Wednesday Apr 02, 2008

New Applications on Network.com!!!

I enabled 7 applications on network.com sometime back. They are not open source softwares, but freewares.

Here is the list of applications and what they do in brief

> ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (fixed pairwise correspondence)
> ASV: Analytical calculation of van der Waals surfaces and volumes.
> CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (pairwise correspondence computed)
> DOG: Docking Geometrically two molecules. (fixed pairwise correspondence)
> POP: Optimal Partition (classification). The number of classes is computed.
> QCM: Quantitative Chirality Measure of a conformer. (graph automorphisms enumeration included)
> RADI, RADI2: Computation of the Radius and Diameter of a spatial set. (computes also various other geometrical parameters)

The freewares are now shared in the Job Catalog of network.com!

Groovy on Solaris 10

I tried installing groovy on solaris 10 today. As expected, groovy 1.5.4 installed smoothly but I encountered a problem post installation. When I tried running groovy, I got the following error!

"startGroovy: syntax error at line 219: `i=$' unexpected"

The startGroovy script has a #!/bin/sh at the top and solaris 10 has problems with the lines
i=$(i+1). There were also other lines in the script that were not compatible with the shell - like the case statement which had

case ($i) in
(0) set -- ;;

This has to be changed to

case ($i) in
0) set --;

This patch will fix these issues with solaris. However, the fix has been put back into the code base recently. I will soon be releasing a groovy package for solaris. Do watch out the blog for updates!

Tuesday Apr 01, 2008

Sun takes April Fool's Day Seriously! :)

Sun is known for its April fool day pranks!!!

Check out some of the best pranks! The 1988 & 1991 & 1993 pranks are the best! :)

Some Famous Sun Pranks!

Freemat 3.5 now on network.com!

Freemat 3.5 is now available on network.com - Sun's Grid Compute Utility.

"FreeMat is a free environment for rapid engineering and scientific prototyping and data processing. It is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source." - freemat.sourceforge.net.

Network.com is Sun's Compute Utility tool where you can 'rent out' Sun's powerful hardware to run / test your applications.
Visit network.com for more info.

How to run Freemat 3.5 on Sun Grid ?

1) Go to the Job Catalog section in network.com and 'Checkout' the Freemat 3.5 Job. It should now appear in your 'jobs' section.
2) Create your 'Freemat Data Resource' - a zip file containing your input files and file called freemat.in.
3) The freemat.in should contain the freemat commands to be run. Note that you need to specify only the arguments to the freemat command in the freemat.in file. "FreeMat -nogui -noX -e" is taken by default.
4) Upload your file and point your Freemat Data Resource to the zip (by editing your Freemat 3.5 job)
5) Save and Run the Job!

A sample freemat.in file would like

HermitianOperatorExample1
HermitianOperatorExample2

This will run two Freemat commands, viz
FreeMat -nogui -noX -e HermitianOperatorExample1
FreeMat -nogui -noX -e HermitianOperatorExample2

You can also compile Freemat on solaris and run it via SGE (Sun Grid Engine)

Download the Sample Resource Zip
Here

Go to the Freemat Home Page

Monday Mar 31, 2008

Compiz on Open Solaris!!!

Compiz is an open source 3D window manager and works great for Open Solaris!

Just download compiz and run the installer!

Download!

sh compiz-0.6.2-for-solaris.sh should do it for you!

A pre-requisite is that you need a nice graphic driver. An NVidia card should serve the purpose.

Re-login to experience the compiz magic! The compiz icon should appear in your panel through which you can configure compiz settings.

Open Source...Should it have been named so?

During the Code for Freedom contest that was held in India from Aug 15th last year to Feb 14th this year, I travelled to various universities as part of the Sun university initiative spreading awareness of Sun's technologies and open source in general to college students. Last week, I was in Chennai and Delhi giving talks on Sun's software portfolio and Netbeans to ISVs. This post is about something that I noticed in common during my experience in these 7-8 months.

