Does matlab throttle thread use for the remainder of the session when available threads are limited?

Hello, I often run multiple jobs (some matlab some other) on our linux servers (RHE6, all 2cpu 8 or 10 core each). I have noticed but cannot yet prove that when I have multiple jobs running on the same server that each use multiple threads, sometimes Matlab seems like it hits a "wall" and drops from consistently using 6 or so threads down to slightly over 1 (i.e. top shows it drop from 650%-ish to 125%) with a dramatic reduction in speed. When run in isolation the same Matlab code continues to use the larger number of threads. I'm wondering if perhaps matlab tried to grab threads, found that they were not available and decided not to try anymore (sorry for the vague description, I'm not a programmer).

In more rare cases I have seen similar behavior with other multi-thread enabled software we run so this may be more an operating system issue than matlab specific. This is a bit problematic though. Something that runs in 41m in isolation now looks like it will take over 8h. Below is the output of top. The top 4 tasks (including matlab) should all be over 500% fairly consistently but are now not. The other three occasionally jump up near normal, but matlab never does.

Any ideas I can try (beyond running a single job at a time?) Thank you.

j

Cpu(s): 9.3%us, 9.7%sy, 0.0%ni, 80.9%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 132181268k total, 54102888k used, 78078380k free, 475360k buffers Swap: 15999992k total, 46048k used, 15953944k free, 2277464k cached

   PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND                                                                                                                                                                
179217 smithjf   20   0 7819m 5.6g  18m R 100.0  4.5 510:58.34 antsRegistratio                                                                                                                                                       
169848 smithjf   20   0 6366m 4.1g  18m R 100.0  3.2 181:04.71 antsRegistratio                                                                                                                                                       
135044 smithjf   20   0 37.1g  32g 130m S 138.7 25.8 108:13.89 MATLAB                                                                                                                                                                
179793 smithjf   20   0 6164m 4.0g  18m R 100.0  3.2 136:47.79 antsRegistratio