Suspend NAMD (to RAM)

From: Ajasja Ljubetič (
Date: Wed Jul 20 2011 - 17:10:06 CDT

Dear All,

Is there an easy way temporarily suspend a running NAMD simulation from the
command line? I'm running NAMD 2.8 on Ubuntu 10.04 (64 bit).
I'm using charmrun +local ... to run my jobs.

The reason I'm asking this is because I have some nodes with two GPUs, where
one GPU keeps overheating (they are just humble GTX 560). I tried increasing
the airflow, but I'm at the limit of what I can do. Since this is only a
problem in the summer I would need a temporary solution. So I would like to
have a script along the lines (in pseudo code):

every 10 seconds do
  if GPU_TEMP>99 then
     suspend namd
     sleep 10 seconds
     resume namd

Actually I have to ideas how I could implement this.
a) I could just kill namd and then sleep for some time and then figuer out
what the latest restart file is and start from there.
b) I could add this check inside the configuration file. So I could run for
a small number of steps, check the GPU temp and then either run for a small
number of steps or sleep for some time. (again in pseudo code)

while i<NUMBER_OF_PARTS do
  if GPU_TEMP>99 then
    sleep 30 seconds
    run 100
    inc i

Any other suggestions are welcome.

Best regards,
Ajasja Ljubetic
Young researcher
Laboratory of biophysics
Department F5
Institute Jozef Stefan
Ljubljana, Slovenia

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