[gmx-users] gromacs 2018 compilation problem with stdlib
David van der Spoel
spoel at xray.bmc.uu.se
Sat Jul 14 07:54:02 CEST 2018
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_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
> 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:
> 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.
> warning #1628: function declared with "noreturn" does retu
> 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.
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