[gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU

[lin hen]

hi,
 
I am testing the dhfr benchmarks with gromacs 4.5.2
 
1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 10000, 
    The GPU version running results shows as following:
   ./mdrun-gpu
    
 Pre-simulation ~15s memtest in progress...done, no errors detected
starting mdrun 'Protein in water'
10000 steps,     20.0 ps.
Writing final coordinates.
Back Off! I just backed up confout.gro to ./#confout.gro.2#
Post-simulation ~15s memtest in progress...done, no errors detected
        OpenMM run - timing based on wallclock.
               NODE (s)   Real (s)      (%)
       Time:     90.796     90.796    100.0
                       1:30
               (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:      0.000      0.060     19.034      1.261
gcq#100: "Jesus Can't Save You, Though It's Nice to Think He Tried" (Black Crowes)

     The CPU version running results shows as following:
    ./mdrun
 
Writing final coordinates.
Back Off! I just backed up confout.gro to ./#confout.gro.3#
 Average load imbalance: 4.7 %
 Part of the total run time spent waiting due to load imbalance: 2.7 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 %

        Parallel run - timing based on wallclock.
               NODE (s)   Real (s)      (%)
       Time:     86.176     86.176    100.0
                       1:26
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    741.634     35.849     20.054      1.197
gcq#0: Thanx for Using GROMACS - Have a Nice Day

 
The gpu version looks slower than cpu version, does it make sense? Is there anyway I could optimize?
 
 
2.  For the CPU benchmark dhfr-impl-1nm.bench, when I run : 
     ./mdrun
     Back Off! I just backed up md.log to ./#md.log.9#
Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
Starting 16 threads
-------------------------------------------------------
Program mdrun, VERSION 4.5.2
Source code file: domdec.c, line: 6428
Fatal error:
There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.02425 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day

 
Where could I modify this nodes#? 
 
3.  for CPU benchmark dhfr-impl-inf.bench
    I modified cpu-imp-RF-inf.mdp:  nsteps  10000
    grompp -f cpu-imp-RF-inf.mdp -o topol.tpr
    it will show: 
    NOTE 1 [file cpu-imp-RF-inf.mdp]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.
Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
NOTE 2 [file topol.top, line 23568]:
  System has non-zero total charge: -1.100000e+01
 
GB parameter(s) missing or negative for atom type 'H0'
-------------------------------------------------------
Program grompp, VERSION 4.5.1
Source code file: grompp.c, line: 870
Fatal error:
Can't do GB electrostatics; the forcefield is missing 1 values for
atomtype radii, or they might be negative
.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"Everybody's Good Enough For Some Change" (LIVE)

and when I run ./mdrun
the steps still -1, infinite time
How could I genete the right topol.tpr?
 
 
Thanks a lot.
 
 
YY 		 	   		  
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