I can see students and ISVs showing tremendous interest in learning Sun Technologies, especially Netbeans and Open Solaris (ZFS, zones and DTrace). Be it the students or the developers, everyone is either passionate or eager to know about Open Source and Sun's technologies. This is a big positive thing for Sun. However, I rarely find people interested in or talking about participation. Everyone seems to like Open Source. But when asked why, their answer is simple - "Its free. Its rocking! I am able to use it to MY advantage!" Of course, its free and no one is preventing you from using it. But is that all open source is about ? Not many people I have seen say "I want to make netbeans better!" May be the concept of open source goes against the usual human mentality - You are done when you get your job done!

"I have a problem that I need to fix. May be this netbeans plugin would be useful. Let me use it. Period!" Thats how most people look at it. Not many go that extra mile - "This plugin is useful..Hmm..how could I make it even better?" And out of the few who go that extra mile, not many complete the circle of open source - putting their 'better code' back to the community. That is a sad reality that needs to be changed.

May be the name 'Open Source' doesn't stand upto its entire concept! The name tells the world the source is open and anyone can take it, but misses out on the crucial piece of contributing.

For those who love open source and have been involved only with the first half of the open source cycle, here is an analogy that I would like to give. Most of us would have gone through forums looking out for interview experiences. And the rest of us would have used some kind of torrent software to download movies! How did the movies or interview experiences land up on the internet? Its because someone dint want to download or retrieve information alone, but also wanted to share the information that he had! Now, imagine everyone wanting to only retrieve information. Will there be any movies to download or any information on the message forums ?

By downloading open source software alone, you increase the gap between people contributing and people retrieving which is not good for open source and ultimately not good for the you the 'open source software downloader'.

Using open source to your benefit and giving back nothing is neither good for open source nor for you! So, Lets Share, Participate, Innovate and Realize the Power of OpenSource!

Sunday Mar 30, 2008

Open Source Captions

Some of the captions & logos I thought of for the recently concluded 2 day IEC Open Source Mela at Sun, Bangalore.

May the Source Be You!

Participate, Innovate!

Freedom Matters!

Friday Mar 28, 2008

Web Developer Summit 2008

Am writing this post from the Web Devloper Summit, Delhi! Am too tired to take my cab after my long presentation and demo on Netbeans!

Sun is organizing the Web Developer Summit across 5 cities in India (Bangalore, Mumbai, Chennai, Hyderabad and today in Delhi). The summit is intented to spread awareness of Sun's technologies amongst ISVs.

The day kicked off with an introduction of Sun and its strategies followed by a presentation on Sun's hardware and software portfolio. Yousuf then spoke on Open Solaris followed by a Netbeans presentation and demo by me.

The ISVs present were attracted by the ZFS and DTrace features in Open Solari and by some cool netbeans editor features and the build in UML, Ruby, SOA and Web Services features of Netbeans!

Do watch out for the 2 day workshop that is going to happen in the same 5 cities where ISVs can get a hands on experience using Solaris, Netbeans and other cool Sun Technologies..

Here's Yousuf presenting on Open Solaris today at the Delhi Summit.

Thursday Mar 27, 2008

Quake III @ the IEC Open Source Mela

As part of the organizing committee for the IEC Open Source, I was asked to setup a gaming event during the 2 day IEC Open Source Fest!

With the Quake III source code GPL-ed, I compiled Quake III on Open Solaris and used the demo arena to setup a 'LAN Party!' The Open Solaris machines of course needed NVidia cards for better and smoother graphics and hence, I used 5 ultra 20 x86 machines with built in NVidia cards.

To run quake3, compile the GPL licences Quake III code (or you can use the packages available at iouqake3.org), use the demo arenas available (place your pak\*.pk3 files in your baseq3 directory) and there you go!!!!

Me, setting up the gaming arcade..

See the video of IEC engineers enjoying Quake III !!!

Wednesday Mar 26, 2008

IEC Open Source Mela!

The IEC Open Source Mela was a two day Sun event at Bangalore to create awareness of Open Source and Open Source technologies amongst Sun Employees. The two day event was held on the 25th and 26th of March. It was a packed two days with demos, talks and lightning talks all day, fun events and some gaming too!

