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# 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
from shutil import Error, copyfile
from spack.package import *
class NetcdfFortran(AutotoolsPackage):
"""NetCDF (network Common Data Form) is a set of software libraries and
machine-independent data formats that support the creation, access, and
sharing of array-oriented scientific data. This is the Fortran
distribution."""
homepage = "https://www.unidata.ucar.edu/software/netcdf"
url = "https://downloads.unidata.ucar.edu/netcdf-fortran/4.5.4/netcdf-fortran-4.5.4.tar.gz"
maintainers = ["skosukhin", "WardF"]
version("4.5.4", sha256="0a19b26a2b6e29fab5d29d7d7e08c24e87712d09a5cafeea90e16e0a2ab86b81")
version("4.5.3", sha256="123a5c6184336891e62cf2936b9f2d1c54e8dee299cfd9d2c1a1eb05dd668a74")
version("4.5.2", sha256="b959937d7d9045184e9d2040a915d94a7f4d0185f4a9dceb8f08c94b0c3304aa")
version("4.4.5", sha256="2467536ce29daea348c736476aa8e684c075d2f6cab12f3361885cb6905717b8")
version("4.4.4", sha256="b2d395175f8d283e68c8be516e231a96b191ade67ad0caafaf7fa01b1e6b5d75")
version("4.4.3", sha256="330373aa163d5931e475b5e83da5c1ad041e855185f24e6a8b85d73b48d6cda9")
variant("pic", default=True, description="Produce position-independent code (for shared libs)")
variant("shared", default=True, description="Enable shared library")
variant("doc", default=False, description="Enable building docs")
depends_on("netcdf-c")
depends_on("netcdf-c@4.7.4:", when="@4.5.3:") # nc_def_var_szip required
depends_on("doxygen", when="+doc", type="build")
# The default libtool.m4 is too old to handle NAG compiler properly:
# https://github.com/Unidata/netcdf-fortran/issues/94
# Moreover, Libtool can't handle '-pthread' flag coming from libcurl,
# doesn't inject convenience libraries into the shared ones, and is unable
# to detect NAG when it is called with an MPI wrapper.
patch("nag_libtool_2.4.2.patch", when="@:4.4.4%nag")
patch("nag_libtool_2.4.6.patch", when="@4.4.5:%nag")
# Enable 'make check' for NAG, which is too strict.
patch("nag_testing.patch", when="@4.4.5%nag")
# File fortran/nf_logging.F90 is compiled without -DLOGGING, which leads
# to missing symbols in the library. Additionally, the patch enables
# building with NAG, which refuses to compile empty source files (see also
# comments in the patch):
patch("logging.patch", when="@:4.4.5")
# Prevent excessive linking to system libraries. Without this patch the
# library might get linked to the system installation of libcurl. See
# https://github.com/Unidata/netcdf-fortran/commit/0a11f580faebbc1c4dce68bf5135709d1c7c7cc1#diff-67e997bcfdac55191033d57a16d1408a
patch("excessive_linking.patch", when="@4.4.5")
# Parallel builds do not work in the fortran directory. This patch is
# derived from https://github.com/Unidata/netcdf-fortran/pull/211
patch("no_parallel_build.patch", when="@4.5.2")
def flag_handler(self, name, flags):
if name == "cflags":
if "+pic" in self.spec:
flags.append(self.compiler.cc_pic_flag)
elif name == "fflags":
if "+pic" in self.spec:
flags.append(self.compiler.f77_pic_flag)
if self.spec.satisfies("%gcc@10:"):
# https://github.com/Unidata/netcdf-fortran/issues/212
flags.append("-fallow-argument-mismatch")
elif self.compiler.name == "cce":
