commit dc4d18a225627f81b9f0b36687964e51f9d23449
parent 408588259eaa2c257937a04dbb3c4f8f0108f07d
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Mon, 30 Oct 2023 15:09:53 +0100
Merge branch 'feature_posix_make' into develop
Diffstat:
20 files changed, 816 insertions(+), 779 deletions(-)
diff --git a/.gitignore b/.gitignore
@@ -1,13 +1,16 @@
.gitignore
-CMakeCache.txt
-CMakeFiles
-Makefile
-tmp
+*.nc
+*.htcp
[Bb]uild*
*.sw[po]
-*.[ao]
-*.orig
+*.[aod]
+*.so
*~
+test*
+!test*.[ch]
+.config
+.test
tags
-*.nc
-*.htcp
+*.pc
+src/les2htcp.h
+les2htcp
diff --git a/Makefile b/Makefile
@@ -0,0 +1,187 @@
+# Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+# Copyright (C) 2018 Centre National de la Recherche Scientifique
+# Copyright (C) 2018 Université Paul Sabatier
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+.POSIX:
+.SUFFIXES: # Clean up default inference rules
+
+include config.mk
+
+LIBNAME_STATIC = libhtcp.a
+LIBNAME_SHARED = libhtcp.so
+LIBNAME = $(LIBNAME_$(LIB_TYPE))
+
+################################################################################
+# Library/program building
+################################################################################
+SRC = src/htcp.c
+OBJ = $(SRC:.c=.o)
+DEP = $(SRC:.c=.d)
+
+default: build_library build_program
+
+build_library: .config $(DEP)
+ @$(MAKE) -fMakefile $$(for i in $(DEP); do echo -f $${i}; done) \
+ $$(if [ -n "$(LIBNAME)" ]; then \
+ echo "$(LIBNAME)"; \
+ else \
+ echo "$(LIBNAME_SHARED)"; \
+ fi)
+
+build_program: .config src/les2htcp.d build_library
+ @$(MAKE) -fMakefile -fsrc/les2htcp.d les2htcp
+
+$(DEP) $(OBJ): config.mk
+
+$(LIBNAME_SHARED): $(OBJ)
+ $(CC) $(CFLAGS_SO) $(RSYS_CFLAGS) -o $@ $(OBJ) $(LDFLAGS_SO) $(RSYS_LIBS)
+
+$(LIBNAME_STATIC): libhtcp.o
+ $(AR) -rc $@ $?
+ $(RANLIB) $@
+
+libhtcp.o: $(OBJ)
+ $(LD) -r $(OBJ) -o $@
+ $(OBJCOPY) $(OCPFLAGS) $@
+
+src/les2htcp.d src/les2htcp.o: config.mk
+
+src/les2htcp.c: src/les2htcp.h
+src/les2htcp.h: src/les2htcp.h.in
+ sed -e 's#@VERSION_MAJOR@#$(VERSION_MAJOR)#g' \
+ -e 's#@VERSION_MINOR@#$(VERSION_MINOR)#g' \
+ -e 's#@VERSION_PATCH@#$(VERSION_PATCH)#g' \
+ src/les2htcp.h.in > $@
+
+les2htcp: src/les2htcp.o
+ $(CC) $(CFLAGS_EXE) $(RSYS_CFLAGS) $(NETCDF_CFLAGS) \
+ -o $@ src/les2htcp.o $(LDFLAGS_EXE) $(RSYS_LIBS) $(NETCDF_LIBS) -lm
+
+.config: config.mk
+ @if ! $(PKG_CONFIG) --atleast-version $(RSYS_VERSION) rsys; then \
+ echo "rsys $(RSYS_VERSION) not found" >&2; exit 1; fi
+ @if ! $(PKG_CONFIG) --atleast-version $(NETCDF_VERSION) netcdf; then \
+ echo "netcdf $(NETCDF_VERSION) not found" >&2; exit 1; fi
+ @echo "config done" > $@
+
+.SUFFIXES: .c .d .o
+.c.d:
+ @$(CC) $(CFLAGS_SO) $(RSYS_CFLAGS) -MM -MT "$(@:.d=.o) $@" $< -MF $@
+
+.c.o:
+ $(CC) $(CFLAGS_SO) $(RSYS_CFLAGS) -DHTCP_SHARED_BUILD -c $< -o $@
+
+src/les2htcp.d: src/les2htcp.c
+ @$(CC) $(CFLAGS_EXE) $(RSYS_CFLAGS) $(NETCDF_CFLAGS) -MM -MT "$(@:.d=.o) $@" \
+ src/les2htcp.c -MF $@
+
+src/les2htcp.o: src/les2htcp.c
+ $(CC) $(CFLAGS_EXE) $(RSYS_CFLAGS) $(NETCDF_CFLAGS) -c src/les2htcp.c -o $@
+
+################################################################################
+# Installation
+################################################################################
+pkg:
+ sed -e 's#@PREFIX@#$(PREFIX)#g'\
+ -e 's#@VERSION@#$(VERSION)#g'\
+ -e 's#@RSYS_VERSION@#$(RSYS_VERSION)#g'\
+ htcp.pc.in > htcp.pc
+
+htcp-local.pc: htcp.pc.in
+ sed -e '1d'\
+ -e 's#^includedir=.*#includedir=./src/#'\
+ -e 's#^libdir=.*#libdir=./#'\
+ -e 's#@VERSION@#$(VERSION)#g'\
+ -e 's#@RSYS_VERSION@#$(RSYS_VERSION)#g'\
+ htcp.pc.in > $@
+
+install: build_library build_program pkg
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/bin" les2htcp
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/lib" $(LIBNAME)
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/lib/pkgconfig" htcp.pc
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/include/high_tune" src/htcp.h
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/share/doc/htcp" COPYING README.md
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/share/man/man1" les2htcp.1
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/share/man/man5" htcp.5
+
+uninstall:
+ rm -f "$(DESTDIR)$(PREFIX)/bin/les2htcp"
+ rm -f "$(DESTDIR)$(PREFIX)/lib/$(LIBNAME)"
+ rm -f "$(DESTDIR)$(PREFIX)/lib/pkgconfig/htcp.pc"
+ rm -f "$(DESTDIR)$(PREFIX)/share/doc/htcp/COPYING"
+ rm -f "$(DESTDIR)$(PREFIX)/share/doc/htcp/README.md"
+ rm -f "$(DESTDIR)$(PREFIX)/include/high_tune/htcp.h"
+ rm -f "$(DESTDIR)$(PREFIX)/share/man/man1/les2htcp.1"
+ rm -f "$(DESTDIR)$(PREFIX)/share/man/man5/htcp.5"
+
+################################################################################
+# Miscellaneous targets
+################################################################################
+all: build_library build_program build_tests
+
+clean: clean_test
+ rm -f $(OBJ) src/les2htcp.o $(TEST_OBJ) $(LIBNAME) les2htcp
+ rm -f .config .test libhtcp.o htcp.pc htcp-local.pc
+
+distclean: clean
+ rm -f $(DEP) src/les2htcp.d src/les2htcp.h $(TEST_DEP)
+
+lint:
+ shellcheck -o all make.sh
+ shellcheck -o all src/dump_netcdf_data.sh
+ shellcheck -o all src/dump_netcdf_desc.sh
+ shellcheck -o all src/test_htcp_load_from_file.sh
+ mandoc -Tlint -Wall les2htcp.1 || [ $$? -le 1 ]
+ mandoc -Tlint -Wall htcp.5 || [ $$? -le 1 ]
+
+################################################################################
+# Tests
+################################################################################
+TEST_SRC =\
+ src/test_htcp.c\
+ src/test_htcp_load.c\
+ src/test_htcp_load_from_file.c
+TEST_OBJ = $(TEST_SRC:.c=.o)
+TEST_DEP = $(TEST_SRC:.c=.d)
+
+PKG_CONFIG_LOCAL = PKG_CONFIG_PATH="./:$${PKG_CONFIG_PATH}" $(PKG_CONFIG)
+HTCP_CFLAGS = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --cflags htcp-local.pc)
+HTCP_LIBS = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --libs htcp-local.pc)
+
+test: build_tests build_program
+ @$(SHELL) make.sh run_test src/test_htcp.c src/test_htcp_load.c
+
+build_tests: build_library $(TEST_DEP) .test
+ @$(MAKE) -fMakefile -f.test $$(for i in $(TEST_DEP); do echo -f"$${i}"; done) test_bin
+
+.test: Makefile make.sh
+ @$(SHELL) make.sh config_test $(TEST_SRC) > $@
+
+clean_test:
+ $(SHELL) make.sh clean_test $(TEST_SRC)
+
+$(TEST_DEP): config.mk htcp-local.pc
+ @$(CC) $(CFLAGS_EXE) $(HTCP_CFLAGS) $(RSYS_CFLAGS) \
+ -MM -MT "$(@:.d=.o) $@" $(@:.d=.c) -MF $@
+
+$(TEST_OBJ): config.mk htcp-local.pc
+ $(CC) $(CFLAGS_EXE) $(HTCP_CFLAGS) $(RSYS_CFLAGS) -c $(@:.o=.c) -o $@
+
+test_htcp \
+test_htcp_load \
+test_htcp_load_from_file \
+: config.mk htcp-local.pc $(LIBNAME)
+ $(CC) $(CFLAGS_EXE) -o $@ src/$@.o $(LDFLAGS_EXE) $(HTCP_LIBS) $(RSYS_LIBS) -lm
diff --git a/README.md b/README.md
@@ -1,32 +1,32 @@
# High-Tune: Cloud Properties
-This project describes the htcp binary fileformat that is used to store the
-some properties of a cloud. The provided `les2htcp` command line tool extracts
-these properties from a LES output stored in a
-[NetCDF](https://www.unidata.ucar.edu/software/netcdf/) file, and converts them
-in the `htcp` fileformat. Finally, a library is provided to load the `htcp`
-fileformat. Since the data to load can be huge, this library silently
-loads/unloads them dynamically allowing to process data that are too large to
-fit in the main memory.
