Re: NAMD job dies on 2-quad core server

From: Axel Kohlmeyer (
Date: Mon Apr 06 2009 - 08:44:54 CDT

On Mon, 2009-04-06 at 04:45 +0000, wrote:
> 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

how should anybody know??? does your input run fine elsewhere? have
you looked at the trajectory? have you looked at the machine logs?
does your os have restrictive limits for interactive use or stack
memory? can you run the same job with less processors? how is the
CPU temperature? is the crash reproducable? ...

this list can go on for much longer. so please keep in mind that
the kind of suggestion you can receive from a mailing list is
directly proportional to the kind and quality of information
you provide. in you case, you just say "it doesn't work". and
only for one specific configuration. that is _very_ little.

> it(NAMD) from scratch?

why? first you have to find out what happens.
blind activism never helps!

> 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.

there has to be more output, and i am pretty certain that there is
some output that indicates what is going wrong.

> All your suggestions will be very helpful.

well, you got a ton of them already. the most important
one is to include more relevant information. there are
many, many cases on this mailing list where people ask
for help with problems, and you can easily derive from
the dialog what information is needed and what _you_
can do beforehand to verify and you are seeing a real
problem and what information is need to narrow it down.


> thanks and regards,
> Vivek
> IMM, India.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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