[gmx-users] Parallel processing

[mariognu-outside at yahoo.com.br]

Hi all.

First, excuse my English, it is not too good, but I'm
learning.

I have a problem with my gromacs. I have a Dell
Precision 470 (2 Xeon processor with 2Gb RAM) and I
can't run mdrun_mpi for 2 processor. I describe what
is happening. 

I installed gromacs-3.3.3-1.x86_64.rpm and
gromacs-mpi-3.3.3-1.x86_64.rpm. My Linux is Fedora 8
x64.

If I run 

mdrun -v -deffnm run

or

mpiexec -np 2 mdrun_mpi -np 2 -v -deffnm run

or

mdrun_mpi -np 2 -v -deffnm run

The time to conclude dynamics is the same. I think
that  the the 2 last command will be more fast. But if
I look to system monitor and analyze process I see the
in the second case the 2 processor is 100%. If I see
in the thirty case the process is alternate in the 2
processor, one is 100% other is near 10%, after one is
near 10% and other is 100%.

If I run 

grompp -f run.mdp -p topol.top -c run -o run -np 2
mpiexec -np 2 mdrun_mpi -np 2 -v -deffnm run

I have this error

-------------------------------------------------------
Program mdrun_mpi, VERSION 3.3.3
Source code file: init.c, line: 69

Fatal error:
run input file run.tpr was made for 2 nodes,
             while mdrun_mpi expected it to be for 1
nodes.
-------------------------------------------------------

And I see that the gromacs is run in one node, but I
put in command to run in two nodes

[mariojose at xxx smase]$ mpiexec -np 2 mdrun_mpi -np 2
-v -deffnm run
NNODES=1, MYRANK=0, HOSTNAME=xxx.unesp.br
     :-)  G  R  O  M  A  C  S  (-:
  Gnomes, ROck Monsters And Chili Sauce
        :-)  VERSION 3.3.3  (-:


I do a test in other machine pentium 4 basic, with one
processor and not hyper threading, and the dynamics
have same speed that my Xeon. It is very strange for
me!!!

I like very much if somebody can help me.

Thanks for all, and excuse my English again! 

Mario Jose
IBILCE - UNESP
www.crystallography.ibilce.unesp.br





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