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serialbox: add new package (#28872)

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Sergey Kosukhin 2022-02-11 09:23:47 +01:00 committed by GitHub
parent cba918c081
commit c80c92aa39
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5 changed files with 273 additions and 0 deletions
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27
var/spack/repos/builtin/packages/serialbox/nag/examples.patch Normal file
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@ -0,0 +1,27 @@
# This patch is applicable starting version 2.3.1
--- a/examples/fortran/simple/m_ser.F90
+++ b/examples/fortran/simple/m_ser.F90
@@ -38 +38 @@ USE utils_ppser, ONLY: &
- REAL(KIND=8), DIMENSION(:,:,:) :: a
+ REAL(KIND=SELECTED_REAL_KIND(15)), DIMENSION(:,:,:) :: a
@@ -59 +59 @@ USE utils_ppser, ONLY: &
- REAL(KIND=8), DIMENSION(:,:,:) :: a
+ REAL(KIND=SELECTED_REAL_KIND(15)), DIMENSION(:,:,:) :: a
@@ -91,2 +91,2 @@ USE utils_ppser, ONLY: &
- REAL(KIND=8), DIMENSION(:,:,:) :: a
- REAL(KIND=8) :: rprecision
+ REAL(KIND=SELECTED_REAL_KIND(15)), DIMENSION(:,:,:) :: a
+ REAL(KIND=SELECTED_REAL_KIND(15)) :: rprecision
@@ -97 +97 @@ USE utils_ppser, ONLY: &
- prefix_ref='SerialboxTest',rprecision=rprecision,rperturb=1.0e-5_8)
+ prefix_ref='SerialboxTest',rprecision=rprecision,rperturb=REAL(1.0e-5,SELECTED_REAL_KIND(15)))
--- a/examples/fortran/simple/main_consumer.F90
+++ b/examples/fortran/simple/main_consumer.F90
@@ -14 +14 @@ PROGRAM main_consumer
- REAL(KIND=8), DIMENSION(5,5,5) :: a
+ REAL(KIND=SELECTED_REAL_KIND(15)), DIMENSION(5,5,5) :: a
--- a/examples/fortran/simple/main_producer.F90
+++ b/examples/fortran/simple/main_producer.F90
@@ -14 +14 @@ PROGRAM main_producer
- REAL(KIND=8), DIMENSION(5,5,5) :: a
+ REAL(KIND=SELECTED_REAL_KIND(15)), DIMENSION(5,5,5) :: a

31
var/spack/repos/builtin/packages/serialbox/nag/ftg.patch Normal file
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@ -0,0 +1,31 @@
# This patch is applicable starting version 2.3.1
--- a/src/serialbox-fortran/m_ser_ftg.f90
+++ b/src/serialbox-fortran/m_ser_ftg.f90
@@ -822,5 +822,5 @@ SUBROUTINE ftg_write_logical_1d(fieldname, field, lbounds, ubounds)
CALL ftg_register_only_internal(fieldname, 'bool', fs_boolsize(), lbounds, ubounds)
END IF
- CALL ftg_add_field_metainfo(TRIM(fieldname), 'ftg:loc', TRIM(ADJUSTL(ftg_loc_hex(C_LOC(field)))))
+ CALL ftg_add_field_metainfo(TRIM(fieldname), 'ftg:loc', 'N/A')
END IF
@@ -853,5 +853,5 @@ SUBROUTINE ftg_write_logical_2d(fieldname, field, lbounds, ubounds)
CALL ftg_register_only_internal(fieldname, 'bool', fs_boolsize(), lbounds, ubounds)
END IF
- CALL ftg_add_field_metainfo(TRIM(fieldname), 'ftg:loc', TRIM(ADJUSTL(ftg_loc_hex(C_LOC(field)))))
+ CALL ftg_add_field_metainfo(TRIM(fieldname), 'ftg:loc', 'N/A')
END IF
@@ -886,5 +886,5 @@ SUBROUTINE ftg_write_logical_3d(fieldname, field, lbounds, ubounds)
CALL ftg_register_only_internal(fieldname, 'bool', fs_boolsize(), lbounds, ubounds)
END IF
- CALL ftg_add_field_metainfo(TRIM(fieldname), 'ftg:loc', TRIM(ADJUSTL(ftg_loc_hex(C_LOC(field)))))
+ CALL ftg_add_field_metainfo(TRIM(fieldname), 'ftg:loc', 'N/A')
END IF
@@ -919,5 +919,5 @@ SUBROUTINE ftg_write_logical_4d(fieldname, field, lbounds, ubounds)
CALL ftg_register_only_internal(fieldname, 'bool', fs_boolsize(), lbounds, ubounds)
END IF
- CALL ftg_add_field_metainfo(TRIM(fieldname), 'ftg:loc', TRIM(ADJUSTL(ftg_loc_hex(C_LOC(field)))))
+ CALL ftg_add_field_metainfo(TRIM(fieldname), 'ftg:loc', 'N/A')
END IF

