[gmx-users] gromacs 2018 compilation problem with stdlib

[David van der Spoel]

Den 2018-07-14 kl. 04:58, skrev Manoel Barrionuevo:
> Hi all,
> 
> I'm trying to compile gromacs 2018.2 and I would like to use intel 
> compilers along with nvidia gpu graphic (GTX 1060) card in a desktop 
> computer with a intel i5 quad-core cpu (the only purpose of it is for 
> learning), in order to do so I was first following the suggested 
> procedures at the INSTALL file distributed along with gromacs, and got 
> the command bellow:
> 
> cmake ../ -DGMX_FFT_LIBRARY="mkl" -DMKL_LIBRARIES="-Wl,--start-group 
> /opt/intel17/mkl/lib/intel64/libmkl_intel_ilp64.a 
> /opt/intel17/mkl/lib/intel64/libmkl_gnu_thread.a 
> /opt/intel17/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lgomp 
> -lpthread -lm -ldl" -DMKL_INCLUDE_DIR="/opt/intel17/mkl/include" 
> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda-9.1/" 
> -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc -DGMX_CXX_FLAGS="-g -O2 
> -std=c++11"
> 
> It worths to say that the OS under current operation is Lubuntu (16.04) 
> and it has both gcc-5.4.1 and g++-5.4.1. Everything goes smoothly 
> without problems, however I noticed a std failure after issuing the 
> "make" command, it says:
> 
> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(250): 
> error: namespace "std" has no member "_Exit"
>        std:: _Exit(returnValue);
Which version of the intel compiler are you using?
icc --version might tell you.

This function should be present since C++11.
https://en.cppreference.com/w/cpp/utility/program/_Exit

>              ^
> 
> /home/yokai/Programs/gromacs-2018.2/src/gromacs/utility/fatalerror.cpp(251): 
> warning #1628: function declared with "noreturn" does retu
> rn
>    }
>    ^
> 
> The same problem can be seen if I start from a very simple "cmake ../" 
> and "make". What am I doing wrong? Is there some environment preparation 
> step to be done prior to everything else, and what should it be?
> 
> I must say that I'm not an expert on compiling things up and I got 
> stuck. Could someone help me out? It would be of great help to know some 
> tips from you guys.
> 
> Thank you all.
> 
> Kind regards,
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se