant

* lammps package: edits for flake8 layout compliance
This commit is contained in:
Marco De La Pierre 2022-06-29 02:22:35 +08:00 committed by GitHub
parent 24048e3be7
commit 38dfec42b7
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 321 additions and 16 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

337
var/spack/repos/builtin/packages/lammps/package.py
View File

@ -24,6 +24,7 @@ class Lammps(CMakePackage, CudaPackage):
version('20220107', sha256='fbf6c6814968ae0d772d7b6783079ff4f249a8faeceb39992c344969e9f1edbb')
version('20211214', sha256='9f7b1ee2394678c1a6baa2c158a62345680a952eee251783e3c246b3f12db4c9')
version('20211027', sha256='c06f682fcf9d5921ca90c857a104e90fba0fe65decaac9732745e4da49281938')
version('20210929.3', sha256='d7df30f7ce0bd8b7c21949cf5bdf1877858815379cddb8a264da7a8cbf699639')
version('20210929.2', sha256='26586c1e82356b60e40359ee474818003c7788214bfe2bfe9128a3dbe5200b4d')
version('20210929.1', sha256='3b792e20864bf88b855332486996f2c540deabb4e3507e48fa4ee96ad79615ec')
version('20210929', sha256='5132f332b582be3006510562ef10bac9ef76d760f34fc08a2af556416c57cf4c')
@ -77,26 +78,39 @@ def url_for_version(self, version):
return "https://github.com/lammps/lammps/archive/patch_{0}{1}.tar.gz".format(
vdate.strftime("%d%b%Y").lstrip('0'), update)
# List of supported optional packages
# Note: package `openmp` in this recipe is called `openmp-package`, to avoid clash
# with the pre-existing `openmp` variant
supported_packages = ['asphere', 'body', 'class2', 'colloid', 'compress',
'coreshell', 'dipole', 'granular', 'kspace',
'coreshell', 'dielectric', 'dipole', 'granular', 'kspace',
'kokkos', 'latte', 'manybody', 'mc', 'meam', 'misc',
'mliap', 'molecule', 'mpiio', 'opt', 'peri', 'poems',
'python', 'qeq', 'replica', 'rigid', 'shock', 'snap',
'spin', 'srd', 'user-atc', 'user-adios',
'user-awpmd', 'user-bocs', 'user-cgsdk',
'mliap', 'ml-iap', 'ml-snap', 'molecule', 'mpiio',
'opt', 'peri', 'plugin', 'poems', 'python', 'qeq', 'replica',
'rigid', 'shock', 'snap', 'spin', 'srd', 'voronoi',
'user-atc', 'user-adios',
'user-awpmd', 'user-bocs', 'user-brownian', 'user-cgsdk',
'user-colvars', 'user-diffraction', 'user-dpd',
'user-drude', 'user-eff', 'user-fep', 'user-h5md',
'user-lb', 'user-manifold', 'user-meamc',
'user-mesodpd', 'user-mesont', 'user-mgpt',
'user-misc', 'user-mofff', 'user-netcdf', 'user-omp',
'user-mesodpd', 'user-mesont', 'user-mgpt', 'user-misc',
'user-mofff', 'user-molfile', 'user-netcdf', 'user-omp',
'user-phonon', 'user-plumed', 'user-ptm', 'user-qtb',
'user-reaction', 'user-reaxc', 'user-sdpd',
'user-smd', 'user-smtbq', 'user-sph', 'user-tally',
'user-uef', 'user-yaff', 'voronoi']
'user-uef', 'user-yaff',
'atc', 'adios', 'awpmd', 'bocs', 'brownian', 'cg-sdk',
'colvars', 'diffraction', 'dpd-basic', 'dpd-meso',
'dpd-react', 'dpd-smooth', 'drude', 'eff', 'extra-compute',
'extra-dump', 'extra-fix', 'extra-molecule', 'extra-pair',
'fep', 'h5md', 'interlayer', 'latboltz', 'machdyn',
'manifold', 'mesont', 'mgpt', 'mofff', 'molfile', 'netcdf',
'openmp-package', 'orient', 'phonon', 'plumed', 'ptm', 'qtb',
'reaction', 'reaxff', 'smtbq', 'sph', 'tally', 'uef', 'yaff']
for pkg in supported_packages:
variant(pkg, default=False,
description='Activate the {0} package'.format(pkg))
description='Activate the {0} package'
.format(pkg.replace('-package', '')))
variant('lib', default=True,
description='Build the liblammps in addition to the executable')
variant('mpi', default=True,
