spack/var/spack/repos/builtin/packages/conduit/package.py
2022-08-23 21:33:49 -06:00

570 lines
23 KiB
Python

# Copyright 2013-2022 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)
import glob
import os
import shutil
import socket
from os import environ as env
import llnl.util.tty as tty
from spack.package import *
def cmake_cache_entry(name, value, vtype=None):
"""
Helper that creates CMake cache entry strings used in
'host-config' files.
"""
if vtype is None:
if value == "ON" or value == "OFF":
vtype = "BOOL"
else:
vtype = "PATH"
return 'set({0} "{1}" CACHE {2} "")\n\n'.format(name, value, vtype)
class Conduit(CMakePackage):
"""Conduit is an open source project from Lawrence Livermore National
Laboratory that provides an intuitive model for describing hierarchical
scientific data in C++, C, Fortran, and Python. It is used for data
coupling between packages in-core, serialization, and I/O tasks."""
homepage = "https://software.llnl.gov/conduit"
url = "https://github.com/LLNL/conduit/releases/download/v0.3.0/conduit-v0.3.0-src-with-blt.tar.gz"
git = "https://github.com/LLNL/conduit.git"
tags = ["radiuss", "e4s"]
version("develop", branch="develop", submodules=True)
# note: the main branch in conduit was renamed to develop, this next entry
# is to bridge any spack dependencies that are still using the name master
version("master", branch="develop", submodules=True)
# note: 2021-05-05 latest tagged release is now preferred instead of develop
version("0.8.4", sha256="55c37ddc668dbc45d43b60c440192f76e688a530d64f9fe1a9c7fdad8cd525fd")
version("0.8.3", sha256="a9e60945366f3b8c37ee6a19f62d79a8d5888be7e230eabc31af2f837283ed1a")
version("0.8.2", sha256="928eb8496bc50f6d8404f5bfa70220250876645d68d4f35ce0b99ecb85546284")
version("0.8.1", sha256="488f22135a35136de592173131d123f7813818b7336c3b18e04646318ad3cbee")
version("0.8.0", sha256="0607dcf9ced44f95e0b9549f5bbf7a332afd84597c52e293d7ca8d83117b5119")
version("0.7.2", sha256="359fd176297700cdaed2c63e3b72d236ff3feec21a655c7c8292033d21d5228a")
version("0.7.1", sha256="460a480cf08fedbf5b38f707f94f20828798327adadb077f80dbab048fd0a07d")
version("0.7.0", sha256="ecaa9668ebec5d4efad19b104d654a587c0adbd5f502128f89601408cb4d7d0c")
version("0.6.0", sha256="078f086a13b67a97e4ab6fe1063f2fef2356df297e45b43bb43d74635f80475d")
version("0.5.1", sha256="68a3696d1ec6d3a4402b44a464d723e6529ec41016f9b44c053676affe516d44")
version("0.5.0", sha256="7efac668763d02bd0a2c0c1b134d9f5ee27e99008183905bb0512e5502b8b4fe")
version("0.4.0", sha256="c228e6f0ce5a9c0ffb98e0b3d886f2758ace1a4b40d00f3f118542c0747c1f52")
version("0.3.1", sha256="7b358ca03bb179876291d4a55d6a1c944b7407a80a588795b9e47940b1990521")
version("0.3.0", sha256="52e9cf5720560e5f7492876c39ef2ea20ae73187338361d2744bdf67567da155")
# note: checksums on github automatic release source tars changed ~9/17
version("0.2.1", sha256="796576b9c69717c52f0035542c260eb7567aa351ee892d3fbe3521c38f1520c4")
version("0.2.0", sha256="31eff8dbc654a4b235cfcbc326a319e1752728684296721535c7ca1c9b463061")
maintainers = ["cyrush"]
###########################################################################
# package variants
###########################################################################
variant("shared", default=True, description="Build Conduit as shared libs")
variant("test", default=True, description="Enable Conduit unit tests")
# variants for python support
variant("python", default=False, description="Build Conduit Python support")
variant("fortran", default=True, description="Build Conduit Fortran support")
# variants for comm and i/o
variant("mpi", default=True, description="Build Conduit MPI Support")
# set to false for systems that implicitly link mpi
variant("blt_find_mpi", default=True, description="Use BLT CMake Find MPI logic")
variant("hdf5", default=True, description="Build Conduit HDF5 support")
# TODO: remove 'compat' variant when VisIt starts distributing HDF5
# binaries
variant(
"hdf5_compat",
default=True,
when="+hdf5",
description="Build Conduit with HDF5 1.8.x (compatibility mode)",
)
variant("silo", default=False, description="Build Conduit Silo support")
variant("adios", default=False, description="Build Conduit ADIOS support")
variant("parmetis", default=True, description="Build Conduit Parmetis support")
