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Aside the point, but your checkpionting issue might be that mdrun
tries to write the file not in $PBS_O_WORKDIR, but somewere where
you don't have more disk quota. Putting "cd $PBS_O_WORKDIR" into
your run script may be a good solution.<br>
<br>
Erik<br>
<br>
Denny Frost skrev 2011-01-28 21.25:
<blockquote
cite="mid:AANLkTiksp4J5RCxM35vBbOV-1HxB+SCHqJQT8qvmVWba@mail.gmail.com"
type="cite">Here's my grompp command:
<div><br>
</div>
<div>grompp_d -nice 0 -v -f md.mdp -c ReadyForMD.gro -o md.tpr -p
top.top</div>
<div><br>
</div>
<div>and my mdrun command is this: </div>
<div><br>
</div>
<div>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</div>
<div><br>
</div>
<div>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.<br>
<br>
<div class="gmail_quote">On Fri, Jan 28, 2011 at 1:18 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im"><br>
<br>
Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
all 8 nodes are running at full capacity, though<br>
<br>
</blockquote>
<br>
</div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div>
<div class="h5">
On Fri, Jan 28, 2011 at 1:13 PM, Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a> <mailto:<a
moz-do-not-send="true" 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
SCFE=Soft-Core/Free Energy<br>
T=Tabulated W3=SPC/TIP3p W4=TIP4p
(single or pairs)<br>
NF=No Forces<br>
<br>
Computing:
M-Number M-Flops % Flops<br>
-----------------------------------------------------------------------------<br>
Coul(T) + VdW(T)
1219164.751609 82903203.109 80.6<br>
Outer nonbonded loop
25980.879385 259808.794 0.3<br>
Calc Weights
37138.271040 1336977.757 1.3<br>
Spread Q Bspline
792283.115520 1584566.231 1.5<br>
Gather F Bspline
792283.115520 4753698.693 4.6<br>
3D-FFT
119163.856212 953310.850 0.9<br>
Solve PME
2527.465668 161757.803 0.2<br>
NS-Pairs
47774.705001 1003268.805 1.0<br>
Reset In Box
371.386080 1114.158 0.0<br>
Shift-X
24758.847360 148553.084 0.1<br>
CG-CoM
1237.953600 3713.861 0.0<br>
Angles
18569.135520 3119614.767 3.0<br>
Propers
14855.308416 3401865.627 3.3<br>
Impropers
3094.855920 643730.031 0.6<br>
Virial
1242.417375 22363.513 0.0<br>
Stop-CM
1237.953600 12379.536 0.0<br>
P-Coupling
12379.423680 74276.542 0.1<br>
Calc-Ekin
12379.436160 334244.776 0.3<br>
Lincs
11760.476208 705628.572 0.7<br>
Lincs-Mat
245113.083072 980452.332 1.0<br>
Constraint-V
23520.928704 188167.430 0.2<br>
Constraint-Vir
11760.452496 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 O U N T I N G<br>
<br>
Computing: Nodes Number
G-Cycles Seconds %<br>
-----------------------------------------------------------------------<br>
Neighbor search 1 99195 8779.027
3300.3 3.8<br>
Force 1 991941
188562.885 70886.8 81.7<br>
PME mesh 1 991941 18012.830
6771.6 7.8<br>
Write traj. 1 41
16.835 6.3<br>
0.0<br>
Update 1 991941
2272.379 854.3 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 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>
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<div class="h5">
<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 moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> |
(540) 231-9080<br>
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<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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