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-rw-r--r--var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch27
-rw-r--r--var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch27
-rw-r--r--var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch11
-rw-r--r--var/spack/repos/builtin/packages/xios/package.py224
4 files changed, 289 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch b/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch
new file mode 100644
index 0000000000..cf2aeaaa4e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch
@@ -0,0 +1,27 @@
+--- a/bld.cfg 2017-12-23 11:41:14.000000000 +1100
++++ b/bld.cfg 2017-12-23 15:34:53.914024629 +1100
+@@ -24,9 +24,6 @@
+
+ search_src true
+ src::zzz .
+-src::date $PWD/extern/boost/src/date_time
+-src::blitz $PWD/extern/blitz/src
+-src::netcdf $PWD/extern/netcdf4
+ bld::lib xios
+ bld::target libxios.a
+ #bld::target generate_fortran_interface.exe
+@@ -37,11 +34,11 @@
+ bld::tool::fc %FCOMPILER
+ bld::tool::fpp %FPP
+ bld::tool::cpp %CPP
+-bld::tool::cppflags %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include
+-bld::tool::fppflags %BASE_INC -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include
++bld::tool::cppflags %CBASE_INC -I${PWD}/extern/rapidxml/include
++bld::tool::fppflags %BASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::ld %LINKER
+ bld::tool::ldflags %LD_FLAGS
+-bld::tool::cflags %CFLAGS %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include
++bld::tool::cflags %CFLAGS %CBASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::fflags %FFLAGS %FBASE_INC
+ bld::tool::cppkeys %CPP_KEY
+ bld::tool::fppkeys %CPP_KEY
diff --git a/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch b/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch
new file mode 100644
index 0000000000..fe52da1192
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch
@@ -0,0 +1,27 @@
+--- a/bld.cfg 2017-12-23 15:21:01.458603785 +1100
++++ b/bld.cfg 2017-12-23 15:36:36.667684136 +1100
+@@ -24,9 +24,6 @@
+
+ search_src true
+ src::zzz .
+-src::date $PWD/extern/boost/src/date_time
+-src::blitz $PWD/extern/blitz/src
+-src::netcdf $PWD/extern/netcdf4
+ src::remap $PWD/extern/remap/src
+ bld::lib xios
+ bld::target libxios.a
+@@ -46,11 +43,11 @@
+ bld::tool::fc %FCOMPILER
+ bld::tool::fpp %FPP
+ bld::tool::cpp %CPP
+-bld::tool::cppflags %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include
+-bld::tool::fppflags %BASE_INC -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include
++bld::tool::cppflags %CBASE_INC -I${PWD}/extern/rapidxml/include
++bld::tool::fppflags %BASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::ld %LINKER
+ bld::tool::ldflags %LD_FLAGS
+-bld::tool::cflags %CFLAGS %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include
++bld::tool::cflags %CFLAGS %CBASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::fflags %FFLAGS %FBASE_INC
+ bld::tool::cppkeys %CPP_KEY
+ bld::tool::fppkeys %CPP_KEY
diff --git a/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch b/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch
new file mode 100644
index 0000000000..9eb5c21950
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch
@@ -0,0 +1,11 @@
+--- a/src/duration.cpp 2017-12-28 10:45:09.000000000 +1100
++++ b/src/duration.cpp 2017-12-28 11:01:40.000000000 +1100
+@@ -43,7 +43,7 @@
+ StdIStream& operator>>(StdIStream& in , CDuration& duration)
+ {
+ duration = NoneDu;
+- double v = 1.0;
++ int v = 1;
+ char c = '/';
+ bool invalidUnit = false;
+ CDuration sentinel = NoneDu;
diff --git a/var/spack/repos/builtin/packages/xios/package.py b/var/spack/repos/builtin/packages/xios/package.py
new file mode 100644
index 0000000000..a3df5e9ca8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/package.py
@@ -0,0 +1,224 @@
+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+#
+from spack import *
+import os
+
+
+class Xios(Package):
+ """XML-IO-SERVER library for IO management of climate models."""
