[gmx-users] Installing GROMACS 5.1.2 om GPU

[Mark Abraham]

Hi,

You need to follow Intel's instructions for accessing the compiler -
including running their magic scripts from each shell that you want to
compile from. (Or save yourself some pain, use gcc, and probably run
slightly faster.)

Mark

‪On Wed, May 25, 2016 at 10:43 AM ‫יוכבד‬‎ <ybaime at gmail.com> wrote:‬

> Hi
>
> I've been having lots of trouble installing gromacs on our GPU machine.
>
> I have Intel2015 Compilers on my machine which are identified correctly
> during configuration.
>
> /private/gnss/cmake-2.8.11.2/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2
> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/
> -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_FFT_LIBRARY=mkl
> -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include
>
> However when I run the make I get alot of warnings and finally the
> following error:
>
> /private/gnss/gromacs-5.1.2/src/external/boost/boost/config/compiler/in
> tel.hpp(93): remark #193: zero used for undefined preprocessing identifier
> "_WCHAR_T_DEFINED"
> # if ((_WCHAR_T_DEFINED + 0) == 0) && ((_WCHAR_T + 0) == 0)
> ^
>
> Linking CXX executable ../../bin/template
> ld: warning: libimf.so, needed by ../../lib/libgromacs.so.1.2.0, not found
> (try using -rpath or -rpath-link)
> ld: warning: libsvml.so, needed by ../../lib/libgromacs.so.1.2.0, not found
> (try using -rpath or -rpath-link)
> ld: warning: libirng.so, needed by ../../lib/libgromacs.so.1.2.0, not found
> (try using -rpath or -rpath-link)
> ld: warning: libintlc.so.5, needed by ../../lib/libgromacs.so.1.2.0, not
> found (try using -rpath or -rpath-link)
> ld: ../../bin/template: hidden symbol `__intel_cpu_features_init_x' in
>
> /opt/intel/composer_xe_2015.5.223/compiler/lib/intel64/libirc.a(cpu_feature_disp.o)
> is referenced by DSO
> ld: final link failed: Nonrepresentable section on output
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> all the files which are not found do exist in the compiler libraries and it
> is added to my path.
>
> Any suggestions how to solve this?
>
> Thanks
>
> Yocheved
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