-
-## How to build
-
-The `les2htcp` program and `htcp` library are compatible GNU/Linux 64-bits.
-They rely on the [CMake](http://www.cmake.org) and the
-[RCMake](https://gitlab.com/vaplv/rcmake/) packages to build. They also depend
-on the [RSys](https://gitlab.com/vaplv/rsys/) library. Furthermore, the
-`les2htcp` tool depends on the
-[NetCDF](https://www.unidata.ucar.edu/software/netcdf/) C library.
-Both eventually depend on [scdoc](https://sr.ht/~sircmpwn/scdoc/)
-which, if available, is used to generate the man pages.
-
-To build them, first ensure that CMake is installed on your system. Then
-install the RCMake package as well as the aforementioned prerequisites. Finally
-generate the project from the `cmake/CMakeLists.txt` file by appending to the
-`CMAKE_PREFIX_PATH` variable the install directories of its dependencies. The
-resulting project can be edited, built, tested and installed as any CMake
-project. Refer to the [CMake](https://cmake.org/documentation) for further
-informations on CMake.
+This project defines a file format for storing the properties of liquid water
+suspended in clouds. See `htcp.5` for the format specification. A C library is
+provided for loading files in this format.
+
+To facilitate interoperability, the `les2htcp` tool converts data to htcp
+format from a [netCDF](https://www.unidata.ucar.edu/software/netcdf/) file.
+While the netCDF format is widely adopted there is no standard or common
+practice for describing cloud properties, whether in terms of data layout,
+variable names or units. The htcp format was developed to circumvent this
+problem: it is a simple file format, independent of netCDF-based data
+formatting, leaving data conversion to third-party translation tools.
+`les2htcp` is one such tool. See `les2htcp.1` for a complete descritpion.
+
+## Requirements
+
+- C compiler
+- POSIX make
+- pkg-config
+- netCDF4
+- [RSys](https://gitlab.com/vaplv/rsys)
+- [mandoc](https://mandoc.bsd.lv)
+
+## Installation
+
+Edit config.mk as needed, then run:
+
+ make clean install
## Release notes
@@ -52,18 +52,18 @@ mixing ratio and the liquid water mixing ratio.
### Version 0.0.1
-- Fix warnings and compilation errors when using the NetCDF library in version
+- Fix warnings and compilation errors when using the netCDF library in version
4.4.0.
- Fix compilation errors on systems with GNU C library version less than 2.19.
-## Copyright notice
+## Copyright
-Copyright (C) 2018, 2020-2023 |Méso|Star> (<contact@meso-star.com>)
-Copyright (C) 2018 Centre National de la Recherche Scientifique
+Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+Copyright (C) 2018 Centre National de la Recherche Scientifique
Copyright (C) 2018 Université Paul Sabatier
## License
`htcp` and `les2htcp` are free software released under the GPL v3+ license: GNU
-GPL version 3 or later. You are welcome to redistribute it under certain
+GPL version 3 or later. You are welcome to redistribute them under certain
conditions; refer to the COPYING file for details.
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
@@ -1,131 +0,0 @@
-# Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
-# Copyright (C) 2018 Centre National de la Recherche Scientifique
-# Copyright (C) 2018 Université Paul Sabatier
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# 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
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-cmake_minimum_required(VERSION 3.1)
-project(htcp)
-enable_testing()
-
-option(NO_TEST "Do not build tests" OFF)
-
-set(HTCP_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../src)
-set(NETCDF_PATH ${PROJECT_SOURCE_DIR}/../ CACHE PATH
- "Path where the NetCDF test files are stored.")
-
-################################################################################
-# Prerequisites
-################################################################################
-find_package(RCMake 0.3 REQUIRED)
-find_package(RSys 0.6 REQUIRED)
-
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${RCMAKE_SOURCE_DIR})
-include(rcmake)
-include(rcmake_runtime)
-
-include_directories(${RSys_INCLUDE_DIR})
-
-if(CMAKE_COMPILER_IS_GNUCC)
- set(MATH_LIB m)
-endif()
-
-################################################################################
-# Test utilities
-################################################################################
-if(NOT NO_TEST)
- function(build_test _name)
- add_executable(${_name}
- ${HTCP_SOURCE_DIR}/${_name}.c)
- target_link_libraries(${_name} htcp ${ARGN})
- endfunction()
-
- function(new_test _name)
- build_test(${_name})
- add_test(${_name} ${_name})
- endfunction()
-endif()
-
-################################################################################
-# Sub projects
-################################################################################
-set(VERSION_MAJOR 0)
-set(VERSION_MINOR 0)
-set(VERSION_PATCH 5)
-set(VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})
-
-add_subdirectory(doc)
-add_subdirectory(htcp)
-add_subdirectory(les2htcp)
-
-################################################################################
-# Test both the les2htcp utility and the htcp library.
-################################################################################
-if(NOT NO_TEST)
- build_test(test_htcp_load_from_file ${MATH_LIB})
-
- set(TEST_FILES
- CEN2D.1.ARMCU.008.diaKCL
- CERK4.1.ARMCu.008
- DZVAR.1.ARMCU.008.diaKCL
- L25km.1.ARMCU.008.diaKCL
- L51km.1.ARMCu.008)
-
- set(VAR_LISTS RVT RCT PABST THT)
-
- set(_script_data ${HTCP_SOURCE_DIR}/dump_netcdf_data.sh)
- set(_script_desc ${HTCP_SOURCE_DIR}/dump_netcdf_desc.sh)
- foreach(_file IN LISTS TEST_FILES)
- set(_netcdf ${NETCDF_PATH}/${_file}.nc)
-
- if(EXISTS ${_netcdf})
- set(_output_base ${CMAKE_CURRENT_BINARY_DIR}/${_file})
-
- add_custom_command(
- OUTPUT ${_output_base}.htcp
- COMMAND les2htcp -m 1000 -i ${_netcdf} -fo ${_output_base}.htcp
- DEPENDS les2htcp
- COMMENT "${_file}.nc: convert to HTCP fileformat"
- VERBATIM)
- add_custom_target(les2htcp-${_file}.nc ALL DEPENDS ${_output_base}.htcp)
-
- add_custom_command(
- OUTPUT ${_output_base}_desc
- COMMAND sh ${_script_desc} ${_netcdf}
- DEPENDS ${_script_desc}
- COMMENT "${_file}.nc: dump descriptor"
- VERBATIM)
- add_custom_target(dump-desc-${_file}.nc ALL DEPENDS ${_output_base}_desc)
-
- set(_ref_files)
- set(_cmds)
- foreach(_var IN LISTS VAR_LISTS)
- set(_cmds ${_cmds} COMMAND sh ${_script_data} ${_var} ${_netcdf})
- set(_ref_files ${_ref_files} ${_output_base}_${_var})
- endforeach()
-
- add_custom_command(
- OUTPUT ${_ref_files}
- ${_cmds}
- DEPENDS ${_script_data}
- COMMENT "${_file}.nc: dump raw data"
- VERBATIM)
- add_custom_target(dump-data-${_file}.nc ALL DEPENDS ${_ref_files})
-
- add_test(test_htcp_load_from_file_${_file}
- test_htcp_load_from_file ${_output_base}.htcp ${CMAKE_CURRENT_BINARY_DIR})
- endif()
- endforeach()
-endif()
-
diff --git a/cmake/doc/CMakeLists.txt b/cmake/doc/CMakeLists.txt
@@ -1,60 +0,0 @@
-# Copyright (C) 2018, 2020-2022 |Méso|Star> (contact@meso-star.com)
-# Copyright (C) 2018 Centre National de la Recherche Scientifique
-# Copyright (C) 2018 Université Paul Sabatier
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# 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
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-set(HTCP_DOC_DIR ${PROJECT_SOURCE_DIR}/../doc)
-
-################################################################################
-# Look for the a2x program
-################################################################################
-find_program(SCDOC NAMES scdoc)
-if(NOT SCDOC)
- message(WARNING
- "The `scdoc' program is missing. "
- "The High-Tune Cloud Properties man pages cannot be generated.")
