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 /<[EMAIL PROTECTED]>/* wrote:
From: Carsten Kutzner <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] mpirun problem
To: [EMAIL PROTECTED], "Discussion list for GROMACS users"
<gmx-users@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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