[gmx-users] intel compiler + amd64: help needed.
Tom Joseph
tom-lists at jambon.ll.cx
Wed May 31 18:14:32 CEST 2006
Can you try to generate a backtrace for the mknb crash using gdb, in
case this offers some insight?
$ gdb mknb
gdb> r -software_invsqrt
...
gdb> bt
(backtrace output appears here)
--Tom
On May 31, 2006, at 11:33 AM, Jones de Andrade wrote:
> 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_func.coul=coulsave;
> ^
>
> mknb_innerloop.c(363): warning #188: enumerated type mixed with
> another type
> mknb_func.vdw=vdwsave;
> ^
>
> 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.
>
> Jones
>
> 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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