Build MPICH with CMake - cmake

I need to force my Cmake to build and link my MPI code with MPICH. My MPICH is installed using the Ubuntu Package manager, in a standard location /usr/lib/mpich/. However, CMake still looks for the OpenMPI libraries, which I do not use. How can I instruct CMake to look for MPICH instead?
Below, you can see the output of some basic diagnostics:
$ whereis openmpi
openmpi:
$ whereis mpich
mpich: /usr/lib/mpich /usr/include/mpich
$ mpicc -v
mpicc for MPICH version 3.2
Below, I also provide the Cmake script and the errors I get from cmake and the mpirun.mpich. My Cmake is 3.5.1 and I run on Ubuntu Xenial 16.04.
cmake_minimum_required(VERSION 3.0)
message (STATUS "Adding mpiService")
find_package(MPI REQUIRED)
set(CMAKE_C_COMPILER mpicc)
set(CMAKE_CXX_COMPILER mpicxx)
set(MPI_GUESS_LIBRARY_NAME MPICH2)
message(STATUS ${MPI_INCLUDE_PATH})
message(STATUS ${MPI_C_LIBRARIES})
#add_definitions(-DOMPI_SKIP_MPICXX)
add_executable(mpiService main.cpp)
set(CMAKE_VERBOSE_MAKEFILE ON)
include_directories(SYSTEM ${MPI_INCLUDE_PATH})
target_link_libraries(
mpiService
PRIVATE
${MPI_C_LIBRARIES}
)
From the Cmake STATUS I get the following output:
/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include/usr/lib/openmpi/include/usr/lib/openmpi/include/openmpi
/usr/lib/openmpi/lib/libmpi.so
And when I run the binary I get the following:
ubuntu#node1:~$ mpirun.mpich -np 2 --host node1,node2 mpiService
mpiService: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory
mpiService: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory

How can I instruct CMake to look for MPICH instead?
According to FindMPI documentation, you may set MPI_<lang>_COMPILER variable to the desired MPI compiler:
Set MPI_<lang>_COMPILER to the MPI wrapper (mpicc, etc.) of your
choice and reconfigure. FindMPI will attempt to determine all the
necessary variables using THAT compiler's compile and link flags.
set(MPI_CXX_COMPILER <path-to-mpich-compiler>)
find_package(MPI REQUIRED)
Alternatively, since CMake version 3.10, variable MPI_EXECUTABLE_SUFFIX can be set instead:
A suffix which is appended to all names that are being looked for. For instance you may set this to .mpich or .openmpi to prefer the one or the other on Debian and its derivatives.
set(MPI_EXECUTABLE_SUFFIX ".mpich")
find_package(MPI REQUIRED)

Herewith my current solution.
find_package(MPI REQUIRED)
# ----------------
# This is the only thing that made it work
# ----------------
set(MPI_C_LIBRARIES "/usr/lib/mpich/lib/libmpich.so")
set(MPI_INCLUDE_PATH "/usr/include/mpich")
# ----------------
add_executable(mpiService main.cpp)
include_directories(SYSTEM ${MPI_INCLUDE_PATH})
target_link_libraries(
mpiService
${MPI_C_LIBRARIES}
)
I personally do not like this solution, as I have to explicitly specify the path. Any other proposed solution was still building with OpenMPI. If I find a better alternative, I will re-post.

Related

Unknown CMake command "CMAKE_DEPENDENT_OPTION"

I faced with an issue that my installed on Ubuntu cmake
cmake --version
cmake version 3.17.2
doesn't recognize CMAKE_DEPENDENT_OPTION command.
So, my CMakeLists.txt with dependent option example from cmake.org/v3.16:
cmake_minimum_required(VERSION 3.4.1)
project(myexe)
CMAKE_DEPENDENT_OPTION(USE_FOO "Use Foo" ON
"USE_BAR;NOT USE_ZOT" OFF)
file(GLOB SRC_FILES "src/*.cpp")
add_executable(${PROJECT_NAME} ${SRC_FILES})
The following error is displayed when running cmake:
CMake Error at CMakeLists.txt:5 (CMAKE_DEPENDENT_OPTION):
Unknown CMake command "CMAKE_DEPENDENT_OPTION".
Why does it happen because the spec says it is supported? Thanks for any help!
You need to add
include(CMakeDependentOption)
before accessing this function.