@ -129,8 +143,11 @@ def url_for_version(self, version):
depends_on('fftw-api@3', when='+kspace')
depends_on('voropp+pic', when='+voronoi')
depends_on('netcdf-c+mpi', when='+user-netcdf')
depends_on('netcdf-c+mpi', when='+netcdf')
depends_on('blas', when='+user-atc')
depends_on('blas', when='+atc')
depends_on('lapack', when='+user-atc')
depends_on('lapack', when='+atc')
depends_on('opencl', when='+opencl')
depends_on('latte@1.0.1', when='@:20180222+latte')
depends_on('latte@1.1.1:', when='@20180316:20180628+latte')
@ -140,8 +157,11 @@ def url_for_version(self, version):
depends_on('lapack', when='+latte')
depends_on('python', when='+python')
depends_on('mpi', when='+user-lb')
depends_on('mpi', when='+latboltz')
depends_on('mpi', when='+user-h5md')
depends_on('mpi', when='+h5md')
depends_on('hdf5', when='+user-h5md')
depends_on('hdf5', when='+h5md')
depends_on('jpeg', when='+jpeg')
depends_on('kim-api', when='+kim')
depends_on('libpng', when='+png')
@ -149,8 +169,15 @@ def url_for_version(self, version):
depends_on('kokkos+deprecated_code+shared@3.0.00', when='@20200303+kokkos')
depends_on('kokkos+shared@3.1:', when='@20200505:+kokkos')
depends_on('adios2', when='+user-adios')
depends_on('adios2', when='+adios')
depends_on('plumed', when='+user-plumed')
depends_on('plumed', when='+plumed')
depends_on('eigen@3:', when='+user-smd')
depends_on('eigen@3:', when='+machdyn')
depends_on('py-cython', when='+mliap+python')
depends_on('py-cython', when='+ml-iap+python')
depends_on('py-numpy', when='+mliap+python')
depends_on('py-numpy', when='+ml-iap+python')
conflicts('+cuda', when='+opencl')
conflicts('+body', when='+poems@:20180628')
@ -158,27 +185,303 @@ def url_for_version(self, version):
conflicts('+python', when='~lib')
conflicts('+qeq', when='~manybody')
conflicts('+user-atc', when='~manybody')
conflicts('+atc', when='~manybody')
conflicts('+user-misc', when='~manybody')
conflicts('+user-phonon', when='~kspace')
conflicts('+user-misc', when='~manybody')
conflicts('+phonon', when='~kspace')
conflicts('%gcc@9:', when='@:20200303+openmp')
conflicts('+kokkos', when='@:20200227')
conflicts('+dielectric', when='~kspace')
conflicts('+dielectric', when='@:20210702~user-misc')
conflicts('+dielectric', when='@20210728:~extra-pair')
conflicts(
'+meam', when='@20181212:',
msg='+meam was removed after @20181212, use +user-meamc instead')
'+meam', when='@20181212:20210527',
msg='+meam is removed between @20181212 and @20210527, use +user-meamc instead')
conflicts(
'+user-meamc', when='@:20181212',
msg='+user-meamc only added @20181212, use +meam instead')
conflicts(
'+user-reaction', when='@:20200303',
msg='+user-reaction only supported for version 20200505 and later')
conflicts(
'+plugin', when='@:20210310',
msg='+plugin only supported for version 20210408 and later')
conflicts(
'+user-brownian', when='@:20210408',
msg='+user-brownian only supported for version 20210514 and later')
conflicts(
'+dielectric', when='@:20210527',
msg='+dielectric only supported for version 20210702 and later')
conflicts(
'+dpd-basic', when='@:20210527',
msg='+dpd-basic only supported for version 20210702 and later')
conflicts('+mliap', when='~snap')
conflicts('+ml-iap', when='~ml-snap')
conflicts(
'+user-adios +mpi', when='^adios2~mpi',
msg='With +user-adios, mpi setting for adios2 and lammps must be the same')
conflicts(
'+user-adios ~mpi', when='^adios2+mpi',
msg='With +user-adios, mpi setting for adios2 and lammps must be the same')
conflicts(
'+adios +mpi', when='^adios2~mpi',