# zfp compression
variant("zfp", default=False, description="Build Conduit ZFP support")
# variants for dev-tools (docs, etc)
variant("doc", default=False, description="Build Conduit's documentation")
# doxygen support is wip, since doxygen has several dependencies
# we want folks to explicitly opt in to building doxygen
variant("doxygen", default=False, description="Build Conduit's Doxygen documentation")
###########################################################################
# package dependencies
###########################################################################
#######################
# CMake
#######################
# cmake 3.14.1 or newer
depends_on("cmake@3.14.1:", type="build")
#######################
# Python
#######################
depends_on("python", when="+python")
extends("python", when="+python")
depends_on("py-numpy", when="+python", type=("build", "run"))
depends_on("py-mpi4py", when="+python+mpi", type=("build", "run"))
#######################
# I/O Packages
#######################
###############
# HDF5
###############
depends_on("hdf5", when="+hdf5")
depends_on("hdf5~shared", when="+hdf5~shared")
# Require older HDF5 to ensure compatibility with VisIt: see #29132
depends_on("hdf5@1.8.0:1.8", when="+hdf5+hdf5_compat")
###############
# Silo
###############
# we are not using silo's fortran features
depends_on("silo+shared", when="+silo+shared")
depends_on("silo~shared", when="+silo~shared")
###############
# ADIOS
###############
depends_on("adios+mpi~hdf5+shared", when="+adios+mpi+shared")
depends_on("adios+mpi~hdf5~shared~blosc", when="+adios+mpi~shared")
depends_on("adios~mpi~hdf5+shared", when="+adios~mpi+shared")
depends_on("adios~mpi~hdf5~shared~blosc", when="+adios~mpi~shared")
#######################
# ZFP
#######################
depends_on("zfp bsws=8", when="+zfp")
# hdf5 zfp plugin when both hdf5 and zfp are on
depends_on("h5z-zfp~fortran", when="+hdf5+zfp")
#######################
# Parmetis
#######################
depends_on("parmetis", when="+parmetis")
depends_on("metis", when="+parmetis")
#######################
# MPI
#######################
depends_on("mpi", when="+mpi")
#######################
# Documentation related
#######################
depends_on("py-sphinx", when="+python+doc", type="build")
depends_on("py-sphinx-rtd-theme", when="+python+doc", type="build")
depends_on("doxygen", when="+doc+doxygen")
# Tentative patch for fj compiler
# Cmake will support fj compiler and this patch will be removed
patch("fj_flags.patch", when="%fj")
patch("bpparametis.patch", when="@0.8.1")
# Add missing include for numeric_limits
# https://github.com/LLNL/conduit/pull/773
patch(
"https://github.com/LLNL/conduit/pull/773.patch?full_index=1",
when="@:0.7.2",
sha256="784d74942a63acf698c31b39848b46b4b755bf06faa6aa6fb81be61783ec0c30",
)
def setup_build_environment(self, env):
env.set("CTEST_OUTPUT_ON_FAILURE", "1")
# conduit uses a <=1.10 api version before 0.8
if "@:0.7 +hdf5" in self.spec and "@1.10:" in self.spec["hdf5"]:
env.append_flags("CFLAGS", "-DH5_USE_110_API")
env.append_flags("CXXFLAGS", "-DH5_USE_110_API")
def url_for_version(self, version):
"""
Provide proper url
"""
v = str(version)
if v == "0.2.0":
return "https://github.com/LLNL/conduit/archive/v0.2.0.tar.gz"
elif v == "0.2.1":
return "https://github.com/LLNL/conduit/archive/v0.2.1.tar.gz"
else:
# starting with v 0.3.0, conduit uses BLT
# (https://github.com/llnl/blt) as a submodule, since github does
# not automatically package source from submodules, conduit
# provides a custom src tarball
return "https://github.com/LLNL/conduit/releases/download/v{0}/conduit-v{1}-src-with-blt.tar.gz".format(
v, v
)
return url
####################################################################
# Note: cmake, build, and install stages are handled by CMakePackage
####################################################################
# provide cmake args (pass host config as cmake cache file)
def cmake_args(self):
host_config = self._get_host_config_path(self.spec)
options = []
options.extend(["-C", host_config, "../spack-src/src/"])
return options
@run_after("build")
@on_package_attributes(run_tests=True)
def build_test(self):
with working_dir("spack-build"):
print("Running Conduit Unit Tests...")
