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] [EMAIL PROTECTED] http://folding.bmc.uu.se
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