Why is process not being displayed by TOP

1

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

AND

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?

dearN

Posted 2012-10-07T14:24:58.860

Reputation: 181

Pls see my reply on this forum – MariusMatutiae – 2015-06-14T16:33:51.530

1Did you try sorting top by memory usage? – Kevin – 2012-10-07T14:39:40.910

And you're right that this isn't a mathematica.SE question, but it'd be better on [SU] or [Unix.SE]. – Kevin – 2012-10-07T14:40:39.693

@Kevin Well that shouldn't be the problem. When I top, the most cpu usage that I see is close to 0% – dearN – 2012-10-07T14:45:34.133

@drN Sort by memory usage; do so by switching the sort field using the > key – artistoex – 2012-10-09T22:19:43.127

@artistoex Yes, I did that. However, there seems to be an issue quite deep. I'll update as soon as I know more. – dearN – 2012-10-11T00:46:23.093

Answers

0

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?

MariusMatutiae

Posted 2012-10-07T14:24:58.860

Reputation: 41 321

Asked: 2012-10-07T14:24:58.860

Viewed: 608 times

Active: 2015-06-14T16:33:29.377