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[ESPResSo-users] 24 Espresso threads consume 32GB memory in 1 hour.

From: Chunda Zhou
Subject: [ESPResSo-users] 24 Espresso threads consume 32GB memory in 1 hour.
Date: Fri, 29 Jul 2011 11:31:36 -0400

Hi guys, 

I am simulating a two-monomer polyelectrolyte in salt solution environment. I 
use Lattice-Boltzman hydrodynamics. 

When I turn on the vtf file output, I put it this way: 

set vtf [open "vtf.vtf" "w"]
set i 0 
while { $i<$n_cycle} {

    puts "   $i/$n_cycle"   
 puts "analyze energy kinetic"
   puts [analyze energy kinetic]
    puts "analyze energy total"
     puts [analyze energy total]

    integrate $n_steps

    analyze set chains 0 1 $l_poly
#    set rg [lindex [analyze rg] 0]

    writevsf $vtf radius {0 2.0 1 auto 2 1.0}

    # if you have turned on the vmd option you can now
    # follow what your simulation is doing
    if { $vmd == "yes" } { imd positions }
# change the position once in a cycle.
    incr i

close $vtf

If I delate the vtf output lines, the whole program will consume 32GB memory in 
10 hours. When i check using top command, it shows that the mpirun thread 
consumes 97% of the whole memory.  

Did I do anything wrong?  

What's the most elegant way to save the current status automatically so that I 
can easily resume it when the computer crashes? 


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