<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
Hello,<br>I got a weird problem by running Gromacs 4.0.7 on a BG/P machine ("Intrepid" at Argonne national lab).<br>The simulated system is a box of SPC water with 648,000 atoms and all MD simulations were performed on 256 CPU cores with MPI. The compiling environment was Linux with IBM compiler and libs.<br>I first compile the code with flags suggested on the Wiki, such as:<br>./configure --prefix=$PREFIX \<br> --host=ppc \<br> --build=ppc64 \<br> --disable-software-sqrt \<br> --enable-ppc-sqrt=1 \<br> &n
bsp; --enable-ppc-altivec \<br> --enable-bluegene \<br> --disable-fortran \<br> --enable-mpi \<br> --with-fft=fftpack \<br> --without-x \<br> CC="mpixlc_r" \<br> CFLAGS="-O3 -qarc
h=450d -qtune=450" \<br> MPICC="mpixlc_r"<br> CXX="mpixlcxx_r"<br> CXXFLAGS="-O3 -qarch=450 -qtune=450"<br> F77="mpixlf77_r"<br> FFLAGS="-O3 -qarch=450 -qtune=450"<br> LIBS="-lmass"<br><br>Here I used fftpack to ensure that the problem is not due to the fftw lib. I got the water system running will with Cut-off for electrostatics. However,
the systems always crashed after a few ( ~100) steps if I used PME. The same system with same PME option runs fine on other non-blue gene clusters I tested. <br>The error message I got was sth like <br>t = 0.100 ps: Water molecule starting at atom 403468 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates.<br><br>and<br><br>2 particles communicated to PME node 63 are more than a cell length out of the domain decomposition cell of their charge group<br><br>From .log file, the kinetic energy is increasing and turned to be "nan". So the system is exploding.<br><br>I found if I turned off the blue gene optimizations during configure, the water system could be run without problem. For example, I used<br> --enable-software-sqrt \<br>
--disable-ppc-sqrt \<br>
--disable-bluegene \<br>and everything else was the same. <br>I suspect there was an issue regarding the blue gene specific code and PME.<br>Could anyone give any comments?<br><br>Thanks a lot.<br>Lanyuan Lu<br> <br /><hr />使用新一代 Windows Live Messenger 轻松交流和共享！ <a href='http://www.windowslive.cn/messenger/' target='_new'>立刻下载！</a></body>
</html>