Gromacs Installation error

User discussions
1

GROMACS version:gromacs-2020.1
GROMACS modification: No

I am porting the gromacs (version 2020.1) application using NEC Compilers.

Environment options:
Export CC=mpincc

Export CXX=mpinc++

  1. Using cmake(version 3.17.0).

  2. Cmake command used:

“cmake … -DCMAKE_C_COMPILER=mpincc -DCMAKE_CXX_COMPILER=mpinc++ -DCMAKE_C_FLAGS=" -report-all -fopenmp " -DCMAKE_CXX_FLAGS=" -report-all -fopenmp " -DGMX_MPI=ON -DCMAKE_PREFIX_PATH=/opt/nec/ve/nlc/2.0.0/ -DCMAKE_INSTALL_PREFIX=/S/home/nti/work/shubham/GROMACS_Intel/gromacs-2020.1/ -DGMX_DOUBLE=on -DFFTW_INCLUDE_DIR=/opt/nec/ve/nlc/2.0.0/include/ -DGMX_FFT_LIBRARY=fftw3 -DFFTW_LIBRARY=/opt/nec/ve/nlc/2.0.0/lib/ ”

  1. Make command: “make”

It results in error:

[ 1%] Built target release-version-info

[ 1%] Built target thread_mpi

[ 1%] Built target lmfit_objlib

[ 4%] Built target tng_io_obj

[ 4%] Built target tng_io_zlib

[ 25%] Built target linearalgebra

Scanning dependencies of target modularsimulator

[ 25%] Building CXX object src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o

"/S/home/nti/work/shubham/GROMACS_Aurora/gromacs-2020.1/src/gromacs/compat/stri

ng_view.h", line 894: error: incomplete type is not allowed

const basic_string_view v;

^

1 error detected in the compilation of “/S/home/nti/work/shubham/GROMACS_Aurora/gromacs-2020.1/src/gromacs/modularsimulator/modularsimulator.cpp”.

make[2]: *** [src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o] Error 1

make[1]: *** [src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/all] Error 2

make: *** [all] Error 2

Can you suggest the possible cause of error.

2

Hi Shubham,

This seems like a bug from the GROMACS side in the code that it uses to emulate the C++17 string_view using https://github.com/martinmoene/string-view-lite . With a change to C++17 in the next release this should be fixed, but to have a look into how to fix this earlier, I generated a bug-report for this on gitlab here:

To confirm, you can try to see if there are any issues with string-view-lite on its own and your NEC compilers; updating compilers is a first guess on an unlikely, but possibly easy fix.

3

Hi Shubham,

can you try to see if this version you can download here fixes the issue?

We’d be very curious to know!

Find the related merge request here:

4

Thanks cblau,
I had made the latest changes in the string-view file but the error remain same.
May be this is the issue with our compiler because the same code works with intel compilers icpc. So as we need to do some urgent basis work so I moved to the oldest version.

thanks for your kind support and quick response.