[gmx-users] Installing GROMACS 5.1.2 om GPU

[יוכבד]

The problem is the gcc installed on our cluster is to old and it is not
possible to upgrade at the moment.

On Wed, May 25, 2016 at 1:44 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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>