We had some discussion about this issue back in January.

For most of the lifetime of BOINC on GPUs, CPU throttling has *not* been 
applied to GPU apps:

it was dis-applied on 27 Oct 2008 - 
http://boinc.berkeley.edu/trac/changeset/3719268f1c3807dcac821c455090e2243133bb8d/boinc-old
and re-applied on 12 Jan 2013 - 
http://boinc.berkeley.edu/trac/changeset/04de2936d47256edc77ba032541b096aff69b2d5/boinc-old

The re-application seemed to be at the request of a single user: David wrote

"I checked in a change so that CPU throttling applies to GPU apps also.
Can anyone think of a reason not to do this?
-- David

On 11-Jan-2013 11:42 PM, Admin Team "St.Petersburg" wrote:
> And here's another. In the client, the CPU has the ability to change power
> steering, and the GPU can not. To do."


That message, and the subsequent discussion, can be followed at 
http://lists.ssl.berkeley.edu/pipermail/boinc_dev/2013-January/019305.html

>From memory (and a very quick refresh view of that thread) the main response 
>was a request for a separate control to throttle GPU apps if desired - we 
>concluded with

"The request for a separate GPU throttling preference is noted; however we're 
not going to get to it immediately.
-- David"



>________________________________
> From: Heinz-Bernd Eggenstein <heinz-bernd.eggenst...@aei.mpg.de>
>To: boinc_dev@ssl.berkeley.edu 
>Sent: Thursday, 4 July 2013, 12:15
>Subject: [boinc_dev] CPU throttling and GPU apps
> 
>
>Hi all!
>
>While hunting for a bug recently, we at Einstein@Home came across a 
>question that I would like to present for discussion here:
>
>If an app has a non zero GPU share ("GPU app" for short), should CPU 
>throttling (as configured thru the preferences setting "Use at most x % of 
>CPU time") be applied to it?
>
>I guess there are several pros and cons, e.g.:
>
>cons: 
>  - one one hand, GPU apps (depending on the CPU share?) get a higher OS 
>prio (in terms of "niceness") to prevent the GPU being starved. Throttling 
>the CPU might very well cause this starvation
>  - if a GPU app has a rather low CPU runtime share in the first place, 
>further CPU throttling does not seem too useful.
>  - in order to avoid GPU load to interfere with the user doing non-BOINC 
>related stuff, there is already the setting "Suspend GPU work while 
>computer is in use".  
>
>pros:
>  I can't think about many, maybe consistency and user expectation?
>
>Volunteer reports at E@H seem to suggest that in the current BOINC client 
>version, GPU apps are indeed CPU throttled, right?
>Browsing thru the source code, my initial impression is that only NCI 
>(non-CPU-intensive) apps are excluded from throttling.
>
>Cheers
>HB 
>
>-----------------------------------------------------------------
>Heinz-Bernd Eggenstein
>Max Planck Institute for Gravitational Physics
>Callinstrasse 38
>D-30167 Hannover,  Germany
>Tel.: +49-511-762-19466 (Room 037)
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