Re: Error on Solaris

From: Marcos Sotomayor (
Date: Sat Jun 25 2005 - 17:53:52 CDT

Hi Tirath,

Note that, as explained in the NAMD tutorial (section 2.1.4), the
simulation is set to run for a "long time" (1 ns) so as to sample well the
quantity of interest. This obviously will take time in a single processor!
Thus, the respective instruction does not have an asterisk (i.e., is not
recommended for a first try with the tutorial, as explained at the
beginning of the chapter; its better look at the provided output files).

The simulation may have filled your disk space, however it would be good
to see the log file it generated in order to understand the error...


On Sun, 26 Jun 2005, Tirath Ramdas wrote:

> Hi all,
> I attempted to run the 2-4-temp tutorial simulation (available from
> on a Solaris machine (with the
> latest executable from the same site) on which I lack root access, and after
> over 50 hours the job died with:
> <----->
> afs: failed to store file (13)
> Bus Error
> <----->
> I have successfully run the earlier namd simulations without any complaints
> on the same system with the same binaries, though they took faarrrr less time
> than 2-4-temp.
> I tried googling {"afs: failed to store file (13)" "Bus Error"}, but got no
> hits. Any hints, anyone?
> (btw, fwiw, I'm a total newbie to this stuff - i.e. molecular biology, as
> well as large scale simulations in general!)
> Apologies if this sort of query is OT on this list.
> Sincerely,
> Tirath Ramdas

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