msg='With +adios, mpi setting for adios2 and lammps must be the same')
conflicts(
'+adios ~mpi', when='^adios2+mpi',
msg='With +adios, mpi setting for adios2 and lammps must be the same')
# In the following, package refactoring at 2 July 2021
conflicts(
'+mliap', when='@20210702:',
msg='+mliap was removed after @20210527, use +ml-iap instead')
conflicts(
'+ml-iap', when='@:20210527',
msg='+ml-iap only added @20210702, use +mliap instead')
conflicts(
'+snap', when='@20210702:',
msg='+snap was removed after @20210527, use +ml-snap instead')
conflicts(
'+ml-snap', when='@:20210527',
msg='+ml-snap only added @20210702, use +snap instead')
#
conflicts(
'+user-atc', when='@20210702:',
msg='+user-atc was removed after @20210527, use +atc instead')
conflicts(
'+atc', when='@:20210527',
msg='+atc only added @20210702, use +user-atc instead')
conflicts(
'+user-adios', when='@20210702:',
msg='+user-adios was removed after @20210527, use +adios instead')
conflicts(
'+adios', when='@:20210527',
msg='+adios only added @20210702, use +user-adios instead')
conflicts(
'+user-awpmd', when='@20210702:',
msg='+user-awpmd was removed after @20210527, use +awpmd instead')
conflicts(
'+awpmd', when='@:20210527',
msg='+awpmd only added @20210702, use +user-awpmd instead')
conflicts(
'+user-bocs', when='@20210702:',
msg='+user-bocs was removed after @20210527, use +bocs instead')
conflicts(
'+bocs', when='@:20210527',
msg='+bocs only added @20210702, use +user-bocs instead')
conflicts(
'+user-brownian', when='@20210702:',
msg='+user-brownian was removed after @20210527, use +brownian instead')
conflicts(
'+brownian', when='@:20210527',
msg='+brownian only added @20210702, use +user-brownian instead')
conflicts(
'+user-cgsdk', when='@20210702:',
msg='+user-cgsdk was removed after @20210527, use +cg-sdk instead')
conflicts(
'+cg-sdk', when='@:20210527',
msg='+cg-sdk only added @20210702, use +user-cgsdk instead')
conflicts(
'+user-colvars', when='@20210702:',
msg='+user-colvars was removed after @20210527, use +colvars instead')
conflicts(
'+colvars', when='@:20210527',
msg='+colvars only added @20210702, use +user-colvars instead')
conflicts(
'+user-diffraction', when='@20210702:',
msg='+user-diffraction was removed after @20210527, use +diffraction instead')
conflicts(
'+diffraction', when='@:20210527',
msg='+diffraction only added @20210702, use +user-diffraction instead')
conflicts(
'+user-dpd', when='@20210702:',
msg='+user-dpd was removed after @20210527, use +dpd-react instead')
conflicts(
'+dpd-react', when='@:20210527',
msg='+dpd-react only added @20210702, use +user-dpd instead')
conflicts(
'+user-drude', when='@20210702:',
msg='+user-drude was removed after @20210527, use +drude instead')
conflicts(
'+drude', when='@:20210527',
msg='+drude only added @20210702, use +user-drude instead')
conflicts(
'+user-eff', when='@20210702:',
msg='+user-eff was removed after @20210527, use +eff instead')
conflicts(
'+eff', when='@:20210527',
msg='+eff only added @20210702, use +user-eff instead')
conflicts(
'+user-fep', when='@20210702:',
msg='+user-fep was removed after @20210527, use +fep instead')
conflicts(
'+fep', when='@:20210527',
msg='+fep only added @20210702, use +user-fep instead')
conflicts(
'+user-h5md', when='@20210702:',
msg='+user-h5md was removed after @20210527, use +h5md instead')
conflicts(
'+h5md', when='@:20210527',
msg='+h5md only added @20210702, use +user-h5md instead')
conflicts(
'+user-lb', when='@20210702:',
