<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Jones,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>There are two things I can think of immediately:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>1. Make sure to set optimization and architecture options for portable code. By default, the intel compiler might generate binaries that use SSE3-specific stuff, although it is unlikely in this part of the code.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>2. Try setting "CC_FOR_BUILD=gcc" before running configure, or as an argument when calling make. This will use a different compiler for code that is executed during the build process (important for cross-compiling, and on systems where you cannot execute mpicc-compiled programs outside the queue).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV><BLOCKQUOTE type="cite"><BR> Program received signal SIGSEGV, Segmentation fault.<BR> 0x00002aaaab15a88c in __find_specmb () from /lib64/tls/libc.so.6<BR> (gdb) where<BR> #0 0x00002aaaab15a88c in __find_specmb () from /lib64/tls/libc.so.6<BR> #1 0x00002aaaab140e6f in vfprintf () from /lib64/tls/libc.so.6<BR> #2 0x00002aaaab15e2a9 in vsprintf () from /lib64/tls/libc.so.6<BR> #3 0x00002aaaab149568 in sprintf () from /lib64/tls/libc.so.6<BR> #4 0x000000000040248b in mknb_code (format=0x40cd2e "s") at mknb_metacode.c:282<BR> #5 0x0000000000401aaf in mknb_declare_real (name=0x7fffffffd0d0 "ix1,iy1,iz1,fix1,fiy1,fiz1") at mknb_metacode.c:104<BR> #6 0x0000000000403e62 in mknb_declare_variables () at mknb_declarations.c:258<BR> #7 0x0000000000400fef in mknb_write_function () at mknb.c:154<BR> #8 0x00000000004017cf in main (argc=1, argv=0x7fffffffd628) at mknb.c:348<BR> <BR>Well, what does this kind of stuff means? It worries about the libc 4 times, but also about the other files. :( What shall I look at?<BR> <BR> David Mathog: thanks also. But, how could I fix that?<BR> <BR> Thanks a lot for everything.<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;"> gdb> where<BR>it will tell you the line in the mknb this was called from.<BR>if you call a library function with garbage data it may crash there...<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><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. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>