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