[gmx-users] gromacs 2018 compilation problem with stdlib

Manoel Barrionuevo manoelvfb at gmail.com
Sat Jul 14 16:30:58 CEST 2018


Currently I have two versions of icc, 18 and 17, but I have already set the environment variables in order to use only icc 17 and icpc 17, that's because cuda-9.1 is not compatible with 18 version of intel's compilers. If I make use of icc 18 I'll get NVCC/C broken warning and the cmake will fail.

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On Jul 14, 2018, 02:54, at 02:54, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>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
>> 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/" 
>> -std=c++11"
>> It worths to say that the OS under current operation is Lubuntu
>> 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
>> 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
>> 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
>> 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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