[gmx-users] mpirun problem

[Carsten Kutzner]

ha salem wrote:
> dear carsten
> I have 110000 particels ,cores of cpu has 90 % usage on one machine but 
> when I run the same
> calculation on 2 machine   the cpu usage of cores reduce to 20% my lan 
> is 100 Mbps
> do you mean with  LAN Gigabit the cpu uasage increase to 90%?
 From the benchmarks I have seen, I can say that you cannot expect any
speedup if your computers are only connected with 100 Mpbs. You will
need at least 1000 Mbps, or better Infiniband/Myrinet.

Carsten

> thank you
> 
> --- On *Sun, 6/15/08, Carsten Kutzner /<ckutzne at gwdg.de>/* wrote:
> 
>     From: Carsten Kutzner <ckutzne at gwdg.de>
>     Subject: Re: [gmx-users] mpirun problem
>     To: greencomp86 at yahoo.com, "Discussion list for GROMACS users"
>     <gmx-users at gromacs.org>
>     Date: Sunday, June 15, 2008, 7:30 PM
> 
>     On 15.06.2008, at 20:19, ha salem wrote:
> 
>>     dear users
>>          I have encouneterd a problem with mpirun I have 2 pc (every
>>     pc has 1 intel
>>          quad core cpu) ,when I run mdrun on 1 machine with  "-np 4 "
>>     option the calculation
>>          run on 4 cores and goes faster ,system monitor show all 4
>>     cores of this cpu are working
>>          every core has 90% cpu usage,and every thing is ok
>>          but now I connect 2 computer to LAN and I executed lamboot -v
>>     lamhosts
>>          then I run mpirun -np 8 but I see the all 8 cores of 2
>>     machines are workinng with
>>          20 % 10% cpu usage and speed is lower than 4 cores of 1 cpu!!!!
>>
>     This could have a lot of reasons. What kind of interconnect do you
>     use? If it is gigabit 
>     Ethernet, you will need at least 80000 particles to be faster on two
>     4 CPU machines compared 
>     to one. With only fast ethernet, do not expect any scaling at all on
>     today's fast processors.
> 
>     Try grompp -shuffle -sort, this will help increase the scaling a bit. 
> 
>     Regards,
>       Carsten
> 
>>
>>          can you help me ?my molecule is part of hsa and is macro molecule
>>        these are my commands
>>     usr/local/share/gromacs_331/bin/grompp -np 8 -f prmd.mdp -c
>>     finalprsp.gro -r finalprsp.gro -p n.top
>>     mpirun -np 8 /usr/local/share/gromacs_331/bin/mdrun -np 8 -s
>>     prmd.tpr -o prmd.trr -c finalprmd.gro -g prmd.log -e prmd.edr -n n.ndx
>>
>>
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> 
>