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siesta: add v4.1.5, v5.0.0 and v5.0.1, add variants and build v5 using cmake (#45518)

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Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
This commit is contained in:
BOUDAOUD34
2024-08-13 12:10:22 +02:00
committed by GitHub
parent 7001a2a65a
commit 7999686856
1 changed files with 248 additions and 37 deletions
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225
var/spack/repos/builtin/packages/siesta/package.py
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@@ -5,16 +5,40 @@
import os
import shutil
from spack.build_systems import cmake
from spack.package import *
class Siesta(MakefilePackage):
class Siesta(MakefilePackage, CMakePackage):
"""SIESTA performs electronic structure calculations and ab initio molecular
dynamics simulations of molecules and solids.
"""
build_system(
conditional("cmake", when="@5:"), conditional("makefile", when="@:4"), default="cmake"
)
homepage = "https://departments.icmab.es/leem/siesta/"
git = "https://gitlab.com/siesta-project/siesta"
version(
"5.0.1",
url="https://gitlab.com/siesta-project/siesta/-/archive/5.0.1/siesta-5.0.1.tar.gz",
sha256="800a22a831c1d36c6f5fe4aa9c49ee510cbd49a0b2f87b3c8bf3edb6ebd0193a",
)
version(
"5.0.0",
url="https://gitlab.com/siesta-project/siesta/-/archive/rel-5.0/siesta-rel-5.0.tar.gz",
sha256="0b40c341dfd47e99e7e191189600bbcaadb0f9af03977fefed6a69836bd523e4",
)
version(
"4.1.5",
url="https://gitlab.com/siesta-project/siesta/-/archive/v4.1.5/siesta-v4.1.5.tar.gz",
sha256="adc88619bf7e17fca2c67ecdcdae1f07ec4b3caf3541c0edf12964c8c330edc9",
)
license("GPL-3.0-or-later")
@@ -30,17 +54,43 @@ class Siesta(MakefilePackage):
url="http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz",
)
depends_on("c", type="build") # generated
depends_on("fortran", type="build") # generated
patch("configure.patch", when="@:4.0")
depends_on("mpi")
variant("mpi", default=True, description="Builds with mpi support")
variant("openmp", default=True, description="Enables OpenMP support")
variant("netcdf", default=False, description="Compile with Netcdf")
variant("metis", default=False, description="Activate Metis as a possible ordering library")
variant("elpa", default=False, description="Use ELPA")
variant("mumps", default=False, description="Compile with support for MUMPS solvers")
variant("pexsi", default=False, description="Compile with PEXSI")
variant(
"cray",
default=False,
description="Enable specific cray settings for using cray-hdf5"
" and cray-netcdf modulefiles",
)
variant("debug", default=False, description="Build in debug mode")
variant(
"build_type",
default="Release",
description="The build type to build",
values=("Debug", "Release", "RelWithDebInfo", "MinSizeRel", "check"),
)
depends_on("mpi", when="+mpi")
depends_on("blas")
depends_on("lapack")
depends_on("scalapack")
depends_on("scalapack", when="+mpi")
depends_on("netcdf-c")
depends_on("netcdf-fortran")
depends_on("cray-libsci+openmp", when="^[virtuals=cray-libsci] cray-libsci")
