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Dear Mark,<br>When I set <span>NOASSEMBLYLOOPS to 1, the simulation could be finished without any problem. So I guess it's related to the assembly loops for BG.<br>Thanks,<br>Lanyuan<br><br></span><br><hr id="stopSpelling">From: mark.abraham@anu.edu.au<br>To: gmx-users@gromacs.org<br>Date: Sat, 5 Jun 2010 03:31:33 +1000<br>Subject: Re: [gmx-users] PME problem on BG/P cluster<br><br><br><br>----- Original Message -----<br>From: LuLanyuan <lulanyuan@msn.com><br>Date: Saturday, June 5, 2010 2:01<br>Subject: [gmx-users] PME problem on BG/P cluster<br>To: gmx-users@gromacs.org<br><br><span> <style>
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</style> <table><tbody><tr><td class="ecxhmmessage"><p><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> Hello,<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I got a weird problem by running Gromacs 4.0.7 on a BG/P machine ("Intrepid" at Argonne national lab).<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I first compile the code with flags suggested on the Wiki, such as:<br><font style="font-style: normal; font-weight: normal; background-
color: rgb(245, 248, 240); font-size: 14px;">> </font>./configure --prefix=$PREFIX \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --host=ppc \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --build=ppc64 \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --disable-software-sqrt \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> &
nbsp; --enable-ppc-sqrt=1 \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> &n bsp; --enable-ppc-altivec \<BR><br><BR>The wiki doesn't suggest this, and it's for another architecture entirely. I don't know if it's causing a problem, but you should see what kernels the .log file reports it is trying to use.<br><BR><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --enable-bluegene \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> &n
bsp; --disable-fortran \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --enable-mpi \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --with-fft=fftpack \<BR><br><BR>This is a waste of a good BlueGene :-) Use FFTW, which has been optimized for BlueGene. [Edit: ah I see why you tried this]<br><BR><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --wit
hout-x \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>&nbs
p; CC="mpixlc_r" \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> CFLAGS="-O3 -qarc h=450d -qtune=450" \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> MPICC="mpixlc_r"<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> CXX="mpixlcxx_r"<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240)
; font-size: 14px;">> </font> CXXFLAGS="-O3 -qarch=450 -qtune=450"<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> F77="mpixlf77_r"<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> FFLAGS="-O3 -qarch=450 -qtune=450"<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> LIBS="-lmass"<br><font style="font-style: normal; font-we
ight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>The error message I got was sth like <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>t = 0.100 ps: Water molecule starting at atom 403468 can not be settled.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 1
4px;">> </font>Check for bad contacts and/or reduce the timestep.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Wrote pdb files with previous and current coordinates.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>and<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>2 particles communicated to PME node 63 are more than a cell length out of the domain decomposition cell of their charge group<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 1
4px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> <
/font>From .log file, the kinetic energy is increasing and turned to be "nan". So the system is exploding.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>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><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --enable-software-sqrt \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> -
-disable-ppc-sqrt \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> --disable-bluegene \<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>and everything else was the same. <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I suspect there was an issue regarding the blue gene specific code and PME.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Could anyone give any comments?<BR><br><BR>First, try without --enable-ppc-altivec in case that's confusing things. Then try setting the enviroment variable NOASSEMBLYLOOPS to 1 before mdrun to see whether the issue really is s
pecific to the BlueGene-kernel. (Consult mpirun documentation about how to set env vars suitably) You might also try compiling with lower optimization levels, to see if its a compiler/optimization issue. Depending what you find above, there are other things to try.<br><BR><br><BR>Mark<br><BR></td></tr></tbody></table></p></span> <br /><hr />聊天+搜索+邮箱 想要轻松出游,手机MSN帮你搞定! <a href='http://3g.msn.cn/' target='_new'>立刻下载！</a></body>
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