siesta: add v4.1.5, v5.0.0 and v5.0.1, add variants and build v5 using cmake (#45518)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
This commit is contained in:
BOUDAOUD34
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commit
7999686856
@ -5,16 +5,40 @@
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import os
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import shutil
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from spack.build_systems import cmake
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from spack.package import *
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class Siesta(MakefilePackage):
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class Siesta(MakefilePackage, CMakePackage):
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"""SIESTA performs electronic structure calculations and ab initio molecular
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dynamics simulations of molecules and solids.
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"""
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build_system(
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conditional("cmake", when="@5:"), conditional("makefile", when="@:4"), default="cmake"
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)
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homepage = "https://departments.icmab.es/leem/siesta/"
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git = "https://gitlab.com/siesta-project/siesta"
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version(
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"5.0.1",
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url="https://gitlab.com/siesta-project/siesta/-/archive/5.0.1/siesta-5.0.1.tar.gz",
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sha256="800a22a831c1d36c6f5fe4aa9c49ee510cbd49a0b2f87b3c8bf3edb6ebd0193a",
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)
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version(
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"5.0.0",
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url="https://gitlab.com/siesta-project/siesta/-/archive/rel-5.0/siesta-rel-5.0.tar.gz",
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sha256="0b40c341dfd47e99e7e191189600bbcaadb0f9af03977fefed6a69836bd523e4",
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)
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version(
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"4.1.5",
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url="https://gitlab.com/siesta-project/siesta/-/archive/v4.1.5/siesta-v4.1.5.tar.gz",
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sha256="adc88619bf7e17fca2c67ecdcdae1f07ec4b3caf3541c0edf12964c8c330edc9",
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)
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license("GPL-3.0-or-later")
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@ -30,17 +54,43 @@ class Siesta(MakefilePackage):
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url="http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz",
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)
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depends_on("c", type="build") # generated
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depends_on("fortran", type="build") # generated
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patch("configure.patch", when="@:4.0")
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depends_on("mpi")
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variant("mpi", default=True, description="Builds with mpi support")
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variant("openmp", default=True, description="Enables OpenMP support")
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variant("netcdf", default=False, description="Compile with Netcdf")
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variant("metis", default=False, description="Activate Metis as a possible ordering library")
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variant("elpa", default=False, description="Use ELPA")
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variant("mumps", default=False, description="Compile with support for MUMPS solvers")
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variant("pexsi", default=False, description="Compile with PEXSI")
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variant(
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"cray",
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default=False,
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description="Enable specific cray settings for using cray-hdf5"
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" and cray-netcdf modulefiles",
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)
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variant("debug", default=False, description="Build in debug mode")
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variant(
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"build_type",
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default="Release",
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description="The build type to build",
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values=("Debug", "Release", "RelWithDebInfo", "MinSizeRel", "check"),
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)
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depends_on("mpi", when="+mpi")
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depends_on("blas")
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depends_on("lapack")
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depends_on("scalapack")
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depends_on("scalapack", when="+mpi")
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depends_on("netcdf-c")
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depends_on("netcdf-fortran")
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depends_on("cray-libsci+openmp", when="^[virtuals=cray-libsci] cray-libsci")
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depends_on("metis@5:", when="+metis")
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depends_on("elpa", when="+elpa")
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depends_on("mumps", when="+mumps")
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depends_on("pexsi", when="+pexsi")
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with when("build_system=cmake"):
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depends_on("cmake@3.20:", type="build")
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def flag_handler(self, name, flags):
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if "%gcc@10:" in self.spec and name == "fflags":
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@ -49,49 +99,210 @@ def flag_handler(self, name, flags):
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def edit(self, spec, prefix):
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sh = which("sh")
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configure_args = [
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"--enable-mpi",
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"--with-blas=%s" % spec["blas"].libs,
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"--with-lapack=%s" % spec["lapack"].libs,
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# need to include BLAS below because Intel MKL's
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# BLACS depends on BLAS, otherwise the compiler
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# test fails
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"--with-blacs=%s" % (spec["scalapack"].libs + spec["blas"].libs),
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"--with-scalapack=%s" % spec["scalapack"].libs,
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"--with-netcdf=%s" % (spec["netcdf-fortran"].libs + spec["netcdf-c"].libs),
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# need to specify MPIFC explicitly below, otherwise
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# Intel's mpiifort is not found
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"MPIFC=%s" % spec["mpi"].mpifc,
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]
