Did this process fail and is the MathKernel just lingering?
Not at all, your program is alive and kicking. This line of your ps output
**dnaneet 20837 12.2 23.3 2234944 1907404 pts/1 Sl 09:23 8:01 /share/apps/mat**
shows that Mathematica is taking up 23.3% of your whole memory, or about 1.87GB. On the other hand, the output of pmap shows that the amount of Resident-Set-Size Memory (RSS) is 1.9GB, the same within rounding errors. The key word here is RSS, the amount of memory which is held in RAM memory.
The 12% you are referring to is the CPU usage.
P.S.: in the end, did you take up that job at a European lab, or did you opt for one of the two faculty positions?