msg='+user-lb was removed after @20210527, use +latboltz instead')
conflicts(
'+latboltz', when='@:20210527',
msg='+latboltz only added @20210702, use +user-lb instead')
conflicts(
'+user-manifold', when='@20210702:',
msg='+user-manifold was removed after @20210527, use +manifold instead')
conflicts(
'+manifold', when='@:20210527',
msg='+manifold only added @20210702, use +user-manifold instead')
conflicts(
'+user-meamc', when='@20210702:',
msg='+user-meamc was removed after @20210527, use +meam instead')
conflicts(
'+user-mesodpd', when='@20210702:',
msg='+user-mesodpd was removed after @20210527, use +dpd-meso instead')
conflicts(
'+dpd-meso', when='@:20210527',
msg='+dpd-meso only added @20210702, use +user-mesodpd instead')
conflicts(
'+user-mesont', when='@20210702:',
msg='+user-mesont was removed after @20210527, use +mesont instead')
conflicts(
'+mesont', when='@:20210527',
msg='+mesont only added @20210702, use +user-mesont instead')
conflicts(
'+user-mgpt', when='@20210702:',
msg='+user-mgpt was removed after @20210527, use +mgpt instead')
conflicts(
'+mgpt', when='@:20210527',
msg='+mgpt only added @20210702, use +user-mgpt instead')
conflicts(
'+user-mofff', when='@20210702:',
msg='+user-mofff was removed after @20210527, use +mofff instead')
conflicts(
'+mofff', when='@:20210527',
msg='+mofff only added @20210702, use +user-mofff instead')
conflicts(
'+user-molfile', when='@20210702:',
msg='+user-molfile was removed after @20210527, use +molfile instead')
conflicts(
'+molfile', when='@:20210527',
msg='+molfile only added @20210702, use +user-molfile instead')
conflicts(
'+user-netcdf', when='@20210702:',
msg='+user-netcdf was removed after @20210527, use +netcdf instead')
conflicts(
'+netcdf', when='@:20210527',
msg='+netcdf only added @20210702, use +user-netcdf instead')
conflicts(
'+user-omp', when='@20210702:',
msg='+user-omp was removed after @20210527, use +openmp-package instead')
conflicts(
'+openmp-package', when='@:20210527',
msg='+openmp-package only added @20210702, use +user-omp instead')
conflicts(
'+user-phonon', when='@20210702:',
msg='+user-phonon was removed after @20210527, use +phonon instead')
conflicts(
'+phonon', when='@:20210527',
msg='+phonon only added @20210702, use +user-phonon instead')
conflicts(
'+user-plumed', when='@20210702:',
msg='+user-plumed was removed after @20210527, use +plumed instead')
conflicts(
'+plumed', when='@:20210527',
msg='+plumed only added @20210702, use +user-plumed instead')
conflicts(
'+user-ptm', when='@20210702:',
msg='+user-ptm was removed after @20210527, use +ptm instead')
conflicts(
'+ptm', when='@:20210527',
msg='+ptm only added @20210702, use +user-ptm instead')
conflicts(
'+user-qtb', when='@20210702:',
msg='+user-qtb was removed after @20210527, use +qtb instead')
conflicts(
'+qtb', when='@:20210527',
msg='+qtb only added @20210702, use +user-qtb instead')
conflicts(
'+user-reaction', when='@20210702:',
msg='+user-reaction was removed after @20210527, use +reaction instead')
conflicts(
'+reaction', when='@:20210527',
msg='+reaction only added @20210702, use +user-reaction instead')
conflicts(
'+user-reaxc', when='@20210702:',
msg='+user-reaxc was removed after @20210527, use +reaxff instead')
conflicts(
'+reaxff', when='@:20210527',
msg='+reaxff only added @20210702, use +user-reaxc instead')
conflicts(
'+user-sdpd', when='@20210702:',
msg='+user-sdpd was removed after @20210527, use +dpd-smooth instead')
conflicts(
'+dpd-smooth', when='@:20210527',
