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

Jones de Andrade johannesrs at gmail.com
Wed Apr 26 16:21:05 CEST 2006

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
 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
-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
-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

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,


P.S.: I'm using the "mixed" run simulation of the "tutor" directory as
a compilation test.

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