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hi,<BR>
<BR>
I am testing the dhfr benchmarks with gromacs 4.5.2<BR>
<BR>
1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 10000, <BR>
The GPU version running results shows as following:<BR>
./mdrun-gpu<BR>
<BR>
Pre-simulation ~15s memtest in progress...done, no errors detected<BR>starting mdrun 'Protein in water'<BR>10000 steps, 20.0 ps.<BR>
Writing final coordinates.<BR>
Back Off! I just backed up confout.gro to ./#confout.gro.2#<BR>
Post-simulation ~15s memtest in progress...done, no errors detected<BR>
OpenMM run - timing based on wallclock.<BR>
<STRONG> NODE (s) Real (s) (%)<BR> Time: 90.796 90.796 100.0<BR> 1:30<BR> (Mnbf/s) (MFlops) (ns/day) (hour/ns)<BR>Performance: 0.000 0.060 19.034 1.261</STRONG><BR>
gcq#100: "Jesus Can't Save You, Though It's Nice to Think He Tried" (Black Crowes)<BR><BR>
The CPU version running results shows as following:<BR>
./mdrun<BR>
<BR>
Writing final coordinates.<BR>
Back Off! I just backed up confout.gro to ./#confout.gro.3#<BR>
Average load imbalance: 4.7 %<BR> Part of the total run time spent waiting due to load imbalance: 2.7 %<BR> Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 %<BR>
<BR> Parallel run - timing based on wallclock.<BR>
<STRONG> NODE (s) Real (s) (%)<BR> Time: 86.176 86.176 100.0<BR> 1:26<BR> (Mnbf/s) (GFlops) (ns/day) (hour/ns)<BR>Performance: 741.634 35.849 20.054 1.197</STRONG><BR>
gcq#0: Thanx for Using GROMACS - Have a Nice Day<BR><BR>
<BR>
The gpu version looks <STRONG>slower </STRONG>than cpu version, does it make sense? Is there anyway I could optimize?<BR>
<BR>
<BR>
2. For the CPU benchmark dhfr-impl-1nm.bench, when I run : <BR>
./mdrun<BR>
Back Off! I just backed up md.log to ./#md.log.9#<BR>Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)<BR>Starting 16 threads<BR>
-------------------------------------------------------<BR>Program mdrun, VERSION 4.5.2<BR>Source code file: domdec.c, line: 6428<BR>
Fatal error:<BR>There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.02425 nm<BR>Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings<BR>Look in the log file for details on the domain decomposition<BR>For more information and tips for troubleshooting, please check the GROMACS<BR>website at <A href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</A><BR>-------------------------------------------------------<BR>
Thanx for Using GROMACS - Have a Nice Day<BR><BR>
<BR>
Where could I modify this nodes#? <BR>
<BR>
3. for CPU benchmark dhfr-impl-inf.bench<BR>
I modified cpu-imp-RF-inf.mdp: nsteps 10000<BR>
grompp -f cpu-imp-RF-inf.mdp -o topol.tpr<BR>
it will show: <BR>
NOTE 1 [file cpu-imp-RF-inf.mdp]:<BR> The Berendsen thermostat does not generate the correct kinetic energy<BR> distribution. You might want to consider using the V-rescale thermostat.<BR>
Generated 2278 of the 2278 non-bonded parameter combinations<BR>Generating 1-4 interactions: fudge = 0.5<BR>Generated 2278 of the 2278 1-4 parameter combinations<BR>Excluding 3 bonded neighbours molecule type 'Protein'<BR>turning all bonds into constraints...<BR>
NOTE 2 [file topol.top, line 23568]:<BR> System has non-zero total charge: -1.100000e+01<BR>
<BR>
GB parameter(s) missing or negative for atom type 'H0'<BR>
-------------------------------------------------------<BR>Program grompp, VERSION 4.5.1<BR>Source code file: grompp.c, line: 870<BR>
Fatal error:<BR>Can't do GB electrostatics; the forcefield is missing 1 values for<BR>atomtype radii, or they might be negative<BR>.<BR>For more information and tips for troubleshooting, please check the GROMACS<BR>website at <A href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</A><BR>-------------------------------------------------------<BR>
"Everybody's Good Enough For Some Change" (LIVE)<BR><BR>
and when I run ./mdrun<BR>
the steps still -1, infinite time<BR>
How could I genete the right topol.tpr?<BR>
<BR>
<BR>
Thanks a lot.<BR>
<BR>
<BR>
YY<BR> </body>
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