Errors while compiling MPI-based GROMACS

User discussions
1

GROMACS version: 2020.4
GROMACS modification: No
Compiling gromacs-2020.4 fetched me these errors when I gave this command in the terminal:

cmake … -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=ON -DGMX_DOUBLE=OFF -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on

Errors are given below
– The C compiler identification is GNU 10.2.0
– The CXX compiler identification is GNU 10.2.0
– Check for working C compiler: /usr/bin/mpicc
– Check for working C compiler: /usr/bin/mpicc – broken
CMake Error at /usr/share/cmake-3.16/Modules/CMakeTestCCompiler.cmake:60 (message):
The C compiler

"/usr/bin/mpicc"

is not able to compile a simple test program.

It fails with the following output:

Change Dir: /home/roshan/gromacs-2020.4/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/gmake cmTC_20912/fast && /usr/bin/gmake -f CMakeFiles/cmTC_20912.dir/build.make CMakeFiles/cmTC_20912.dir/build
gmake[1]: Entering directory '/home/roshan/gromacs-2020.4/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_20912.dir/testCCompiler.c.o
/usr/bin/mpicc    -o CMakeFiles/cmTC_20912.dir/testCCompiler.c.o   -c /home/roshan/gromacs-2020.4/build/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTC_20912
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_20912.dir/link.txt --verbose=1
/usr/bin/mpicc      CMakeFiles/cmTC_20912.dir/testCCompiler.c.o  -o cmTC_20912 
/usr/bin/ld: cannot find -lmpi
/usr/bin/ld: cannot find -lopen-rte
/usr/bin/ld: cannot find -lopen-pal
/usr/bin/ld: cannot find -lhwloc
/usr/bin/ld: cannot find -levent
/usr/bin/ld: cannot find -levent_pthreads
collect2: error: ld returned 1 exit status
gmake[1]: *** [CMakeFiles/cmTC_20912.dir/build.make:87: cmTC_20912] Error 1
gmake[1]: Leaving directory '/home/roshan/gromacs-2020.4/build/CMakeFiles/CMakeTmp'
gmake: *** [Makefile:121: cmTC_20912/fast] Error 2

CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:58 (project)

– Configuring incomplete, errors occurred!
See also “/home/roshan/gromacs-2020.4/build/CMakeFiles/CMakeOutput.log”.
See also “/home/roshan/gromacs-2020.4/build/CMakeFiles/CMakeError.log”.

When I checked the error log file, I can see the following warnings:
/usr/bin/ld: cannot find -lmpi_cxx
/usr/bin/ld: cannot find -lmpi
/usr/bin/ld: cannot find -lopen-rte
/usr/bin/ld: cannot find -lopen-pal
/usr/bin/ld: cannot find -lhwloc
/usr/bin/ld: cannot find -levent
/usr/bin/ld: cannot find -levent_pthreads

Looking forward to your suggestions. Thanks.

2

Hi Roshan,

you might miss the the necessary MPI librarires. If you are using ubuntu, you should be able to get them via typing:

sudo apt install mpich
3

And hwloc is missing, which you can get with
sudo apt install hwloc