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hdf: new version, variants and refactoring (#16469)

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* hdf: new version, variants and refactoring.

* libc provides rpc

* Fix szip-related configure argument.

* Update dependent packages.
This commit is contained in:
Sergey Kosukhin 2020-05-26 02:20:04 +02:00 committed by GitHub
parent 15d2883abe
commit ff44a6d03f
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
7 changed files with 141 additions and 32 deletions
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1
etc/spack/defaults/packages.yaml
View file

@ -40,6 +40,7 @@ packages:
opencl: [pocl]
pil: [py-pillow]
pkgconfig: [pkgconf, pkg-config]
rpc: [libtirpc]
scalapack: [netlib-scalapack]
sycl: [hipsycl]
szip: [libszip, libaec]

4
var/spack/repos/builtin/packages/gdal/package.py
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@ -297,8 +297,8 @@ def configure_args(self):
if '+hdf4' in spec:
args.append('--with-hdf4={0}'.format(spec['hdf'].prefix))
hdf4 = self.spec['hdf']
if '+libtirpc' in hdf4:
libs.append('-ltirpc')
if '+external-xdr' in hdf4 and hdf4['rpc'].name != 'libc':
libs.append(hdf4['rpc'].libs.link_flags)
else:
args.append('--with-hdf4=no')

11
var/spack/repos/builtin/packages/hdf/disable_doclint.patch Normal file
View file

@ -0,0 +1,11 @@
--- a/java/src/Makefile.in
+++ b/java/src/Makefile.in
@@ -818,7 +818,7 @@ $(jarfile): classhdf_java.stamp classes docs
.PHONY: docs classes
docs:
- $(JAVADOC) -sourcepath $(srcdir) -d javadoc -use -splitIndex -windowtitle $(WINDOWTITLE) -doctitle $(DOCTITLE) -J-Xmx180m -verbose -overview $(top_srcdir)/java/src/hdf/overview.html -classpath $(CLASSPATH_ENV) hdf.hdflib
+ $(JAVADOC) -sourcepath $(srcdir) -d javadoc -use -splitIndex -windowtitle $(WINDOWTITLE) -doctitle $(DOCTITLE) -J-Xmx180m -verbose -overview $(top_srcdir)/java/src/hdf/overview.html -classpath $(CLASSPATH_ENV) hdf.hdflib -Xdoclint:none
clean:
rm -rf $(JAVAROOT)/*

