[maker-devel] maker low cpu utilization

[Daniel Ence]

Hi Christian, I think what you have described is normal behavior for MAKER. It spawns many child processes, most of which complete very quickly. What dataset were you running with MAKER? Did it complete successfully?

~Daniel


Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

> On Mar 10, 2016, at 7:53 AM, Christian Meesters <meesters at uni-mainz.de> wrote:
> 
> Dear maker-developers,
> 
> As a computational scientist of our local HPC-Team, I recently installed maker and its tools.
> 
> We encountered a most peculiar problem: Distributed over 2 nodes, 64 cores each (AMD OPT6272 "bulldozer"), all started processes take up ~20 % of the possible CPU whilst the node show a full load of processes. Amongst this 20 % there is some system overhead (~4%).
> 
> We then wrote a little wrapper / submission script, such that the ctl-Files were altered and all reference input is copied unto ramdisks (each node provides the same path, there are then 2 copies of each reference file, prior to starting maker). Still no change - IO is not a bottleneck, here.
> 
> I then wanted to trace individual PIDs, but they are frequently changing. However, I saw > 170 instances ps concurrently running and the same amount of 'sh'.
> 
> Only augustus should about 100% CPU usage, all other (except maker itself) showed lower usage.
> 
> Have you ever experienced something similar and could perhaps provide a pointer to the cause? Could this perhaps be related to the nature of the input data (can some input data cause frequent switches of processes and therefore OS scheduler overhead)?
> 
> Thanks a lot in advance,
> Best regards,
> Christian Meesters
> 
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