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

Justin Lemkul jalemkul at vt.edu
Tue Sep 3 20:39:57 CEST 2013

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
> -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, 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Outdated compilers can't be expected to handle all the best features Gromacs has 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 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 | (410) 706-7441


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