- return()
-endif()
-
-################################################################################
-# ROFF man pages
-################################################################################
-set(MAN_NAMES htcp.5 les2htcp.1)
-set(MAN5_FILES)
-set(MAN1_FILES)
-
-foreach(_man IN LISTS MAN_NAMES)
- set(_src ${HTCP_DOC_DIR}/${_man}.scd)
- add_custom_command(
- OUTPUT ${_man}
- COMMAND ${SCDOC} < ${_src} > ${_man}
- DEPENDS ${_src}
- COMMENT "Build ROFF man page ${_man}"
- VERBATIM)
- list(APPEND MAN_FILES ${_man})
-
- string(REGEX MATCH "^.*.5$" _man5 ${_man})
- string(REGEX MATCH "^.*.1$" _man1 ${_man})
- if(_man1)
- list(APPEND MAN1_FILES ${CMAKE_CURRENT_BINARY_DIR}/${_man1})
- elseif(_man5)
- list(APPEND MAN5_FILES ${CMAKE_CURRENT_BINARY_DIR}/${_man5})
- else()
- message(FATAL_ERROR "Unexpected man type")
- endif()
-endforeach()
-add_custom_target(man-roff ALL DEPENDS ${MAN_NAMES})
-install(FILES ${MAN1_FILES} DESTINATION share/man/man1)
-install(FILES ${MAN5_FILES} DESTINATION share/man/man5)
diff --git a/cmake/htcp/CMakeLists.txt b/cmake/htcp/CMakeLists.txt
@@ -1,62 +0,0 @@
-# Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
-# Copyright (C) 2018 Centre National de la Recherche Scientifique
-# Copyright (C) 2018 Université Paul Sabatier
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# 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
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-cmake_minimum_required(VERSION 3.1)
-project(htcp-library C)
-
-################################################################################
-# Configure and define targets
-################################################################################
-set(HTCP_FILES_SRC htcp.c)
-set(HTCP_FILES_INC )
-set(HTCP_FILES_INC_API htcp.h)
-set(HTCP_FILES_DOC COPYING)
-
-# Prepend each file in the `HTCP_FILES_<SRC|INC>' list by `HTCP_SOURCE_DIR'
-rcmake_prepend_path(HTCP_FILES_SRC ${HTCP_SOURCE_DIR})
-rcmake_prepend_path(HTCP_FILES_INC ${HTCP_SOURCE_DIR})
-rcmake_prepend_path(HTCP_FILES_INC_API ${HTCP_SOURCE_DIR})
-rcmake_prepend_path(HTCP_FILES_DOC ${PROJECT_SOURCE_DIR}/../../)
-
-add_library(htcp SHARED ${HTCP_FILES_SRC} ${HTCP_FILES_INC} ${HTCP_FILES_INC_API})
-target_link_libraries(htcp RSys)
-
-set_target_properties(htcp PROPERTIES
- DEFINE_SYMBOL HTCP_SHARED_BUILD
- VERSION ${VERSION}
- SOVERSION ${VERSION_MAJOR})
-
-rcmake_setup_devel(htcp HTCP ${VERSION} high_tune/htcp_version.h)
-
-################################################################################
-# Add tests
-################################################################################
-if(NOT NO_TEST)
- new_test(test_htcp)
- new_test(test_htcp_load)
-endif()
-
-################################################################################
-# Define output & install directories
-################################################################################
-install(TARGETS htcp
- ARCHIVE DESTINATION bin
- LIBRARY DESTINATION lib
- RUNTIME DESTINATION bin)
-install(FILES ${HTCP_FILES_INC_API} DESTINATION include/high_tune)
-install(FILES ${HTCP_FILES_DOC} DESTINATION share/doc/htcp)
-
diff --git a/cmake/les2htcp/CMakeLists.txt b/cmake/les2htcp/CMakeLists.txt
@@ -1,66 +0,0 @@
-# Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
-# Copyright (C) 2018 Centre National de la Recherche Scientifique
-# Copyright (C) 208 Université Paul Sabatier
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-cmake_minimum_required(VERSION 3.1)
-project(les2htcp C)
-
-# Required by netcdf.h header that some versions contains C99 comments
-set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=gnu89")
-
-################################################################################
-# Check dependencies
-################################################################################
-get_filename_component(_current_source_dir ${CMAKE_CURRENT_LIST_FILE} PATH)
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${_current_source_dir})
-
-find_package(NetCDF REQUIRED)
-
-include_directories(
- ${NETCDF_C_INCLUDE_DIRS}
- ${CMAKE_CURRENT_BINARY_DIR})
-
-################################################################################
-# Generate files
-################################################################################
-configure_file(${HTCP_SOURCE_DIR}/les2htcp.h.in
- ${CMAKE_CURRENT_BINARY_DIR}/les2htcp.h @ONLY)
-
-################################################################################
-# Configure and define targets
-################################################################################
-set(LES2HTCP_FILES_SRC les2htcp.c)
-set(LES2HTCP_FILES_INC les2htcp.h.in)
-set(LES2HTCP_FILES_DOC COPYING)
-
-# Prepend each file in the `HTNC_FILES_<SRC|INC>' list by `HTCP_SOURCE_DIR'
-rcmake_prepend_path(LES2HTCP_FILES_SRC ${HTCP_SOURCE_DIR})
-rcmake_prepend_path(LES2HTCP_FILES_INC ${HTCP_SOURCE_DIR})
-rcmake_prepend_path(LES2HTCP_FILES_DOC ${PROJECT_SOURCE_DIR}/../../)
-
-add_executable(les2htcp ${LES2HTCP_FILES_SRC})
-target_link_libraries(les2htcp RSys ${NETCDF_C_LIBRARIES} m)
-
-set_target_properties(les2htcp PROPERTIES
- VERSION ${VERSION}
- SOVERSION ${VERSION_MAJOR})
-
-################################################################################
-# Define output & install directories
-################################################################################
-install(TARGETS les2htcp RUNTIME DESTINATION bin)
-install(FILES ${LES2HTCP_FILES_DOC} DESTINATION share/doc/les2htcp)
-
diff --git a/cmake/les2htcp/FindNetCDF.cmake b/cmake/les2htcp/FindNetCDF.cmake
@@ -1,119 +0,0 @@
-# - Find NetCDF
-# Find the native NetCDF includes and library
-#
-# NETCDF_INCLUDE_DIR - user modifiable choice of where netcdf headers are
-# NETCDF_LIBRARY - user modifiable choice of where netcdf libraries are
-#
-# Your package can require certain interfaces to be FOUND by setting these
-#
-# NETCDF_CXX - require the C++ interface and link the C++ library
-# NETCDF_F77 - require the F77 interface and link the fortran library
-# NETCDF_F90 - require the F90 interface and link the fortran library
-#
-# Or equivalently by calling FindNetCDF with a COMPONENTS argument containing one or
-# more of "CXX;F77;F90".