depends_on("metis@5:", when="+metis")
depends_on("elpa", when="+elpa")
depends_on("mumps", when="+mumps")
depends_on("pexsi", when="+pexsi")
with when("build_system=cmake"):
depends_on("cmake@3.20:", type="build")
def flag_handler(self, name, flags):
if "%gcc@10:" in self.spec and name == "fflags":
@@ -49,6 +99,10 @@ def flag_handler(self, name, flags):
def edit(self, spec, prefix):
sh = which("sh")
if "+cray" in spec:
netcdff_prefix = os.environ.get("NETCDF_DIR", "")
hdf5_prefix = os.environ.get("HDF5_DIR", "")
if spec.satisfies("@:4.0.2 +mpi"):
configure_args = [
"--enable-mpi",
"--with-blas=%s" % spec["blas"].libs,
@@ -58,12 +112,23 @@ def edit(self, spec, prefix):
# test fails
"--with-blacs=%s" % (spec["scalapack"].libs + spec["blas"].libs),
"--with-scalapack=%s" % spec["scalapack"].libs,
"--with-netcdf=%s" % (spec["netcdf-fortran"].libs + spec["netcdf-c"].libs),
# need to specify MPIFC explicitly below, otherwise
# Intel's mpiifort is not found
"MPIFC=%s" % spec["mpi"].mpifc,
]
if "+cray" in spec:
configure_args += ["--with-netcdf={0}/lib/libnetcdff.so".format(netcdff_prefix)]
else:
configure_args += [
"--with-netcdf=%s" % (spec["netcdf-fortran"].libs + spec["netcdf-c"].libs)
]
if self.spec.satisfies("%gcc"):
if "+cray" in spec:
configure_args.append(
"FCFLAGS=-ffree-line-length-0 -I{0}/include".format(netcdff_prefix)
)
else:
configure_args.append("FCFLAGS=-ffree-line-length-0")
for d in ["Obj", "Obj_trans"]:
with working_dir(d, create=True):
@@ -75,9 +140,97 @@ def edit(self, spec, prefix):
f.write("$(INCFLAGS) $(FPPFLAGS) $<")
sh("../Src/obj_setup.sh")
elif self.spec.satisfies("@:4.1.5"):
with working_dir("Obj", create=True):
sh("../Src/obj_setup.sh")
if spec.satisfies("@:4.1.5%gcc"):
shutil.copy("./gfortran.make", "./arch.make")
libs_arg = []
fppflags_arg = []
arch_make = FileFilter("./arch.make")
arch_make.filter(
"FFLAGS = .*",
"FFLAGS = {0}".format(
"-O2 -fPIC -ftree-vectorize -fallow-argument-mismatch"
),
)
if "+debug" in spec:
arch_make.filter("FFLAGS_DEBUG=.*", "FFLAGS_DEBUG= -g -O1")
if "^cray-libsci" in spec:
libs_arg.append("-L{0}/lib -lsci_gnu".format(spec["cray-libsci"].prefix))
with open("arch.make", "a") as f:
if "+mpi" in spec:
arch_make.filter("CC = .*", "CC = {0}".format(spec["mpi"].mpicc))
arch_make.filter("FC = .*", "FC = {0}".format(spec["mpi"].mpifc))
if "^cray-libsci" in spec:
libs_arg.append("-lsci_gnu_mpi")
f.write("MPI_INTERFACE = libmpi_f90.a\n")
f.write("MPI_INCLUDE = .\n")
f.write("LIBS += " + spec["scalapack"].libs.ld_flags + "\n")
fppflags_arg.append("-DMPI ")
if "+openmp" in spec:
f.write("FFLAGS += -fopenmp\n")
f.write("LIBS += -fopenmp\n")
if "+netcdf" in spec:
if "+cray" in spec:
libs_arg.append(
"-L{0}/lib -lnetcdff -lnetcdf".format(netcdff_prefix)
)
libs_arg.append(
"-L{0}/lib -lhdf5_fortran -lhdf5".format(hdf5_prefix)
)
else:
libs_arg.append(
"-L{0}/lib -lnetcdff -lnetcdf".format(
spec["netcdf-fortran"].prefix
)
)
libs_arg.append(
"-L{0}/lib -lhdf5_fortran -lhdf5".format(spec["hdf5"].prefix)
)
if "+metis" in spec:
