[gmx-users] REMD problem
Liu, Liang
liu4gre at gmail.com
Thu Sep 29 01:53:56 CEST 2011
Not know. I will update the result tomorrow, as the 50000 steps take really
long time :(
On Wed, Sep 28, 2011 at 4:38 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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>
>>>
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>>> >>
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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
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>>> <tel:%28540%29%20231-9080>
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>>>
>>
>>
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--
Best,
Liang Liu
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