+
+ homepage = "https://forge.ipsl.jussieu.fr/ioserver/wiki"
+ url = "https://forge.ipsl.jussieu.fr/ioserver"
+
+ version('1.0', revision=910,
+ svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0')
+ version('develop', svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk')
+
+ variant('mode', values=('debug', 'dev', 'prod'), default='dev',
+ description='Build for debugging, development or production')
+ # NOTE: oasis coupler could be supported with a variant
+
+ # Use spack versions of blitz and netcdf for compatibility
+ # with recent compilers and optimised platform libraries:
+ patch('bld_extern_1.0.patch', when='@:1.0')
+ patch('bld_extern_1.x.patch', when='@1.1:')
+
+ # Workaround bug #17782 in llvm, where reading a double
+ # followed by a character is broken (e.g. duration '1d'):
+ patch('llvm_bug_17782.patch', when='@1.1: %clang')
+
+ depends_on('netcdf+mpi')
+ depends_on('netcdf-fortran')
+ depends_on('hdf5+mpi')
+ depends_on('mpi')
+ depends_on('boost')
+ depends_on('blitz')
+ depends_on('perl', type='build')
+ depends_on('perl-uri-escape', type='build')
+ depends_on('gmake', type='build')
+
+ @when('%clang')
+ def patch(self):
+ """Fix type references that are ambiguous for clang."""
+ for dirpath, dirnames, filenames in os.walk('src'):
+ for filename in filenames:
+ filepath = os.path.join(dirpath, filename)
+ # Use boost definition of type shared_ptr:
+ filter_file(r'([^:/])shared_ptr<',
+ r'\1boost::shared_ptr<', filepath)
+ # Use type long for position in output stream:
+ filter_file(r'oss.tellp\(\) *- *startPos',
+ r'(long)oss.tellp() - startPos', filepath)
+
+ def xios_env(self):
+ file = join_path('arch', 'arch-SPACK.env')
+ touch(file)
+
+ def xios_path(self):
+ file = join_path('arch', 'arch-SPACK.path')
+ spec = self.spec
+ paths = {'NETCDF_INC_DIR': spec['netcdf'].prefix.include,
+ 'NETCDF_LIB_DIR': spec['netcdf'].prefix.lib,
+ 'HDF5_INC_DIR': spec['hdf5'].prefix.include,
+ 'HDF5_LIB_DIR': spec['hdf5'].prefix.lib}
+ text = r"""
+NETCDF_INCDIR="-I {NETCDF_INC_DIR}"
+NETCDF_LIBDIR="-L {NETCDF_LIB_DIR}"
+NETCDF_LIB="-lnetcdff -lnetcdf"
+
+MPI_INCDIR=""
+MPI_LIBDIR=""
+MPI_LIB=""
+
+HDF5_INCDIR="-I {HDF5_INC_DIR}"
+HDF5_LIBDIR="-L {HDF5_LIB_DIR}"
+HDF5_LIB="-lhdf5_hl -lhdf5"
+
+OASIS_INCDIR=""
+OASIS_LIBDIR=""
+OASIS_LIB=""
+"""
+ with open(file, 'w') as f:
+ f.write(text.format(**paths))
+
+ def xios_fcm(self):
+ file = join_path('arch', 'arch-SPACK.fcm')
+ spec = self.spec
+ param = dict()
+ param['MPICXX'] = spec['mpi'].mpicxx
+ param['MPIFC'] = spec['mpi'].mpifc
+ param['CC'] = self.compiler.cc
+ param['FC'] = self.compiler.fc
+ param['BOOST_INC_DIR'] = spec['boost'].prefix.include
+ param['BOOST_LIB_DIR'] = spec['boost'].prefix.lib
+ param['BLITZ_INC_DIR'] = spec['blitz'].prefix.include
