[gmx-users] Slow Runs
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 28 21:32:02 CET 2011
Denny Frost wrote:
> Here's my grompp command:
>
> grompp_d -nice 0 -v -f md.mdp -c ReadyForMD.gro -o md.tpr -p top.top
>
> and my mdrun command is this:
>
> time mpiexec mdrun_mpi -np 8 -cpt 30000 -nice 0 -nt 1 -s
> $PBS_O_WORKDIR/md.tpr -o $PBS_O_WORKDIR/mdDone.trr -x
> $PBS_O_WORKDIR/mdDone.xtc -c $PBS_O_WORKDIR/mdDone.gro -e
> $PBS_O_WORKDIR/md.edr -g $PBS_O_WORKDIR/md.log 1> $PBS_JOBID.pgm.out 4>
> $PBS_JOBID.pgm.err
>
The -np option of mdrun is nonexistent, but mdrun does not check for proper
command line arguments, so you won't get an error. But then you've said that 8
processors are active, so I still suspect that mdrun was compiled incorrectly or
in such a way that it's incompatible with your system. The output from the .log
file indicates that only one processor was used. Maybe your admins can help you
on this one, if the jobs spit out any useful diagnostic information.
For our cluster, we use e.g.:
mpirun -np 8 mdrun_mpi -deffnm md
-Justin
> I know the -cpt option is 30000 because I don't want a checkpoint file
> because every time it tries to make it, it fails due to quota issues and
> kills the job. I'm not sure why this happens, but I think it's a
> separate issue to take up with my supercomputing facility.
>
> On Fri, Jan 28, 2011 at 1:18 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Denny Frost wrote:
>
> all 8 nodes are running at full capacity, though
>
>
> What is your mdrun command line? How did you compile it? What can
> happen is something went wrong during installation, so you think you
> have an MPI-enabled binary, but it is simply executing 8 copies of
> the same job.
>
> -Justin
>
> On Fri, Jan 28, 2011 at 1:13 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Denny Frost wrote:
>
> Here's what I've got:
>
> M E G A - F L O P S A C C O U N T I N G
>
> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free
> Energy
> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or
> pairs)
> NF=No Forces
>
> Computing: M-Number
> M-Flops % Flops
>
> -----------------------------------------------------------------------------
> Coul(T) + VdW(T) 1219164.751609
> 82903203.109 80.6
> Outer nonbonded loop 25980.879385
> 259808.794 0.3
> Calc Weights 37138.271040
> 1336977.757 1.3
> Spread Q Bspline 792283.115520
> 1584566.231 1.5
> Gather F Bspline 792283.115520
> 4753698.693 4.6
> 3D-FFT 119163.856212
> 953310.850 0.9
> Solve PME 2527.465668
> 161757.803 0.2
> NS-Pairs 47774.705001
> 1003268.805 1.0
> Reset In Box 371.386080
> 1114.158 0.0
> Shift-X 24758.847360
> 148553.084 0.1
> CG-CoM 1237.953600
> 3713.861 0.0
> Angles 18569.135520
> 3119614.767 3.0
> Propers 14855.308416
> 3401865.627 3.3
> Impropers 3094.855920
> 643730.031 0.6
> Virial 1242.417375
> 22363.513 0.0
> Stop-CM 1237.953600
> 12379.536 0.0
> P-Coupling 12379.423680
> 74276.542 0.1
> Calc-Ekin 12379.436160
> 334244.776 0.3
> Lincs 11760.476208
> 705628.572 0.7
> Lincs-Mat 245113.083072
> 980452.332 1.0
> Constraint-V 23520.928704
> 188167.430 0.2
> Constraint-Vir 11760.452496
> 282250.860 0.3
>
> -----------------------------------------------------------------------------
> Total
> 102874947.133 100.0
>
> -----------------------------------------------------------------------------
>
>
> R E A L C Y C L E A N D T I M E A C C O U N T
> I N G
>
> Computing: Nodes Number G-Cycles
> Seconds %
>
> -----------------------------------------------------------------------
> Neighbor search 1 99195 8779.027 3300.3
> 3.8
> Force 1 991941 188562.885
> 70886.8 81.7
> PME mesh 1 991941 18012.830 6771.6
> 7.8
> Write traj. 1 41 16.835
> 6.3
> 0.0
> Update 1 991941 2272.379
> 854.3 1.0
> Constraints 1 991941 11121.146
> 4180.8 4.8
> Rest 1 2162.628
> 813.0 0.9
>
> -----------------------------------------------------------------------
> Total 1 230927.730
> 86813.1 100.0
>
> -----------------------------------------------------------------------
>
> -----------------------------------------------------------------------
> PME spread/gather 1 1983882 17065.384
> 6415.4 7.4
> PME 3D-FFT 1 1983882 503.340
> 189.2
> 0.2
> PME solve 1 991941 427.136
> 160.6 0.2
>
> -----------------------------------------------------------------------
>
> Does that mean it's only using 1 node? That would
> explain the
> speed issues.
>
>
> That's what it looks like to me.
>
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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