For the last couple of days, my home computer with SolydXK was overheating. The situation was so bad that, by the time I can gain control of the machine, it gets so overheated that it shuts down automatically as the critical temperatures have reached.
I initially suspected acpi_call (just a hunch, because I have set up the OS on this machine quite recently and haven't tweaked the system much yet, except turning off the discrete graphics card using acpi_call). But removing the corresponding kernel module didn't do the trick. I booted into recovery mode, edited the /etc/rc.local to prevent loading the acpi_call kernel module and turning off the discrete graphics card. Although this sounds counter intuitive, because usually turning on the discrete graphics card causes the overheating, I saw some errors related to acpi_call during boot time too, which is why I targeted that first.
But a reboot after exiting the recovery mode, now without acpi_call loaded, didn't prevent the laptop from overheating. So, I tried to chase my second suspect. Before the system would go down again reaching the critical temperature, I quickly ran apt upgrade, suspecting that some unstable package might be messing up the system. While running the upgrade, I also checked "top" as a sanity check (looking for a third suspect). The apt upgrade appeared to have upgraded some causual packages such as mendeley etc. It is the top result in which I found the culprit: a process called freshclam, running at 100%. I slaughtered it immediately (sudo killall freshclam). Result immediately showed up; the temperature slowly started to reduce. The next cpu hungry process in the race was dropbox. I killed it too. The computer became sane again (well, I could have safely spared dropbox, but I didn't want to take any chance at all :-P).
I googled to find out what freshclam process was. The freshclam process was part of the clamav antivirus software!. It must have bundled in the default SolydXK distro. As I never previously used any antivirus software on any of my linux systems, I didn't see an immediate need for it now. So, I removed the clamav software for now (sudo apt purge clamav clamav-freshclam; there was a third package too, whose name probably was clamav-common).
After this, everything was good. So, I re-enabled the acpi_call and turning off the discrete graphics card, by uncommenting those lines in /etc/rc.local. Everything has been running smooth ever since.
I wanted to start analysing genome-scale metabolic models. I am interested in metabolic modelling to study human diseases. At least as of now, my idea is to use R for the analysis. This post describes all the technical set-up that I am doing on my ubuntu 10.04 LTS machine in order to eventually start working with these models. As I am interested in human metabolic network, my model of interest is the reconstructed human metabolic model, recon 2. I googled to see where I can download it from. It has a web site http://humanmetabolism.org/. But the model is available for download from the supplementary material of this paper . There was a zip file that contained many files which I interpret as the generic human model and cell specific models for a variety of cell types. I first wanted to see the contents of these files with my eyes. I know that I could open these files with any text editor, but I also knew that there is something called SBML editor which is specifically designed fo...
Comments