STM32 Project with CMake

I am trying to create and compile an ARM-based STM32 project using CMake.
CMakeLsts.txt is the following:
cmake_minimum_required(VERSION 3.7)
SET(CMAKE_SYSTEM_NAME Generic)
SET(CMAKE_SYSTEM_VERSION 1)
# Enable logging messages
#set(CMAKE_VERBOSE_MAKEFILE ON)
# Project name
set(PROJECT_NAME FixtureTACO)
PROJECT(${PROJECT_NAME} C CXX ASM)
SET(CMAKE_CXX_STANDARD 11)
###################### CHIP CONFIGURATION ##########################
SET(ROOT_PROJ ${CMAKE_CURRENT_SOURCE_DIR})
SET(CPU "cortex-m4")
SET(ARCH_NAME "arm")
SET(ARCH_VER "v7e-m")
SET(FAMILY "stm32f3")
SET(CHIP "STM32F303xC")
SET(ARCH "${ARCH_NAME}${ARCH_VER}")
####################################################################
# MCU Config
set(FPU "-mfpu=fpv4-sp-d16")
set(FLOAT_ABI "-mfloat-abi=hard")
# Toolchain path
set(TOOLCHAIN_PATH "")
set(ARM_LIB "/usr/lib/arm-none-eabi/lib/${ARCH}")
# Specify C, C++ and ASM compilers
SET(CMAKE_C_COMPILER ${TOOLCHAIN_PATH}arm-none-eabi-gcc)
SET(CMAKE_CXX_COMPILER ${TOOLCHAIN_PATH}arm-none-eabi-g++)
set(AS ${TOOLCHAIN_PATH}arm-none-eabi-as)
set(AR ${TOOLCHAIN_PATH}arm-none-eabi-ar)
set(OBJCOPY ${TOOLCHAIN_PATH}arm-none-eabi-objcopy)
set(OBJDUMP ${TOOLCHAIN_PATH}arm-none-eabi-objdump)
set(SIZE ${TOOLCHAIN_PATH}arm-none-eabi-size)
set(GDB ${TOOLCHAIN_PATH}arm-none-eabi-gdb)
set(SIZE ${TOOLCHAIN_PATH}arm-none-eabi-size)
# Definitions passed at compile time (#defines)
add_definitions(-DFAMILY=${FAMILY})
add_definitions(-DCHIP=${CHIP})
add_definitions(-D${CHIP})
add_definitions(-DUSE_FULL_LL_DRIVER)
add_definitions(-USE_HAL_DRIVER)
add_definitions(-DHSE_VALUE=8000000)
add_definitions(-DHSE_STARTUP_TIMEOUT=100)
add_definitions(-DLSE_STARTUP_TIMEOUT=5000)
add_definitions(-DLSE_VALUE=32768)
add_definitions(-DHSI_VALUE=8000000)
add_definitions(-DLSI_VALUE=40000)
add_definitions(-DDD_VALUE=3300)
add_definitions(-DPREFETCH_ENABLE=1)
# Compilation flags
add_compile_options(-mcpu=${CPU})
add_compile_options(-march=${ARCH})
add_compile_options(-mthumb)
add_compile_options(${FPU})
add_compile_options(${FLOAT_ABI})
add_compile_options(-Og)
add_compile_options(-Wall)
add_compile_options(-fdata-sections)
add_compile_options(-ffunction-sections)
# Only for debugging
add_compile_options(-g -gdwarf-2)
# Linker script path
file(GLOB_RECURSE LINKER_SCRIPT ${ROOT_PROJ}/platforms/${FAMILY}/Linker/*.ld)
# Variables initialized first time
SET(CMAKE_CXX_FLAGS_INIT "-std=c++11")
SET(CMAKE_C_FLAGS_INIT "-std=gnu99")
################################## Source code ###############################################################
# Retrieve all sources # "platforms/${FAMILY}/Startup/*.s"
file(GLOB SOURCES "platforms/${FAMILY}/Startup/*.s" "src/*.cpp" "src/*.c" "platforms/${FAMILY}/Hal/src/*.c" "platforms/${FAMILY}/Device/*.c")
#Retrieve all locations of headers
file(GLOB_RECURSE HEADERS "includes/*.h" "src/*.h" "platforms/${FAMILY}*.h")
set (INCLUDE_DIRS "")
foreach (_headerFile ${HEADERS})
get_filename_component(_dir ${_headerFile} PATH)
list (APPEND INCLUDE_DIRS ${_dir})
endforeach()
list(REMOVE_DUPLICATES INCLUDE_DIRS)
include_directories(${INCLUDE_DIRS})
link_directories(${ARM_LIB})
################################## Source code END ###########################################################
set(EXE_NAME "${PROJECT_NAME}_${CHIP}")
add_executable(${EXE_NAME}.elf ${SOURCES} ${LINKER_SCRIPT})
set(CMAKE_EXE_LINKER_FLAGS "-mcpu=${CPU} -mthumb ${FPU} ${FLOAT_ABI} --specs=nano.specs -T${LINKER_SCRIPT} -Wl,-Map=${PROJECT_BINARY_DIR}/${PROJECT_NAME}.map,--cref -Wl,--gc-sections")
# Libs and external dependencies
target_link_libraries(${EXE_NAME}.elf -lc -lm -lnosys)
# Outputs
set(ELF_FILE ${PROJECT_BINARY_DIR}/${EXE_NAME}.elf)
set(HEX_FILE ${PROJECT_BINARY_DIR}/${EXE_NAME}.hex)
set(BIN_FILE ${PROJECT_BINARY_DIR}/${EXE_NAME}.bin)
add_custom_command(TARGET "${EXE_NAME}.elf" POST_BUILD
