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bredelings / BAli-Phy

Bayesian co-estimation of phylogenies and multiple alignments via MCMC
http://www.bali-phy.org/
GNU General Public License v2.0
45 stars 16 forks source link

Please check the free() or other scripts related with memory #15

Closed starsareintherose closed 2 years ago

starsareintherose commented 2 years ago

OS: ArchLinux Installation: https://github.com/BioArchLinux/Packages/blob/master/BioArchLinux/bali-phy/PKGBUILD

When I finished running this problem and then It is still running in the background and quickly fills up the CPU. I don't want to repeat it, but it's still a problem for other users.

bredelings commented 2 years ago

Thanks for the bug report. Can you please give more information?

Do you mean it fills up the RAM, or the CPU?

After compilation, the installation process should run tests that take up the CPU. That is not a bug.

starsareintherose commented 2 years ago

sorry, not compiling the process, but after using it and it finished running. It starts to take up the RAM or CPU, I use the https://extensions.gnome.org/extension/2986/runcat/ extension, it shows that it quickly to 100%. Monitor shows that CPU occupy is quite large for Bali-phy, but it has finished the running

bredelings commented 2 years ago

Hmm... what do you see if you run the top command in the terminal? That gives more information than the 'runcat' command.

Also, what kind of input are you giving to bali-phy? How many sequences? How long are the sequences?

starsareintherose commented 2 years ago

very short sequence, just 3 samples CO1 section. and it has been finished. I don't want to repeat it, it will make my PC broken

bredelings commented 2 years ago

Can you send me the data set so I can test it?

starsareintherose commented 2 years ago

okay, no problem, I will send you a large dataset, and the original seq is just for testing some software, it has been deleted. CO1.fas.txt

bredelings commented 2 years ago

I ran your example, and I'm not seeing a problem, either with memory usage or with CPU usage.

Note that a program cannot break your computer by using 100% CPU. If you have two programs that try to use the CPU, they will share it.

What command line did you use?

How do you know that the analysis is finished?

starsareintherose commented 2 years ago

This program make CPU occupy to 100% shown by the gnome extension I will report it when I would like to repeat it.