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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