<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Can you try to generate a backtrace for the mknb crash using gdb, in case this offers some insight?<DIV><BR class="khtml-block-placeholder"></DIV><DIV>$ gdb mknb</DIV><DIV>gdb> r -software_invsqrt</DIV><DIV>...</DIV><DIV>gdb> bt<DIV>(backtrace output appears here)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV><DIV>--Tom</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>On May 31, 2006, at 11:33 AM, Jones de Andrade wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Hi David.<BR> <BR> First, thanks for your time. ;)<BR> <BR> Unfortunatelly, it seems that the simple flag it is not quite enough still... :(<BR> <BR> 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. :(<BR> <BR> 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... :( ):<BR> *********************************************************************************************************************<BR> CruNumMac# rm *.o<BR> CruNumMac# rm mknb<BR> CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb.o mknb.c<BR> CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_metacode.o mknb_metacode.c<BR> CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_common.o mknb_common.c<BR> CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_declarations.o mknb_declarations.c<BR> CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_outerloop.o mknb_outerloop.c<BR> CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_innerloop.o mknb_innerloop.c<BR> mknb_innerloop.c(362): warning #188: enumerated type mixed with another type<BR> mknb_func.coul=coulsave;<BR> ^<BR> <BR> mknb_innerloop.c(363): warning #188: enumerated type mixed with another type<BR> mknb_func.vdw=vdwsave;<BR> ^<BR> <BR> CruNumMac# /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../../../src -g -c -o mknb_interactions.o mknb_interactions.c<BR> 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<BR> CruNumMac# rm -f kernel-stamp<BR> CruNumMac# ./mknb -software_invsqrt<BR> >>> Gromacs nonbonded kernel generator (-h for help)<BR> >>> Generating single precision functions in C.<BR> >>> Using Gromacs software version of 1/sqrt(x).<BR> Falha de segmentaēćo<BR> ****************************************************************************************************************<BR> <BR> 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?<BR> <BR> Thanks a lot in advance.<BR> <BR> Jones<BR><BR><DIV><SPAN class="gmail_quote">On 5/31/06, <B class="gmail_sendername">David van der Spoel</B> <<A href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</A>> wrote:</SPAN><BLOCKQUOTE class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> > The error I get is still the following:<BR>> ******************************************************************************<BR>> ./mknb -software_invsqrt<BR>> >>> Gromacs nonbonded kernel generator (-h for help) <BR>> >>> Generating single precision functions in C.<BR>> >>> Using Gromacs software version of 1/sqrt(x).<BR>> make[5]: *** [kernel-stamp] Falha de segmentaēćo<BR>> make[5]: Leaving directory <BR>> `/home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel'<BR>> make[4]: ** [all-recursive] Erro 1<BR>> *****************************************************************************<BR><BR>your problem here is that the mknb program crashes with a SEGV, which is <BR>weird. You could try<BR>make CFLAGS=-g mknb<BR>./mknb -software_invsqrt<BR>make install<BR><BR>Obviously if mknb crashed due to compiler bugs then you might not want<BR>to use that compiler anyway, but if there is a real problem in the <BR>program you will be able to debug it.<BR><BR>--<BR>David.<BR>________________________________________________________________________<BR>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>Dept. of Cell and Molecular Biology, Uppsala University. <BR>Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>phone: 46 18 471 4205 fax: 46 18 511 755<BR><A href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</A> <A href="mailto:spoel@gromacs.org">spoel@gromacs.org </A> <A href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR> </BLOCKQUOTE></DIV><BR><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. 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