Ubuntu: Increase processor utilisation of one application/program



Question:

I use ClustalX to align few unusually big sequences on my home desktop, this takes more than a week to complete and runs well below the maximum capacity of the machine.

The top | grep clustalx gives the following output

5985 @username 0 -20 1971048 105428 9012 R 99.9 2.7 5829:27 clustalx

It shows the CPU usage is ~100 and the memory usage ~3% RAM. But the system monitor says otherwise,

CPU Usage history and Memory history

There are 2 CPU cores running at maximum in the picture, that's because I am using firefox and the system monitor, otherwise its just one. I have also set the priority of clustalx to Very high and yet, there is no considerable improvement I could see.

What more should I do that it utilises more CPU and RAM. Any suggestions would be useful.

Load average ~2.7(when I'm using other programs also)

I have seen the following post related to this, but they don't answer my question:

How to increase cpu usage [closed]

System specifications:
Ubuntu 64 bit 14.04 LTS on 154GB HDD partition, 4GB RAM, Intel Core i3-4130 CPU @ 3.40GHz × 4 processor, and 10 GB swap.

Program Spcification: ClustalX for linux - Used in biological sequence alignment.

To determine if my program is 32/64 bit, I used

find /usr/bin/clustalx

/usr/bin/clustalx: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),...


Solution:1

Easy: run your program as many times as you have cores...

I do the same to transcode video in multiple formats: not all video-encoders are multi-core/multi-CPU-aware, so I run a video-encore for one resolution on one core and the other one (with different command-line parameters) on another core.

Low-quality reviewers: some complex problems have exceedingly simple solutions.


Solution:2

According to this:

https://www.biostars.org/p/44231/

it sounds like clustalx will only the one core, and you need to use clustal omega or mafft.


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