diff options
| -rw-r--r-- | etc/spack/defaults/packages.yaml | 1 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/gdal/package.py | 4 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/hdf/disable_doclint.patch | 11 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/hdf/package.py | 143 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/libc/package.py | 9 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/libtirpc/package.py | 2 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/netcdf-c/package.py | 7 |
7 files changed, 143 insertions, 34 deletions
diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml index 2c91b75e45..dcfbf76b51 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 88075f8a4e..5aafdb44a1 100644 --- a/var/spack/repos/builtin/packages/gdal/package.py +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -297,8 +297,8 @@ class Gdal(AutotoolsPackage): 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 0000000000..221d8c77c6 --- /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 67c2744470..d3076b35f9 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 a4fa9ac3a6..e328c40ea1 100644 --- a/var/spack/repos/builtin/packages/libc/package.py +++ b/var/spack/repos/builtin/packages/libc/package.py @@ -7,13 +7,16 @@ from spack import * 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 e6ce06e0ea..f83c7499a0 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 153a1057b1..6043e1122d 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 @@ class NetcdfC(AutotoolsPackage): 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 @@ class NetcdfC(AutotoolsPackage): 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. |