make("test")
@run_after("install")
@on_package_attributes(run_tests=True)
def check_install(self):
"""
Checks the spack install of conduit using conduit's
using-with-cmake example
"""
print("Checking Conduit installation...")
spec = self.spec
install_prefix = spec.prefix
example_src_dir = join_path(install_prefix, "examples", "conduit", "using-with-cmake")
print("Checking using-with-cmake example...")
with working_dir("check-conduit-using-with-cmake-example", create=True):
cmake_args = ["-DCONDUIT_DIR={0}".format(install_prefix), example_src_dir]
cmake(*cmake_args)
make()
example = Executable("./conduit_example")
example()
print("Checking using-with-make example...")
example_src_dir = join_path(install_prefix, "examples", "conduit", "using-with-make")
example_files = glob.glob(join_path(example_src_dir, "*"))
with working_dir("check-conduit-using-with-make-example", create=True):
for example_file in example_files:
shutil.copy(example_file, ".")
make("CONDUIT_DIR={0}".format(install_prefix))
example = Executable("./conduit_example")
example()
def _get_host_config_path(self, spec):
sys_type = spec.architecture
# if on llnl systems, we can use the SYS_TYPE
if "SYS_TYPE" in env:
sys_type = env["SYS_TYPE"]
host_config_path = "{0}-{1}-{2}-conduit-{3}.cmake".format(
socket.gethostname(), sys_type, spec.compiler, spec.dag_hash()
)
dest_dir = spec.prefix
host_config_path = os.path.abspath(join_path(dest_dir, host_config_path))
return host_config_path
@run_before("cmake")
def hostconfig(self):
"""
This method creates a 'host-config' file that specifies
all of the options used to configure and build conduit.
For more details about 'host-config' files see:
http://software.llnl.gov/conduit/building.html
"""
spec = self.spec
if not os.path.isdir(spec.prefix):
os.mkdir(spec.prefix)
#######################
# Compiler Info
#######################
c_compiler = env["SPACK_CC"]
cpp_compiler = env["SPACK_CXX"]
if "+fortran" in spec:
f_compiler = env["SPACK_FC"]
else:
