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

David van der Spoel spoel at xray.bmc.uu.se
Thu Apr 27 08:44:48 CEST 2006


Jones de Andrade wrote:
> 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?
> 
only the one in the function that the compiler complains about. goto 
line 313 and then upwards from there until you find the offensive 
declaration.

> Thanks a lot,
> 
> Jones
> 
> On 4/26/06, *David van der Spoel* <spoel at xray.bmc.uu.se 
> <mailto: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
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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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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