-#
-# When interfaces are requested the user has access to interface specific hints:
-#
-# NETCDF_${LANG}_INCLUDE_DIR - where to search for interface header files
-# NETCDF_${LANG}_LIBRARY - where to search for interface libraries
-#
-# This module returns these variables for the rest of the project to use.
-#
-# NETCDF_FOUND - True if NetCDF found including required interfaces (see below)
-# NETCDF_LIBRARIES - All netcdf related libraries.
-# NETCDF_INCLUDE_DIRS - All directories to include.
-# NETCDF_HAS_INTERFACES - Whether requested interfaces were found or not.
-# NETCDF_${LANG}_INCLUDE_DIRS/NETCDF_${LANG}_LIBRARIES - C/C++/F70/F90 only interface
-#
-# Normal usage would be:
-# set (NETCDF_F90 "YES")
-# find_package (NetCDF REQUIRED)
-# target_link_libraries (uses_everthing ${NETCDF_LIBRARIES})
-# target_link_libraries (only_uses_f90 ${NETCDF_F90_LIBRARIES})
-
-#search starting from user editable cache var
-if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
- # Already in cache, be silent
- set (NETCDF_FIND_QUIETLY TRUE)
-endif ()
-
-set(USE_DEFAULT_PATHS "NO_DEFAULT_PATH")
-if(NETCDF_USE_DEFAULT_PATHS)
- set(USE_DEFAULT_PATHS "")
-endif()
-
-find_path (NETCDF_INCLUDE_DIR netcdf.h
- PATHS "${NETCDF_DIR}/include")
-mark_as_advanced (NETCDF_INCLUDE_DIR)
-set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
-
-find_library (NETCDF_LIBRARY NAMES netcdf
- PATHS "${NETCDF_DIR}/lib"
- HINTS "${NETCDF_INCLUDE_DIR}/../lib")
-mark_as_advanced (NETCDF_LIBRARY)
-
-set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})
-
-#start finding requested language components
-set (NetCDF_libs "")
-set (NetCDF_includes "${NETCDF_INCLUDE_DIR}")
-
-get_filename_component (NetCDF_lib_dirs "${NETCDF_LIBRARY}" PATH)
-set (NETCDF_HAS_INTERFACES "YES") # will be set to NO if we're missing any interfaces
-
-macro (NetCDF_check_interface lang header libs)
- if (NETCDF_${lang})
- #search starting from user modifiable cache var
- find_path (NETCDF_${lang}_INCLUDE_DIR NAMES ${header}
- HINTS "${NETCDF_INCLUDE_DIR}"
- HINTS "${NETCDF_${lang}_ROOT}/include"
- ${USE_DEFAULT_PATHS})
-
- find_library (NETCDF_${lang}_LIBRARY NAMES ${libs}
- HINTS "${NetCDF_lib_dirs}"
- HINTS "${NETCDF_${lang}_ROOT}/lib"
- ${USE_DEFAULT_PATHS})
-
- mark_as_advanced (NETCDF_${lang}_INCLUDE_DIR NETCDF_${lang}_LIBRARY)
-
- #export to internal varS that rest of project can use directly
- set (NETCDF_${lang}_LIBRARIES ${NETCDF_${lang}_LIBRARY})
- set (NETCDF_${lang}_INCLUDE_DIRS ${NETCDF_${lang}_INCLUDE_DIR})
-
- if (NETCDF_${lang}_INCLUDE_DIR AND NETCDF_${lang}_LIBRARY)
- list (APPEND NetCDF_libs ${NETCDF_${lang}_LIBRARY})
- list (APPEND NetCDF_includes ${NETCDF_${lang}_INCLUDE_DIR})
- else ()
- set (NETCDF_HAS_INTERFACES "NO")
- message (STATUS "Failed to find NetCDF interface for ${lang}")
- endif ()
- endif ()
-endmacro ()
-
-list (FIND NetCDF_FIND_COMPONENTS "CXX" _nextcomp)
-if (_nextcomp GREATER -1)
- set (NETCDF_CXX 1)
-endif ()
-list (FIND NetCDF_FIND_COMPONENTS "F77" _nextcomp)
-if (_nextcomp GREATER -1)
- set (NETCDF_F77 1)
-endif ()
-list (FIND NetCDF_FIND_COMPONENTS "F90" _nextcomp)
-if (_nextcomp GREATER -1)
- set (NETCDF_F90 1)
-endif ()
-NetCDF_check_interface (CXX netcdfcpp.h netcdf_c++)
-NetCDF_check_interface (F77 netcdf.inc netcdff)
-NetCDF_check_interface (F90 netcdf.mod netcdff)
-
-#export accumulated results to internal varS that rest of project can depend on
-list (APPEND NetCDF_libs "${NETCDF_C_LIBRARIES}")
-set (NETCDF_LIBRARIES ${NetCDF_libs})
-set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
-
-# handle the QUIETLY and REQUIRED arguments and set NETCDF_FOUND to TRUE if
-# all listed variables are TRUE
-include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args (NetCDF
- DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS NETCDF_HAS_INTERFACES)
diff --git a/config.mk b/config.mk
@@ -0,0 +1,85 @@
+VERSION_MAJOR = 0
+VERSION_MINOR = 0
+VERSION_PATCH = 5
+VERSION = $(VERSION_MAJOR).$(VERSION_MINOR).$(VERSION_PATCH)
+PREFIX = /usr/local
+
+LIB_TYPE = SHARED
+#LIB_TYPE = STATIC
+
+BUILD_TYPE = RELEASE
+#BUILD_TYPE = DEBUG
+
+################################################################################
+# Tools
+################################################################################
+AR = ar
+CC = cc
+LD = ld
+OBJCOPY = objcopy
+PKG_CONFIG = pkg-config
+RANLIB = ranlib
+
+################################################################################
+# Dependencies
+################################################################################
+PCFLAGS_SHARED =
+PCFLAGS_STATIC = --static
+PCFLAGS = $(PCFLAGS_$(LIB_TYPE))
+
+RSYS_VERSION = 0.14
+RSYS_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags rsys)
+RSYS_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs rsys)
+
+NETCDF_VERSION = 4
+NETCDF_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags netcdf)
+NETCDF_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs netcdf)
+
+################################################################################
+# Compilation options
+################################################################################
+WFLAGS =\
+ -Wall\
+ -Wcast-align\
+ -Wconversion\
+ -Wextra\
+ -Wmissing-declarations\
+ -Wmissing-prototypes\
+ -Wshadow
+
+# Increase the security and robustness of generated binaries
+CFLAGS_HARDENED =\
+ -D_FORTIFY_SOURCES=2\
+ -fcf-protection=full\
+ -fstack-clash-protection\
+ -fstack-protector-strong
+
+CFLAGS_COMMON =\
+ -std=c89\
+ -pedantic\
+ -fvisibility=hidden\
+ -fstrict-aliasing\
+ $(CFLAGS_HARDENED)\
+ $(WFLAGS)
+
+CFLAGS_DEBUG = -g $(CFLAGS_COMMON)
+CFLAGS_RELEASE = -O2 -DNDEBUG $(CFLAGS_COMMON)
+CFLAGS = $(CFLAGS_$(BUILD_TYPE))
+
+CFLAGS_SO = $(CFLAGS) -fPIC
+CFLAGS_EXE = $(CFLAGS) -fPIE
+
+################################################################################
+# Linker options
+################################################################################
+LDFLAGS_HARDENED = -Wl,-z,relro,-z,now
+LDFLAGS_DEBUG = $(LDFLAGS_HARDENED)
+LDFLAGS_RELEASE = -s $(LDFLAGS_HARDENED)
+LDFLAGS = $(LDFLAGS_$(BUILD_TYPE))
+
+LDFLAGS_SO = $(LDFLAGS) -shared -Wl,--no-undefined
+LDFLAGS_EXE = $(LDFLAGS) -pie
+
+OCPFLAGS_DEBUG = --localize-hidden
+OCPFLAGS_RELEASE = --localize-hidden --strip-unneeded
+OCPFLAGS = $(OCPFLAGS_$(BUILD_TYPE))
diff --git a/doc/htcp.5.scd b/doc/htcp.5.scd
@@ -1,98 +0,0 @@
-htcp(5)
-
-; Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
-; Copyright (C) 2018 Centre National de la Recherche Scientifique
-; Copyright (C) 2018 Université Paul Sabatier
-;
-; This program is free software: you can redistribute it and/or modify
-; it under the terms of the GNU General Public License as published by
-; the Free Software Foundation, either version 3 of the License, or
-; (at your option) any later version.
