[gmx-users] Slow Runs
Justin A. Lemkul
jalemkul at vt.edu
Sat Jan 29 00:01:23 CET 2011
Denny Frost wrote:
> I didn't do the install myself, so I'm not sure what options they used.
> What potentially could have gone wrong?
>
Tons of things. Most directly, forgetting --enable-mpi during configuration,
but then specifying the _mpi program suffix and continuing to compile mdrun.
-Justin
> On Fri, Jan 28, 2011 at 3:49 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Denny Frost wrote:
>
> I tried using mpiexec -n 8 mdrun_mpi, but I still can't get the
> output to that it used anything but just 1 Node. Is there
> something I was supposed to specify in the grompp command?
>
>
> No, grompp has nothing to do with parallelization (at least, not
> since version 3.3.3). Are you sure the mdrun executable was
> properly compiled with MPI support? I believe mpiexec will happily
> run a serial version of mdrun over all the processors, rather than
> invoke the properly-compiled one.
>
> -Justin
>
> On Fri, Jan 28, 2011 at 3:43 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:
>
> In the log file, when gromacs specifies "Nodes," does it mean
> processors?
>
>
> Yes. For instance, on my dual-core workstation, the "nodes" are
> correctly reported as 2.
>
> -Justin
>
> On Fri, Jan 28, 2011 at 1:44 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:
>
> 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>
> <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 <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 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>>
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> <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
> <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>>>
> <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 <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>>>
> <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 <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>>
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> <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
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> <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
> <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>>>
> <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 <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>
> <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>
> <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
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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>
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> 231-9080
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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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