I am using cmake 3.10.2. I have both openmpi and mpich installed. However I need to load only mpich. So I found from the documentation the following
MPI_EXECUTABLE_SUFFIX
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.
My CMake file goes like this
set(MPI_EXECUTABLE_SUFFIX ".mpich")
FIND_PACKAGE(MPI REQUIRED)
INCLUDE_DIRECTORIES(${MPI_INCLUDE_DIRS})
LINK_DIRECTORIES(${MPI_LIBRARY_DIRS})
message(${MPI_INCLUDE_PATH})
However this shows
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/usr/lib/x86_64-linux-gnu/openmpi/include...
Where am I going wrong. Could you please help me with this
Also
mpicc -show
gcc -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -pthread -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi
mpicc.mpich -show
gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -I/usr/include/mpich -L/usr/lib/x86_64-linux-gnu -lmpich
the best is to use modules for switch between openmpi and mpich:
$ module load mpich
$ module unload mpich
$ module load openmpi
http://modules.sourceforge.net/
The default mpicc is not your choice. You can specify it manually in the cmake file, or update the $PATH variable with your mpicc included before the default one. Personally, I installed the mpich in the /usr/local/ directory.
Regards
Related
I have installed msys2/mingw64 because I need the g++ compiler. Now, I want to compile some c++ oce which requires openblas. I have installed the package using pacman -S mingw-w64-x86_64-openblas. However, compiling the code fails with
fatal error: cblas.h: No such file or directory
Clearly, the include path does not contain the headers from openblas which are located at C:\msys64\mings64\include\openblas. This is easy to fix by passing -I<include path> as an additional argument to g++.
Now, I was wondering whether there is an automated way to include include files/headers of installed packages in the g++ include path. The same problem also holds for libraries.
For example, pacman might be able to atomatically append these paths onto some environment variable which g++ checks.
The standard way to get compilation and linking options for a library on MSYS2 and other Unix-like systems is to run this command:
pkg-config --cflags --libs openblas
If you're just compiling, use --cflags by itself.
If you're just linking, use --libs by itself.
Here's an example Bash command you could use to compile a single-file program:
g++ foo.cpp $(pkg-config --cflags --libs openblas) -o foo
I find myself going against the grain configuring cmake paths with ccmake over and over again as with every change of for ex. compiler some of my library paths get lost.
In particular paths to (unlinked) lapack, lapacke, gsl get either lost or set to system defaults instead the ones I've installed with brew.
There has to be a way to tell cmake to "ignore" system libraries and instead look in homebrew paths (say. /opt/homebrew/lib, /opt/homebrew/include etc.).
I'd prefer not to link those libraries as this is not recommend and I'm not experienced in switching environments.
[EDIT] MRE:
git clone https://gitlab.physik.uni-muenchen.de/AG-Scrinzi/tRecX.git
cd tRecX
cmake . -DCMAKE_BUILD_TYPE=Parallel
make -j 8
I add the following to .bash_profile/.zshrc:
export LDFLAGS="-L/opt/homebrew/opt/lapack/lib -L/opt/homebrew/opt/lapack/lib"
export CPPFLAGS="-I/opt/homebrew/opt/lapack/include -I/opt/homebrew/opt/openblas/include"
export PKG_CONFIG_PATH="/opt/homebrew/opt/lapack/lib/pkgconfig /opt/homebrew/opt/openblas/lib/pkgconfig"
then I try:
cmake . -DCMAKE_PREFIX_PATH=/opt/homebrew -DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER -DCMAKE_FIND_USE_CMAKE_SYSTEM_PATH=FALSE -DCMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH=FALSE -DMPI_CXX_COMPILER=/opt/homebrew/bin/mpicxx -DMPI_C_COMPILER=/opt/homebrew/bin/mpicc -DCMAKE_CXX_COMPILER=/opt/homebrew/bin/g++-11 -DCMAKE_C_COMPILER=/opt/homebrew/bin/gcc-11
The most common solution is to just set CMAKE_PREFIX_PATH to /opt/homebrew. CMake will then look preferentially in /opt/homebrew for everything. Since you're on Apple, you might need to set CMAKE_FIND_FRAMEWORK and CMAKE_FIND_APPBUNDLE to LAST or NEVER, too.
You can skip the standard platform search paths by setting CMAKE_FIND_USE_CMAKE_SYSTEM_PATH to FALSE at the command line, in a preset, or in a toolchain file. You might also wish to disable looking at the PATH environment variable by setting CMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH to FALSE.
