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I am running a Mathematica script (this question probably doesn't fit in Mathematica.SE however) and I know that it generally takes up a lot of RAM and loads up my cores. However, althought pgrep MathKernel is showing a pid, I find that top doesn't show this in the top processes, although I notice that it is taking up about 2.25GB of the 8GB available to me.

pmap -x my_process_id

total kB         2243132 1907404 1892108


ps aux | grep MathKernel
dnaneet  20837 12.6 23.3 2234944 1907404 pts/1 Sl   09:23  
 8:01 /share/apps/mathematica/8.0.4/SystemFiles/Kernel/Binaries/Linux-x86-64/MathKernel   -runfirst $TopDirectory="/share/apps/mathematica/8.0.4" -script 
./dcm_10micrometer_2x -- ./dcm_10micrometer_2x

ps aux shows that the process is taking about 12% (In asterisks)

dnaneet  20601  0.0  0.0  68264  1660 pts/1    Ss   09:15   0:00 -bash
**dnaneet  20837 12.2 23.3 2234944 1907404 pts/1 Sl   09:23   8:01 /share/apps/mat**
dnaneet  21922  0.0  0.0  65604   948 pts/1    R+   10:29   0:00 ps -aux

Did this process fail and is the MathKernel just lingering?

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migrated from Oct 7 '12 at 21:13

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Did you try sorting top by memory usage? – Kevin Oct 7 '12 at 14:39
And you're right that this isn't a mathematica.SE question, but it'd be better on Super User or Unix & Linux. – Kevin Oct 7 '12 at 14:40
@Kevin Well that shouldn't be the problem. When I top, the most cpu usage that I see is close to 0% – drN Oct 7 '12 at 14:45
@drN Sort by memory usage; do so by switching the sort field using the > key – artistoex Oct 9 '12 at 22:19
@artistoex Yes, I did that. However, there seems to be an issue quite deep. I'll update as soon as I know more. – drN Oct 11 '12 at 0:46

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?

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