[gmx-users] parallel problem

[Osmany Guirola Cruz]

hi
What did you think about put this option in the configure lammpi
tcp-short=524288 for use 512kb
is it rigth?


David wrote:

>On Thu, 2003-09-04 at 01:52, Osmany Guirola Cruz wrote:
>  
>
>>No i have dual PIII 933MHz   coupled by tcp/ip
>>
>>It is 100 Mbit 
>>
>>My cluster  have a switch  i have 32 dual in a sub-net and only one
>>machine is in my network (PBS)
>>
>>I do a simulation whit 9500  molecules of water (SOL) 129 proteins
>>residue
>>
>>No i dont do the gromacs benchmarks , HOW COULD I DO IT?
>>    
>>
>Download them from gromacs.org...
>I have done the test with a switched 100 Mbit/s network with dual 800
>MHz P3s, up until 10 nodes (i.e. 20 cpus). 
>
>  
>
>> i forget something , my simulations whith cutoff are shorter than PME
>>    
>>
>
>To efficiently use the dual processors you have to select another lam
>option (rcp=usysv or rcp=sysv).
>
>Now the real problem performancewise is PME. In the current 3.1.4
>version PME does not behave well at all in parallel. On a Scali network
>I use at most 4 dual Xeon nodes  for my runs which have 30000 waters.
>Since your system is smaller, performance will be even worse. Note that
>the gromacs scaling benchmark is done with a (twin-range) cut-off rather
>than PME. If you can live with a cut-off (and after all, the GROMOS96
>force field was developed for use with a cut-off) you could maybe scale
>to somewhat more processors:
>nstlist  = 5
>rlist    = 0.9
>rcoulomb = 1.4
>rvdw     = 1.4
>
>See how far you can go with that. Furthermore you want to control how
>PBS/LAM allocates your processors. The communication is on a ring
>topology in principle, so if you have two dual processor nodes
>N0-p0, N0-p1, N1-p0, N1-p1
>you want the jobs to be allocated in this order (to use the shared
>memory communication) rather than
>N0-p0, N1-p0, N0-p1, N1-p1
>
>In the first example two of the four communications use shared memory,
>in the other example none of them do.
>
>
>
>
>
>  
>
>>Really i need help, i have 32 machines and  only use one for my
>>simulations :-( 
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>David wrote:
>>    
>>
>>>On Wed, 2003-09-03 at 22:16, Osmany Guirola Cruz wrote:
>>>  
>>>      
>>>
>>>>This is not the first time that i make the same question, how should i do gromacs work well whith lam in my linux cluster , a simulation in one machine is shorter than two machines , my last steep was compile the lammpi source whith the option  tcp-short=524288 (512kb) and nothing  happens . 
>>>>
>>>>PLEASE HELPMEEEEEEEEEEEEEEEEEEEEEE
>>>>    
>>>>        
>>>>
>>>I'll just assume you have single processor machines coupled by tcp/ip
>>>network, is that correct?
>>>
>>>Is it 10 Mbit/s, 100 Mbit/s or better?
>>>
>>>Do you have a switch between the machines or a hub?
>>>
>>>How large is your system to simulate?
>>>
>>>Did you try to reproduce the gromacs benchmarks?
>>>
>>>  
>>>      
>>>
>>>>    
>>>>        
>>>>

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