Finally, if you're in a cross-compiling scenario or toolchain file, you can change the definition of the system directories by setting CMAKE_SYSROOT. Note that the sysroot will have to contain the language runtime libraries (e.g. glibc) and will be passed to the --sysroot flag (or equivalent). Just be aware of those effects, too.
All of this is documented here:
https://cmake.org/cmake/help/latest/command/find_package.html#search-procedure
https://cmake.org/cmake/help/latest/variable/CMAKE_FIND_FRAMEWORK.html#variable:CMAKE_FIND_FRAMEWORK
https://cmake.org/cmake/help/latest/variable/CMAKE_FIND_APPBUNDLE.html#variable:CMAKE_FIND_APPBUNDLE
The following homebrew.cmake toolchain file worked for me:
set(HOMEBREW_PREFIX "/usr/local"
CACHE PATH "Path to Homebrew installation")
set(CMAKE_C_COMPILER "${HOMEBREW_PREFIX}/bin/gcc-11")
set(CMAKE_CXX_COMPILER "${HOMEBREW_PREFIX}/bin/g++-11")
set(CMAKE_PREFIX_PATH
"${HOMEBREW_PREFIX}"
# These libraries are keg-only and not loaded into
# the root prefix by default (to avoid clashes).
"${HOMEBREW_PREFIX}/opt/lapack"
"${HOMEBREW_PREFIX}/opt/openblas"
"${HOMEBREW_PREFIX}/opt/gcc/lib/gcc/11"
)
list(TRANSFORM CMAKE_PREFIX_PATH APPEND "/include"
OUTPUT_VARIABLE CMAKE_CXX_STANDARD_INCLUDE_DIRECTORIES)
set(CMAKE_C_STANDARD_INCLUDE_DIRECTORIES "${CMAKE_CXX_STANDARD_INCLUDE_DIRECTORIES}")
set(CMAKE_FIND_FRAMEWORK NEVER)
set(CMAKE_FIND_APPBUNDLE NEVER)
set(CMAKE_FIND_USE_CMAKE_SYSTEM_PATH FALSE)
set(CMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH FALSE)
I built with the following commands:
$ ls
tRecX homebrew.cmake
$ cmake -G Ninja -S tRecX -B tRecX-build \
-DCMAKE_TOOLCHAIN_FILE=$PWD/homebrew.cmake \
-DCBLAS=/usr/local/opt/openblas/lib/libblas.dylib \
-DCMAKE_EXE_LINKER_FLAGS="-Wl,-undefined,dynamic_lookup" \
-DCMAKE_SHARED_LINKER_FLAGS="-Wl,-undefined,dynamic_lookup" \
-DCMAKE_BUILD_TYPE=Parallel
[ ... output clipped ... ]
Boost found -- full functionality
Build "Parallel" with C++ flags -D_USE_BOOST_ -O3 -pthread -D_USE_FFTW_, return to default by -UCMAKE_BUILD_TYPE
Compiler: /usr/local/bin/g++-11, change by -DCMAKE_CXX_COMPILER=[path_to_complier]
-- Linking to libraries Boost::system;Boost::filesystem;/usr/local/lib/libfftw3.dylib;/usr/local/opt/gcc/lib/gcc/11/libgfortran.dylib;alglib;/usr/local/lib/libarpack.dylib;Boost::system;Boost::filesystem;/usr/local/opt/lapack/lib/liblapacke.dylib;/usr/local/opt/openblas/lib/libblas.dylib;/usr/local/opt/lapack/lib/liblapack.dylib;/usr/local/opt/lapack/lib/libblas.dylib;m
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/alexreinking/Development/tRecX-build
$ cmake --build tRecX-build
I had to set CBLAS manually because libblas.dylib provides the OpenBLAS CBLAS interface, but the build system specifically looks for a library named libcblas. There's no other option in this case.
The code and build have issues with its linking model and dependencies. I was able to paper over these by setting -Wl,-undefined,dynamic_lookup. However, note that this will just defer linker errors to runtime and might impose a large startup cost.
If you can make commits to the project, I would store these settings in a preset, maybe name it homebrew-parallel or something:
-DCMAKE_TOOLCHAIN_FILE=$PWD/homebrew.cmake \
-DCBLAS=/usr/local/opt/openblas/lib/libblas.dylib \
-DCMAKE_EXE_LINKER_FLAGS="-Wl,-undefined,dynamic_lookup" \
-DCMAKE_SHARED_LINKER_FLAGS="-Wl,-undefined,dynamic_lookup" \
-DCMAKE_BUILD_TYPE=Parallel
Then you could just run cmake --preset=homebrew-parallel
So I am trying to include an installed Fortran library to a CMake project. I know the directory where the module (.mod) file is located, but my project can't seem to find it unless I set CMAKE_Fortran_MODULE_DIRECTORY.