-;
-; 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
-; GNU General Public License for more details.
-;
-; You should have received a copy of the GNU General Public License
-; along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# NAME
-
-htcp - High-Tune: Cloud Properties file format
-
-# DESCRIPTION
-
-*htcp* is a binary file format that describes properties on liquid water
-content in suspension within clouds. The *les2htcp*(1) command can be used to
-generate a *htcp* file from cloud properties saved in a NetCDF file format.
-
-The cloud properties are actually spatio temporal double precision floating
-point data, structured in a 4D grid whose definition and spatial origin is
-given by the _<definition>_ and the _<lower-pos>_ fields. The size of a grid
-cell along the X and Y dimension is constant while the size along the Z axis
-can be irregular. Is such case, the _<is-Z-irregular>_ header flag is set to 1
-and the sizes of the cells in Z are explicitly listed in _<voxel-size>_. Note
-that in *htcp*, the spatial dimensions are defined in meters, i.e. values
-listed in _<lower-pos>_ and _<voxel-size>_ are meters.
-
-For a given property, the list of its spatio temporal data are linearly listed
-along the X, Y, Z and time dimension, in that order. The address where its
-first data is stored is aligned on the value defined by the file header field
-_<pagesize>_; several bytes of padding can be thus added priorly to a property
-in order to ensure that its first data is correctly aligned.
-
-Available cloud properties are:
-
-- _<RVT>_: water vapor mixing ratio in kg of water per m^3 of dry air.
-- _<RCT>_: liquid water in suspension mixing ratio in kg of water per m^3 of dry
- air.
-- _<PABST>_: pressure in Pascal.
-- _<T>_: temperature in Kelvin.
-
-# BINARY FILE FORMAT
-
-Data are encoded with respect to the little endian bytes ordering, i.e. least
-significant bytes are stored first.
-
-```
-<htcp> ::= <header>
- <definition>
- <lower-pos>
- <voxel-size>
- <padding>
- <RVT>
- <padding>
- <RCT>
- <padding>
- <PABST>
- <padding>
- <T>
- <padding>
-
-<header> ::= <pagesize> <is-Z-irregular>
-<definition> ::= <X> <Y> <Z> <time> # Spatial and temporal definition
-<lower-pos> ::= DOUBLE DOUBLE DOUBLE # Spatial origin of the grid
-<voxel-size> ::= DOUBLE DOUBLE # Size of a cell in X and Y
- DOUBLE [ DOUBLE ... ] # Size of the cells in Z
-
-<pagesize> ::= INT64
-<is-Z-irregular>
- ::= INT8
-
-<X> ::= INT32
-<Y> ::= INT32
-<Z> ::= INT32
-<time> ::= INT32
-
-<RVT> ::= DOUBLE [ DOUBLE ... ] # Water vapor mixing ratio
-<RCT> ::= DOUBLE [ DOUBLE ... ] # Liquid water in suspension mixing ratio
-<PABST> ::= DOUBLE [ DOUBLE ... ] # Pressure
-<T> ::= DOUBLE [ DOUBLE ... ] # Temperature
-
-<padding> ::= [ BYTE ... ]
-```
-
-# SEE ALSO
-
-*les2htcp*(1)
diff --git a/doc/les2htcp.1.scd b/doc/les2htcp.1.scd
@@ -1,131 +0,0 @@
-les2htcp(1)
-
-; Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
-; Copyright (C) 2018 Centre National de la Recherche Scientifique
-; Copyright (C) 2018 Université Paul Sabatier
-;
-; This program is free software: you can redistribute it and/or modify
-; it under the terms of the GNU General Public License as published by
-; the Free Software Foundation, either version 3 of the License, or
-; (at your option) any later version.
-;
-; 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
-; GNU General Public License for more details.
-;
-; You should have received a copy of the GNU General Public License
-; along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# NAME
-
-les2htcp - convert cloud properties from NetCDF to htcp(5) file format
-
-# SYNOPSIS
-
-les2htcp [_option_] ... -i _NetCDF_
-
-# DESCRIPTION
-*les2htcp* generates a *htcp*(5) file from cloud properties stores in a NetCDF
-file [1]. Expected variables in the submitted NetCDF file are:
-
-- _W_E_direction_ *and* _S_N_direction_: one dimensional list of position of the
- center of each cell along the West-East and South-North horizontal axis,
- respectively. This should be a homogeneous mesh: each cell should have the
- same width along each axis. The unit is assumed to be the meter but it can
- be adjusted by the *-m* option.
-- _VLEV_ *or* _vertical_levels_: position of the center of each cell along the
- vertical axis. The vertical mesh can possibly be inhomogeneous: each cell
- can have different vertical extent. At least one of this variable must be
- defined. Note that _VLEV_ is a four dimensional variable while
- _vertical_levels_ is assumed to be one dimensional. In all cases, *les2htcp*
- assumes that the vertical columns are the same for each cell along the
- West-East and South-North axis. The unit is assumed to be the meter but it
- can be adjusted by the *-m* option.
-- _RVT_: water vapor mixing ratio in each grid cell; in kg of water per kg of
- air.
-- _RCT_: liquid water (in suspension) mixing ratio in each grid cell; in kg of
- water per kg of dry air.
-- _PABST_: pressure in each grid cell in Pascal.
-- _THT_: potential temperature in each grid cell in Kelvin.
-
-# OPTIONS
-
-*-c*
- Advanced checks on the validity of the submitted _NetCDF_ file with respect
- to the *les2htcp* prerequisites on the NetCDF data. Note that this option
- can increase significantly the conversion time.
-
-*-f*
- Force overwrite of the _output_ file.
-
-*-h*
- List short help and exit.
-
-*-i* _NetCDF_
- NetCDF file to convert.
-
-*-m* _float-to-meter_
- Scale factor from floating point unit to meters. By default it is set to 1.
-
-*-o* _output_
- Destination file where the *htcp*(5) file is written. If not defined, the
- results are written to standard output.
-
-*-p* _page-size_
- Targeted page size in bytes; must be a power of 2. The size of the converted
- NetCDF data and their starting address into the *htcp*(5) file are aligned
- according to _page-size_. By default, _page-size_ is 4096 bytes.
-
-*-q*
- Write nothing to _output_. Might be used in conjunction of the *-c* option
- to only check the submitted _NetCDF_.
-
-*-v*
- Display version information and exit.
-
-# EXAMPLES
-
-Convert the _clouds.nc_ NetCDF file. Write the resulting *htcp*(5) file in
-_cloud.htcp_ excepted if the file already exists; in this case an error is
-notified, the program stops and the _cloud.htcp_ file remains unchanged:
-
-```
-les2htcp -i clouds.nc -o clouds.htcp
-```
-
-Convert the _clouds_km.nc_ file to *htcp*(5) file format. Use the *-f* option
-to write the output file _clouds.htcp_ even though it already exists. The
-_clouds_km.nc_ file to convert has its spatial unit in kilo-meters while the
-*htcp*(5) file format assumes meters: use the *-m* _1000_ option to map
-kilo-meters to meters:
-
-```
-les2htcp -i clouds_km.nc -m 1000 -o clouds.htcp
-```
-
-Check that the submitted _clouds.nc_ file is valid regarding the
-*les2htcp* constraints. Use the *-q* option to disable the generation of
-output data:
-
-```
-les2htcp -c -i clouds.nc -q
-```
-
-# COPYRIGHT
-
-Copyright © 2018, 2020 |Méso|Star> <contact@meso-star.com>++
-Copyright © 2018 Centre National de la Recherche Scientifique++
-Copyright © 2018 Université Paul Sabatier <contact-edstar@laplace.univ-tlse.fr>
-
-# LICENSE
-
-*les2htcp* is free software released under the GPLv3+ license: GNU GPL version
-3 or later <https://gnu.org/licenses/gpl.html>. You are free to change and
-redistribute it. There is NO WARRANTY, to the extent permitted by law.
