[gmx-users] gromacs 2018 compilation problem with stdlib

Manoel Barrionuevo manoelvfb at gmail.com
Sat Jul 14 04:58:14 CEST 2018

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/" 

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);

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,

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