NAMD job dies on 2-quad core server

From: vivek.viv.sharma_at_gmail.com
Date: Sun Apr 05 2009 - 23:45:28 CDT

Hello everyone,

We have recently bought a machine with the following configuration:

2 quad core processors each with 2.33GHz clock rate.
8 GB RAM
500GB total hard disk

I have simply used the "NAMD_2.6_Linux-i686" binaries. And, started the
simulation (membrane protein with membrane, water, ions.). The simulation
starts fine with the command

./charmrun ++local +p 8 ./namd2 config.txt > config.log &

But after 4390 steps the job dies, without giving any error message. Would
you please suggest what is happening? Do I need to install it(NAMD) from
scratch?

NAMD in log file shows clearly:

>> Info: Running on 8 processors.

I observed from 'top', indeed simulation runs on all 8 processors, using
more or less efficiently all the processors.

All your suggestions will be very helpful.

thanks and regards,

Vivek
IMM, India.

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