-
-# SEE ALSO
-
-. Network Common Data Form - <https://www.unidata.ucar.edu/software/netcdf/>
-
-*htcp*(5)
diff --git a/htcp.5 b/htcp.5
@@ -0,0 +1,112 @@
+.\" Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+.\" Copyright (C) 2018 Centre National de la Recherche Scientifique
+.\" Copyright (C) 2018 Université Paul Sabatier
+.\"
+.\" This program is free software: you can redistribute it and/or modify
+.\" it under the terms of the GNU General Public License as published by
+.\" the Free Software Foundation, either version 3 of the License, or
+.\" (at your option) any later version.
+.\"
+.\" 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
+.\" GNU General Public License for more details.
+.\"
+.\" You should have received a copy of the GNU General Public License
+.\" along with this program. If not, see <http://www.gnu.org/licenses/>.
+.Dd September 4, 2023
+.Dt HTCP 5
+.Os
+.Sh NAME
+.Nm htcp
+.Nd High-Tune: Cloud Properties
+.Sh DESCRIPTION
+.Nm
+is a binary file format for storing the properties of liquid water content
+suspended in clouds.
+Cloud properties are double-precision spatio-temporal floating-point values,
+structured in a 4D grid whose definition and origin are stored in the
+.Va definition
+and
+.Va lower-pos
+fields.
+The size of a grid cell can be irregular.
+In such case, the
+.Va is-Z-irregular
+flag is set to 1 and the sizes of the cells in Z are explicitly listed in
+.Va voxel-size
+.Pq in meters .
+The size of a grid cell along the X and Y axes is constant, whereas the size
+along the Z axis may be irregular.
+In this case, the
+.Va is-Z-irregular
+flag is set to 1 and the Z cell size is explicitly indicated in
+.Va voxel-size
+.Pq in meters .
+.Pp
+For each property, the list of its data is enumerated linearly along the X, Y,
+Z and time dimensions, in that order.
+The address where its first data is stored is aligned with the value defined by
+the
+.Va pagesize
+field; several padding bytes can therefore be added before a property to ensure
+data alignment.
+Padding bytes are also added at the end of the file to align its overall size
+with the size of a page.
+.Pp
+The stored cloud properties are as follows:
+.Bl -dash -offset indent -compact
+.It
+.Va RVT :
+water vapor mixing ratio in kg of water per m^3 of dry air.
+.It
+.Va RCT :
+liquid water in suspension mixing ratio in kg of water per m^3 of dry air.
+.It
+.Va PABST :
+pressure in Pascal.
+.It
+.Va T :
+temperature in Kelvin.
+.El
+.Pp
+Data are encoded with respect to the little endian bytes ordering, i.e. least
+significant bytes are stored first.
+.Pp
+The file format is as follows:
+.Bl -column (is-Z-irregular) (::=) ()
+.It Ao Va htcp Ac Ta ::= Ta Ao Va pagesize Ac Ao Va is-Z-irregular Ac
+.It Ta Ta Aq Va definition
+.It Ta Ta Aq Va lower-pos
+.It Ta Ta Aq Va voxel-size
+.It Ta Ta Aq Va padding
+.It Ta Ta Aq Va RVT
+.It Ta Ta Aq Va padding
+.It Ta Ta Aq Va RCT
+.It Ta Ta Aq Va padding
+.It Ta Ta Aq Va PABST
+.It Ta Ta Aq Va padding
+.It Ta Ta Aq Va T
+.It Ta Ta Aq Va padding
+.It \ Ta Ta
+.It Ao Va pagesize Ac Ta ::= Ta Vt uint64_t
+.It Ao Va is-Z-irregular Ac Ta ::= Ta Vt int8_t
+.It \ Ta Ta
+.It Ao Va definition Ac Ta ::= Ta Ao Va X Ac Ao Va Y Ac Ao Va Z Ac Ao Va time Ac
+.It Ao Va lower-pos Ac Ta ::= Ta Vt double double double
+# In m
+.It Ao Va voxel-size Ac Ta ::= Ta Vt double double double ...
+# In m
+.It Ao Va X Ac Ta ::= Ta Vt uint32_t
+.It Ao Va Y Ac Ta ::= Ta Vt uint32_t
+.It Ao Va Z Ac Ta ::= Ta Vt uint32_t
+.It Ao Va time Ac Ta ::= Ta Vt uint32_t
+.It \ Ta Ta
+.It Ao Va RVT Ac Ta ::= Ta Vt double ...
+.It Ao Va RCT Ac Ta ::= Ta Vt double ...
+.It Ao Va PABST Ac Ta ::= Ta Vt double ...
+.It Ao Va T Ac Ta ::= Ta Vt double ...
+.It Ao Va padding Ac Ta ::= Ta Op Vt int8_t ...
+.El
+.Sh SEE ALSO
+.Xr les2htcp 1
diff --git a/htcp.pc.in b/htcp.pc.in
@@ -0,0 +1,10 @@
+prefix=@PREFIX@
+includedir=${prefix}/include
+libdir=${prefix}/lib
+
+Requires: rsys >= @RSYS_VERSION@
+Name: htcp
+Description: High-Tune Cloud Properties
+Version: @VERSION@
+Libs: -L${libdir} -lhtcp
+CFlags: -I${includedir}
diff --git a/les2htcp.1 b/les2htcp.1
@@ -0,0 +1,177 @@
+.\" Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+.\" Copyright (C) 2018 Centre National de la Recherche Scientifique
+.\" Copyright (C) 2018 Université Paul Sabatier
+.\"
+.\" This program is free software: you can redistribute it and/or modify
+.\" it under the terms of the GNU General Public License as published by
+.\" the Free Software Foundation, either version 3 of the License, or
+.\" (at your option) any later version.
+.\"
+.\" 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
+.\" GNU General Public License for more details.
+.\"
+.\" You should have received a copy of the GNU General Public License
+.\" along with this program. If not, see <http://www.gnu.org/licenses/>.
+.Dd September 5, 2023
+.Dt LES2HTCP 1
+.Os
+.Sh NAME
+.Nm les2htcp
+.Nd convert cloud properties from netCDF to
+.Xr htcp 5
+.Sh SYNOPSIS
+.Nm
+.Op Fl cfhqv
+.Op Fl m Ar float_to_meter
+.Op Fl o Ar output
+.Op Fl p Ar pagesize
+.Fl i Ar netcdf
+.Sh DESCRIPTION
+.Nm
+generates a
+.Xr htcp 5
+file from cloud properties stored in a netCDF file.
+The variables expected in the submitted netCDF file are:
+.Bl -dash -offset indent
+.It
+.Va W_E_direction
+and
+.Va S_N_direction :
+one-dimensional list of the position at the center of each cell along the
+west-east and south-north horizontal axis, respectively.
+The mesh must be homogeneous: each cell must have the same width along each
+axis.
+The unit is assumed to be meters, but this can be adjusted via
+the
+.Fl m
+option.
+.It
+.Va VLEV
+or
+.Va vertical_levels :
+position at the center of each cell along the vertical axis.
+The vertical mesh can be inhomogeneous, i.e. each cell can have a different
+vertical extent.
+At least one of these variables must be defined.
+Note that
+.Va VLEV
+is a four-dimensional variable, whereas
+.Va vertical_levels
+is assumed to be one-dimensional.
+In all cases
+.Nm
+assumes that the vertical columns are
+the same for each cell along the west-east and south-north axes.
+The unit is assumed to be meters, but this can be adjusted via the
+.Fl m
+option.
+.It
+.Va RCT :
+mixing ratio of liquid suspended water in each grid cell; in kg of water per kg
+of dry air.
+.It
+.Va PABST :
+pressure in each grid cell in Pascal.
+.It
+.Va THT :
+potential temperature in each grid cell in Kelvin.
+.El
+.Pp
+The options are as follows:
+.Bl -tag -width Ds
+.It Fl c
+Advanced checks of the validity of the input
+.Ar netcdf
+file against
+.Nm
+prerequisites on netCDF data.
+Note that this option can significantly increase conversion time.
