Re: [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  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 
> 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  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
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
>
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Re: [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 
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  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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
-- 
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Re: [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  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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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[gmx-users] Installing GROMACS 5.1.2 om GPU

[יוכבד]

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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