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if self.spec.satisfies("%gcc"):
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configure_args.append("FCFLAGS=-ffree-line-length-0")
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for d in ["Obj", "Obj_trans"]:
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with working_dir(d, create=True):
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sh("../Src/configure", *configure_args)
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if spec.satisfies("@:4.0%intel"):
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with open("arch.make", "a") as f:
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f.write("\natom.o: atom.F\n")
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f.write("\t$(FC) -c $(FFLAGS) -O1")
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f.write("$(INCFLAGS) $(FPPFLAGS) $<")
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if "+cray" in spec:
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netcdff_prefix = os.environ.get("NETCDF_DIR", "")
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hdf5_prefix = os.environ.get("HDF5_DIR", "")
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if spec.satisfies("@:4.0.2 +mpi"):
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configure_args = [
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"--enable-mpi",
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"--with-blas=%s" % spec["blas"].libs,
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"--with-lapack=%s" % spec["lapack"].libs,
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# need to include BLAS below because Intel MKL's
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# BLACS depends on BLAS, otherwise the compiler
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# test fails
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"--with-blacs=%s" % (spec["scalapack"].libs + spec["blas"].libs),
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"--with-scalapack=%s" % spec["scalapack"].libs,
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# need to specify MPIFC explicitly below, otherwise
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# Intel's mpiifort is not found
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"MPIFC=%s" % spec["mpi"].mpifc,
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]
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if "+cray" in spec:
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configure_args += ["--with-netcdf={0}/lib/libnetcdff.so".format(netcdff_prefix)]
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else:
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configure_args += [
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"--with-netcdf=%s" % (spec["netcdf-fortran"].libs + spec["netcdf-c"].libs)
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]
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if self.spec.satisfies("%gcc"):
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if "+cray" in spec:
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configure_args.append(
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"FCFLAGS=-ffree-line-length-0 -I{0}/include".format(netcdff_prefix)
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)
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else:
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configure_args.append("FCFLAGS=-ffree-line-length-0")
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for d in ["Obj", "Obj_trans"]:
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with working_dir(d, create=True):
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sh("../Src/configure", *configure_args)
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if spec.satisfies("@:4.0%intel"):
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with open("arch.make", "a") as f:
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f.write("\natom.o: atom.F\n")
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f.write("\t$(FC) -c $(FFLAGS) -O1")
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f.write("$(INCFLAGS) $(FPPFLAGS) $<")
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sh("../Src/obj_setup.sh")
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elif self.spec.satisfies("@:4.1.5"):
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with working_dir("Obj", create=True):
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sh("../Src/obj_setup.sh")
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if spec.satisfies("@:4.1.5%gcc"):
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shutil.copy("./gfortran.make", "./arch.make")
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libs_arg = []
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fppflags_arg = []
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arch_make = FileFilter("./arch.make")
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arch_make.filter(
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"FFLAGS = .*",
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"FFLAGS = {0}".format(
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"-O2 -fPIC -ftree-vectorize -fallow-argument-mismatch"
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),
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)
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if "+debug" in spec:
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arch_make.filter("FFLAGS_DEBUG=.*", "FFLAGS_DEBUG= -g -O1")
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if "^cray-libsci" in spec:
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libs_arg.append("-L{0}/lib -lsci_gnu".format(spec["cray-libsci"].prefix))
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with open("arch.make", "a") as f:
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if "+mpi" in spec:
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arch_make.filter("CC = .*", "CC = {0}".format(spec["mpi"].mpicc))
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arch_make.filter("FC = .*", "FC = {0}".format(spec["mpi"].mpifc))
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if "^cray-libsci" in spec:
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libs_arg.append("-lsci_gnu_mpi")
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f.write("MPI_INTERFACE = libmpi_f90.a\n")
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f.write("MPI_INCLUDE = .\n")
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f.write("LIBS += " + spec["scalapack"].libs.ld_flags + "\n")
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fppflags_arg.append("-DMPI ")
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if "+openmp" in spec:
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f.write("FFLAGS += -fopenmp\n")
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f.write("LIBS += -fopenmp\n")
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if "+netcdf" in spec:
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if "+cray" in spec:
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libs_arg.append(
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"-L{0}/lib -lnetcdff -lnetcdf".format(netcdff_prefix)
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)
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libs_arg.append(
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"-L{0}/lib -lhdf5_fortran -lhdf5".format(hdf5_prefix)
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)
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else:
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libs_arg.append(
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"-L{0}/lib -lnetcdff -lnetcdf".format(
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spec["netcdf-fortran"].prefix
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)
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)
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libs_arg.append(
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"-L{0}/lib -lhdf5_fortran -lhdf5".format(spec["hdf5"].prefix)
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)
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if "+metis" in spec:
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libs_arg.append("-L{0} -lmetis".format(self.spec["metis"].prefix.lib))
