[gmx-developers] GPU memory issue?

[Justin A. Lemkul]

Hello all,

We have a new GPU workstation equipped with a Tesla C2075.  I installed Gromacs 
4.5.5 and tried to run the DHFR benchmark but got a fatal error that the 
pre-simulation memory test had failed.  This was the first time anything had 
been run on the GPU, so it struck me as odd.  I saw the discussion on this list 
a few days ago regarding memory exhaustion, so I used Szilard's script to see 
what was going on.  I got the following:

[2012-03-12 08:37:36]  Memory usage: virt      10736	res       4920
[2012-03-12 08:37:46]  Memory usage: virt     148428	res      71188
[2012-03-12 08:37:56]  Memory usage: virt     148428	res      71188
...
[2012-03-12 08:52:18]  Memory usage: virt     148428	res      71188
[2012-03-12 08:52:28]  Memory usage: virt     148428	res      71188
[2012-03-12 08:52:38]  Memory usage: virt     149348	res      72256
[2012-03-12 08:52:48]  Memory usage: virt     149348	res      72256
[2012-03-12 08:52:58]  Memory usage: virt     149348	res      72256
[2012-03-12 08:53:08]  Memory usage: virt     149348	res      72256
[2012-03-12 08:53:18]  Memory usage: virt     149348	res      72256
[2012-03-12 08:53:28]  Memory usage: virt     149348	res      72256
...
(and onward to completion)

Is this increase in memory usage indicative of a problem?  If so, is there 
anything that can be done?  I imagine that the bump in the beginning is simply 
an effect of the simulation starting up, or is that not correct?

Looking at the observables in the simulation, there seems to be nothing wrong - 
no abnormal structures or RMSD spikes, energy terms are very stable, etc. 
Should I be looking at other things?  The error that comes up about failing the 
memory test seems to indicate that I should expect catastrophic problems, so I'd 
like to fully investigate any issues before we invest serious time in doing data 
collection.

I would also note that on the Gromacs website, it states that the Tesla C2075 is 
supported, but it is not present in the hard-coded list.  Thus I have to use 
"force-device=yes" in my mdrun-gpu command.  I suppose this is something to be 
fixed, if it hasn't already been.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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