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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto: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> <http://vt.edu>
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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> | (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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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
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