+.It Fl f
+Forces overwriting of
+.Ar output
+file.
+.It Fl h
+Display short help.
+.It Fl i Ar netcdf
+netCDF file to convert.
+.It Fl m Ar float_to_meter
+Scale factor to be applied to floating-point number
+.Li 1.0 to convert it to meters. By default, it is set to
+.Li 1 .
+.It Fl o Ar output
+Output file.
+If not defined, data is written to standard output.
+.It Fl p Ar pagesize
+Page size in bytes on which htcp data will be aligned.
+It must be a power of 2 and greater than or equal to the size of a system page,
+which is the default value
+.Pq see Xr sysconf 3 .
+.It Fl q
+Writes nothing to the output.
+Can be used in conjunction with the
+.Fl c
+option to check only the validity of the input netCDF.
+.It Fl v
+Display the version number and exit.
+.El
+.Sh EXIT STATUS
+.Ex -std
+.Sh EXAMPLES
+Convert the netCDF
+.Pa clouds.nc
+file.
+The resulting
+.Xr htcp 5
+file is stored in the
+.Pa cloud.htcp
+file unless it already exists; in this case, an error is notified, the program
+stops and the
+.Pa cloud.htcp
+file remains unchanged:
+.Pp
+.Dl les2htcp -i clouds.nc -o clouds.htcp
+.Pp
+Converts netCDF file
+.Pa clouds_km.nc
+to
+.Xr htcp 5
+format.
+Use the
+.Fl f
+option to write the output file
+.Pa clouds.htcp
+even if it already exists.
+The input file to be converted has its spatial unit in kilo-meters, whereas the
+htcp file format assumes meters; use the
+.Fl m Ar 1000
+option to perform the conversion:
+.Pp
+.Dl les2htcp -i clouds_km.nc -m 1000 -o clouds.htcp
+.Pp
+Check that the netCDF file
+.Pa clouds.nc
+is a valid input file for
+.Nm .
+Use the
+.Fl q
+option to disable file conversion:
+.Pp
+.Dl les2htcp -c -i clouds.nc -q
+.Sh SEE ALSO
+.Xr htrdr 1 ,
+.Xr sysconf 3 ,
+.Xr htcp 5
+.Sh STANDARDS
+.Rs
+.%A Edward Hartnett
+.%D March 2011
+.%R ESDS-RFC-022v1
+.%T netCDF4/HDF5 File Format
+.Re
+.Sh HISTORY
+.Nm
+has been developed to generate cloud properties as input to the
+.Xr htrdr 1
+program.
diff --git a/make.sh b/make.sh
@@ -0,0 +1,73 @@
+#!/bin/sh
+
+# Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+# Copyright (C) 2018 Centre National de la Recherche Scientifique
+# Copyright (C) 2018 Université Paul Sabatier
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+set -e
+
+config_test()
+{
+ for i in "$@"; do
+ test=$(basename "${i}" ".c")
+ test_list="${test_list} ${test}"
+ printf "%s: %s\n" "${test}" "src/${test}.o"
+ done
+ printf "test_bin: %s\n" "${test_list}"
+}
+
+run_test()
+{
+ for i in "$@"; do
+ test=$(basename "${i}" ".c")
+
+ printf "%s " "${test}"
+ if "./${test}" > /dev/null 2>&1; then
+ printf "\033[1;32mOK\033[m\n"
+ else
+ printf "\033[1;31mError\033[m\n"
+ fi
+ done 2> /dev/null
+}
+
+
+clean_test()
+{
+ for i in "$@"; do
+ rm -f "$(basename "${i}" ".c")"
+ done
+}
+
+install()
+{
+ prefix=$1
+ shift 1
+
+ mkdir -p "${prefix}"
+
+ for i in "$@"; do
+ dst="${prefix}/${i##*/}"
+
+ if cmp -s "${i}" "${dst}"; then
+ printf "Up to date %s\n" "${dst}"
+ else
+ printf "Installing %s\n" "${dst}"
+ cp "${i}" "${prefix}"
+ fi
+ done
+}
+
+"$@"
diff --git a/src/dump_netcdf_data.sh b/src/dump_netcdf_data.sh
@@ -1,7 +1,8 @@
-#!/bin/sh
+#!/bin/sh -e
-# Copyright (C) 2018, 2020-2022 |Méso|Star> (contact@meso-star.com)
-# Copyright (C) CNRS, Université Paul Sabatier
+# Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+# Copyright (C) 2018 Centre National de la Recherche Scientifique
+# Copyright (C) 2018 Université Paul Sabatier
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -19,21 +20,22 @@
set -e
if [ $# -lt 2 ]; then
- >&2 echo "Usage: $0 VAR-NAME LES-NETCDF "
+ printf "usage: %s variable netcdf\n" "${0##*/}" >&2
exit 1
fi
if [ ! -f "$2" ]; then
- >&2 echo "\"$2\" is not a valid file."
+ printf "\"%s\" is not a valid file\n" "$2" >&2
exit 1
fi
name=$(basename "$2")
name=${name%.*}
+blanks="[[:blank:]]\{0,\}"
ncdump -v "$1" "$2" \
- | sed -n "/^ *$1 *=/,\$p" \
- | sed "s/^ *$1 *= *//g" \
- | sed 's/[;} ]//g' \
- | sed 's/,/\n/g' \
- | sed '/^ *$/d' > "${name}_${1}"
+ | sed -n "/^${blanks}$1${blanks}=/,\$p" \
+ | sed "s/^${blanks}$1${blanks}=${blanks}//g" \
+ | sed "s/[;} ]//g" \
+ | sed "s/,/\n/g" \
+ | sed "/^${blanks}$/d" > "${name}_${1}"
diff --git a/src/dump_netcdf_desc.sh b/src/dump_netcdf_desc.sh
@@ -1,7 +1,8 @@
-#!/bin/sh
+#!/bin/sh -e
-# Copyright (C) 2018, 2020-2022 |Méso|Star> (contact@meso-star.com)
-# Copyright (C) CNRS, Université Paul Sabatier
+# Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+# Copyright (C) 2018 Centre National de la Recherche Scientifique
+# Copyright (C) 2018 Université Paul Sabatier
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -18,22 +19,35 @@
set -e
if [ $# -lt 1 ]; then
- >&2 printf "Usage: %s -NAME LES-NETCDF\n" "$0"
+ printf "usage: %s variable netcdf\n" "${0##*/}" >&2
exit 1
fi
-dimensions=$(ncdump -h "$1" | sed '/^ *variables/,$d' | sed '1,2d')
-nx=$(echo "${dimensions}" | sed -n 's/^.*W_E_direction *= *\([0-9]\{1,\}\) *;.*$/\1/p')
-ny=$(echo "${dimensions}" | sed -n 's/^.*S_N_direction *= *\([0-9]\{1,\}\) *;.*$/\1/p')
-nz=$(echo "${dimensions}" | sed -n 's/^.*vertical_levels *= *\([0-9]\{1,\}\) *;.*$/\1/p')
-ntimes=$(echo "${dimensions}" | sed -n 's/^.*time *= *\([0-9]\{1,\}\) *;.*$/\1/p')
+
+b="[[:blank:]]\{0,\}" # Blanks
+c=".\{0,\}" # Any chars
+
+dimensions=$(ncdump -h "$1" | sed "/^${b}variables/,\$d" | sed '1,2d')
+nx=$(echo "${dimensions}" | \
+ sed -n "s/^${c}W_E_direction${b}=${b}\([0-9]\{1,\}\)${b};${c}$/\1/p")
+ny=$(echo "${dimensions}" | \
+ sed -n "s/^${c}S_N_direction${b}=${b}\([0-9]\{1,\}\)${b};${c}$/\1/p")
+nz=$(echo "${dimensions}" | \
+ sed -n "s/^${c}vertical_levels${b}=${b}\([0-9]\{1,\}\)${b};${c}$/\1/p")
+ntimes=$(echo "${dimensions}" | \
+ sed -n "s/^${c}time${b}=${b}\([0-9]\{1,\}\)${b};${c}$/\1/p")
if [ -z "${ntimes}" ]; then
- ntimes=$(echo "${dimensions}" | sed -n 's/^.*time *=.*\/\/ *(\([0-9]\{1,\}\) currently).*$/\1/p')
+ ntimes=$(echo "${dimensions}" | \
+ sed -n "s/^${c}time${b}=${c}\/\/${b}(\([0-9]\{1,\}\) currently)${c}$/\1/p")
