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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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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