# Build .hex and .bin files
COMMAND ${OBJCOPY} -Obinary ${ELF_FILE} ${BIN_FILE}
COMMAND ${OBJCOPY} -Oihex ${ELF_FILE} ${HEX_FILE}
COMMENT "Building ${PROJECT_NAME}.bin and ${PROJECT_NAME}.hex"
# Copy files to a custom build directory
COMMAND ${CMAKE_COMMAND} -E copy ${ELF_FILE} "${ROOT_PROJ}/builds/${CHIP}/${EXE_NAME}.elf"
COMMAND ${CMAKE_COMMAND} -E copy ${HEX_FILE} "${ROOT_PROJ}/builds/${CHIP}/${EXE_NAME}.hex"
COMMAND ${CMAKE_COMMAND} -E copy ${BIN_FILE} "${ROOT_PROJ}/builds/${CHIP}/${EXE_NAME}.bin"
# Display sizes
COMMAND ${SIZE} --format=berkeley ${EXE_NAME}.elf ${EXE_NAME}.hex
COMMENT "Invoking: Cross ARM GNU Print Size"
)
add_custom_target(UPLOAD
${GDB} -iex "target remote tcp:127.0.0.1:3333"
-iex "monitor program ${EXE_NAME}.elf"
-iex "monitor reset init"
-iex "disconnect" -iex "quit ")
When I try to compile I am getting the following errors:
[ 82%] Building C object CMakeFiles/FixtureTACO_STM32F303xC.elf.dir/platforms/stm32f3/Hal/src/stm32f3xx_ll_utils.c.obj
[ 86%] Building ASM object CMakeFiles/FixtureTACO_STM32F303xC.elf.dir/platforms/stm32f3/Startup/startup_stm32f303xc.s.obj
cc: warning: ‘-mcpu=’ is deprecated; use ‘-mtune=’ or ‘-march=’ instead
cc: error: unrecognized command line option ‘-mthumb’; did you mean ‘-mtbm’?
cc: error: unrecognized command line option ‘-mfpu=fpv4-sp-d16’
cc: error: unrecognized command line option ‘-mfloat-abi=hard’
The error occurs ONLY when an assembly file (startup.s in this case) is present in source files and when FPU and FLOAR_ABI flags are present. As you can see, error occurs when startup_stm32f303xc.s is compiled.
I suspect that I am adding those flags in the wrong place but I have no clue where to add them in order to get it works.
Later edit: I already have installed arm 7 compiler on my ubuntu system. I can use it without specifying any path as it is already present in environment variables. I can compile without problems ARM code (from Makefiles) for other targets on machine. My problem is with cmake.
In your line set(TOOLCHAIN_PATH "") you must add a path to compiler. First go to get your free GCC ARM ToolChain. Download for your OS. and then just copy to your favorite location. If you using Linux you can use my path configurations:
1.) Copy gcc arm compirel to /opt/ directory:
sudo tar xjfv ~/Downloads/gcc-arm-none-eabi-7-2018-q2-update-linux.tar.bz2 -C /opt/
For more "sexy" path you can do symbolic link:
sudo ln -s /opt/gcc-arm-none-eabi-7-2018-q2-update/ /opt/gcc-arm-none-eabi
After that go to your CMakeLists.txt and rewrite your set command to:
set(TOOLCHAIN_PATH "/opt/gcc-arm-none-eabi/bin")
But there is better solution to build your project for STM32, but with already done stm32-cmake template project, specifically made for STM32 family. It is mush easier done with something working. You will also need two prerequisites STM32CubeMX installed and again GCC ARM ToolChain. If you want to know how to use this template just DM me and I will you give a quick guidance.
OK, I finally managed to figure it out!
I had to replace
set(AS ${TOOLCHAIN_PATH}arm-none-eabi-as)
with
set(CMAKE_ASM_COMPILER ${TOOLCHAIN_PATH}arm-none-eabi-gcc)
It is not a mistake, it is gcc compiler. You can also append these flags: -x assembler-with-cpp.
CMake didn't know about my custom ASM compiler so it was using default system ASM compiler unless I force it by writing CMAKE_ASM_COMPILER. Now the project is being build and works fine on microcontroller.
The other answers were ok, but had half of the solution. Only ASM filese were compiled with wrong compiler.
I think you try to compile code for ARM using x86 compiler. It will not work. You need to download the ARM toolchain and use the correct compiler.
-mcpu is depreciated in the x86 branch, but is not in the ARM branch
another options just not exist in the x86 compiler.