f_compiler = None
#######################################################################
# Directly fetch the names of the actual compilers to create a
# 'host config' file that works outside of the spack install env.
#######################################################################
sys_type = spec.architecture
# if on llnl systems, we can use the SYS_TYPE
if "SYS_TYPE" in env:
sys_type = env["SYS_TYPE"]
# are we on a specific machine
on_blueos = "blueos" in sys_type
##############################################
# Find and record what CMake is used
##############################################
cmake_exe = spec["cmake"].command.path
# get hostconfig name
host_cfg_fname = self._get_host_config_path(spec)
cfg = open(host_cfg_fname, "w")
cfg.write("##################################\n")
cfg.write("# spack generated host-config\n")
cfg.write("##################################\n")
cfg.write("# {0}-{1}\n".format(sys_type, spec.compiler))
cfg.write("##################################\n\n")
# Include path to cmake for reference
cfg.write("# cmake from spack \n")
cfg.write("# cmake executable path: %s\n\n" % cmake_exe)
#######################
# Compiler Settings
#######################
cfg.write("#######\n")
cfg.write("# using %s compiler spec\n" % spec.compiler)
cfg.write("#######\n\n")
cfg.write("# c compiler used by spack\n")
cfg.write(cmake_cache_entry("CMAKE_C_COMPILER", c_compiler))
cfg.write("# cpp compiler used by spack\n")
cfg.write(cmake_cache_entry("CMAKE_CXX_COMPILER", cpp_compiler))
cfg.write("# fortran compiler used by spack\n")
if "+fortran" in spec:
cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "ON"))
cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER", f_compiler))
else:
cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "OFF"))
if "+shared" in spec:
cfg.write(cmake_cache_entry("BUILD_SHARED_LIBS", "ON"))
else:
cfg.write(cmake_cache_entry("BUILD_SHARED_LIBS", "OFF"))
# use global spack compiler flags
cppflags = " ".join(spec.compiler_flags["cppflags"])
if cppflags:
# avoid always ending up with ' ' with no flags defined
cppflags += " "
cflags = cppflags + " ".join(spec.compiler_flags["cflags"])
if cflags:
cfg.write(cmake_cache_entry("CMAKE_C_FLAGS", cflags))
cxxflags = cppflags + " ".join(spec.compiler_flags["cxxflags"])
if cxxflags:
cfg.write(cmake_cache_entry("CMAKE_CXX_FLAGS", cxxflags))
fflags = " ".join(spec.compiler_flags["fflags"])
if self.spec.satisfies("%cce"):
fflags += " -ef"
if fflags:
cfg.write(cmake_cache_entry("CMAKE_Fortran_FLAGS", fflags))
if (f_compiler is not None) and ("gfortran" in f_compiler) and ("clang" in cpp_compiler):
libdir = os.path.join(os.path.dirname(os.path.dirname(f_compiler)), "lib")
flags = ""
for _libpath in [libdir, libdir + "64"]:
if os.path.exists(_libpath):
flags += " -Wl,-rpath,{0}".format(_libpath)
description = "Adds a missing libstdc++ rpath"
if flags:
cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS", flags, description))
#######################
# Unit Tests
#######################
if "+test" in spec:
cfg.write(cmake_cache_entry("ENABLE_TESTS", "ON"))
else:
cfg.write(cmake_cache_entry("ENABLE_TESTS", "OFF"))
# extra fun for blueos
if on_blueos:
# All of BlueOS compilers report clang due to nvcc,
# override to proper compiler family
if "xlc" in c_compiler:
cfg.write(cmake_cache_entry("CMAKE_C_COMPILER_ID", "XL"))
if "xlC" in cpp_compiler:
cfg.write(cmake_cache_entry("CMAKE_CXX_COMPILER_ID", "XL"))
if "+fortran" in spec:
if "xlf" in f_compiler:
cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER_ID", "XL"))
if (f_compiler is not None) and ("xlf" in f_compiler):
# Fix missing std linker flag in xlc compiler
flags = "-WF,-C! -qxlf2003=polymorphic"
cfg.write(cmake_cache_entry("BLT_FORTRAN_FLAGS", flags))
# Grab lib directory for the current fortran compiler
libdir = os.path.join(os.path.dirname(os.path.dirname(f_compiler)), "lib")
rpaths = "-Wl,-rpath,{0} -Wl,-rpath,{0}64".format(libdir)
flags = "${BLT_EXE_LINKER_FLAGS} -lstdc++ " + rpaths
cfg.write(cmake_cache_entry("BLT_EXE_LINKER_FLAGS", flags))
if "+shared" in spec:
flags = "${CMAKE_SHARED_LINKER_FLAGS} " + rpaths
cfg.write(cmake_cache_entry("CMAKE_SHARED_LINKER_FLAGS", flags))
#######################
# Python
#######################
cfg.write("# Python Support\n")
if "+python" in spec:
cfg.write("# Enable python module builds\n")
