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spack/var/spack/repos/builtin/packages/conduit/package.py
adityakavalur 9f89a7e9f7
Update package.py (#19513) 
On Cori(Cray-XC40), I need to pass the entire path for the compilers, this is what is saved in c_compiler, cpp_compiler, f_compiler. Therefore, when for the MPI wrappers only the binary name is provided I run into the same issue. There is no drawback of passing the entire path, this is set by the user through the compiler path anyways.
2020-10-27 13:24:09 -05:00

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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)
from spack import *
import socket
import os
import glob
import shutil
import llnl.util.tty as tty
from os import environ as env
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(Package):
"""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 = "http://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"
version('master', branch='master', submodules=True, preferred=True)
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")
variant("hdf5", default=True, description="Build Conduit HDF5 support")
variant("hdf5_compat", default=True,
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")
# 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 3.8.2 or newer
depends_on("cmake@3.8.2:", 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
###############
# TODO: cxx variant is disabled due to build issue Cyrus
# experienced on BGQ. When on, the static build tries
# to link against shared libs.
#
# Use HDF5 1.8, for wider output compatibly
# variants reflect we are not using hdf5's mpi or fortran features.
depends_on("hdf5@1.8.19:1.8.999~cxx", when="+hdf5+hdf5_compat+shared")
depends_on("hdf5@1.8.19:1.8.999~shared~cxx", when="+hdf5+hdf5_compat~shared")
depends_on("hdf5~cxx", when="+hdf5~hdf5_compat+shared")
depends_on("hdf5~shared~cxx", when="+hdf5~hdf5_compat~shared")
###############
# Silo
###############
# we are not using silo's fortran features
depends_on("silo~fortran", when="+silo+shared")
depends_on("silo~shared~fortran", 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", when="+zfp")
#######################
# 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')
# build phases used by this package
phases = ["configure", "build", "install"]
def flag_handler(self, name, flags):
if name in ('cflags', 'cxxflags', 'fflags'):
# the package manages these flags in another way
return (None, None, None)
return (flags, None, None)
def setup_build_environment(self, env):
env.set('CTEST_OUTPUT_ON_FAILURE', '1')
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
def configure(self, spec, prefix):
"""
Configure Conduit.
"""
with working_dir('spack-build', create=True):
py_site_pkgs_dir = None
if "+python" in spec:
py_site_pkgs_dir = site_packages_dir
host_cfg_fname = self.create_host_config(spec,
prefix,
py_site_pkgs_dir)
# save this filename for
# other package recipe steps to access
self.host_cfg_fname = host_cfg_fname
cmake_args = []
# if we have a static build, we need to avoid any of
# spack's default cmake settings related to rpaths
# (see: https://github.com/spack/spack/issues/2658)
if "+shared" in spec:
cmake_args.extend(std_cmake_args)
else:
for arg in std_cmake_args:
if arg.count("RPATH") == 0:
cmake_args.append(arg)
cmake_args.extend(["-C", host_cfg_fname, "../src"])
print("Configuring Conduit...")
cmake(*cmake_args)
def build(self, spec, prefix):
"""
Build Conduit.
"""
with working_dir('spack-build'):
print("Building Conduit...")
make()
@run_after('build')
@on_package_attributes(run_tests=True)
def test(self):
with working_dir('spack-build'):
print("Running Conduit Unit Tests...")
make("test")
def install(self, spec, prefix):
"""
Install Conduit.
"""
with working_dir('spack-build'):
make("install")
# install copy of host config for provenance
print("Installing Conduit CMake Host Config File...")
install(self.host_cfg_fname, prefix)
@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 create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
"""
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
Note:
The `py_site_pkgs_dir` arg exists to allow a package that
subclasses this package provide a specific site packages
dir when calling this function. `py_site_pkgs_dir` should
be an absolute path or `None`.
This is necessary because the spack `site_packages_dir`
var will not exist in the base class. For more details
on this issue see: https://github.com/spack/spack/issues/6261
"""
#######################
# Compiler Info
#######################
c_compiler = env["SPACK_CC"]
cpp_compiler = env["SPACK_CXX"]
f_compiler = None
if self.compiler.fc:
# even if this is set, it may not exist
# do one more sanity check
if os.path.isfile(env["SPACK_FC"]):
f_compiler = env["SPACK_FC"]
#######################################################################
# By directly fetching the names of the actual compilers we appear
# to doing something evil here, but this is necessary 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
host_cfg_fname = "%s-%s-%s-conduit.cmake" % (socket.gethostname(),
sys_type,
spec.compiler)
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 and f_compiler is not None:
cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "ON"))
cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER",
f_compiler))
else:
cfg.write("# no fortran compiler found\n\n")
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 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))
# only set dest python site packages dir if passed
if py_site_pkgs_dir:
cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
py_site_pkgs_dir))
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 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 "+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))
else:
cfg.write("# hdf5 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")
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)
return host_cfg_fname
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