A CMake build system for cfl3d and some bug fixes (at least in Linux)

.gitignore

@@ -1,55 +1,7 @@
 # Untracked files:
-*.o
-build/makefile
-build/tools/seq/*.F*
-build/splitcmplx/seq/*.F*
-build/split/seq/*.F*
-build/ron/seq/*.F*
-build/preron/seq/*.F*
-build/precfl/seq/*.F*
-build/mag/seq/*.F*
-build/cflcmplx/seq/*.F*
-build/cflcmplx/mpi/*.F*
-build/cflcmplx/libs/*.F*
-build/cflcmplx/libs/bessel.c
-build/cfl/libs/bessel.c
-build/cfl/seq/*.F*
-build/cfl/mpi/*.F*
-build/cfl/libs/*.F*
-build/cfl/libs/*.mod
-libcommon.a
-libdist.a
-cfl3d_seq
-cfl3d_mpi
-cfl3dcmplx_seq
-cfl3dcmplx_mpi
-maggie
-precfl3d
-preronnie
-ronnie
-splitter
-splittercmplx
-build/mag/seq/mag1.h
-build/tools/seq/Get_FD
-build/tools/seq/INGRID_to_p3d
-build/tools/seq/XINTOUT_to_ovrlp
-build/tools/seq/cfl3d_to_nmf
-build/tools/seq/cfl3d_to_pegbc
-build/tools/seq/cfl3dinp_to_FVBND
-build/tools/seq/cgns_readhist
-build/tools/seq/cgns_to_cfl3dinput
-build/tools/seq/everyother_xyz
-build/tools/seq/grid_perturb
-build/tools/seq/grid_perturb_cmplx
-build/tools/seq/initialize_field
-build/tools/seq/libs.a
-build/tools/seq/moovmaker
-build/tools/seq/nmf_to_cfl3dinput
-build/tools/seq/p3d_to_INGRID
-build/tools/seq/p3d_to_cfl3drst
-build/tools/seq/plot3dg_to_cgns
-build/tools/seq/v6_restart_mod
-build/tools/seq/v6_ronnie_mod
-build/tools/seq/v6inpdoubhalf
-build/tools/seq/gridswitchijk
-build/tools/seq/v6inpswitchijk
+build/
+testcase/
+
+*.swp
+bin/
+external/cgns/cgnslib_2.5/

