Category Archives: Biomedical Engineering

Biomedical Engineering

The cluster is basically done

I started setting up the hardware at around 1600h yesterday.

I finished setting up the underlying software today at around 1900h today.

Not too shabby, eh? According to wwtop:


Cluster totals: 20 nodes, 40 cpus, 96200 MHz, 39.18 GB mem

Here’s a snapshot of the front of the status page:

What an ordeal. Now we have to start compiling PETSC on it.

New Cluster Set-Up

When moving to JHU, we took our 20 cluster nodes which are Evolocity II units from Linux Networx. They were part of a larger cluster at Tulane’s Center for Computational Science. As such, we didn’t need to worry about them — the CCS sysadmin took care of them.

Now that they are here at JHU, they need to be set up on their own. “Who will set them up?” you ask.

*looks around*

Oh, right. So, I’m looking at using Warewulf. It’s targeted to Fedora Core head nodes, and our fileserver Lagniappe is already running Ubuntu 6.06 LTS Server, so I may have a few difficulties there. Also, Warewulf prefers PXE boot, and our nodes use Etherboot on LinuxBIOS. Supposedly this is “backward” compatible with PXE boot, but I’m not sure whether our nodes have a current version of LinuxBIOS or not, so I don’t know if they feature that capability. Luckily, assuming I get Warewulf set up, there’s no difference administratively between running 5 nodes and 500 nodes.

Once it is complete, I will need to install MPI, the intel compilers, and so on.

Science Attacked From All Sides

You may have heard me complain about the Intelligent Design movement, what a load of bunk it is, and how much damage its proponents are doing to scientific understanding and progress. However vast and harmful that may be, in degree it doesn’t hold a candle to firebombing people’s houses, bomb threats, and the other nastiness perpetrated by the hypocritical animal rights groups.

Look, I’m vegetarian. I’m a Buddhist. I don’t think we should be eating animals en masse for a variety of reasons, the most important of which is health. I don’t have a problem with animal research, though. There are strict guidelines in place to ensure that it is done in a “humane” way. And even if that weren’t the case, is threatening someone, and firebombing their house a better way to act? What if that molotov cocktail had exploded, the house had burned down, and someone had died?

The ethical hypocrisy from these groups is monstrous.

Please, no matter how much you love animals, and want to see them treated well, do not let words like these (from the article) come out of your mouth, ever:

… force is a poor second choice, but if that’s the only thing that will work … there’s certainly moral justification for that.

ADDENDUM: You really should read the comments over there. Some of the comments from the animal rights nuts leave me agape. They also reveal a bit of a misunderstanding: they seem to think scientists like vivisection, like the pure glee of it drives them to do it. They seem to think if research is not on AIDS or cancer, then it’s “esoteric” and frivolous, and that no benefit can come from it.

Clearly there’s a major gap between public perception and reality when it comes to scientific research. What can we do to eliminate that gap?

ADDENDUM 2: I think we need to call the science nazi, as I mentioned with regard to ID a little while ago.