xios: I/O management for climate models (#6796)
* xios: XML-IO-SERVER library for IO management of climate models * xios: install to prefix directory * xios: add a test case * xios: define versions to use cache and mirror directories * xios: use proper svn URL for version 910 * xios: package url must be defined, otherwise uninstall fails * xios: add trunk version to allow building latest revision * xios: enable parallel build * xios: allow installation with mpif90 compiler wrappers * xios: use mpi variants of dependencies * xios: allow user to specify MPI launcher via MPIRUN environment variable * xios: prefer spack versions of blitz and boost (needed for gcc@7) * xios: enable builds with clang+gfortran on OSX * xios: use numeric versions for releases, @develop for trunk * xios: different patches required for @1.0 and @develop * xios: patch function for clang works across revisions * xios: link blitz library * xios: workaround bug 17782 in llvm * xios: whitespace adjustments for flake8 * xios: avoid bare except clause * xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
This commit is contained in:
Milton Woods
Adam J. Stewart
parent
75f1a91821
commit
70d589a14e
27
var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch
Normal file
27
var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch
Normal file
@ -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
|
||||
27
var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch
Normal file
27
var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch
Normal file
@ -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
|
||||
11
var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch
Normal file
11
var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch
Normal file
@ -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;
|
||||
224
var/spack/repos/builtin/packages/xios/package.py
Normal file
224
var/spack/repos/builtin/packages/xios/package.py
Normal file
@ -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.')
|
||||
Loading…
Reference in New Issue
Block a user