9
var/spack/repos/builtin/packages/serialbox/nag/interface.patch Normal file
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@ -0,0 +1,9 @@
# This patch is applicable starting version 2.0.1
--- a/src/serialbox-fortran/utils_ppser.f90
+++ b/src/serialbox-fortran/utils_ppser.f90
@@ -33 +33 @@ MODULE utils_ppser
-USE iso_fortran_env
+USE f90_unix_proc; USE iso_fortran_env
@@ -66 +66 @@ SUBROUTINE ppser_initialize(directory, prefix, mode, prefix_ref, mpi_rank, rprec
- REAL(KIND=8), OPTIONAL, INTENT(IN) :: rprecision, rperturb
+ REAL(KIND=SELECTED_REAL_KIND(15)), OPTIONAL, INTENT(IN) :: rprecision, rperturb

183
var/spack/repos/builtin/packages/serialbox/package.py Normal file
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@ -0,0 +1,183 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
class Serialbox(CMakePackage):
"""Serialbox is a serialization library and tools for C/C++, Python3 and
Fortran. Serialbox is used in several projects for building validation
frameworks against reference runs."""
homepage = "https://github.com/GridTools/serialbox"
url = "https://github.com/GridTools/serialbox/archive/v2.6.1.tar.gz"
maintainers = ['skosukhin']
version('2.6.1', sha256='b795ce576e8c4fd137e48e502b07b136079c595c82c660cfa2e284b0ef873342')
version('2.6.0', sha256='9199f8637afbd7f2b3c5ba932d1c63e9e14d553a0cafe6c29107df0e04ee9fae')
version('2.5.4', sha256='f4aee8ef284f58e6847968fe4620e222ac7019d805bbbb26c199e4b6a5094fee')
version('2.5.3', sha256='696499b3f43978238c3bcc8f9de50bce2630c07971c47c9e03af0324652b2d5d')
variant('c', default=True, description='enable C interface')
variant('python', default=False, description='enable Python interface')
variant('fortran', default=False, description='enable Fortran interface')
variant('ftg', default=False,
description='enable FortranTestGenerator frontend')
variant('sdb', default=False, description='enable stencil debugger')
variant('shared', default=True, description='build shared libraries')
variant('examples', default=False, description='build the examples')
variant('logging', default=True,
description='enable the logging infrastructure')
variant('async-api', default=True,
description='enable the asynchronous API')
variant('netcdf', default=False,
description='build the NetCDF archive backend')
variant('std-filesystem', default=True,
description='use std::experimental::filesystem (no dependency on '
'compiled boost libs)')
depends_on('cmake@3.12:', type='build')
# We might be provided with an external vanilla cmake, and we need one with
# with https://gitlab.kitware.com/cmake/cmake/-/merge_requests/5025
depends_on('cmake@3.19:', when='%pgi', type='build')
depends_on('boost@1.54:', type='build')
depends_on('boost+filesystem+system',
when='~std-filesystem', type=('build', 'link'))
depends_on('netcdf-c', when='+netcdf')
depends_on('python@3.4:', when='+python', type=('build', 'run'))
depends_on('py-numpy', when='+python', type=('build', 'run'))
# pp_ser fails to process source files containing Unicode character with
# Python 3 (https://github.com/GridTools/serialbox/pull/249):
patch('ppser_py3.patch', when='@2.2.1:')
# NAG patches:
patch('nag/interface.patch', when='@2.0.1:%nag+fortran')
patch('nag/examples.patch', when='@2.3.1:%nag+fortran+examples')
patch('nag/ftg.patch', when='@2.3.1:%nag+ftg')
conflicts('+ftg', when='~fortran',
msg='the FortranTestGenerator frontend requires the Fortran '
'interface')
conflicts('+ftg', when='@:2.2.999',
msg='the FortranTestGenerator frontend is supported only '
'starting version 2.3.0')
conflicts('+sdb', when='~python',
msg='the stencil debugger requires the Python interface')
conflicts('+fortran', when='~c',
msg='the Fortran interface requires the C interface')
conflicts('+python', when='~c',
msg='the Python interface requires the C interface')
conflicts('+python', when='~shared',
msg='the Python interface requires the shared libraries')
def patch(self):
