It can be maintained via user-defined resourses too.
All that need is ability of BOINC to learn new <coproc> tag values and schedule 
task accordingly to these <coproc> shares.
For exampe, if one project uses CPU and another one uses GPU (let say ATI GPU 
so <coproc> tag has ATI value) these 2 projects will be naturally paired, they 
tasks will always run together as long as both have work to do.

I propose extend this <coproc> tag to allow new, user-defined resourses.
I already proposed that regarding support of currently unknown to BOINC new 
coprocessors or another hardware resourses.
But this approach could be used to solve project pairing problem too.
As was mentioned many times it's better to run different apps on different 
cores in multiprocessor system. Especially if it's HT-enabled one.

So let's define new <coproc> tags like CORE1, CORE2 and so on.
That way user could be able set <coproc> tag for one app as CORE1 and as CORE2 
for another app (even no matter will it be the same project with 2 apps as 
SETI's MB and AP or 2 different projects). Then BOINC will be able to schedule 
such app correctly, avoiding to run many instances of the same app that will 
give better CPU usage and ensure project diversity too.
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