CMakeLists.txt

@@ -0,0 +1,155 @@
+cmake_minimum_required(VERSION 3.0.2)
+cmake_policy(SET CMP0048 NEW) #used to set Version Number
+project(CFL3D VERSION 6.7)
+enable_language(Fortran C)
+SET (CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/include CACHE PATH "Single Directory for all fortran modules.")
+
+## options
+option(USE_SINGLE "use single precision? " OFF)
+option(USE_CGNS "use CGNS? " ON)
+option(USE_NO_REDIRECT "use no-redirect? " OFF)
+option(USE_FASTIO "use fast-io of mpi? It is effective when mpi is found. " ON)
+option(BUILD_MPI "build MPI version? " ON)
+option(BUILD_CMPLX "build complex version? " ON)
+
+## default Build Type is Release
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release)
+endif(NOT CMAKE_BUILD_TYPE)
+
+## no redirect
+if(USE_NO_REDIRECT)
+	add_definitions(-DNOREDIRECT)
+endif(USE_NO_REDIRECT)
+
+
+## use options to setup flags and find libraries
+if(USE_SINGLE)
+	# do nothing
+else(USE_SINGLE)
+	add_definitions(-DDBLE_PRECSN)
+
+	if(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
+		message(STATUS "Using the Intel Fortran compiler")
+		add_compile_options(-r8)
+	elseif(CMAKE_Fortran_COMPILER_ID MATCHES GNU)
+		message(STATUS "Using the GNU Fortran compiler")
+		add_compile_options(-fdefault-real-8)
+	else(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
+		message(WARNING "compiler do not match Intel/GNU! use Intel's setting instead.")
+		add_compile_options(-r8)
+	endif(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
+
+endif(USE_SINGLE)
+
+
+# no FindCGNS in CMake release
+# using Paraview's FindCGNS.cmake
+# https://github.com/Kitware/ParaView/raw/master/CMake/FindCGNS.cmake
+# modified to find `cgnslib_f.h` and `libcgns.a`
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+
+if(USE_CGNS)
+	find_package(CGNS 2.4 REQUIRED)
+	if(CGNS_FOUND)
+		message("Found CGNS for CFL3D")
+		message("CGNS include dir: ${CGNS_INCLUDE_DIR}")
+		message("CGNS library: ${CGNS_LIBRARY}")
+		add_library(cgns STATIC IMPORTED)
+		set_property(TARGET cgns PROPERTY IMPORTED_LOCATION ${CGNS_LIBRARY})
+		set_property(TARGET cgns PROPERTY IMPORTED_LINK_INTERFACE_LANGUAGES Fortran)
+		set_property(TARGET cgns PROPERTY INTERFACE_INCLUDE_DIRECTORIES $<BUILD_INTERFACE:${CGNS_INCLUDE_DIR}>)
+		set_property(TARGET cgns PROPERTY INTERFACE_COMPILE_DEFINITIONS CGNS)
+		# If using libcgns.so in system lib, it is required to find and use libhdf5.so
+		#find_package(HDF5 REQUIRED)
+		#if(HDF5_FOUND)
+		#	message("HDF5_lib:${HDF5_hdf5_LIBRARY_RELEASE}")
+		#	set_property(TARGET cgns PROPERTY INTERFACE_LINK_LIBRARIES ${HDF5_hdf5_LIBRARY_RELEASE})
+		#else(HDF5_FOUND)
+		#	message(WARNING "HDF5 not found, there might be some error when linking to libcgns.so")
+		#endif(HDF5_FOUND)
+	else(CGNS_FOUND)
+		message(WARNING "system CGNS not found for CFL3D")
+		set(USE_CGNS OFF CACHE BOOL "use CGNS? (not available)" FORCE) # set the CGNS not available
+	endif(CGNS_FOUND)
+else(USE_CGNS)
+endif(USE_CGNS)
+
+if(BUILD_MPI)
+	find_package(MPI 1.0 REQUIRED)
+	if(MPI_Fortran_FOUND)
+		message("Found MPI for Fortran")
+		## add mpi library
+		add_library(mpi STATIC IMPORTED)
+		set_property(TARGET mpi PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${MPI_Fortran_INCLUDE_PATH})
+		set(other_elems ${MPI_Fortran_LIBRARIES})
+		list(GET other_elems 0 first_elem)
+		list(REMOVE_AT other_elems 0)
+		set_property(TARGET mpi PROPERTY IMPORTED_LOCATION ${first_elem})
+		set_property(TARGET mpi PROPERTY INTERFACE_LINK_LIBRARIES ${other_elems})
+		set_property(TARGET mpi APPEND PROPERTY INTERFACE_COMPILE_DEFINITIONS "DIST_MPI")
+		set_property(TARGET mpi APPEND PROPERTY LINK_FLAGS "${MPI_Fortran_LINK_FLAGS}")
+		set_property(TARGET mpi APPEND PROPERTY INTERFACE_COMPILE_OPTIONS "${MPI_Fortran_COMPILE_FLAGS}")
+		## FAST-io
+		if(USE_FASTIO)
+			set_property(TARGET mpi APPEND PROPERTY INTERFACE_COMPILE_DEFINITIONS "FASTIO")
+		endif(USE_FASTIO)
+	else(MPI_Fortran_FOUND)
+		## FAST-io
+		if(USE_FASTIO)
+			message(WARNING "no mpi, no fast-io.")
+			set(USE_FASTIO OFF CACHE BOOL "build MPI? (not available)" FORCE) # set the fastio not available
+		endif(USE_FASTIO)
+		set(BUILD_MPI OFF CACHE BOOL "build MPI? (not available)" FORCE) # set the MPI not available
+	endif(MPI_Fortran_FOUND)
+else(BUILD_MPI)
+endif(BUILD_MPI)
+
+# in LINUX system
+if(UNIX AND NOT APPLE)
+	add_definitions(-DLINUX)
+	## usually the Linux OS uses `ld` as linker, so add `-z muldefs` option
+	SET( CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -z muldefs" )
+endif(UNIX AND NOT APPLE)
+
+## project compiler dependent settings
+if(${CMake_Fortran_COMPILER_ID} MATCHES Intel)
+	add_definitions(-DINTEL)
+	add_compile_options(-xHost )
+	add_compile_options(-traceback)
+	add_compile_options(-fpe0) # 
+	#add_compile_options(-w) #bad behavior, old codes usually use common block incorrectly. However, the warning is harmless. 
+	add_compile_options(-ip) # interprocedural optimization
+	add_compile_options(-fno-alias) #gcc by default uses `-fargument-noalias-global` 
+elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES GNU)
+	add_compile_options(-march=native)
+	add_compile_options(-Wno-align-commons) #suppress some warnings about the padding of commons
+	add_compile_options(-fbacktrace)
+else(${CMAKE_Fortran_COMPILER_ID} MATCHES Intel)
+	message(WARNING "Unsupported compiler iD: " ${CMAKE_Fortran_COMPILER_ID})
+	message(WARNING "Supported compiler iD: Intel/GNU")
+	message(WARNING "Try to use GNU options")
+	add_compile_options(-march=native)
+	add_compile_options(-Wno-align-commons) #suppress some warnings about the padding of commons
+	add_compile_options(-fbacktrace)
+endif(${CMake_Fortran_COMPILER_ID} MATCHES Intel)
+
+# it seems always use P3D_SINGLE in original Install script
+add_definitions(-DP3D_SINGLE)
+
+message("---------------------CFL3D programs summary--------------------------")
+message("Build type? " ${CMAKE_BUILD_TYPE})
+message("CMAKE_Fortran_COMPILER full path: " ${CMAKE_Fortran_COMPILER})
+message("CMAKE Fortran compiler ID: " ${CMAKE_Fortran_COMPILER_ID})
+message("---------------------------------------------------------------------")
+
+# set output library
+# use CMAKE_XXX_OUTPUT_DIRECTORY to set the default dirs when create targets
+# set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/lib/fortran)
+# set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
+# set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
+
+add_subdirectory(source) 
+#add_subdirectory(testcases) 
+