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fppflags_arg.append("-DSIESTA__METIS ")
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if "elpa" in spec:
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elpa = spec["elpa"]
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elpa_suffix = "_openmp" if "+openmp" in elpa else ""
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elpa_incdir = elpa.headers.directories[0]
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libs_arg.append(
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"-L{0} -lelpa{1}".format(self.spec["elpa"].prefix.lib, elpa_suffix)
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)
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fppflags_arg.append(
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"-DSIESTA__ELPA -I{0}".format(join_path(elpa_incdir, "modules"))
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)
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if "mumps" in spec:
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libs_arg.append(
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"-L{0} -lmumps_common -lzmumps".format(
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self.spec["mumps"].prefix.lib
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)
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)
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fppflags_arg.append("-DSIESTA__MUMPS ")
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if "+pexsi" in spec:
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libs_arg.append(
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"-L{0} -lpexsi_linux".format(self.spec["pexsi"].prefix.lib)
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)
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fppflags_arg.append("-DSIESTA__PEXSI ")
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f.write("INCFLAGS += -I{0}/include".format(self.spec["pexsi"].prefix))
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arch_make.filter("^LIBS =.*", "LIBS = {0}".format(" ".join(libs_arg)))
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f.write("FPPFLAGS = {0}".format(" ".join(fppflags_arg)))
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def build(self, spec, prefix):
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with working_dir("Obj"):
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make(parallel=False)
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with working_dir("Obj_trans"):
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make("transiesta", parallel=False)
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with working_dir("Util"):
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sh = which("sh")
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sh("build_all.sh")
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if spec.satisfies("@:4.0.2"):
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with working_dir("Obj_trans"):
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make("transiesta", parallel=False)
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with working_dir("Util"):
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sh = which("sh")
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sh("build_all.sh")
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def install(self, spec, prefix):
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mkdir(prefix.bin)
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with working_dir("Obj"):
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install("siesta", prefix.bin)
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with working_dir("Obj_trans"):
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install("transiesta", prefix.bin)
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if spec.satisfies("@:4.0.2"):
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with working_dir("Obj_trans"):
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install("transiesta", prefix.bin)
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for root, _, files in os.walk("Util"):
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for fname in files:
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fname = join_path(root, fname)
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if os.access(fname, os.X_OK):
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install(fname, prefix.bin)
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class CMakeBuilder(cmake.CMakeBuilder):
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"""Use the new CMake build system to build siesta@5.0.0:."""
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def cmake_args(self):
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spec = self.spec
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args = []
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args += ["-DBLAS_LIBRARIES={0}".format(self.spec["blas"].libs.link_flags)]
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args += ["-DLAPACK_LIBRARIES={0}".format(self.spec["lapack"].libs.link_flags)]
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if "+mpi" in spec:
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args += [
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"-DCMAKE_C_COMPILER=%s" % spec["mpi"].mpicc,
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"-DCMAKE_CXX_COMPILER=%s" % spec["mpi"].mpicxx,
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"-DCMAKE_Fortran_COMPILER=%s" % spec["mpi"].mpifc,
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]
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args += ["-DSIESTA_WITH_MPI=ON"]
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args += ["-DSCALAPACK_LIBRARY={0}".format(spec["scalapack"].libs.joined(";"))]
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if "+openmp" in spec:
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args += ["-DSIESTA_WITH_OPENMP=ON"]
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if "+cray" in spec:
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args += ["-DFortran_FLAGS=-fopenmp"]
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if "build_type=Debug" in spec:
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args += [
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"-DFortran_FLAGS=-Og -g -Wall -fcheck=all -fbacktrace"
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" -Warray-bounds -Wunused -Wuninitialized"
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]
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else:
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args += ["-DFortran_FLAGS=-O2 -fPIC -ftree-vectorize -fallow-argument-mismatch"]
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if "+netcdf" in spec:
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args += ["-DSIESTA_WITH_NETCDF=ON"]
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if "+cray" in spec:
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args += ["-DNetCDF_PATH={0}".format(os.environ.get("NETCDF_DIR", ""))]
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else:
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args += ["-DNetCDF_PATH={0}".format(spec["netcdf-fortran"].prefix)]
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if "+elpa" in spec:
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args += ["-DSIESTA_WITH_ELPA=ON"]
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if "+mumps" in spec:
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args += ["-DSIESTA__MUMPS=ON"]
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args += [
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"-DSIESTA_LINKER_FLAGS=-L{0} -lmumps_common -lzmumps".format(
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self.spec["mumps"].prefix.lib
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)
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]
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if "+metis" in spec:
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args += ["-DSIESTA__METIS=ON"]
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args += ["-DSIESTA_LINKER_FLAGS=-L{0} -lmetis".format(self.spec["metis"].prefix.lib)]
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return args
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