fi
-if [ -z "${nx}" ] || [ -z "${ny}" ] || [ -z "${nz}" ] || [ -z "${ntimes}" ]; then
- >&2 printf "%s: Error retrieving the dimensions of \"%s\"\n" "$0" "$1"
+if [ -z "${nx}" ] \
+|| [ -z "${ny}" ] \
+|| [ -z "${nz}" ] \
+|| [ -z "${ntimes}" ]
+then
+ >&2 printf "%s: error retrieving the dimensions of \"%s\"\n" "$0" "$1"
exit 1
fi
diff --git a/src/les2htcp.c b/src/les2htcp.c
@@ -28,7 +28,7 @@
#include <errno.h>
#include <netcdf.h>
#include <string.h>
-#include <unistd.h> /* getopt */
+#include <unistd.h> /* getopt, sysconf */
#include <fcntl.h> /* open */
#include <sys/stat.h> /* S_IRUSR & S_IWUSR */
@@ -45,46 +45,15 @@ struct args {
int no_output;
int quit; /* Quit the application */
};
-#define ARGS_DEFAULT__ {NULL,NULL,1.0,4096,0,0,0,0}
+#define ARGS_DEFAULT__ {NULL,NULL,1.0,-1,0,0,0,0}
static const struct args ARGS_DEFAULT = ARGS_DEFAULT__;
-static void
-print_help(const char* cmd)
+static INLINE void
+usage(const char* cmd)
{
ASSERT(cmd);
- (void)cmd;
-
- printf(
-"Usage: les2htcp -i INPUT [OPTIONS]\n"
-"Convert the LES data stored into INPUT from NetCDF to the htcp fileformat.\n\n");
- printf(
-" -c advanced check of the validity of the submitted LES file.\n");
- printf(
-" -f overwrite the OUTPUT file if it already exists.\n");
- printf(
-" -h display this help and exit.\n");
- printf(
-" -i INPUT path of the LES file to convert.\n");
- printf(
-" -m FLT_TO_METER scale factor to convert from floating point units to\n"
-" meters. By default, it is set to %g.\n",
- ARGS_DEFAULT.fp_to_meter);
- printf(
-" -o OUTPUT write results to OUTPUT. If not defined, write results to\n"
-" standard output.\n");
- printf(
-" -p targeted page size in bytes. Must be a power of 2. By\n"
-" default, the page size is %li Bytes.\n",
- ARGS_DEFAULT.pagesize);
- printf(
-" -q do not write results to OUTPUT.\n");
- printf(
-" -v display version information and exit.\n");
- printf("\n");
- printf(
-"les2htcp is free software released under the GNU GPL license, version 3 or\n"
-"later. You are free to change or redistribute it under certain conditions\n"
-"<http://gnu.org/licenses/gpl.html>\n");
+ printf("usage: %s [-cfhqv] [-m float_to_meter] [-o output] [-p pagesize] "
+ "-i netcdf\n", cmd);
}
static void
@@ -97,16 +66,26 @@ args_release(struct args* args)
static res_T
args_init(struct args* args, const int argc, char** argv)
{
+ long system_pagesize;
int opt;
res_T res = RES_OK;
ASSERT(args && argc && argv);
+ system_pagesize = sysconf(_SC_PAGESIZE);
+ if(system_pagesize == -1) {
+ fprintf(stderr,
+ "Error when querying the size of a system page -- %s\n",
+ strerror(errno));
+ res = RES_BAD_OP;
+ goto error;
+ }
+
while((opt = getopt(argc, argv, "cfhi:m:o:p:qv")) != -1) {
switch(opt) {
case 'c': args->check = 1; break;
case 'f': args->force_overwrite = 1; break;
case 'h':
- print_help(argv[0]);
+ usage(argv[0]);
args_release(args);
args->quit = 1;
goto exit;
@@ -119,14 +98,15 @@ args_init(struct args* args, const int argc, char** argv)
case 'p':
res = cstr_to_long(optarg, &args->pagesize);
if(res == RES_OK && !IS_POW2(args->pagesize)) res = RES_BAD_ARG;
+ if(res == RES_OK && args->pagesize < system_pagesize) res = RES_BAD_ARG;
break;
case 'q': args->no_output = 1; break;
case 'v':
printf("%s %d.%d.%d\n",
argv[0],
- LES2HTLES_VERSION_MAJOR,
- LES2HTLES_VERSION_MINOR,
- LES2HTLES_VERSION_PATCH);
+ LES2HTCP_VERSION_MAJOR,
+ LES2HTCP_VERSION_MINOR,
+ LES2HTCP_VERSION_PATCH);
args->quit = 1;
goto exit;
default: res = RES_BAD_ARG; break;
@@ -148,9 +128,15 @@ args_init(struct args* args, const int argc, char** argv)
if(args->no_output) args->output = NULL;
+ /* Use the default page size if not explicitly defined by the caller. */
+ if(args->pagesize < system_pagesize) {
+ args->pagesize = system_pagesize;
+ }
+
exit:
return res;
error:
+ usage(argv[0]);
args_release(args);
goto exit;
}
diff --git a/src/les2htcp.h.in b/src/les2htcp.h.in
@@ -1,6 +1,6 @@
-/* Copyright (C) 2018, 2020-2022 |Méso|Star> (contact@meso-star.com)
- * Copyright (C) 2018 CNRS
- * Copyright (C) 2018 Université Paul Sabatier (contact-edstar@laplace.univ-tlse.fr)
+/* Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+ * Copyright (C) 2018 Centre National de la Recherche Scientifique
+ * Copyright (C) 2018 Université Paul Sabatier
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
@@ -15,12 +15,12 @@
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>. */
-#ifndef LES2HTLES_H
-#define LES2HTLES_H
+#ifndef LES2HTCP_H
+#define LES2HTCP_H
-#define LES2HTLES_VERSION_MAJOR @VERSION_MAJOR@
-#define LES2HTLES_VERSION_MINOR @VERSION_MINOR@
-#define LES2HTLES_VERSION_PATCH @VERSION_PATCH@
+#define LES2HTCP_VERSION_MAJOR @VERSION_MAJOR@
+#define LES2HTCP_VERSION_MINOR @VERSION_MINOR@
+#define LES2HTCP_VERSION_PATCH @VERSION_PATCH@
-#endif /* LES2HTLES_H */
+#endif /* LES2HTCP_H */
diff --git a/src/test_htcp_load_from_file.sh b/src/test_htcp_load_from_file.sh
@@ -0,0 +1,55 @@
+#!/bin/sh -e
+
+# Copyright (C) 2018, 2020-2023 |Méso|Star> (contact@meso-star.com)
+# Copyright (C) 2018 Centre National de la Recherche Scientifique
+# Copyright (C) 2018 Université Paul Sabatier
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>. */
+
+dump_data() {
+ variable="$1"
+ netcdf="$2"
+ printf "Dump the variable \"%s\" from \"%s\"\n" "${variable}" "${netcdf}"
+ dump_netcdf_data.sh "${variable}" "${netcdf}"
+}
+
+if [ $# -ne 1 ]; then
+ printf "usage: %s netcdf\n" "${0##*/}" >&2
+ exit 1
+fi
+
+nc="$1"
+
+if [ ! -f "${nc}" ]; then
+ printf "Invalid netcdf: %s\n" "${nc}" >&2
+ exit 1
+fi
+
+prefix=$(basename "${nc}")
+prefix=${prefix%.*}
+htcp="${prefix}.htcp"
+path=$(pwd)
+
+printf "Convert \"%s\" to \"%s\"\n" "${nc}" "${htcp}"
+les2htcp -m 1000 -i "${nc}" -fo "${htcp}"
+
+printf "Dump the descriptor of \"%s\"\n" "${nc}"
+dump_netcdf_desc.sh "${nc}"
+
+dump_data "PABST" "${nc}"
+dump_data "RCT" "${nc}"
+dump_data "RVT" "${nc}"
+dump_data "THT" "${nc}"
+
+test_htcp_load_from_file "${prefix}.htcp" "${path}"