cfg.write(cmake_cache_entry("ENABLE_PYTHON", "ON"))
cfg.write("# python from spack \n")
cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE", spec["python"].command.path))
try:
cfg.write("# python module install dir\n")
cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX", python_platlib))
except NameError:
# spack's won't exist in a subclass
pass
else:
cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
if "+doc" in spec:
if "+python" in spec:
cfg.write(cmake_cache_entry("ENABLE_DOCS", "ON"))
cfg.write("# sphinx from spack \n")
sphinx_build_exe = join_path(spec["py-sphinx"].prefix.bin, "sphinx-build")
cfg.write(cmake_cache_entry("SPHINX_EXECUTABLE", sphinx_build_exe))
if "+doxygen" in spec:
cfg.write("# doxygen from uberenv\n")
doxygen_exe = spec["doxygen"].command.path
cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
else:
cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF"))
#######################
# MPI
#######################
cfg.write("# MPI Support\n")
if "+mpi" in spec:
mpicc_path = spec["mpi"].mpicc
mpicxx_path = spec["mpi"].mpicxx
mpifc_path = spec["mpi"].mpifc if "+fortran" in spec else None
# if we are using compiler wrappers on cray systems
# use those for mpi wrappers, b/c spec['mpi'].mpicxx
# etc make return the spack compiler wrappers
# which can trip up mpi detection in CMake 3.14
if spec["mpi"].mpicc == spack_cc:
mpicc_path = c_compiler
mpicxx_path = cpp_compiler
mpifc_path = f_compiler
cfg.write(cmake_cache_entry("ENABLE_MPI", "ON"))
cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path))
cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path))
if "+blt_find_mpi" in spec:
cfg.write(cmake_cache_entry("ENABLE_FIND_MPI", "ON"))
else:
cfg.write(cmake_cache_entry("ENABLE_FIND_MPI", "OFF"))
if "+fortran" in spec:
cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path))
mpiexe_bin = join_path(spec["mpi"].prefix.bin, "mpiexec")
if os.path.isfile(mpiexe_bin):
# starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
# vs the older versions which expect MPIEXEC
if self.spec["cmake"].satisfies("@3.10:"):
cfg.write(cmake_cache_entry("MPIEXEC_EXECUTABLE", mpiexe_bin))
else:
cfg.write(cmake_cache_entry("MPIEXEC", mpiexe_bin))
else:
cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
#######################
# ZFP
#######################
cfg.write("# zfp from spack \n")
if "+zfp" in spec:
cfg.write(cmake_cache_entry("ZFP_DIR", spec["zfp"].prefix))
else:
cfg.write("# zfp not built by spack \n")
#######################################################################
# I/O Packages
#######################################################################
cfg.write("# I/O Packages\n\n")
#######################
# HDF5
#######################
cfg.write("# hdf5 from spack \n")
if "+hdf5" in spec:
cfg.write(cmake_cache_entry("HDF5_DIR", spec["hdf5"].prefix))
if "zlib" in spec:
# HDF5 depends on zlib
cfg.write(cmake_cache_entry("ZLIB_DIR", spec["zlib"].prefix))
else:
cfg.write("# hdf5 not built by spack \n")
#######################
# h5z-zfp
#######################
cfg.write("# h5z-zfp from spack \n")
if "+hdf5+zfp" in spec:
cfg.write(cmake_cache_entry("H5ZZFP_DIR", spec["h5z-zfp"].prefix))
else:
cfg.write("# h5z-zfp not built by spack \n")
#######################
# Silo
#######################
cfg.write("# silo from spack \n")
if "+silo" in spec:
cfg.write(cmake_cache_entry("SILO_DIR", spec["silo"].prefix))
else:
cfg.write("# silo not built by spack \n")
#######################
# ADIOS
#######################
cfg.write("# ADIOS from spack \n")
if "+adios" in spec:
cfg.write(cmake_cache_entry("ADIOS_DIR", spec["adios"].prefix))
else:
cfg.write("# adios not built by spack \n")
#######################
# Parmetis
#######################
cfg.write("# parmetis from spack \n")
if "+parmetis" in spec:
cfg.write(cmake_cache_entry("METIS_DIR", spec["metis"].prefix))
cfg.write(cmake_cache_entry("PARMETIS_DIR", spec["parmetis"].prefix))
else:
cfg.write("# parmetis not built by spack \n")
#######################
# Finish host-config
#######################
cfg.write("##################################\n")
cfg.write("# end spack generated host-config\n")
cfg.write("##################################\n")
cfg.close()
host_cfg_fname = os.path.abspath(host_cfg_fname)
tty.info("spack generated conduit host-config file: " + host_cfg_fname)