serialbox: add new package (#28872)

5 files changed, 273 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/serialbox/nag/examples.patch b/var/spack/repos/builtin/packages/serialbox/nag/examples.patch
new file mode 100644
index 0000000000..91857d0d6c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/serialbox/nag/examples.patch
@@ -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
diff --git a/var/spack/repos/builtin/packages/serialbox/nag/ftg.patch b/var/spack/repos/builtin/packages/serialbox/nag/ftg.patch
new file mode 100644
index 0000000000..6794227a91
--- /dev/null
+++ b/var/spack/repos/builtin/packages/serialbox/nag/ftg.patch
@@ -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
+ 
diff --git a/var/spack/repos/builtin/packages/serialbox/nag/interface.patch b/var/spack/repos/builtin/packages/serialbox/nag/interface.patch
new file mode 100644
index 0000000000..abb79bf396
--- /dev/null
+++ b/var/spack/repos/builtin/packages/serialbox/nag/interface.patch
@@ -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
diff --git a/var/spack/repos/builtin/packages/serialbox/package.py b/var/spack/repos/builtin/packages/serialbox/package.py
new file mode 100644
index 0000000000..49f57249d3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/serialbox/package.py
@@ -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
diff --git a/var/spack/repos/builtin/packages/serialbox/ppser_py3.patch b/var/spack/repos/builtin/packages/serialbox/ppser_py3.patch
new file mode 100644
index 0000000000..1a15de7274
--- /dev/null
+++ b/var/spack/repos/builtin/packages/serialbox/ppser_py3.patch
@@ -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))