[gmx-users] REMD problem
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Sep 29 01:38:31 CEST 2011
On 29/09/2011 7:20 AM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>> Yes, they are updated like:
>> ...
>> Replica exchange at step 5700 time 11.4
>> Repl ex 0 1 x 2 3 x 4 5 x 6 7 8 9 x 10 11 x
>> 12 13 14 15 x 16 17 x 18 19 x 20 21 x 22 23 24 25 x
>> 26 27 28 29 x 30 31 32 33 x 34 35 36 37 x 38 39
>> 40 41 x 42 43 x 44 45 x 46 47 48 49
>> Repl pr 1.0 1.0 1.0 .00 1.0
>> 1.0 .00 1.0 1.0 1.0 1.0 .00
>> 1.0 .00 1.0 .00 1.0 .00 .46
>> .00 1.0 .78 1.0 .00
>>
>> Replica exchange at step 5750 time 11.5
>> Repl 0 <-> 1 dE = -7.583e+00
>> Repl ex 0 x 1 2 3 4 x 5 6 x 7 8 x 9 10 x 11
>> 12 x 13 14 x 15 16 x 17 18 x 19 20 21 22 23 24 x 25
>> 26 27 28 x 29 30 31 32 x 33 34 35 36 37 38 39
>> 40 x 41 42 x 43 44 45 46 47 48 49
>> Repl pr 1.0 .00 1.0 1.0 1.0 1.0
>> 1.0 1.0 1.0 1.0 .48 .11 1.0
>> .00 1.0 .00 1.0 .00 .00 .01
>> 1.0 1.0 .00 .01 .01
>>
>> Step Time Lambda
>> 5800 11.60000 0.00000
>>
>> Energies (kJ/mol)
>> Angle Proper Dih. Improper Dih. LJ-14
>> Coulomb-14
>> 9.69806e+02 1.32207e+03 3.34938e+01 4.93171e+02
>> -3.91111e+03
>> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Position
>> Rest.
>> 3.14374e+04 -6.42258e+02 -1.88529e+05 -2.01604e+04
>> 0.00000e+00
>> Potential Kinetic En. Total Energy Conserved En.
>> Temperature
>> -1.78987e+05 4.57462e+04 -1.33240e+05 1.23302e+10
>> 5.62201e+02
>> Pres. DC (bar) Pressure (bar) Constr. rmsd
>> -2.12803e+02 -5.47109e+02 2.21484e-05
>> ...
>>
>
> Perhaps someone else can offer an explanation. It should not be
> possible to run multiple replicas on a single processor. Also note
> that your exchange probability is extremely high; you're likely not
> obtaining meaningful sampling.
If the MPI configuration allows physical processors to be
over-allocated, then GROMACS is none the wiser.
Mark
>
> -Justin
>
>> On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Liu, Liang wrote:
>>
>> Thanks. currently what I see is the program runs very slowly,
>> but get .log file for all the 50 replicas, does this mean all of
>> them are running?
>>
>>
>> Are the log files being updated, or do they all simply contain a
>> fatal error message that there are insufficient nodes? I cannot
>> think of a reason why 50 simulations could possibly run on 2
>> processors.
>>
>> -Justin
>>
>> On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>> Liu, Liang wrote:
>>
>> Well, although this makes sense, why all the 50
>> replicas are
>> running when I run "mpirun
>> -np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on
>> my own
>> computer with only 2 cores?
>>
>>
>> I can offer no explanation for this behavior, but I expect
>> that
>> either not all of them are actually running, or at the
>> very least
>> you will get horribly slow performance.
>>
>>
>> By the way, would you please show me where I can find the
>> reasonable replex number information in the literature?
>> I did
>> not find it in the link you posted and the manual either.
>>
>>
>> A few minutes of real literature searching will be far more
>> valuable
>> than some random person on the Internet giving you a value
>> that you
>> blindly use ;)
>>
>> -Justin
>>
>> Thanks.
>>
>>
>> -- Best,
>> Liang Liu
>>
>>
>> -- ==============================____==========
>>
>> 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 <tel:%28540%29%20231-9080>
>> <tel:%28540%29%20231-9080>
>>
>> http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
>> <http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
>>
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>>
>>
>> -- Best,
>> Liang Liu
>>
>>
>> -- ==============================__==========
>>
>> 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
>> <tel:%28540%29%20231-9080>
>> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
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>>
>>
>> --
>> Best,
>> Liang Liu
>
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