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<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<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>
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<p class=MsoNormal><font size=4 color=white face=Verdana><span
style='font-size:14.0pt;font-family:Verdana;color:white'>Shawn T. Brown<o:p></o:p></span></font></p>
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color=white face=Verdana><span style='font-size:10.0pt;font-family:
Verdana;color:white'><img width=45 height=49 id="_x0000_i1025"
src="cid:image001.jpg@01C6626B.2C74E980" border=0><o:p></o:p></span></font></p>
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height:.75pt'>
<p class=MsoNormal><i><font size=1 color="#4e81c4" face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:#4E81C4;font-style:
italic'>Senior Scientific Support Specialist</span></font></i><font
size=1 color="#4e81c4" face=Verdana><span style='font-size:8.0pt;
font-family:Verdana;color:#4E81C4'> <o:p></o:p></span></font></p>
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<p class=MsoNormal align=right style='text-align:right'><st1:City
w:st="on"><st1:place w:st="on"><b><font size=1 color="#4e81c4"
face=Verdana><span style='font-size:8.0pt;font-family:Verdana;
color:#4E81C4;font-weight:bold'>Pittsburgh</span></font></b></st1:place></st1:City><b><font
size=1 color="#4e81c4" face=Verdana><span style='font-size:8.0pt;
font-family:Verdana;color:#4E81C4;font-weight:bold'> Supercomputing
Center</span></font></b><font size=1 color="#4e81c4" face=Verdana><span
style='font-size:8.0pt;font-family:Verdana;color:#4E81C4'><br>
<a
href="http://maps.yahoo.com/py/maps.py?Pyt=Tmap&addr=Rm+%23369&csz=Pittsburgh%2C+PA+15213&country=us"
target="_blank"><font color="#4e81c4"><span style='color:#4E81C4;
text-decoration:none'>Carnegie Mellon University<br>
Pittsburgh Supercomputing Center<br>
Rm #369<br>
Pittsburgh, PA 15213</span></font></a> <o:p></o:p></span></font></p>
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href="mailto:stbrown@psc.edu" target="_blank"><font color="#4e81c4"><span
style='color:#4E81C4;text-decoration:none'>stbrown@psc.edu</span></font></a>
<o:p></o:p></span></font></p>
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color="#4e81c4" face=Verdana><span style='font-size:8.0pt;font-family:
Verdana;color:#4E81C4'>tel: <o:p></o:p></span></font></p>
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color="#4e81c4" face=Verdana><span style='font-size:8.0pt;font-family:
Verdana;color:#4E81C4'>412-268-4635 <o:p></o:p></span></font></p>
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color="#4e81c4" face=Verdana><span style='font-size:8.0pt;font-family:
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<p class=MsoNormal><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><a
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