139
var/spack/repos/builtin/packages/hdf/package.py
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@ -15,45 +15,138 @@ class Hdf(AutotoolsPackage):
list_url = "https://support.hdfgroup.org/ftp/HDF/releases/"
list_depth = 2
version('4.2.15', sha256='dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459')
version('4.2.14', sha256='2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a')
version('4.2.13', sha256='be9813c1dc3712c2df977d4960e1f13f20f447dfa8c3ce53331d610c1f470483')
version('4.2.12', sha256='dd419c55e85d1a0e13f3ea5ed35d00710033ccb16c85df088eb7925d486e040c')
version('4.2.11', sha256='c3f7753b2fb9b27d09eced4d2164605f111f270c9a60b37a578f7de02de86d24')
variant('szip', default=False, description="Enable szip support")
variant('libtirpc', default=False, description="Use xdr library from libtirpc package; if false, will use system or hdf internal")
variant('external-xdr', default=True,
description="Use an external XDR backend")
variant('netcdf', default=False,
description='Build NetCDF API (version 2.3.2)')
variant('fortran', default=False,
description='Enable Fortran interface')
variant('java', default=False,
description='Enable Java JNI interface')
variant('shared', default=False, description='Enable shared library')
variant('pic', default=True,
description='Produce position-independent code')
depends_on('jpeg@6b:')
depends_on('szip', when='+szip')
depends_on('libtirpc', when='+libtirpc')
depends_on('zlib@1.1.4:')
depends_on('jpeg')
depends_on('szip', when='+szip')
depends_on('rpc', when='+external-xdr')
depends_on('bison', type='build')
depends_on('flex', type='build')
depends_on('java@7:', when='+java', type=('build', 'run'))
# https://forum.hdfgroup.org/t/cant-build-hdf-4-2-14-with-jdk-11-and-enable-java/5702
patch('disable_doclint.patch', when='@:4.2.14^java@9:')
conflicts('^libjpeg@:6a')
# configure: error: Cannot build shared fortran libraries.
# Please configure with --disable-fortran flag.
conflicts('+fortran', when='+shared')
# configure: error: Java requires shared libraries to be built
conflicts('+java', when='~shared')
# configure: WARNING: unrecognized options: --enable-java
conflicts('+java', when='@:4.2.11')
# The Java interface library uses netcdf-related macro definitions even
# when netcdf is disabled and the macros are not defined, e.g.:
# hdfsdsImp.c:158:30: error: 'MAX_NC_NAME' undeclared
conflicts('+java', when='@4.2.12:4.2.13~netcdf')
# TODO: '@:4.2.14 ~external-xdr' and the fact that we compile for 64 bit
# architecture should be in conflict
@property
def libs(self):
"""HDF can be queried for the following parameters:
- "shared": shared libraries (default if '+shared')
- "static": static libraries (default if '~shared')
- "transitive": append transitive dependencies to the list of static
libraries (the argument is ignored if shared libraries are
requested)
:return: list of matching libraries
"""
libraries = ['libmfhdf', 'libdf']
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 not 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))
if not shared and 'transitive' in query_parameters:
libs += self.spec['jpeg:transitive'].libs
libs += self.spec['zlib:transitive'].libs
if '+szip' in self.spec:
libs += self.spec['szip:transitive'].libs
if ('+external-xdr' in self.spec and
self.spec['rpc'].name != 'libc'):
libs += self.spec['rpc:transitive'].libs
return libs
def flag_handler(self, name, flags):
if '+pic' in self.spec:
if name == 'cflags':
flags.append(self.compiler.cc_pic_flag)
elif name == 'fflags':
flags.append(self.compiler.f77_pic_flag)
return flags, None, None
def configure_args(self):
spec = self.spec
config_args = ['--enable-production',
'--enable-static',
'--with-zlib=%s' % self.spec['zlib'].prefix,
'--with-jpeg=%s' % self.spec['jpeg'].prefix]
config_args = [
'CFLAGS={0}'.format(self.compiler.cc_pic_flag),
'--with-jpeg={0}'.format(spec['jpeg'].prefix),
'--with-zlib={0}'.format(spec['zlib'].prefix),
'--disable-netcdf', # must be disabled to build NetCDF with HDF4
'--enable-fortran',
'--disable-shared', # fortran and shared libs are not compatible
'--enable-static',
'--enable-production'
]
config_args += self.enable_or_disable('shared')
config_args += self.enable_or_disable('netcdf')
config_args += self.enable_or_disable('fortran')
config_args += self.enable_or_disable('java')
# Szip support
if '+szip' in spec:
config_args.append('--with-szlib={0}'.format(spec['szip'].prefix))
if '+szip' in self.spec:
config_args.append('--with-szlib=%s' % self.spec['szip'].prefix)
else:
config_args.append('--without-szlib')
if '+libtirpc' in spec:
config_args.append('LIBS=-ltirpc')
config_args.append('CPPFLAGS=-I{0}/include/tirpc'.format(
spec['libtirpc'].prefix))
if '~external-xdr' in self.spec:
config_args.append('--enable-hdf4-xdr')
elif self.spec['rpc'].name != 'libc':
# We should not specify '--disable-hdf4-xdr' due to a bug in the
# configure script.
config_args.append('LIBS=%s' % self.spec['rpc'].libs.link_flags)
return config_args
# Otherwise, we randomly get:
# SDgetfilename:
# incorrect file being opened - expected <file755>, retrieved <file754>
def check(self):
with working_dir(self.build_directory):
make('check', parallel=False)

9
var/spack/repos/builtin/packages/libc/package.py
View file

@ -7,13 +7,16 @@
class Libc(Package):
"""Dummy libc package to provide `iconv` virtual package"""
"""Dummy package to provide interfaces available in libc."""
homepage = "https://en.wikipedia.org/wiki/C_standard_library"
url = ""
has_code = False
phases = []
version('1.0') # Dummy
variant('iconv', default=False, description='Set to True if libc provides iconv')
variant('iconv', default=False, description='Provides interfaces for Localization Functions')
variant('rpc', default=False, description='Provides interfaces for RPC')
provides('iconv', when='+iconv')
provides('rpc', when='+rpc')

2
var/spack/repos/builtin/packages/libtirpc/package.py
View file

@ -15,6 +15,8 @@ class Libtirpc(AutotoolsPackage):
version('1.1.4', sha256='2ca529f02292e10c158562295a1ffd95d2ce8af97820e3534fe1b0e3aec7561d')
provides('rpc')
# FIXME: build error on macOS
# auth_none.c:81:9: error: unknown type name 'mutex_t'

7
var/spack/repos/builtin/packages/netcdf-c/package.py
View file

@ -75,7 +75,7 @@ def url_for_version(self, version):
depends_on('libtool', type='build', when='@4.7.0')
depends_on("m4", type='build')
depends_on("hdf", when='+hdf4')
depends_on("hdf~netcdf", when='+hdf4')
# curl 7.18.0 or later is required:
# http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
@ -219,9 +219,8 @@ def configure_args(self):
if '+szip' in hdf4:
# This should also come from hdf4.libs
libs.append('-lsz')
if '+libtirpc' in hdf4:
# This should also come from hdf4.libs
libs.append('-ltirpc')
if '+external-xdr' in hdf4 and hdf4['rpc'].name != 'libc':
libs.append(hdf4['rpc'].libs.link_flags)
# Fortran support
# In version 4.2+, NetCDF-C and NetCDF-Fortran have split.