In the log file, when gromacs specifies "Nodes," does it mean processors?<br><br><div class="gmail_quote">On Fri, Jan 28, 2011 at 1:44 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im"><br>
<br>
Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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? <br>
</blockquote>
<br></div>
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.<br><font color="#888888">
<br>
-Justin<br>
<br>
</font><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Fri, Jan 28, 2011 at 1:32 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Denny Frost wrote:<br>
<br></div><div><div></div><div class="h5">
Here's my grompp command:<br>
<br>
grompp_d -nice 0 -v -f md.mdp -c ReadyForMD.gro -o md.tpr -p top.top<br>
<br>
and my mdrun command is this:<br>
time mpiexec mdrun_mpi -np 8 -cpt 30000 -nice 0 -nt 1 -s<br>
$PBS_O_WORKDIR/md.tpr -o $PBS_O_WORKDIR/mdDone.trr -x<br>
$PBS_O_WORKDIR/mdDone.xtc -c $PBS_O_WORKDIR/mdDone.gro -e<br>
$PBS_O_WORKDIR/md.edr -g $PBS_O_WORKDIR/md.log 1><br>
$PBS_JOBID.pgm.out 4> $PBS_JOBID.pgm.err<br>
<br>
<br>
The -np option of mdrun is nonexistent, but mdrun does not check for<br>
proper command line arguments, so you won't get an error. But then<br>
you've said that 8 processors are active, so I still suspect that<br>
mdrun was compiled incorrectly or in such a way that it's<br>
incompatible with your system. The output from the .log file<br>
indicates that only one processor was used. Maybe your admins can<br>
help you on this one, if the jobs spit out any useful diagnostic<br>
information.<br>
<br>
For our cluster, we use e.g.:<br>
<br>
mpirun -np 8 mdrun_mpi -deffnm md<br>
<br>
-Justin<br>
<br>
I know the -cpt option is 30000 because I don't want a<br>
checkpoint file because every time it tries to make it, it fails<br>
due to quota issues and kills the job. I'm not sure why this<br>
happens, but I think it's a separate issue to take up with my<br>
supercomputing facility.<br>
<br>
On Fri, Jan 28, 2011 at 1:18 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Denny Frost wrote:<br>
<br>
all 8 nodes are running at full capacity, though<br>
<br>
<br>
What is your mdrun command line? How did you compile it?<br>
What can<br>
happen is something went wrong during installation, so you<br>
think you<br>
have an MPI-enabled binary, but it is simply executing 8<br>
copies of<br>
the same job.<br>
<br>
-Justin<br>
<br>
On Fri, Jan 28, 2011 at 1:13 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>>> wrote:<br>
<br>
<br>
<br>
Denny Frost wrote:<br>
<br>
Here's what I've got:<br>
<br>
M E G A - F L O P S A C C O U N T I N G<br>
<br>
RF=Reaction-Field FE=Free Energy<br>
SCFE=Soft-Core/Free<br>
Energy<br>
T=Tabulated W3=SPC/TIP3p W4=TIP4p<br>
(single or<br>
pairs)<br>
NF=No Forces<br>
<br>
Computing: M-Number<br>
M-Flops % Flops<br>
-----------------------------------------------------------------------------<br>
Coul(T) + VdW(T) 1219164.751609<br>
82903203.109 80.6<br>
Outer nonbonded loop 25980.879385<br>
259808.794 0.3<br>
Calc Weights 37138.271040<br>
1336977.757 1.3<br>
Spread Q Bspline 792283.115520<br>
1584566.231 1.5<br>
Gather F Bspline 792283.115520<br>
4753698.693 4.6<br>
3D-FFT 119163.856212<br>
953310.850 0.9<br>
Solve PME 2527.465668<br>
161757.803 0.2<br>
NS-Pairs 47774.705001<br>
1003268.805 1.0<br>
Reset In Box 371.386080<br>
1114.158 0.0<br>
Shift-X 24758.847360<br>
148553.084 0.1<br>
CG-CoM 1237.953600<br>
3713.861 0.0<br>
Angles 18569.135520<br>
3119614.767 3.0<br>
Propers 14855.308416<br>
3401865.627 3.3<br>
Impropers 3094.855920<br>
643730.031 0.6<br>
Virial 1242.417375<br>
22363.513 0.0<br>
Stop-CM 1237.953600<br>
12379.536 0.0<br>
P-Coupling 12379.423680<br>
74276.542 0.1<br>
Calc-Ekin 12379.436160<br>
334244.776 0.3<br>
Lincs 11760.476208<br>
705628.572 0.7<br>
Lincs-Mat 245113.083072<br>
980452.332 1.0<br>
Constraint-V 23520.928704<br>
188167.430 0.2<br>
Constraint-Vir 11760.452496<br>
282250.860 0.3<br>
-----------------------------------------------------------------------------<br>
Total 102874947.133 100.0<br>
-----------------------------------------------------------------------------<br>
<br>
<br>
R E A L C Y C L E A N D T I M E A C C<br>
O U N T<br>
I N G<br>
<br>
Computing: Nodes Number G-Cycles<br>
Seconds %<br>
-----------------------------------------------------------------------<br>
Neighbor search 1 99195 8779.027 3300.3<br>
3.8<br>
Force 1 991941 188562.885<br>
70886.8 81.7<br>
PME mesh 1 991941 18012.830 6771.6<br>
7.8<br>
Write traj. 1 41 16.835 6.3<br>
0.0<br>
Update 1 991941 2272.379<br>
854.3 1.0<br>
Constraints 1 991941 11121.146 4180.8 4.8<br>
Rest 1 2162.628 813.0 0.9<br>
-----------------------------------------------------------------------<br>
Total 1 230927.730 86813.1 100.0<br>
-----------------------------------------------------------------------<br>
-----------------------------------------------------------------------<br>
PME spread/gather 1 1983882 17065.384 6415.4 7.4<br>
PME 3D-FFT 1 1983882 503.340 189.2<br>
0.2<br>
PME solve 1 991941 427.136 160.6 0.2<br>
-----------------------------------------------------------------------<br>
<br>
Does that mean it's only using 1 node? That would<br>
explain the<br>
speed issues.<br>
<br>
<br>
That's what it looks like to me.<br>
<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>><br>
<<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<br>
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<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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