# The following is implemented as a method to avoid having two sets of
# almost identical patch files: one with the CR symbols (for versions
# 2.5.x) and one without them (for versions 2.6.x).
# Remove hard-coded -march=native
# (see https://github.com/GridTools/serialbox/pull/233):
if self.spec.satisfies('@2.0.1:2.6.0'):
filter_file(
r'^(\s*set\(CMAKE_CXX_FLAGS.*-march=native)',
r'#\1', 'CMakeLists.txt')
# Do not fallback to boost::filesystem:
if '+std-filesystem' in self.spec:
filter_file(
r'(message\()'
r'STATUS( "std::experimental::filesystem not found).*("\))',
r'\1FATAL_ERROR\2\3', 'CMakeLists.txt')
@property
def libs(self):
query_parameters = self.spec.last_query.extra_parameters
shared = '+shared' in self.spec
query2libraries = {
tuple(): ['libSerialboxCore'],
('c', 'fortran'): [
'libSerialboxFortran',
'libSerialboxC',
'libSerialboxCore',
],
('c',): [
'libSerialboxC',
'libSerialboxCore',
],
('fortran',): [
'libSerialboxFortran',
'libSerialboxC',
'libSerialboxCore'
]
}
key = tuple(sorted(query_parameters))
libraries = query2libraries[key]
if self.spec.satisfies('@2.5.0:2.5'):
libraries = [
'{0}{1}'.format(name, 'Shared' if shared else 'Static')
for name in libraries]
libs = find_libraries(
libraries, root=self.prefix, shared=shared, recursive=True)
if libs:
return libs
msg = 'Unable to recursively locate {0} libraries in {1}'
raise spack.error.NoLibrariesError(
msg.format(self.spec.name, self.spec.prefix))
def flag_handler(self, name, flags):
cmake_flags = []
if name == 'cxxflags':
# Intel (at least up to version 19.0.1, version 19.0.4 works) and
# PGI (at least up to version 19.9, version 20.1.0 works) compilers
# have problems with C++11 name mangling. An attempt to link to
# libSerialboxCore leads to:
# undefined reference to
# `std::experimental::filesystem::v1::__cxx11::path::
# _M_find_extension[abi:cxx11]() const'
if any(self.spec.satisfies('{0}+std-filesystem'.format(x))
for x in ['%intel@:19.0.1', '%pgi@:19.9']):
cmake_flags.append('-D_GLIBCXX_USE_CXX11_ABI=0')
return flags, None, (cmake_flags or None)
def cmake_args(self):
args = [
'-DBOOST_ROOT:PATH=%s' % self.spec['boost'].prefix,
# https://cmake.org/cmake/help/v3.15/module/FindBoost.html#boost-cmake
self.define('Boost_NO_BOOST_CMAKE', True),
self.define_from_variant('SERIALBOX_ENABLE_C', 'c'),
self.define_from_variant('SERIALBOX_ENABLE_PYTHON', 'python'),
self.define_from_variant('SERIALBOX_ENABLE_FORTRAN', 'fortran'),
self.define_from_variant('SERIALBOX_ENABLE_FTG', 'ftg'),
self.define_from_variant('SERIALBOX_ENABLE_SDB', 'sdb'),
self.define_from_variant('SERIALBOX_BUILD_SHARED', 'shared'),
self.define_from_variant('SERIALBOX_EXAMPLES', 'examples'),
self.define_from_variant('SERIALBOX_LOGGING', 'logging'),
self.define_from_variant('SERIALBOX_ASYNC_API', 'async-api'),
# CMake scripts of Serialbox (at least up to version 2.6.0) are
# broken and do not instruct the compiler to link to the OpenSSL
# libraries:
self.define('SERIALBOX_USE_OPENSSL', False),
self.define_from_variant('SERIALBOX_ENABLE_EXPERIMENTAL_FILESYSTEM',
'std-filesystem'),
self.define_from_variant('SERIALBOX_USE_NETCDF', 'netcdf'),
self.define('SERIALBOX_TESTING', self.run_tests),
]
if '+netcdf' in self.spec:
args.append('-DNETCDF_ROOT:PATH=%s' % self.spec['netcdf-c'].prefix)
return args

23
var/spack/repos/builtin/packages/serialbox/ppser_py3.patch Normal file
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@ -0,0 +1,23 @@
# This patch is applicable starting version 2.2.1
--- a/src/serialbox-python/pp_ser/pp_ser.py
+++ b/src/serialbox-python/pp_ser/pp_ser.py
@@ -51 +51 @@ __email__ = 'oliver.fuhrer@meteoswiss.ch'
-def to_ascii(text):
+def open23(name, mode='r'):
@@ -53 +53,9 @@ def to_ascii(text):
- return bytes(text, 'ascii')
+ return open(name, mode,
+ encoding=(None if 'b' in mode else 'UTF-8'))
+ else:
+ return open(name, mode)
+
+
+def bytes23(text):
+ if sys.version_info[0] == 3:
+ return bytes(text, 'UTF-8')
@@ -815 +823 @@ class PpSer:
- input_file = open(os.path.join(self.infile), 'r')
+ input_file = open23(os.path.join(self.infile), 'r')
@@ -860 +868 @@ class PpSer:
- output_file.write(to_ascii(self.__outputBuffer))
+ output_file.write(bytes23(self.__outputBuffer))