[gmx-users] Benching against different compilers - Help needed

[Jones de Andrade]

Hi.

Sorry if it looks like a stupidy question (and it is), but I'm quite bad on
C (fortran addicted).

I found 4 entries in the file like the one you told me to change. May I
change all them, or which ones?

Thanks a lot,

Jones

On 4/26/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Jones de Andrade wrote:
> > Hi all.
> >
> > Well, some time ago I decided to bench gromacs on AMD64 machines
> > compiled with different compilers (both single and double precision,
> > both internal and external blas and lapack, just FFTw 3 for fourier)
> > in order to see which one performs better.
> >
> > To time, I have available GCC, PGI and Intel compilers. Pathscale is a
> > future option.
> >
> > Unfortunatelly, I was able to properly compile it just with GCC (all 4
> > flavours, despite the fact that the external libraries of ACML didn't
> > seem to improve so much the performance as I expected), but failed on
> > both PGI and Intel compilers at different points. So, I'm asking for
> > help on those compilation issues.
> >
> > For Intel, the compilation ends up with a segmentation fault at the
> > following point:
> >
> >
> ***********************************************************************************
> > ./mknb   -software_invsqrt
> >  >>> Gromacs nonbonded kernel generator (-h for help)
> >  >>> Generating single precision functions in C.
> >  >>> Using Gromacs software version of 1/sqrt(x).
> >  make[5]: *** [kernel-stamp] Falha de segmentação
> >  make[5]: Leaving directory
> > `/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel'
> >  make[4]: ** [all-recursive] Erro 1
> >
> ***********************************************************************************
> >
> > And, for PGI, it dies at the following point (after using the
> > --without-x --without-motif-libraries -- without-motif-includes flags
> > for configure):
> >
> >
> ****************************************************************************************
> > source='gmx_sgangle.c' object='gmx_sgangle.lo' libtool=yes \
> >  DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
> >  /bin/sh ../../libtool --mode=compile --tag=CC
> > /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I. -I.
> > -I../../src  -I../../include
> > -DGMXLIBDIR=\"/usr/local/bin/chemistry/gromacs/PSI//share/top\"
> > -I/usr/local/lib64/fftw/pgi/include  -tp=k8-64 -fastsse -Mipa=fast
> > -Mipa=inline -c -o gmx_sgangle.lo gmx_sgangle.c
> >   /usr/local/pgi/linux86-64/6.0/bin/pgcc -DHAVE_CONFIG_H -I. -I.
> > -I../../src -I../../include
> > -DGMXLIBDIR=\"/usr/local/bin/chemistry/gromacs/PSI//share/top\"
> > -I/usr/local/lib64/fftw/pgi/include -tp=k8-64 -fastsse -Mipa=fast
> > -Mipa=inline -c gmx_sgangle.c -o gmx_sgangle.o
> >  PGC-S-0090-Scalar data type required for logical expression
> > (gmx_sgangle.c: 313)
> >  PGC-S-0090-Scalar data type required for logical expression
> > (gmx_sgangle.c: 320)
> >  PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with severe errors
> >
> **************************************************************************************
> >
> Shitty compiler...
>
> replace in the header of the function
> matrix box,
> by
> rvec *box
>
>
> > Did anyone run into those problems before when trying to compile
> > gromacs with those compilers?
> >
> > Any help will be very welcome. :)
> >
> > Thanks a lot in advance,
> >
> > Jones
> >
> > P.S.: I'm using the "mixed" run simulation of the "tutor" directory as
> > a compilation test.
> > _______________________________________________
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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