[gmx-users] gromacs 2018 make error with multiple compilers and GPU support

Kevin Boyd kevin.boyd at uconn.edu
Mon May 7 19:38:22 CEST 2018


I've been trying to install gromacs 2018 on a cluster running Centos7.
In keeping with the guidelines for maximizing performance, I'm
compiling with a recent (7.3.0) GCC version. However, Cuda 9.0 on
Centos 7.x needs to be compiled with GCC 4.8.5, so my cmake command
included -DCUDA_HOST_COMPILER=/path/to/gcc4.8.5. When installing, the
following error occurred.

[ 98%] Built target libgromacs
[ 98%] Linking CXX executable ../../bin/template
../../lib/libgromacs.so.4.0.0: undefined reference to
`gmx::formatString(char const*, ...)'
../../lib/libgromacs.so.4.0.0: undefined reference to
std::char_traits<char>, std::allocator<char> >*)'
../../lib/libgromacs.so.4.0.0: undefined reference to
../../lib/libgromacs.so.4.0.0: undefined reference to

The same error (or at least part of the error) shows up trying Gromacs
2018, 2018.1, and the current master branch.

My full cmake configuration command was

cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/prefix    \
              -DGMX_GPU=ON                                               \
              -DGMX_SIMD=AVX2_256                                  \
              -DGMX_FFT_LIBRARY=fftw3                             \
              -DCUDA_HOST_COMPILER=/path/to/gcc4.8.5 \

I can compile and run successfully if I turn off GPU support (with GCC
7.3.0), or by using GCC 4.8.5 for the entire install (with GPUs), so
I'm assuming the issue has something to do with using both compilers.

Has anyone else run into similar issues?



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