# Cray compiler generates module files with uppercase names by
# default, which is not handled by the makefiles of
# NetCDF-Fortran:
# https://github.com/Unidata/netcdf-fortran/pull/221.
# The following flag forces the compiler to produce module
# files with lowercase names.
flags.append("-ef")
# Note that cflags and fflags should be added by the compiler wrapper
# and not on the command line to avoid overriding the default
# compilation flags set by the configure script:
return flags, None, None
@property
def libs(self):
libraries = ["libnetcdff"]
query_parameters = self.spec.last_query.extra_parameters
if "shared" in query_parameters:
shared = True
elif "static" in query_parameters:
shared = False
else:
shared = "+shared" in self.spec
libs = find_libraries(libraries, root=self.prefix, shared=shared, recursive=True)
if libs:
return libs
msg = "Unable to recursively locate {0} {1} libraries in {2}"
raise spack.error.NoLibrariesError(
msg.format("shared" if shared else "static", self.spec.name, self.spec.prefix)
)
def configure_args(self):
config_args = ["--enable-static"]
config_args += self.enable_or_disable("shared")
config_args += self.enable_or_disable("doxygen", variant="doc")
netcdf_c_spec = self.spec["netcdf-c"]
if "+mpi" in netcdf_c_spec or "+parallel-netcdf" in netcdf_c_spec:
# Prefixing with 'mpiexec -n 4' is not necessarily the correct way
# to launch MPI programs on a particular machine (e.g. 'srun -n 4'
# with additional arguments might be the right one). Therefore, we
# make sure the parallel tests are not launched at all (although it
# is the default behaviour currently):
config_args.append("--disable-parallel-tests")
if self.spec.satisfies("@4.5.0:4.5.2"):
# Versions from 4.5.0 to 4.5.2 check whether the Fortran MPI
# interface is available and fail the configuration if it is
# not. However, the interface is needed for a subset of the test
# programs only (the library itself does not need it), which are
# not run by default and explicitly disabled above. To avoid the
# configuration failure, we set the following cache variable:
config_args.append("ac_cv_func_MPI_File_open=yes")
return config_args
@run_after("configure")
def patch_libtool(self):
"""AOCC support for NETCDF-F"""
if "%aocc" in self.spec:
# Libtool does not fully support the compiler toolchain, therefore
# we have to patch the script. The C compiler normally gets
# configured correctly, the variables of interest in the
# 'BEGIN LIBTOOL CONFIG' section are set to non-empty values and,
# therefore, are not affected by the replacements below. A more
# robust solution would be to extend the filter_file function with
# an additional argument start_at and perform the replacements
# between the '# ### BEGIN LIBTOOL TAG CONFIG: FC' and
# '# ### END LIBTOOL TAG CONFIG: FC' markers for the Fortran
# compiler, and between the '# ### BEGIN LIBTOOL TAG CONFIG: F77'
# and '# ### END LIBTOOL TAG CONFIG: F77' markers for the Fortran 77
# compiler.
# How to pass a linker flag through the compiler:
filter_file(r'^wl=""$', 'wl="{0}"'.format(self.compiler.linker_arg), "libtool")
# Additional compiler flags for building library objects (we need
# this to enable shared libraries when building with ~pic). Note
# that the following will set fc_pic_flag for both FC and F77, which
# in the case of AOCC, should not be a problem. If it is, the
# aforementioned modification of the filter_file function could be
# a solution.
filter_file(
r'^pic_flag=""$', 'pic_flag=" {0}"'.format(self.compiler.fc_pic_flag), "libtool"
)
# The following is supposed to tell the compiler to use the GNU
# linker. However, the replacement does not happen (at least for
# NetCDF-Fortran 4.5.3) because the replaced substring (i.e. the
# first argument passed to the filter_file function) is not present
# in the file. The flag should probably be added to 'ldflags' in the
# flag_handler method above (another option is to add the flag to
# 'ldflags' in compilers.yaml automatically as it was done for other
# flags in https://github.com/spack/spack/pull/22219).
filter_file(
r"\${wl}-soname \$wl\$soname",
r"-fuse-ld=ld -Wl,-soname,\$soname",
"libtool",
string=True,
)
# TODO: resolve the NAG-related issues in a similar way: remove the
# respective patch files and tune the generated libtool script instead.
@when("@:4.4.5")
def check(self):
with working_dir(self.build_directory):
make("check", parallel=False)
@run_after("install")
def cray_module_filenames(self):
# Cray compiler searches for module files with uppercase names by
# default and with lowercase names when the '-ef' flag is specified.
# To avoid warning messages when compiler user applications in both
# cases, we create copies of all '*.mod' files in the prefix/include
# with names in upper- and lowercase.
if self.spec.compiler.name != "cce":
return
with working_dir(self.spec.prefix.include):
for f in glob.glob("*.mod"):
name, ext = os.path.splitext(f)
try:
# Create a copy with uppercase name:
copyfile(f, name.upper() + ext)
except Error:
# Assume that the exception tells us that the file with
# uppercase name already exists. Try to create a file with
# lowercase name then:
try:
copyfile(f, name.lower() + ext)
except Error:
pass
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