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<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2>Hello</FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>I just got done
running the gmxbench mark on a small cluster and am noticing some odd results. I
am currently only running d.villin</FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>I am using a version
of mpich provided by our infiniband supplier, not sure how it was built. fftw is
2.1.5 with --enable-mpi and --enable-float options.</FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>gromacs 3.2 compiled
with --enable-mpi and --program-suffix=_mpi. </FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>The systems are dual
2.4 GHz Xeons running rh 7.3 linux with 2.4.18-27.7.xsmp as the
kernel.</FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>When I run on as 2
processes on the smp machine I see a about 75% improvement, however if I run as
2 processes each on a different machine over infiniband I see 85%
improvement. </FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>This seems counter
intuitive.</FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>My typical run is
grompp -np 2 -v ; mpirun -np -hostfile host mdrun_mpi -v</FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>I also tried
mdrun_mpi -v -shuffle.</FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial size=2>Any help or
suggestions would be appreciated.</FONT></SPAN></DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=285385718-26022004><FONT face=Arial
size=2>Denis</FONT></SPAN></DIV></BODY></HTML>