README.md

@@ -24,3 +24,52 @@ distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
 WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the 
 License for the specific language governing permissions and limitations 
 under the License.
+
+------------
+## About the CMake branch
+As a practice of cmake, I had ported the make system of cfl3d to CMake, a modern industry-level build system. Which is much more easy to use, understand, modify and maintain.
+
+### Compilation
+```shell
+## prerequirement (tested in Ubuntu 16.04)
+sudo apt-get install libopenmpi-dev gfortran build-essential git cmake -y
+# in RHEL/CentOS, you may try this:
+# sudo yum install openmpi-devel gcc gcc-gfortran git cmake
+
+## download the CMake branch only 
+git clone -b CMake --single-branch https://github.com/chengdi123000/CFL3D.git
+
+## manually build cgns 2.5 without hdf5 and mpi
+# you can also use your own cgns library if you put your cgnslib_f.h and libcgns.a in /usr/share/include and /usr/share/lib respectively
+cd CFL3D/external/cgns
+./build_cgns
+
+## build cfl3d executables out of source
+cd ../../build
+cmake ..
+make
+# or you may benefit from parallel run, try:
+# make -j`nproc`
+# There will be a lot of warnings because I do not turn off all warnings as the original CFL3D build system do.
+```
+
+### Test
+First set the PATH
+```shell
+## When completed, the executables will be in CFL3D/build/bin directory.
+# suggest to use this line of script to add executables to PATH
+# export PATH=$PWD/bin:$PATH
+# You can use following line of script to add a command `use_cfl3d` to load executables ready to run after re-login
+# echo "alias use_cfl3d='export PATH=$PWD/bin:\$PATH'">>$HOME/.bashrc
+```
+Then you need to download testcases
+```shell
+cd CFL3D/testcase
+./download_testcases #wget is needed.
+cd cfl3d.larc.nasa.gov/Cfl3dv6/2DTestcases/Flatplate
+tar xvf Flatplate.tar.Z
+# use_cfl3d
+splitter < split.inp_1blk 
+cfl3d_seq < grdflat5.inp &
+tail -f cfl3d.out #monitor the steps and residuals
+```