msg='+dpd-smooth only added @20210702, use +user-sdpd instead')
conflicts(
'+user-smd', when='@20210702:',
msg='+user-smd was removed after @20210527, use +machdyn instead')
conflicts(
'+machdyn', when='@:20210527',
msg='+machdyn only added @20210702, use +user-smd instead')
conflicts(
'+user-smtbq', when='@20210702:',
msg='+user-smtbq was removed after @20210527, use +smtbq instead')
conflicts(
'+smtbq', when='@:20210527',
msg='+smtbq only added @20210702, use +user-smtbq instead')
conflicts(
'+user-sph', when='@20210702:',
msg='+user-sph was removed after @20210527, use +sph instead')
conflicts(
'+sph', when='@:20210527',
msg='+sph only added @20210702, use +user-sph instead')
conflicts(
'+user-tally', when='@20210702:',
msg='+user-tally was removed after @20210527, use +tally instead')
conflicts(
'+tally', when='@:20210527',
msg='+tally only added @20210702, use +user-tally instead')
conflicts(
'+user-uef', when='@20210702:',
msg='+user-uef was removed after @20210527, use +uef instead')
conflicts(
'+uef', when='@:20210527',
msg='+uef only added @20210702, use +user-uef instead')
conflicts(
'+user-yaff', when='@20210702:',
msg='+user-yaff was removed after @20210527, use +yaff instead')
conflicts(
'+yaff', when='@:20210527',
msg='+yaff only added @20210702, use +user-yaff instead')
# In the following, package refactoring at 28 July 2021
conflicts(
'+user-misc', when='@20210728:',
msg='+user-misc was removed after @20210702, and split over multiple packages')
conflicts(
'+extra-compute', when='@:20210702',
msg='+extra-compute only added @20210728, use +user-misc instead')
conflicts(
'+extra-dump', when='@:20210702',
msg='+extra-dump only added @20210728, use +user-misc instead')
conflicts(
'+extra-fix', when='@:20210702',
msg='+extra-fix only added @20210728, use +user-misc instead')
conflicts(
'+extra-molecule', when='@:20210702',
msg='+extra-molecule only added @20210728, use +user-misc instead')
conflicts(
'+extra-pair', when='@:20210702',
msg='+extra-pair only added @20210728, use +user-misc instead')
conflicts(
'+interlayer', when='@:20210702',
msg='+interlayer only added @20210728, use +user-misc instead')
conflicts(
'+orient', when='@:20210702',
msg='+orient only added @20210728, use +user-misc instead')
patch("lib.patch", when="@20170901")
patch("660.patch", when="@20170922")
@ -235,7 +538,7 @@ def cmake_args(self):
args.append(self.define_from_variant('WITH_FFMPEG', 'ffmpeg'))
for pkg in self.supported_packages:
opt = '-D{0}_{1}'.format(pkg_prefix, pkg.upper())
opt = '-D{0}_{1}'.format(pkg_prefix, pkg.replace('-package', '').upper())
if '+{0}'.format(pkg) in spec:
args.append('{0}=ON'.format(opt))
else:
@ -255,18 +558,20 @@ def cmake_args(self):
# for reduced memory use and parallel communication costs
# for transposing 3d FFT data.
args.append(self.define('FFT_SINGLE', True))
if '^cray-fftw' in spec:
args.append('-DFFT=FFTW3')
if '+kokkos' in spec:
args.append('-DEXTERNAL_KOKKOS=ON')
if '+user-adios' in spec:
if '+user-adios' in spec or '+adios' in spec:
args.append('-DADIOS2_DIR={0}'.format(self.spec['adios2'].prefix))
if '+user-plumed' in spec:
if '+user-plumed' in spec or '+plumed' in spec:
args.append('-DDOWNLOAD_PLUMED=no')
if '+shared' in self.spec['plumed']:
args.append('-DPLUMED_MODE=shared')
else:
args.append('-DPLUMED_MODE=static')
if '+user-smd' in spec:
if '+user-smd' in spec or '+machdyn' in spec:
args.append('-DDOWNLOAD_EIGEN3=no')
args.append('-DEIGEN3_INCLUDE_DIR={0}'.format(
self.spec['eigen'].prefix.include))