Day 1:

After the inaugral and inspirational talk by KNR, IEC engineers were in for a series of talks surrounding open source! It was an excellent opportunity indeed to learn plenty of stuff about open source and more importantly to be aware of the work happening at Sun, India around Open Source!! The talks were around Sun's open source products like Netbeans, how to contribute to open source, etc. Simultaneously, there were demos happening to enlighten Sun fellow engineers on what Open Source Evangelists at IEC are upto!

The 'Gaming Arcade' was opened up post lunch and attracted plenty!!! Everyone tried their hands on 'Quake III' over the LAN! It was fun indeed to see people frag each other!!!

At the end of the day were some fun events followed by prize distribution for a few events that happened before the mela - the caption and logo contest and the acrostic puzzle! (I won the first prize! ;) )

Day 2:

The day kicked off with an excellent talk on the 'Do s and Dont s' in open source communities followed by some more amazing talks around virtualization, virtual desktops. The demos and the gaming arcade were there today too!! At the end of the day was a luck draw amongst those who attended many talks!

The IEC Open Source mela was a huge success indeed and of course sent the message across loud and straight - Open Source is the way of the future!!!!

Here's Swathi and me talking about the 2 day event!

A small quote that was put up during one of the talks - Open Source is a religion. Those who dont follow it go to hell! ;)

To catch up all the action on the IEC Open Source Mela - check out the blog.

Ruby Native Gem Support on Open Solaris

We integrated Ruby into Open Solaris build 78! From build 78 onwards, you can use ruby 1.8.6 and ruby gems 0.9.4 with Openssl, Curses, Readline, and Tcl/Tk extensions enabled :)

Ruby and Ruby Gems are available in /usr/ruby and have been linked form /usr/bin for easy use! So, in case you want to install a gem, all you need to do is issue the '(/usr/bin/)gem install ' command! If you are behind a proxy, do not forget to set your proxy - export http_proxy="http://:"

However, for native gems, you need to make some changes to your rbconfig.file (in /usr/ruby/1.8/lib/ruby/1.8/-solaris-)

If you are using Sun Studio, make sure you have /opt/SUNWspro/bin in your path and make the following changes to your rbconfig.rb file.

CONFIG["CC"] = "cc"
CONFIG["CFLAGS"] = "-xO3 -xbuiltin=%all -xinline=auto -xprefetch=auto -xdepend -KPIC"
CONFIG["LDFLAGS"] = "-L. -L/usr/sfw/lib -R/usr/sfw/lib"
CONFIG["CPPFLAGS"] = "-DTEXT_DOMAIN=\\"\\" -I/usr/sfw/include -I/usr/include"
CONFIG["CPP"] = "cc -E
CONFIG["CCDLFLAGS"] = "-KPIC"

If you are using GNU compiler tools, make sure you have gcc, g++, etc (usually /usr/sfw/bin) in your path and make the following changes to your rbconfig.rb file.

CONFIG["CC"] = "gcc"
CONFIG["CFLAGS"] = "-g -O3 -fPIC"
CONFIG["LDFLAGS"] = "-L. -L/usr/sfw/lib -R/usr/sfw/lib"
CONFIG["CPPFLAGS"] = "-DTEXT_DOMAIN=\\"\\" -I/usr/sfw/include -I/usr/include"
CONFIG["CPP"] = "gcc -E"
CONFIG["CCDLFLAGS"] = "-fPIC"

Voila! you are done and ready to use the gem command to install native gems on the fly!!
Well, this is just for the time being, these changes will also be integrated into Open Solaris soon so that native gem support too will be enabled by default! Shall blog about that once the integration is done!

Tuesday Oct 16, 2007

The Code For Freedom Movement

The Code For Freedom Contest is on and rocking!

Sun invites all students across India to join the open source m'ovement and make an impact!

Within a couple of months of its launch, the no. of registrations have already rocketed and touched the four figure mark!

What is the contest about ?

Students can participate in teams of two and contribute to Sun's popular open source technolgies - Netbeans, Open Solaris, Apache Derby, Glassfish and Open Portal.

Students can contribute to one or many of these technologies by either providing feature enhancements or by fixing bugs or by providing documentation.

Benefits :
- Rewards for every contributor.
- Excellent exposure to world class technologies.
- Opportunities to interact with actual developers of these technologies.
- Excellent value add to your resume ;) !!

