[gmx-users] Installing GROMACS 5.1.2 om GPU

[Mark Abraham]

Hi,

So did you try the other half of my suggestion? (And ask harder -
installing gcc is no harder than installing icc, and there is no point
buying CUDA GPUs without funding for people to install compilers that
support them.)

Mark

‪On Thu, May 26, 2016 at 11:39 AM ‫יוכבד‬‎ <ybaime at gmail.com> wrote:‬

> 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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>>
>