Monthly Archive for August, 2007

What to do with a broken Rubik’s Cube: make a fused cube

on 2007 August 27
in Hard Hacks
. 0 Comments

This is a relatively overdue post. I will use this to introduce myself in the Philippine Cubers Association (PCA) forum.

I bought a Rubik’s Cube a few months ago from national bookstore. It was too late when I found a factory defect. The center face cube was broken and is not attached firmly into the kernel (the internal piece that makes the cube work). Gluing it was not an option since it will immobilize a face on the cube. Thinking on the constraints made me think of an idea: a fused cube!

There are already a lot of fused versions of the Rubik’s cube. A simple Google search will gives you Rubik’s Fusion, Rubik’s Fusion+, Siamese Cubes. Some of these “cube mods” are actually available online. I also found DIY sites on how to make them. And the easiest to build was called a “Fused Cube” in TwistyPuzzles.com.

Constructing the cube was fairly simple. As seen in Ton’s Puzzle Building Corner, One has to first create quarter circle grooves on the 3 center faces of each cube. Here is a picture of the kernel found on his site:

I made the grooves as found in the picture by drilling the initial cuts on the center faces. The final sculpturing for finishing the quarter circle cut was made using a grinder and a file. The image below shows both modded kernels pre-assembled with the other cube pieces.

fused cube internals

Both cubes were attached together using Mighty Bond (superglue). Solving this cube was more challenging and requires more thinking because of you cannot move the center pies. I will make another post regarding my solution for solving this fused cube.

fused cube

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Building a 1.2 Terabyte server

on 2007 August 20
in Hard Hacks and Soft Hacks
. 2 Comments

At last after several months of processing paperwork through the Purchasing Office, our 1.2 terabyte Beowulf cluster server has finally arrived! This will be used to replace our recently decommissioned Beowulf cluster deployed last 2001. It will serve the scientific community of Ateneo de Manila for various numerically intensive problems like bioinformatics, climate modeling, gellation of natural products, coding theory, etc. The server uses Promise FastTrak SX8300 raid controller to be able to create a RAID 5 image of the 6 320 Gb hard disks. The picture below shows the 6 channel hot swap bay:

6 driver hotswap bay

We were having problems in creating the RAID image during the first few days of our installation. I called the vendor’s supplier, PC Trends for basic troubleshooting and support. They were very responsive with our concerns and replaced our controller with a new one in their site visit. Now I was able to succesfully create a RAID array (called an LD device in the FastTrak manual).

The next step is installing the operating system itself. We used the Rocksclusters system [1] developed at the San Diego Supercomputing Center. I downloaded their latest version, v. 4.3 Mars Hill. Their solution based based on CentOS 4.4 which in turn is a rebuild of Redhat EL 4 update 4. In order for the OS to recognize the images, drivers from RAID cd must be installed. Unfortunately they only built disk drivers (dd images) for the first release of Redhat EL. Issuing a “frontend dd” on the isolinux boot prompt was not able to successfully recognized this driver disk since they have different update version of the 2.6.9 kernel. Thus I have to first install the OS without recognizing the RAID device, and then build a disk driver from it using the Partial Linux source code driver.

Building the driver was very straightforward since the README file describes how to build the modules. Their partial source code generates the modules napa.ko. Then the next step is to integrate it with the disk driver image to create a new one dedicated for Rocksclusters. The first is to create the modules.cgz file inside the image. Assume that we are building for kernel version 2.6.9-xxEL

DRIVER_ROOT$mkdir -p`uname -r`/i686
DRIVER_ROOT$cp napa.ko `uname -r`/i686
DRIVER_ROOT$ls -1 `uname -r`*/i686/* | cpio -Hcrc -o | gzip -9 > modules.cgz

Mount the pre-built image found on the FastTrak driver CD and copy modules.cgz. Also edit the install file to update the base_ver variable with the kernel version. Notice I also built a driver for the SMP version of the kernel.

#!/bin/sh
drv_basename=napa
remove_module=
base_ver=”2.6.9-5.EL 2.6.9-5.ELsmp”
drvname=”${drv_basename}.ko”

Using the install script from the driver image, I installed the kernel module after installing the OS. I am having a bit of trouble integrating the disk driver during the OS installation itself. After loading the module at the start of the installation process, the machine restarts. It is not any of my concern as of the moment to get the disk driver working during the installation. Now I am able to recognize our RAID controller. Just take a look at that 1.2 Tb of disk space

df -h

Here are my modules.cgz builds both for Rocksclusters 4.2.1 and Rocks 4.3.

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WIPAS propagation studies

on 2007 August 17
in Theoretical Hacks
. 0 Comments

Classes have been suspended for three consecutive days due to heavy rain. At last I can slack off preparing for class and concentrate on the other side of academic work: research.

The ECCE Department is very interested in studying its properties in the context of Philippine tropical rain. We have various publications exhibiting the crazy stuff we do these days. One of our projects it to characterize rain in terms of its effects on wireless telecommunications systems. A few weeks ago, we went out to the field to make key field measurements of its received signal levels over some distances. It makes sense that the distance between two directional transceivers increases, it is harder to align them.

Here are some pictures during the propagation studies. The operation was performed ona clear sunny day.

wipas: site view 1wipas: site view 2wipas: site view 3

wipas: alignment 2wipas: alignment 1

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Lecture: Biomedical applications using the grid

on 2007 August 8
in Teaching
. 0 Comments

For my CE21 B students:  Those who were not able to attend the lecture may find the lecture slides on the course website. montagnat-grid.pdf

Title:  Biomedical applications using the grid
Speaker:  Johan Montagnat, Ph.D

Abstract:

With the generalization of digital imaging in medicine and the emergence of ever growing medical archives, efficient tools for retrieving clinically relevant data are needed. Medical images are usually indexed with medical records (patient information, acquisition parameters, etc.) but for applications such as epidemiology or diagnostic assistance, images also need to be identified from their content. Content-based image retrieval in medical databases is challenging both in terms of computing power (size of image databases, complexity of algorithms) and in terms of performance of image content analysis algorithms (difficulty to identify relevant features in medical images).
Our research project is addressing the problem of content-based medical image retrieval in large databases. We are exploiting grids to tackle the computational requirement of this problem. We developed strategies to optimize the load distribution over the very large scale EGEE (Enabling Grids for E-sciencE) grid infrastructure, taking into account its properties and load. We have explored several
strategies to identify relevant images. Texture features extracted using Gabor filters proved to be an efficient and relevant mean of indexing medical databases. The texture feature could be correlated to image modality, tissues, and subtle changes such as myocardium tissues variation using the cardiac cycle.

About the Speaker:

Dr. Johan Montagnat has obtained his PhD in Computer Science (with highest honors) from the University of Nice-Sophia Antipolis (France). He is currently a research scientist at the French National Center for Scientific Research (CNRS), working in the fields of medical image processing and grid computing. Dr. Montagnat is a co-principal investigator of the ONCO-MEDIA project ( http://www.onco-media.com), an international research collaboration on biomedical applications of grid computing, wherein Ateneo de Manila University is one of the partner institutions.

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