<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV>Providing a backtrace or two would really help. Given the exact same input files and run conditions, does it sometimes segfault and sometimes not? Does this happen on a login node (full glibc and such) or just the compute nodes (POSIX subset)?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Separately, is it a better idea to use fftw2 since it supports MPI?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>(Hopefully soon my Teragrid access will extend to bigben, so I'm especially interested in this...)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Tom</DIV><BR><DIV><DIV>On Apr 17, 2006, at 10:06 PM, Shawn T. Brown wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><O:SMARTTAGTYPE namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="City"> <O:SMARTTAGTYPE namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="place"> <DIV class="Section1"><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Hello, I am trying to port GROMACS 3.3.1 to the CRAY XT3, which is essentially an Opteron machine with the PGI compilers. I can get everything to compile, but when I run mdrun, I am “randomly” getting segmentation faults. This seems to happen no matter what input file I use. It happens in init_forcerec (line 1001), in add_gbond, and in solvent_check. Some times it runs fine. I am configuring with the following command:<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">./configure --with-fft=fftw3 --disable-nice --enable-mpi --program-suffix="_xt3" --enable-float --with-external-blas --with-external-lapack --disable-threads --prefix=/usr/local/packages/gromacs-3.3.1<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">I am wondering if anyone else has seen these types of problems and knows how to fix them. I have tried compiling the code without optimization, to no avail.<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial"><O:P> </O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Thanks in advance,<O:P></O:P></SPAN></FONT></P><P class="MsoNormal"><FONT size="2" face="Arial"><SPAN style="font-size:10.0pt; font-family:Arial">Shawn</SPAN></FONT></P><P class="MsoNormal"><FONT class="Apple-style-span" face="Arial" size="4"><SPAN class="Apple-style-span" style="font-size: 13.3333px;"></SPAN></FONT></P></DIV></O:SMARTTAGTYPE></O:SMARTTAGTYPE></BLOCKQUOTE></DIV></BODY></HTML>