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

[Tom Joseph]

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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> ++++
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060531/9f94c2f1/attachment.html>