[gmx-users] intel compiler + amd64: help needed.

Jones de Andrade johannesrs at gmail.com
Wed May 31 17:33:46 CEST 2006

Hi David.

First, thanks for your time. ;)

Unfortunatelly, it seems that the simple flag it is not quite enough
still... :(

If it was not a well known fact that intel compiler yelds you some extra
performance for gromacs, and if I would not want to try to make QM/MM of
gromacs+cpmd (and, in this case, I DO prefer to not mix compilers), I would
have gave up this compiler already. :(

Well, here is what I got: I tried to put the suggested "CFLAGS" as an option
in the "make" line, and that didn't work. So I set the CFLAGS by hand before
the make. Since tht was not enough too, I did the compilations by hand, one
compilation line after the other. Here we go (before anybody asks: it failed
at the exact same point...  :(  ):
CruNumMac# rm *.o
CruNumMac# rm mknb
CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I.
-I../../../../src -g -c -o mknb.o mknb.c
CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I.
-I../../../../src -g -c -o mknb_metacode.o mknb_metacode.c
CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I.
-I../../../../src -g -c -o mknb_common.o mknb_common.c
CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I.
-I../../../../src -g -c -o mknb_declarations.o mknb_declarations.c
CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I.
-I../../../../src -g -c -o mknb_outerloop.o mknb_outerloop.c
CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I.
-I../../../../src -g -c -o mknb_innerloop.o mknb_innerloop.c
mknb_innerloop.c(362): warning #188: enumerated type mixed with another type

mknb_innerloop.c(363): warning #188: enumerated type mixed with another type

CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I.
-I../../../../src -g -c -o mknb_interactions.o mknb_interactions.c
CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I.
-I../../../../src -g -o mknb mknb.o mknb_metacode.o mknb_common.o
mknb_declarations.o mknb_outerloop.o mknb_innerloop.o mknb_interactions.o
CruNumMac# rm -f kernel-stamp
CruNumMac# ./mknb   -software_invsqrt
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating single precision functions in C.
>>> Using Gromacs software version of 1/sqrt(x).
Falha de segmentação

Unfortunately, it means that I'm back to the beggining. I've also tried the
"-debug extended" option instead of "-g", and that yelded exactly same
results... :( Any suggestion at this point?

Thanks a lot in advance.


On 5/31/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> > The error I get is still the following:
> >
> ******************************************************************************
> > ./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
> >
> *****************************************************************************
> your problem here is that the mknb program crashes with a SEGV, which is
> weird. You could try
> make CFLAGS=-g mknb
> ./mknb -software_invsqrt
> make install
> Obviously if mknb crashed due to compiler bugs then you might not want
> to use that compiler anyway, but if there is a real problem in the
> program you will be able to debug it.
> --
> 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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