Friday, February 26, 2010

Amaha Linux Home Server

Amaha Linux Home Server is not a Linux Distro but a collection of software packed as presented with a web-managed console. It sits on top of the version of Fedora 12.

The Amahi Linux Home Server core purpose makes your home networking simple. According to the Project website, it has a number of features that
  1. Audio Streaming with the Amahi Tunes, a customised Firefly Media Server.
  2. VPN using preconfigured OpenVPN
  3. Networking including DNS, Web Servers and NAS Server
  4. File Sharing
  5. Hardware monitoring
  6. Amaha Private Wiki
  7. Backup to a network share
  8. Vista Calendar Integration 
  9. Outlook Integration
  10. ICal Integration
  11. For more information, do look at Amahi Feature Gallery

Before you install Amahi Linux Home Server, you have to install Fedora 12 and add the Amahi repository in. Use the web-based console to configure the services you need.

Monday, February 22, 2010

Using Linux Console to Send Message

If you need to send a message using the linux console, you can use the command write
write userid [ttyname]
To exit write, just do a ^C and you will see a EOF at the end of the message.

Overview of MAUI Scheduler Commands

Finally, I thought I summarise the documentation of MAUI Schduler Commands in one nice blog entry "Overview of MAUI Scheduler Commands". Hopefully, this will help summarise the commands used for system administration of the MAUI Scheduler

Phoronix Test Suite

The Phoronix Test Suite is the most comprehensive testing and benchmarking platform available for the Linux operating system. This software is designed to effectively carry out both qualitative and quantitative benchmarks in a clean, reproducible, and easy-to-use manner. The Phoronix Test Suite consists of a lightweight processing core (pts-core) with each benchmark consisting of an XML-based profile with related resource scripts. Some of the key features are
  • 120+ Test Profiles
  • 50+ Test Suites
  • Extensible (XML-based) Testing Architecture
  • Optional Linux-based LiveDVD/USB Testing Distribution (PTS Desktop Live)
  • Automated Test Installation
  • Dependency Management Support
  • Module-based Plug-In Architecture
  • Integrated Results Viewer
  • PNG, JPG, Adobe SWF, SVG Graph Rendering Support
  • Autonomous Batch Mode Support
  • Global Database For Result Uploads, Benchmark Comparisons
  • HTML Documentation Covering Test Profiles, Module Framework
  • Installed Software, Hardware Detection
  • System Monitoring Support
  • GTK2 Graphical User Interface + Command-Line Interface
  • Runs On Linux, OpenSolaris, Mac OS X, & BSD Operating Systems

Sunday, February 21, 2010

Inkscape - Open Source Scalable Vector Graphics Editor

Inkscape is an Open Source vector graphics editor, with capabilities similar to Illustrator, CorelDraw, or Xara X, using the W3C standard Scalable Vector Graphics (SVG) file format.

Inkscape supports many advanced SVG features (markers, clones, alpha blending, etc.) and great care is taken in designing a streamlined interface. It is very easy to edit nodes, perform complex path operations, trace bitmaps and much more. We also aim to maintain a thriving user and developer community by using open, community-oriented development.'

Available for both Mac, Linux and Windows

Screenshots of Inkscape

Saturday, February 20, 2010

How to split your large file into smaller chunk using Linux

There are many ways to send a large file across. Using Bittorrent, P2P, FTP etc. But what if you encounter scenario like sending a email attachment with very limited attachment size, you may find this tool useful

For example, you have  a media file of size 20M and you wish to break it up to 10M chunk, just use the split command that comes with Linux
split -b 10M test-split.wmv
Consequently, the command will break the test-split.wmv into 2 chunk xaa and xab. "xaa" and "xab" are generated by the split command. If you split into more chunk, it will follow the alphabetical order xac, xad etc

To join back the 2 file into a single entity again, just use the good old cat
cat xab >> xaa.
(Do use ">>" as it append data from one file to another)

Friday, February 19, 2010

Understanding memory usage from top and htop

Actually from htop and top utilities, you can find how the memory is used and buffered.

When you run top, you will notice that a lot of memory are being used even though there may not be much applications currently running. The reasons for this huge usage is that the kernel allocates memory that isn't in active use by processes to things like filesystem caches to improve performance. If there is demand on the memory by another application or data, the kernel will free up the memory.

If you run top,  you will notice buffers and cached. "Buffers" represent how much portion of RAM is dedicated to cache disk block. "Cached" is similar like "Buffers", only this time it caches pages from file reading.