libs_arg.append("-L{0} -lmetis".format(self.spec["metis"].prefix.lib))
fppflags_arg.append("-DSIESTA__METIS ")
if "elpa" in spec:
elpa = spec["elpa"]
elpa_suffix = "_openmp" if "+openmp" in elpa else ""
elpa_incdir = elpa.headers.directories[0]
libs_arg.append(
"-L{0} -lelpa{1}".format(self.spec["elpa"].prefix.lib, elpa_suffix)
)
fppflags_arg.append(
"-DSIESTA__ELPA -I{0}".format(join_path(elpa_incdir, "modules"))
)
if "mumps" in spec:
libs_arg.append(
"-L{0} -lmumps_common -lzmumps".format(
self.spec["mumps"].prefix.lib
)
)
fppflags_arg.append("-DSIESTA__MUMPS ")
if "+pexsi" in spec:
libs_arg.append(
"-L{0} -lpexsi_linux".format(self.spec["pexsi"].prefix.lib)
)
fppflags_arg.append("-DSIESTA__PEXSI ")
f.write("INCFLAGS += -I{0}/include".format(self.spec["pexsi"].prefix))
arch_make.filter("^LIBS =.*", "LIBS = {0}".format(" ".join(libs_arg)))
f.write("FPPFLAGS = {0}".format(" ".join(fppflags_arg)))
def build(self, spec, prefix):
with working_dir("Obj"):
make(parallel=False)
if spec.satisfies("@:4.0.2"):
with working_dir("Obj_trans"):
make("transiesta", parallel=False)
with working_dir("Util"):
@@ -88,6 +241,7 @@ def install(self, spec, prefix):
mkdir(prefix.bin)
with working_dir("Obj"):
install("siesta", prefix.bin)
if spec.satisfies("@:4.0.2"):
with working_dir("Obj_trans"):
install("transiesta", prefix.bin)
for root, _, files in os.walk("Util"):
@@ -95,3 +249,60 @@ def install(self, spec, prefix):
fname = join_path(root, fname)
if os.access(fname, os.X_OK):
install(fname, prefix.bin)
class CMakeBuilder(cmake.CMakeBuilder):
"""Use the new CMake build system to build siesta@5.0.0:."""
def cmake_args(self):
spec = self.spec
args = []
args += ["-DBLAS_LIBRARIES={0}".format(self.spec["blas"].libs.link_flags)]
args += ["-DLAPACK_LIBRARIES={0}".format(self.spec["lapack"].libs.link_flags)]
if "+mpi" in spec:
args += [
"-DCMAKE_C_COMPILER=%s" % spec["mpi"].mpicc,
"-DCMAKE_CXX_COMPILER=%s" % spec["mpi"].mpicxx,
"-DCMAKE_Fortran_COMPILER=%s" % spec["mpi"].mpifc,
]
args += ["-DSIESTA_WITH_MPI=ON"]
args += ["-DSCALAPACK_LIBRARY={0}".format(spec["scalapack"].libs.joined(";"))]
if "+openmp" in spec:
args += ["-DSIESTA_WITH_OPENMP=ON"]
if "+cray" in spec:
args += ["-DFortran_FLAGS=-fopenmp"]
if "build_type=Debug" in spec:
args += [
"-DFortran_FLAGS=-Og -g -Wall -fcheck=all -fbacktrace"
" -Warray-bounds -Wunused -Wuninitialized"
]
else:
args += ["-DFortran_FLAGS=-O2 -fPIC -ftree-vectorize -fallow-argument-mismatch"]
if "+netcdf" in spec:
args += ["-DSIESTA_WITH_NETCDF=ON"]
if "+cray" in spec:
args += ["-DNetCDF_PATH={0}".format(os.environ.get("NETCDF_DIR", ""))]
else:
args += ["-DNetCDF_PATH={0}".format(spec["netcdf-fortran"].prefix)]
if "+elpa" in spec:
args += ["-DSIESTA_WITH_ELPA=ON"]
if "+mumps" in spec:
args += ["-DSIESTA__MUMPS=ON"]
args += [
"-DSIESTA_LINKER_FLAGS=-L{0} -lmumps_common -lzmumps".format(
self.spec["mumps"].prefix.lib
)
]
if "+metis" in spec:
args += ["-DSIESTA__METIS=ON"]
args += ["-DSIESTA_LINKER_FLAGS=-L{0} -lmetis".format(self.spec["metis"].prefix.lib)]
return args