More about the process can be found HERE.

I shall keep mosting more on the contest itself in the contest blog.

Saturday Jul 28, 2007

200 CPU Hrs Free

Join network.com now and get 200 CPU hrs free!!!

Guess the offer is valid for a limited time only! So hurry!

Enjoy the power of grid computing!

Friday Jul 27, 2007

Burning CD / DVD s on Solaris

I initially had a tough time burning CDs / DVDs on Solaris - Not anymore!

Just in case the Lauch->Places->CD/DVD Writer doesnt work good for you, here is what you can do!

Steps :

1> Place all your files / folders to be written in a directory say '/export/home/user/myNewDisc'

2> Make an ISO image out of it using the following command. Let say the iso image name is myImage

[gKrish]#mkisofs -J -R -o /export/home/user/myImage.iso /export/home/user/myNewDisc

3> Optional: You can test if the image created can be properly mounted.

[gKrish]# lofiadm -a /export/home/user/myImage.iso
/dev/lofi/1
[gKrish]# mount -F hsfs /dev/lofi/1 /mnt
[gKrish]# cd /mnt

4> Burn the CD / DVD

[gKrish]# cdrw -i /export/home/user/myImage.iso
Looking for CD devices...
Initializing device...done.
Preparing to write DVD
Writing track 1...done.
Finalizing (Can take several minutes)...done.

Voila!

Thursday Jul 12, 2007

Solaris Package Creator Plugin For Netbeans!!!

Now, you can create solaris packages of your solaris compliant applications from within netbeans! :)

The plugin can be accessed from
Solaris-Pkg-Creator.dev.java.net or from
Nebeans Plugins Portal

Note : In both the above links, the plugin comes as an add on to the "Sun Grid Enable My App" plugin.

Note : For clearer screenshots, visit Solaris-Pkg-Creator.dev.java.net

How to use this plugin ?

The plugin is an easy to use 5 step wizard based process to create solaris packages for any application. It can be invoked from the Tools Menu by clicking on 'Create Solaris Pkg'.

Step 1 :

Choose / create a directory to organize your application (to create your bin, lib, docs, man, etc. This may not be needed in some scenarios. Ex, a C application where you performed a configure –prefix=dir and a gmake install. Here, you can choose the prefix dir itself as it will contain all the files that need to be packaged.)

Step 2 :

The file system is displayed in the left side tree. You can copy files to the right side tree which displays the directory chosen in Step 1, thereby designing the way your package should look. Multiple Selection is allowed thereby enabling copying / deleting of multiple files / folders. Right click the right side tree to create new folders.

Step 3.

Enter the prototype file information (user, group and options to include pre, post and checkinstall files). Also, you can edit the generated prototype file to include any advanced options.

Then, in the table provided, enter the pkginfo file information. The first 5 rows marked in RED are mandatory. Information about each field will be displayed when the field is selected.

Step 4.

This screen lets you customize your package post package creation. You can either convert it to a file format by doing a pkgtrans, or perform a zip (.tar, .zip .tar.gz) or both. After the zip operation, you can also choose the destination of the final package zip created.

Step 5.

Nothing to do here! Just enjoy the output of your package creation process! In case of errors, you can go back and rectify any wrong information you entered. When you go back to Step 4, the folder where you are designing your package will be cleaned up viz, the created package files will be deleted.

Wednesday Jul 11, 2007

Netbeans plugin to enable your applications on network.com!

Now, you can enable your applications on network.com from within Netbeans!

Go, get the netbeans 'Grid Enable My App' plugin from any of the following places :

1. sun-grid-enabler.dev.java.net
2. netbeans.org/PluginPortal

How to use the plugin?

Download the zip file from the cvs repository of the dev.java.net page or from the netbeans plugin portal.

Extract the zip file and save the three .nbm files on your local machine. (This plugin works on solaris and partly on linux).

Install the three .nbm (netbeans module) files from Netbeans. (For 5.0, Tools -> Update Center -> Manually Install Modules)

Now, in the tools menu, you will have two new options :

1. Solaris Package Creator
2. Sun Grid Enable My App

The first is to create a solaris package for your application
The second is oto enable your application on the grid / network.com . You can create an app resource, a data resource if necessary and generate scripts with various options. After the script generation, you can zip the app and data resource along with the script generated and can upload them on network.com

Sample screen shot of the Grid Enable My App Plugin.