Why does CMake force the use of libcublas with separable compilation?

I use CMake 3.11 to build the following tiny CUDA-based project:
CMakeLists.txt:
cmake_minimum_required(VERSION 3.1)
find_package(CUDA 7.0 REQUIRED)
set(CUDA_SEPARABLE_COMPILATION ON)
cuda_add_executable(dummy dummy.cu)
dummy.cu:
int main() { }
Strangely enough, when building, the following command is used for the dlink phase:
/path/to/cuda/bin/nvcc -m64 -ccbin /opt/gcc-5.4.0/bin/gcc -dlink /home/joeuser/src/dummy/CMakeFiles/dummy.dir//./dummy_generated_dummy.cu.o /path/to/cuda/lib64/libcublas_device.a -o /home/joeuser/src/dummy/CMakeFiles/dummy.dir/./dummy_intermediate_link.o
Why is CMake linking against cublas where it supposedly doesn't need it?
Note: If I remove the SEPARABLE_COMPILATION line, cublas is not added to the dlink command arguments.
Partial answer:
This doesn't seem to happen if we use CMake's native CUDA language support, e.g.
cmake_minimum_required(VERSION 3.1)
enable_language(CUDA)
add_executable(dummy dummy.cu)
instead of the above - works. I can't make it not have separable compilation though, even if I set:
set_property(TARGET dummy PROPERTY CUDA_SEPARABLE_COMPILATION OFF)

