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

Mark Abraham mark.j.abraham at gmail.com
Tue Sep 3 21:35:34 CEST 2013

On Tue, Sep 3, 2013 at 7:47 PM, Guanglei Cui
<amber.mail.archive at gmail.com> 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

I can't imagine you'll benefit from threaded FFTW, but feel free to try...

> 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.

As Justin said, get an up-to-date compiler. gcc regularly outperforms
icc, anyway. You can use cmake -DGMX_CPU_ACCELERATION=SSE2 to get a
least-common-denominator build, but if you care about threaded FFTW
then you care enough to get a new compiler!


> 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)
> --
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