App Resource & Data Resource Creation

Script Generation

Job Run

Wednesday Jun 06, 2007

Running multiple commands in parallel on the Sun Grid

A sample grid script to execute a simple command on the sun grid can look like this.

#$ -N jobName
#$ -S /bin/sh
#$ -cwd
myCommand

However, if one needs to run multiple independent commands in parallel, the following procedure can be followed.

Enter all the commands in a file called myCommands.in, say.

#$ -N jobName
#$ -S /bin/sh
#$ -cwd

PATH=.:$PATH
export PATH

inputFile=myCommands.in
i=1
while read inputLine
do
echo "#\\$ -N Command$i" > script$i.sh
echo "#\\$ -S /bin/sh" >> script$i.sh
echo "#\\$ -cwd" >> script$i.sh
echo "PATH=.:\\$PATH" >> script$i.sh
echo "export PATH" >> script$i.sh
echo $inputLine >> script$i.sh
$SGE_BINARY_PATH/qsub script$i.sh
i=`expr $i + 1`
done < $inputFile

HTH

Friday Mar 16, 2007

Nice Video

Animation, showing the effects of Sun Grid Compute Utility.

--The Network Is The Computer--

Wednesday Mar 14, 2007

Network.com ... A Cool New Look :)

Yippie!!! Network.com also has a new look along with the addition of the Application Catalog. Looks really cool!

Useful Links
------------

Want to know more about the Application Catalog?

Amazed by the power of the Grid? Want to be a part of it? Become a Sun Grid Developer!

You can also become an ISV Partner

Current list of applications available on th catalog.

-----------------------------------------------------------------------------------------

Well, here is the new look of network.com!!! :) :) :)

SUN Grid Adds Application Catalog!!!

Sun Microsystems Inc. today announced it has added additional features to its Network.com pay-per-use offering, giving developers and open source communities the ability to just "click and run" applications online and a unique new way to create personalized application playlists... More on GridToday

--The Network Is The Computer--

Monday Mar 12, 2007

More applications!!!

Below are some more applications that are currently available on the SUN Grid Application Catalog.

IMPACT https://impact.dev.java.net
OFELI https://ofeli.dev.java.net
FASTA https://fasta.dev.java.net
HMMER https://hmmer.dev.java.net

You can access any application and use it from the Job Catalog based on the information available.

Click here - Information on how to use the Job Catalog
Click here - Information on how to use FASTA from the Job Catalog.

-- The Network Is The Computer --

FASTA on the Sun Grid

What is FASTA?

FASTA is a set of biological sequence comparison programs for searching protein and DNA sequence databases. More information on FASTA can be found here

FASTA on SUN Grid

Why?

Protein sequences and databases can be extremely huge. FASTA uses MPI to make the sequence search and comparison algorithms parallel in nature, meaning they can run simultaneously across multiple nodes. This makes FASTA an ideal candidate for the SUN Grid which is a network of high compute power nodes with MPI support.

How?

If you are expecting a FASTA download link and instructions to compile the source code, you have not realised the power of SUN Grid yet ;) FASTA binaries are already available in the SUN Grid's Application Catalog. All you need to do is check out FASTA from the catalog, prepare your set of inputs and feed it to the application! After checking out the job, see the details of the job for instructions on how to prepare the data and the corresponding fasta command with / without mpi support.

Sample Data

A sample data to test run the FASTA application can be found here.
This data resource contains many sequence / database files to test run both the MPI and non-MPI versions of FASTA.

Resources

FASTA HOME - http://fasta.bioch.virginia.edu
DEV.JAVA.NET - https://fasta.dev.java.net
SUN GRID USER GUIDE - http://www.sun.com/service/sungrid/SunGridUG.pdf


Wow!!! A Job Catalog for The Sun Grid!!!

The wait is over!!!! Network.com has more to it now !!!

I caught Google scanning/indexing/crawling (whatever you call it) network.com when the site was being upgraded! Have a look!





