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

Wed Sep 4 16:06:41 CEST 2013

I was following
http://www.gromacs.org/Documentation/Installation_Instructions. The link to
4.6.3 regression test set isn't obvious. Following the pattern, I
downloaded the 4.6.3 regression test tarball (which apparently unpacks to a
folder named for 4.6.2). Now, GMX_CPU_ACCELERATION=None passes all tests.
SSE4.1 fails only 1 of the kernel tests
(nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4) and nothing else.

Again, thanks for everyone's help.

Regards,
Guanglei

On Wed, Sep 4, 2013 at 2:54 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Please test using the test set version that matches the code!
> On Sep 4, 2013 5:16 AM, "Guanglei Cui" <amber.mail.archive at gmail.com>
> wrote:
>
> > 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)
> > > >> > --
> > > >> > gmx-users mailing list    gmx-users at gromacs.org
> > > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > >> > * Please search the archive at
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> > > >> > www interface or send it to gmx-users-request at gromacs.org.
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> > > >> --
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> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > Guanglei Cui
> > > > --
> > > > gmx-users mailing list    gmx-users at gromacs.org
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> >
> >
> >
> > --
> > Guanglei Cui
> > --
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-- 
Guanglei Cui