CMake error: For MinGW make to work correctly sh.exe must NOT be in your path

I am trying to built a "Hello World" project with Qt 5 and cmake under MinGW.
This is the CMakeLists.txt file (taken from the on-line doc):
project(Qt5_cmake_test)
cmake_minimum_required(VERSION 2.8.11)
set(CMAKE_PREFIX_PATH "C:/Qt/Qt5.1.1/5.1.1/mingw48_32")
# Find includes in corresponding build directories
set(CMAKE_INCLUDE_CURRENT_DIR ON)
# Instruct CMake to run moc automatically when needed.
set(CMAKE_AUTOMOC ON)
# Find the QtWidgets library
find_package(Qt5Widgets)
# Add the source files from the current directory
aux_source_directory(. SRC_LIST)
# Tell CMake to create the executable
add_executable(${PROJECT_NAME} WIN32 ${SRC_LIST})
# Use the Widgets module from Qt5
target_link_libraries(${PROJECT_NAME} Qt5::Widgets)
The source code is the one generated automatically when creating a new project (which produces an empty window).
Configuring from the Windows command prompt with: cmake -G "MinGW Makefiles" ..\Qt5_cmake_test
I get these errors:
CMake Error at C:/Program Files (x86)/CMake 2.8/share/cmake-2.8/Modules/CMakeMinGWFindMake.cmake:20 (message):
sh.exe was found in your PATH, here:
C:/Program Files (x86)/Git/bin/sh.exe
For MinGW make to work correctly sh.exe must NOT be in your path.
Run cmake from a shell that does not have sh.exe in your PATH.
If you want to use a UNIX shell, then use MSYS Makefiles.
Call Stack (most recent call first):
CMakeLists.txt:8 (project)
CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly.
Missing variable is:
CMAKE_C_COMPILER_ENV_VAR
CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly.
Missing variable is:
CMAKE_C_COMPILER
CMake Error: Could not find cmake module file:C:/Users/pietro.mele/projects/tests/buildSystem_test/Qt5_cmake_test-build/CMakeFiles/2.8.11.2/CMakeCCompiler.cmake
CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly.
Missing variable is:
CMAKE_CXX_COMPILER_ENV_VAR
CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly.
Missing variable is:
CMAKE_CXX_COMPILER
CMake Error: Could not find cmake module file:C:/Users/pietro.mele/projects/tests/buildSystem_test/Qt5_cmake_test-build/CMakeFiles/2.8.11.2/CMakeCXXCompiler.cma
ke
CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
-- Configuring incomplete, errors occurred!
So it seems it is not able to find the compiler. Is there a way to let cmake find it on its own, or just giving it the CMAKE_PREFIX_PATH directory?
Do I have to manually specify all those variables in the makefile or as environment variables in Windows?
I tried both from the standard Windows command prompt and from the one provided by Qt, with the same result. Is it OK to build from the Windows command prompt, or should I do it from the MinGW's shell?
Platform:
Qt 5.1
CMake 2.8.11.2
MinGW/GCC 4.8
Windows 7
Get the git path out of your PATH before running cmake.
Here is the magic to do that:
set PATH=%PATH:C:/Program Files (x86)/Git/bin;=%
This CMakeLists.txt file works properly:
project(Qt5_cmake_test)
cmake_minimum_required(VERSION 2.8.11)
set(CMAKE_PREFIX_PATH "C:/Qt/Qt5.1.1/5.1.1/mingw48_32")
# Find includes in corresponding build directories
set(CMAKE_INCLUDE_CURRENT_DIR ON)
# Instruct CMake to run moc automatically when needed.
set(CMAKE_AUTOMOC ON)
# Find the Qt libraries
find_package(Qt5Core REQUIRED)
find_package(Qt5Widgets REQUIRED)
# Add the source files from the current directory
aux_source_directory(. SRC_LIST)
# Tell CMake to create the executable
add_executable(${PROJECT_NAME} WIN32 ${SRC_LIST})
# Use Qt5 modules
target_link_libraries(${PROJECT_NAME}
Qt5::Widgets
Qt5::WinMain)
The changes are:
Added find_package(Qt5Core REQUIRED).
Added Qt5::WinMain to target_link_libraries.
In some of my answer here on SO, I have described. CMake does not like sh.exe.
sh.exe was found in your PATH, here:
C:/Program Files (x86)/Git/bin/sh.exe
Solution : Rename C:/Program Files (x86)/Git/bin/sh.exe shortly.
For example:
C:/Program Files (x86)/Git/bin/shxx.exe
But do not forget when everything is built. rename properly again.