Well, network.com now has a new feature - The Job Catalog

The Job or Application Catalog is a venue where ISV And Open Source Applications can be easily accessed. An example is the application 'POVRay', a ray tracer. This sample application comes by default as part of the Job Catalog when you request a Sun Grid Account in NETWORK.COM. Also, do not forget the 10$ CPU-hr you get to try out this application and more!!!

Advantages

\* Use Sun as your one-stop application shop
\* Easy Access to the applications you use in an on-demand enviornment
\* Plug Into Sun's Infrastructure, Use the applications on an as-needed basis

Steps to access the applications from the Job Catalog

1. Check out the job from the Job Catalog
2. Click on 'View Details' of the checked out job to see the instructions that will provide information how to use the application, how to provide your input data etc.
3. Edit the Job and add any additional data resource if any as per Step 2.
4. Save and Run the Job!

There you go!!! Let the job run. You can start running your other jobs till then!!!

The network is truly becoming the computer!!!

Monday Mar 05, 2007

Cheers to Numbers!!!




Disclaimer : All details mentioned in this article are true to the best of the author's knowledge, though, sometimes, the reader may feel that the author is lying!!!

I do not drive to office. On lucky days, my roommates drop me, else, I take an autorikshaw. Hence, I spend most of my travel time observing vehicle numbers, searching for some patterns or co-incidences. Nothing like I am a math whiz, but just on a lookout for interesting numbers to while away my travel time!!

(Time travel, rather than travel time would have made things different tho! ;) )

/\* The beginning

I once saw a black pulsar - KA - 07 EQ 049. A7 was the code for my specialization in college(Computer Science) and 049 was my college id no! Why not search for my
roommates' id nos too ?

The End of the Beginning \*/

Sixteen days, all nos found!!!! 049, 063, 099, 084, 031. And in the process, I also encountered some nos like these - 9931, 8463 etc!!! Well, is there any way to calculate the probability of such an event?! Well, what is the sample space then?? I leave that to the reader as I already mentioned I am not a math whiz!!

I was amazed that I was able to find all these nos in sixteen days, jus by looking at car nos for 30 mts a day!! This interested me and I wanted to try more. So, this time, I chose squares. I guess it was one fine day in mid Feb that I noticed 8 square nos!!!! And once, I even came up with a couple of arithmetic progression triplets on the same day!!!!

These interesting patterns (or co-incidence if u want to call it) continues to amaze me...

N here's the best - Two cars, both black Hyundai Accents - with the following nos
KA 01 \*\* 1729
KA 01 \*\* 1729

(\*\* - I remember having tried to recollect the 4 letters a thousand times in vain)

FYI - 1729 is called the Hardy Ramanujam number - The only no that can be expressed as the sum of 2 cubes in 2 different ways - 10 cube + 3 cube and 12 cube + 1 cube.

I still wonder why it dint strike me to take a picture of both cars standing together. Afterall, my mobile with a 1.3 mega pixel camera was there in my jeans pocket!! :( But, going by past experiences, I am sure I will get a chance to click the same cars together, if not something better!!

What is it that makes these vehicles come together to generate patterns? Is it just co-incidence? If yes, then why me? May be because I am the one who doesnt own a bike! Probably, when I own one, I wont have the time to notice all these as I would be busy concentrating on protecting my life from the extremely dangerous bangalore traffic.

Cheers to numbers, probability, and co-incidences!

Friday Mar 02, 2007

SAMP Setup

This is an excellent article that gives detailed steps to setup SAMP (Solaris, Apache 2, MySql 5, PHP5) on Solaris 10.

The steps worked fine for Solaris 11 too! :)

http://www.sun.com/bigadmin/features/articles/samp_setup.html

Thursday Nov 23, 2006

Awaiting FOSS.in too...

FOSS.in begins tomorrow in IISc, Bangalore. Shouldnt be a surprise that SUN is a platinum sponsor for the event. It is going to be mind blowing and I am excited!!!!
Here is the schedule for the three day event.

What a way to start the year - spending my bday at a science symposium!!!