SET(LIB_INCLUDE_DIR /usr/local/include)
SET(EX_FILES main.f90 file1.f90 file2.f90)
INCLUDE_DIRECTORIES(${LIB_INCLUDE_DIR})
ADD_EXECUTABLE(test ${EX_FILES})
TARGET_LINK_LIBRARIES(test lib1)
Where the error is
use lib1
1
Fatal Error: Can't open module file 'lib1.mod' for reading at (1): No such file or directory
unless I include the line
SET(CMAKE_Fortran_MODULE_DIRECTORY ${LIB_INCLUDE_DIR})
And then it can find the file just fine. But I'm running into a little problem. By setting CMAKE_Fortran_MODULE_DIRECTORY, CMake tries to write all generated modules to this directory rather than the CMAKE_BINARY_DIR (where I would like it).
From the documentation, I know that CMAKE_Fortan_MODULE_DIRECTORY is meant to be set to specify where to write generated module files, but some compilers look to that directory to find modules. Is there any way to set multiple directories so that if it can't find in/write to one directory, it searches the second? When I try to set CMAKE_Fortran_MODULE_DIRECTORY to be multiple directories, it only looks at the first directory.
If it helps I am on a Ubuntu 14.04 LTS system using gfortran 4.8.4
EDIT:
So by Alexander Vogt's suggestion I ran with VERBOSE=1 and got
cd /home/user/Repos/build/src && gfortran -I/home/user/Repos/build/src -isystem /usr/local/include -c /home/user/Repos/test_project/src/main.f90 -o CMakeFiles/test.dir/main.f90.o
when I did NOT set CMAKE_Fortran_MODULE_DIRECTORY and
cd /home/user/Repos/build/src && gfortran -J/usr/local/include -I/home/user/Repos/build/src -isystem /usr/local/include -c /home/user/Repos/test_project/src/main.f90 -o CMakeFiles/test.dir/main.f90.o
when I did.
It seems the only difference is the -J flag, which sets exactly what CMAKE_Fortran_MODULE_DIRECTORY sets. Is there some flag that sets just where to look for compiled modules, and not where to put them?
I want to generate a dll file in MinGW, I have several object dependencies in order to do that, one of my object dependencies is libdl.so, I add this object in unix simply as :
g++ xx.o yy.o /usr/lib/libdl.so -o module.so
but in MinGW, I don't have any idea how to add this object. any ideas?
There is a MinGW port of libdl that you can use just like under Unix. Quote from the website:
This library implements a wrapper for dlfcn, as specified in POSIX and SUS, around the dynamic link library functions found in the Windows API.
It requires MinGW to build.
You may get pre-built binaries (with MinGW gcc 3.4.5) and a bundled source code from the Downloads section.
The following commands build and install it in a standard MinGW installation (to be run from your MinGW shell):
./configure --prefix=/ --libdir=/lib --incdir=/include && make && make install
To compile your library as a DLL, use the following command:
g++ -shared xx.o yy.o -ldl -o module.dll
I encountered the same problem (msys2, 32bit version of compiler etc.).
For me I found out that the libdl.a was available in /usr/lib but not in /mingw32/lib. I was able to solve the problem by linking it to the /mingw32/lib folder:
ln -s /usr/lib/libdl.a /mingw32/lib
Can someone please tell me how to compile custom kinect code on MAC.
I have downloaded and built the OpenKinect as instructed by the guide(and yes glview works fine)
I am following this: http://openkinect.org/wiki/C%2B%2B_GL_Example
But I am not able to produce any output file.
g++ -g -Wall `pkg-config --cflags libfreenect` -lopengl32 -lglut32 `pkg-config --libs libfreenect` -lGL -lGLU -lglut -c main.cpp
Package libfreenect was not found in the pkg-config search path.
Perhaps you should add the directory containing `libfreenect.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libfreenect' found
Package libfreenect was not found in the pkg-config search path.
Perhaps you should add the directory containing `libfreenect.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libfreenect' found
In file included from main.cpp:27:
/usr/local/include/libfreenect.hpp:29:25: error: libfreenect.h: No such file or directory
In file included from main.cpp:27:
/usr/local/include/libfreenect.hpp:46: error: expected `)' before ‘*’ token