However if you run htop, the memory used is smaller. Both utilities are not wrong, it is a different representation of the memory usage

For more information, you may want to read an excellent article on Using Top More Efficiently 

Wednesday, February 17, 2010

Using ImageMagick to edit image at command line

ImageMagick is one of the oldest but still widely used graphics editing software. One of the strength of ImageMagick is the ability to do batch processing like shrinking the size of the images etc.

There are very good examples on the ImageMagick tutorial itself.
  1. Example (​Usage/)
  2. Stream (​stream.​php)
  3. Animate (Animate:​php)
  4. Command-line-Options (
  5. Image Format (
  6. API (
  7. ImageMagick Studio (
To install ImageMagick, just type
# yum install ImageMagick

To view the image, just type
$ display

Click Top left-hand corner to launch the ImageMagick

Friday, February 12, 2010

OpenFOAM - Open Source CFD

OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

Thursday, February 11, 2010

ImageJ - Image Processing and Analysis in Java

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.

It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.

Wednesday, February 10, 2010


NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PL0OR.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Monday, February 8, 2010

Installing Devede on Fedora 11

DeVeDe is a program to create video DVDs and CDs (VCD, sVCD or CVD), suitables for home players, from any number of video files, in any of the formats supported by Mplayer. The big advantage over other utilites is that it only needs Mplayer, Mencoder, DVDAuthor, VCDImager and MKisofs (well, and Python, PyGTK and PyGlade), so its dependencies are really small.

To install devede on Fedora 11, first you have to install RPM Fusion. For more information on RPM Fusion installation, see Blog Entry RPM Fusion Repository. Remember to do a "yum check-update" after you have install the repository

Step 1: Install devede
# yum install devede

Step 2: Launch devede
$ devede

Step 2: Explore the options. Some of the key features are
  • Selection of Video output format (PAL, NTSC)
  • Customised Menu Title Background, Music, Font
  • Video Output size in relations to Video Medium
  • Can burn to ISO or MPEG
  • etc

Wednesday, February 3, 2010

SSH Error : Permission denied (publickey, gssapi-with-mic,password)

One of our Linux accounts was having this issue with SSH
"Permission denied (publickey,gssapi-with-mic,password)"
One obvious symptoms of this problem is that it was possible to SSH in from external machine, but was unable SSH out of the problematic machine

To resolve this issue, you have to go to
$ cd /home/youruserid/.ssh/
$ vim config

Change the configuration to
BatchMode no
The option BatchMode specifies whether a username and password querying on connect will be disabled. This option is useful when you create scripts and dont want to supply the password. e.g. Scripts that use the scp command to make backups over the network.

For more information on SSH configuration, see
See also
  1. Unspecified GSS failure from SSH causes slow login 
  2. Resolving Slow SSH Login

Tuesday, February 2, 2010 warning: warning: feupdateenv is not implemented and will always fail

After you have compiled OpenMPI with the Intel Compilers, as
and when execuing mpirun on your program, you enconter " warning: warning: feupdateenv is not implemented and will always fail"
$ mpicc hello.c -o hello warning: warning: feupdateenv is not implemented and will always fail

This resolution to the issue can be found at OpenMPI FAQ to resolve this issue, you have to include the
$ mpicc hello.c -o hello -shared-intel

The default behavior of Open MPI's wrapper compilers can be changed to automatically include this -shared-intel flag so that it is unnecessary to specify it on the command line when linking MPI applications.

RCSB Protein Database Bank

RCSB Protein Database Bank is a Resource for Studying Biological Macromolecules. The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.

The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.

Pupil - Program for User Package Interface and Linking

PUPIL,Program for User Package Interface and Linking, is a software environment,- the program,- to allow developers to quickly and efficiently link together multiple pieces of software,- the user packages,- that have been and are actively being developed by researchers.

With its current 1.3 version, it is able to
  • Graphic User Interface to build the main simulation input file.
  • Simulation Manager to lead the multi-scale simulation between different Calculation Units.
  • Interface with Amber v10
  • Interface with DLPOLY v2.18
  • Interface with Gaussian03
  • Interface with deMon2k
  • Interface with NWChem
  • Interface with Siesta v2.0 (Start/Stop and CycleQM behaviors)
  • Interface with mndo97 (Start/Stop QM role behaviors)
  • stubMD. Stub program for interface sample and testing playing a Molecular Dynamics Calculation Unit role.
  • stubQM. Stub program for interface sample and testing, playing a Cycle Quantum Mechanics Calculation Unit role.
  • stubDI. Stub program for interface sample and testing, playing an external Domain Identifier Calculation Unit role.