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

[Guanglei Cui]

Hi Szilard,

Thanks for your reply. I may try your suggestions tomorrow when I get back
to work.

Feeling curious, I downloaded and compiled gmx 4.6.3 on my home computer
(gcc-4.6.3 and ubuntu 12.04). Even with the default (below), kernel (38 out
of 142) and freeenergy (2 out of 9) tests would still fail. I'm not sure
what is going on. Perhaps I should try an earlier version that matches the
regressiontests?

cmake .. -DGMX_BUILD_OWN_FFTW=on
-DREGRESSIONTEST_PATH=/home/cuigl/Downloads/regressiontests-4.6.1

Regards,
Guanglei


On Tue, Sep 3, 2013 at 7:40 PM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:

> On Tue, Sep 3, 2013 at 9:50 PM, Guanglei Cui
> <amber.mail.archive at gmail.com> wrote:
> > Hi Mark,
> >
> > I agree with you and Justin, but let's just say there are things that are
> > out of my control ;-) I just tried SSE2 and NONE. Both failed the
> > regression check.
>
> That's alarming, with GMX_CPU_ACCELERATION=None only the plain C
> kernels get compiled which should pass the regressiontests even with
> icc 11 - although I have not tried myself.
>
> Some things that don't take much time and may be useful to try:
> - make sure that when GMX_CPU_ACCELERATION=None the resulting binary
> does not get compiled with flags that instruct the compiler to
> auto-generate SSE4.1 code (e.g. -msse4.1 or -xHOST);
> - run with the GMX_NOOPTIMIZEDKERNELS environment variable set which
> disables the architecture-specific kernels at runtime (regardless of
> what mdrun was compiled with); the end result should be the same as
> above: the plain C kernels should be used (although with
> GMX_CPU_ACCELERATION != None the instructions of requested instruction
> set will be generated by the compiler as an optimization).
>
> --
> Szilárd
>
> > I think I've spent enough time on this, which justifies
> > escalating this to someone with the control, but is failing regression
> > check with no CPU/instruction optimization normal?
> >
> > Regards,
> > Guanglei
> >
> >
> > On Tue, Sep 3, 2013 at 3:35 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
> >
> >> 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
> >> > -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.
> >>
> >> 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!
> >>
> >> Mark
> >>
> >> > 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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> >
> >
> >
> > --
> > Guanglei Cui
> > --
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-- 
Guanglei Cui