From: Tirath Ramdas (Tirath.Ramdas_at_eng.monash.edu.au)
Date: Sat Jun 25 2005 - 20:10:21 CDT
Hi Marcos,
On 26/06/2005, at 8:53 AM, Marcos Sotomayor wrote:
>
> 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).
>
Yep, I was aware that it would take a "long time", but I decided to
run it anyway. I even ran the bloody thing on my iBook for the past
few days, lol! Took 95 hours, CPUTime. :-)
I was engaged with some other activity over the past week, and
therefore had to put aside working through the tutorial for a while,
which is why I gave the 2-4-temp namd simulation a run - to gain a
sense for how long my actual simulations will take on the systems at
my disposal.
> 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...
That thought occurred to me too... `fs quota` reveals I have 63% of
my quota left, which should come up to over 80MB remaining. ubq-
nve.log is 2.1MB. `tail ubq-nve.log` shows the following:
<----->
PRESSAVG: 265650 0 0 0 0 0 0 0 0 0
GPRESSAVG: 265650 0 0 0 0 0 0 0 0 0
ENERGY: 265650 182.7499 610.9642 366.7911
36.0723 -24428.7147 2026.1854 0.6125
0.0000 3298.2906 -17907.0486 243.8157
-17892.3390 -17893.1002 243.2147
PRESSURE: 265700 0 0 0 0 0 0 0 0 0
GPRESSURE: 265700 0 0 0 0 0 0 0 0 0
PRESSAVG: 265700 0 0 0 0 0 0 0 0 0
GPRESSAVG: 265700 0 0 0 0 0 0 0 0 0
ENERGY: 265700 208.9778 586.8624 376.2380
33.9850 -24300.7110 1892.1172 2.1558
0.0000 3292.5690 -17907.8058 243.3927
-17893.4380 -17892.5894 242.8721
<----->
I tried grepping ubq-nve.log for "afs", as well as "error", but found
nothing. What else should I be doing?
-tirath
>
> Marcos
>
>
> On Sun, 26 Jun 2005, Tirath Ramdas wrote:
>
>
>> Hi all,
>>
>> I attempted to run the 2-4-temp tutorial simulation (available
>> from http://www.ks.uiuc.edu/Training/Tutorials/) 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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