[gmx-users] gromacs 4.6.3 and Intel compiiler 11.x

[Guanglei Cui]

Hi Justin,

Thanks for the response. Right now, I will just have to get around this by
using a slower code. How do I switch off SSE4.1 and use a different CPU
optimization scheme?

Regards,
Guanglei


On Tue, Sep 3, 2013 at 2:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/3/13 1:47 PM, Guanglei Cui wrote:
>
>> Dear GMX users,
>>
>> I'm attempting to compile gromacs 4.6.3 with an older Intel compiler (ver
>> 11.x). Here is how I compiled FFTW,
>>
>> ./configure CC=icc F77=ifort CFLAGS="-O3 -gcc"
>> --prefix=/tmp/gromacs-4.6.3/**fftw-3.3.3/build-intel-threads
>> --enable-threads
>> --enable-sse2 --with-combined-threads --with-our-malloc16 --enable-float
>>
>> And, here is how I invoked cmake,
>>
>> CC=icc CXX=icpc ../cmake-2.8.11/bin/cmake .. -DGMX_FFT_LIBRARY=fftw3
>> -DFFTWF_LIBRARY=/tmp/gromacs-**4.6.3/fftw-3.3.3/build-intel-**
>> threads/lib/libfftw3f.a
>> -DFFTWF_INCLUDE_DIR=/tmp/**gromacs-4.6.3/fftw-3.3.3/**
>> build-intel-threads/include
>> -DBUILD_SHARED_LIBS=no
>> -DCMAKE_INSTALL_PREFIX=/home/**gc603449/APPLICATIONS/gromac-**
>> 4.6.3/thread-float-static
>> -DREGRESSIONTEST_PATH=/tmp/**gromacs-4.6.3/regressiontests-**4.6.1
>>
>> When I ran 'make check', 39 out of 142 kernel tests failed, and 2 out of 9
>> free energy tests failed.
>>
>> This is my first time to compile gromacs, which I am not very familiar
>> with. I wonder if anyone can kindly point out what has gone wrong, and
>> where to look for hints. Any help is much appreciated.
>>
>> Best regards,
>> --
>> Guanglei Cui
>> PS: I am aware of a warning about using older Intel compilers with 4.6.3,
>> but that's the only quality compiler I got. The gcc compiler I have access
>> to is too old (ver 4.1.x)
>>
>
> I assume what you're referring to is http://redmine.gromacs.org/**
> issues/1126 <http://redmine.gromacs.org/issues/1126>, so it should be
> pretty clear (and cmake reminds you) that there are expected regression
> test failures with this compiler and SSE4.1.  I suppose a workaround is to
> use a different CPU acceleration, but you'll pay a price in performance.
> Outdated compilers can't be expected to handle all the best features
> Gromacs has to offer :)
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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-- 
Guanglei Cui