CMake cannot find MPI in standard installation path

#1

The following is my CMakeLists.txt file and actually it works well on my server4. However, I tried to configure it on my server3 and then it could not find the MPI package.


project(CUDA_MPI LANGUAGES CXX CUDA)
set(CMAKE_CXX_FLAGS "-lrt")
find_package(CUDA REQUIRED)
find_package(MPI REQUIRED)

add_library(Timer STATIC timer.h 
						 timer.cpp)
add_library(Coll STATIC  collectives.h 
						collectives.cu)
add_executable(CUDA_MPI ${CMAKE_CURRENT_SOURCE_DIR}/test/test.cpp)

target_link_libraries(Coll PUBLIC Timer)
target_link_libraries(CUDA_MPI PUBLIC Coll MPI_LIB ${CUDA_LIBRARIES})

I have checked the installation path of OpenMPI and it seems that both server are exact same. The path is

openmpi: /usr/lib/x86_64-linux-gnu/openmpi

I want to provide any hints for my CMakeLists file and it also failed. I am confused that why I cannot find the MPI on the server3 but I can do it on another machine. Is it because my different installation way?

The error log is as the following.

Performing C++ SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_c1a8d/fast && /usr/bin/make -f CMakeFiles/cmTC_c1a8d.dir/build.make CMakeFiles/cmTC_c1a8d.dir/build
make[1]: Entering directory '/home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_c1a8d.dir/src.cxx.o
/home/szhangcj/.conda/envs/distributed/bin/x86_64-conda_cos6-linux-gnu-c++    -lrt -L/home/szhangcj/.conda/envs/distributed/lib -DCMAKE_HAVE_LIBC_PTHREAD   -o CMakeFiles/cmTC_c1a8d.dir/src.cxx.o -c /home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp/src.cxx
Linking CXX executable cmTC_c1a8d
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_c1a8d.dir/link.txt --verbose=1
/home/szhangcj/.conda/envs/distributed/bin/x86_64-conda_cos6-linux-gnu-c++  -lrt -L/home/szhangcj/.conda/envs/distributed/lib -DCMAKE_HAVE_LIBC_PTHREAD  -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/szhangcj/.conda/envs/distributed/lib -Wl,-rpath-link,/home/szhangcj/.conda/envs/distributed/lib -L/home/szhangcj/.conda/envs/distributed/lib  CMakeFiles/cmTC_c1a8d.dir/src.cxx.o  -o cmTC_c1a8d 
/home/szhangcj/.conda/envs/distributed/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/cmTC_c1a8d.dir/src.cxx.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5'
/home/szhangcj/.conda/envs/distributed/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/szhangcj/.conda/envs/distributed/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_c1a8d.dir/build.make:86: recipe for target 'cmTC_c1a8d' failed
make[1]: *** [cmTC_c1a8d] Error 1
make[1]: Leaving directory '/home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp'
Makefile:121: recipe for target 'cmTC_c1a8d/fast' failed
make: *** [cmTC_c1a8d/fast] Error 2


Source file was:
#include <pthread.h>

void* test_func(void* data)
{
  return data;
}

int main(void)
{
  pthread_t thread;
  pthread_create(&thread, NULL, test_func, NULL);
  pthread_detach(thread);
  pthread_join(thread, NULL);
  pthread_atfork(NULL, NULL, NULL);
  pthread_exit(NULL);

  return 0;
}

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_5b4c9/fast && /usr/bin/make -f CMakeFiles/cmTC_5b4c9.dir/build.make CMakeFiles/cmTC_5b4c9.dir/build
make[1]: Entering directory '/home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_5b4c9.dir/CheckFunctionExists.cxx.o
/home/szhangcj/.conda/envs/distributed/bin/x86_64-conda_cos6-linux-gnu-c++    -lrt -L/home/szhangcj/.conda/envs/distributed/lib -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_5b4c9.dir/CheckFunctionExists.cxx.o -c /home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CheckLibraryExists/CheckFunctionExists.cxx
Linking CXX executable cmTC_5b4c9
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_5b4c9.dir/link.txt --verbose=1
/home/szhangcj/.conda/envs/distributed/bin/x86_64-conda_cos6-linux-gnu-c++  -lrt -L/home/szhangcj/.conda/envs/distributed/lib -DCHECK_FUNCTION_EXISTS=pthread_create  -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/szhangcj/.conda/envs/distributed/lib -Wl,-rpath-link,/home/szhangcj/.conda/envs/distributed/lib -L/home/szhangcj/.conda/envs/distributed/lib  CMakeFiles/cmTC_5b4c9.dir/CheckFunctionExists.cxx.o  -o cmTC_5b4c9 -lpthreads 
/home/szhangcj/.conda/envs/distributed/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_5b4c9.dir/build.make:86: recipe for target 'cmTC_5b4c9' failed
make[1]: *** [cmTC_5b4c9] Error 1
make[1]: Leaving directory '/home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp'
Makefile:121: recipe for target 'cmTC_5b4c9/fast' failed
make: *** [cmTC_5b4c9/fast] Error 2



The MPI test test_mpi for CXX in mode normal failed to compile with the following output:
Change Dir: /home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_01687/fast && /usr/bin/make -f CMakeFiles/cmTC_01687.dir/build.make CMakeFiles/cmTC_01687.dir/build
make[1]: Entering directory '/home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_01687.dir/test_mpi.cpp.o
/home/szhangcj/.conda/envs/distributed/bin/x86_64-conda_cos6-linux-gnu-c++    -lrt -L/home/szhangcj/.conda/envs/distributed/lib    -pthread -o CMakeFiles/cmTC_01687.dir/test_mpi.cpp.o -c /home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/FindMPI/test_mpi.cpp
/home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/FindMPI/test_mpi.cpp:1:10: fatal error: mpi.h: No such file or directory
 #include <mpi.h>
          ^~~~~~~
compilation terminated.
CMakeFiles/cmTC_01687.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_01687.dir/test_mpi.cpp.o' failed
make[1]: *** [CMakeFiles/cmTC_01687.dir/test_mpi.cpp.o] Error 1
make[1]: Leaving directory '/home/szhangcj/HPC/MPI/baidu-allreduce/build/CMakeFiles/CMakeTmp'
Makefile:121: recipe for target 'cmTC_01687/fast' failed
make: *** [cmTC_01687/fast] Error 2
#2

Do you have the actual error output available? The literal MPI_LIB looks…suspicious to me.

#3

I have edited my question. Please check it.

#4

It seems like something went wrong with the MPI compiler wrapper detection? @chuckatkins Thoughts?

#5

But I can check the configure of my mpicc as the following.

Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.4.0-1ubuntu1~18.04.1' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1)

By the way, I still cannot find the MPI package even I tried to install the MPI by using conda.

#6

The problem seems to be that FindMPI is not extracting the information directly from it properly or something. It is good that the wrappers do work though :slight_smile: .

#7

Yes. I do not know why it is.