Monday Nov 20, 2006

Java Party

JavaParty allows easy port of multi-threaded Java programs to distributed environments such as clusters. Regular Java already supports parallel applications with threads and synchronization mechanisms. While multi-threaded Java programs are limited to a single address space, JavaParty extends the capabilities of Java to distributed computing environments.

The previous post talks about the Impact program which uses Java Party for distributive computing. For more on how to use Java Party, refer to JavaParty page. Cool stuff indeed to use with the Grid Engine! :)

An 'Impact' On the Sun Grid Engine

Impact is an open source finite element program suite which can be used to predict most dynamic events such as car crashes or metal sheet punch operations. They usually involve large deformations and high velocities. More information on Impact can be found at The Impact Project Homepage.

Impact is a java based application and usually involves huge computations which consume plenty of time. Hence, a parallel version of Impact is also packaged alongwith, which uses as a distributed computing environment to distribute the computations across different nodes.

Since Impact is supported by such a tool like JavaParty, one can take advantage of it to use it with Sun Grid Engine. Now to make it run on the Sun Grid Engine, a script (similar to the one for hmmer 2.3.2) has to be written. This script can be generated automatically with the help of the Sun Grid Script Generator too. A simple script to use one single Impact command at a time is provided here.

1 #!/bin/sh
2 #Tue Nov 18 15:28:55 IST 2006
3 #Script File Generator for the SUN Grid Engine
4
5 #Grid Engine Settings
6 #####################
7
8 #$ -N Impact
9 #$ -S /bin/sh
10
11 #Create an output file
12 #$ -e impact.output
13
14 #Create an error file
15 #$ -e impact.err
16
17 #$ -cwd
18 PATH=/home/gkrish/programFiles/jp-karmi/bin:$SGE_BINARY_PATH:$PATH
19 export PATH
20 $SGE_BINARY_PATH/qconf -sel >> .jp-nodefile
21 JPQ_NODEFILE=.jp-nodefile
22 JPQ_RSH=qrsh
23 export JPQ_NODEFILE
24 export JPQ_RSH
25
26 bash /home/gkrish/gridApps/Impact/Cluster.sh /home/gkrish/gridApps/Impact/examples/Ver_01.in

This script specifies the input and output files for the grid engine, adds javaparty to the PATH variable, sets required variables for JP to function properly and then executes an Impact command.

Here, "qconf -sel >> .jp-nodefile" adds the list of available hosts to the .jp-nodefile, which is a requisite for java party. I shall update this soon with more info on javaparty :) Now, here's a screenshot of a sample output of Impact!

Thursday Nov 02, 2006

Sun Grid Script Generator

The Sun Grid Script Generator is a tool that will help you enable your application to run on the Sun Grid. The tool generates necessary scripts for the Sun Grid Engine (SGE) and even generates a zip file that can be directly uploaded to the Sun Grid. The Script Writer is a Java based Swing utility with a Graphical User interface to ease the selection of various options available for the Sun Grid.

The tool is available at developer.network.com. More information about the tool and the instructions to use it are availabe in the tool's help tab.

Here is a screenshot of the tool.

Developed by :
Gopala Krishnan S & Jeevan Kumar R

Saturday Sep 30, 2006

My Time Machine...

How many of you believe there is a clock ticking within you, inside your skull, somewhere in the cerebrum?

Well, I do!!!

All of us have our own sleeping trends. As for me, I used to be an early riser when I was in school. There was no attendence in college and I was not bothered about the 8 AM tutorials either, so waking up post 9 became a routine and thats how I am still. And obviously, no morning alarms!

Of course, there are exceptions. You would not want to miss a Federer-Nadal clash that happens at 5 in the morning. You might want to leave for a team outing at 6 the next day.

On each of those 'exception' days, I set my alarm before going to bed. Not a single day have I woken up to switch off the alarm. I always end up waking up a few minutes before my nokia 6020 starts ringing!!!

May be you know for sure that you will have to wake up. Thats your last thought before sleep. May be when you set the alarm in your cell phone, you start off your 'brain clock' unknowingly. I do not know if there is any science here. But all I know is I have a 100% strike rate at this and this makes me feel that my brain too has 'somethin' in it! ;)

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gkrish

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