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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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