diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml
index 2c91b75e45d68545a4ebc302372df00e7ca4577d..dcfbf76b51b715d67d4bb101cd1886c3c08a3af0 100644
--- a/etc/spack/defaults/packages.yaml
+++ b/etc/spack/defaults/packages.yaml
@@ -40,6 +40,7 @@ packages:
opencl: [pocl]
pil: [py-pillow]
pkgconfig: [pkgconf, pkg-config]
+ rpc: [libtirpc]
scalapack: [netlib-scalapack]
sycl: [hipsycl]
szip: [libszip, libaec]
diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
index 88075f8a4e11d3ec7c4140ed64aa228fb1aef628..5aafdb44a1a7a86b548a6b6a88d424c4031baca1 100644
--- a/var/spack/repos/builtin/packages/gdal/package.py
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -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')
diff --git a/var/spack/repos/builtin/packages/hdf/disable_doclint.patch b/var/spack/repos/builtin/packages/hdf/disable_doclint.patch
new file mode 100644
index 0000000000000000000000000000000000000000..221d8c77c6cfb0c14ad994f1414c9fdfea0e59b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf/disable_doclint.patch
@@ -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)/*
diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py
index 67c2744470c055a332100fded7d0b7018441e8dd..d3076b35f9ac50eae3661e3252d7fed6acba84bd 100644
--- a/var/spack/repos/builtin/packages/hdf/package.py
+++ b/var/spack/repos/builtin/packages/hdf/package.py
@@ -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 = [
- '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'
- ]
-
- # Szip support
- if '+szip' in spec:
- config_args.append('--with-szlib={0}'.format(spec['szip'].prefix))
+ config_args = ['--enable-production',
+ '--enable-static',
+ '--with-zlib=%s' % self.spec['zlib'].prefix,
+ '--with-jpeg=%s' % self.spec['jpeg'].prefix]
+
+ 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')
+
+ 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)
diff --git a/var/spack/repos/builtin/packages/libc/package.py b/var/spack/repos/builtin/packages/libc/package.py
index a4fa9ac3a64c08b774871827bdfb906ac0adc403..e328c40ea1fe7e6f3356091d98b6831c5ec40a0b 100644
--- a/var/spack/repos/builtin/packages/libc/package.py
+++ b/var/spack/repos/builtin/packages/libc/package.py
@@ -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')
diff --git a/var/spack/repos/builtin/packages/libtirpc/package.py b/var/spack/repos/builtin/packages/libtirpc/package.py
index e6ce06e0ea02e22745499060eff501a3262e2784..f83c7499a098798ac3158fa4aec0d7bca7fcbfa0 100644
--- a/var/spack/repos/builtin/packages/libtirpc/package.py
+++ b/var/spack/repos/builtin/packages/libtirpc/package.py
@@ -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'
diff --git a/var/spack/repos/builtin/packages/netcdf-c/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py
index 153a1057b172c672255af5af8fcbf25bfda3fdb9..6043e1122d765d37f99cc6c68b130215cdba3c75 100644
--- a/var/spack/repos/builtin/packages/netcdf-c/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-c/package.py
@@ -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.