Compiling with cmake and include debug information

cmake version 2.8.5
I am trying to compile my project using cmake. However, when i compile I don't think I am including the debug cflags i.e. -ggdb -D_DEBUG. As when I try and debug there is no debub info.
Is there any problem with the CMakeLists.txt files. I have 3 of them
# Mimimum version of cmake required
CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
# Name of project
PROJECT(sdp_creator C)
# Check for correct compiler
# Using C compiler GNUCXX for c++ compiler
IF(CMAKE_COMPILER_IS_GNUCC)
MESSAGE(STATUS "=== GCC C COMPILER DETECTED")
SET(CMAKE_C_FLAGS "-m32 -ggdb -D_DEBUG -Wextra -Wall -Wunreachable-code -O0 -D_LARGEFILE64_SOURCE")
ENDIF(CMAKE_COMPILER_IS_GNUCC)
# Using windows compiler i.e. msvc++
IF(WIN32)
MESSAGE(STATUS "=== MSVC COMPILER DETECTED")
ENDIF(WIN32)
# Location of directory where include files are kept
INCLUDE_DIRECTORIES($ENV{HOME}/projects/sdp_creator/src/sdp)
INCLUDE_DIRECTORIES($ENV{HOME}/projects/sdp_creator/src/apr/inc)
# Location of directory where libraries are kept
LINK_DIRECTORIES($ENV{HOME}/projects/sdp_creator/src/apr/lib)
# Add subdirectories
ADD_SUBDIRECTORY(driver)
ADD_SUBDIRECTORY(sdp)
building shared library:
# Create a shared library called libsdp from sdp.c
# NOTE: static is the default
# NOTE: the lib prefix is automatically added
ADD_LIBRARY(sdp SHARED sdp.c)
Creating executable:
# Add executable called sdp_creator from source file
ADD_EXECUTABLE(sdp_creator main.c)
# Link the sdp library and other libraries with the excutable
#if using windows compiler add additional windows libraries
IF(WIN32)
TARGET_LINK_LIBRARIES(sdp_creator libsdp ws2_32)
MESSAGE(STATUS "=== Linking executable with windows libraries")
ENDIF(WIN32)
# if using gcc compiler
# NOTE: no need to add the -l prefix i.e. -lsdp, no automatically
IF(CMAKE_COMPILER_IS_GNUCC)
TARGET_LINK_LIBRARIES(sdp_creator sdp apr-1)
MESSAGE(STATUS "=== Linking executable with posix libraries")
ENDIF(CMAKE_COMPILER_IS_GNUCC)
Many thanks for any advice,
If you're using the "Unix Makefiles" (or any Makefile-based) generator, set the variable CMAKE_BUILD_TYPE to "Debug"
cmake -DCMAKE_BUILD_TYPE=Debug ../src
That will automatically add the right definitions and flags for your compiler. You should not have to add any flags yourself.
With multi-configuration generators, (like Visual Studio and Xcode), CMAKE_BUILD_TYPE is ignored, because the choice of whether to build a Debug or Release configuration is left up to the developer at build-time, and is not known at CMake configure time.
You can check the exact steps used in make by setting VERBOSE=1. That will tell you if the flags were included or not.
cmake project_dir
make VERBOSE=1
You can also check the CMakeCache.txt to see what value is assigned to CMAKE_C_FLAGS variable.
you can use the CMAKE_C_FLAGS and CMAKE_CXX_FLAGS flags with -g0/1/2 (debug information flag for the compiler. -g2 is the highest information):
cmake ... -DCMAKE_C_FLAGS="-g2" -DCMAKE_CXX_FLAGS="-g2" ...
Another option, if unix Makefiles are used to build the project, is to set CMAKE_BUILD_TYPE in CMakeLists.txt file directly:
set(CMAKE_BUILD_TYPE Debug)
You can find more in
$ man cmakevars
Look for CMAKE_BUILD_TYPE