[gmx-users] Slow Runs
Justin A. Lemkul
jalemkul at vt.edu
Fri Jan 28 21:44:59 CET 2011
Denny Frost wrote:
> I'm leaning toward the possibility that it is actually only running 8
> copies of the same job on different processors. My question is how does
> gromacs4.5 know how many processors it has available to parallelize a
> job? Is it specified in grompp or does it just detect it?
>
If you're using MPI, it comes from mpiexec/mpirun/whatever. Setting a proper
flag there is what tells mdrun how many nodes to use.
-Justin
> On Fri, Jan 28, 2011 at 1:32 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto: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>
> <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> <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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