+ param['BLITZ_LIB_DIR'] = spec['blitz'].prefix.lib
+ if spec.satisfies('%clang platform=darwin'):
+ param['LIBCXX'] = '-lc++'
+ else:
+ param['LIBCXX'] = '-lstdc++'
+
+ if any(map(spec.satisfies, ('%gcc', '%intel', '%clang'))):
+ text = r"""
+%CCOMPILER {MPICXX}
+%FCOMPILER {MPIFC}
+%LINKER {MPIFC}
+
+%BASE_CFLAGS -ansi -w -D_GLIBCXX_USE_CXX11_ABI=0 \
+ -I{BOOST_INC_DIR} -I{BLITZ_INC_DIR}
+%PROD_CFLAGS -O3 -DBOOST_DISABLE_ASSERTS
+%DEV_CFLAGS -g -O2
+%DEBUG_CFLAGS -g
+
+%BASE_FFLAGS -D__NONE__
+%PROD_FFLAGS -O3
+%DEV_FFLAGS -g -O2
+%DEBUG_FFLAGS -g
+
+%BASE_INC -D__NONE__
+%BASE_LD -L{BOOST_LIB_DIR} -L{BLITZ_LIB_DIR} -lblitz {LIBCXX}
+
+%CPP {CC} -E
+%FPP {CC} -E -P -x c
+%MAKE gmake
+""".format(**param)
+ elif spec.satisfies('%cce'):
+ # In the CC compiler prior to cce/8.3.7,
+ # optimisation must be reduced to avoid a bug,
+ # as reported by Mike Rezny at the UK Met Office:
+ if spec.satisfies('%cce@8.3.7:'):
+ param.update({'CC_OPT_DEV': '-O2', 'CC_OPT_PROD': '-O3'})
+ else:
+ param.update({'CC_OPT_DEV': '-O1', 'CC_OPT_PROD': '-O1'})
+
+ text = r"""
+%CCOMPILER {MPICXX}
+%FCOMPILER {MPIFC}
+%LINKER {MPIFC}
+
+%BASE_CFLAGS -DMPICH_SKIP_MPICXX -h msglevel_4 -h zero -h gnu \
+ -I{BOOST_INC_DIR} -I{BLITZ_INC_DIR}
+%PROD_CFLAGS {CC_OPT_PROD} -DBOOST_DISABLE_ASSERTS
+%DEV_CFLAGS {CC_OPT_DEV}
+%DEBUG_CFLAGS -g
+
+%BASE_FFLAGS -em -m 4 -e0 -eZ
+%PROD_FFLAGS -O3
+%DEV_FFLAGS -G2
+%DEBUG_FFLAGS -g
+
+%BASE_INC -D__NONE__
+%BASE_LD -D__NONE__ -L{BOOST_LIB_DIR} -L{BLITZ_LIB_DIR} -lblitz
+
+%CPP cpp
+%FPP cpp -P -CC
+%MAKE gmake
+""".format(**param)
+ else:
+ raise InstallError('Unsupported compiler.')
+
+ with open(file, 'w') as f:
+ f.write(text)
+
+ def install(self, spec, prefix):
+ env['CC'] = spec['mpi'].mpicc
+ env['CXX'] = spec['mpi'].mpicxx
+ env['F77'] = spec['mpi'].mpif77
+ env['FC'] = spec['mpi'].mpifc
+
+ options = ['--full',
+ '--%s' % spec.variants['mode'].value,
+ '--arch', 'SPACK',
+ '--netcdf_lib', 'netcdf4_par',
+ '--job', str(make_jobs)]
+
+ self.xios_env()
+ self.xios_path()
+ self.xios_fcm()
+
+ make_xios = Executable('./make_xios')
+ make_xios(*options)
+
+ mkdirp(spec.prefix)
+ install_tree('bin', spec.prefix.bin)
+ install_tree('lib', spec.prefix.lib)
+ install_tree('inc', spec.prefix.include)
+ install_tree('etc', spec.prefix.etc)
+ install_tree('cfg', spec.prefix.cfg)
+
+ @run_after('install')
+ @on_package_attributes(run_tests=True)
+ def check_build(self):
+ mpirun = os.getenv('MPIRUN')
+ if mpirun is None:
+ mpirun = 'mpiexec'
+ mpiexec = Executable(mpirun)
+ with working_dir('inputs'):
+ try:
+ mpiexec('-n', '2', join_path('..', 'bin', 'test_client.exe'))
+ except Exception:
+ raise InstallError(
+ 'Test failed; defining MPIRUN variable may help.')
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-11-05 16:20:28 +0000