On the turning away

NAMD and Charm++ - some cool research projects from UIUC

UIUC has a cool research project going called NAMD. 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-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. The tutorials show you how to use NAMD and VMD for biomolecular modeling.

                                        I know for sure that the Gordon Bell Award is a big deal. I looked around and realised that they had no distribution for Solaris 10 operating system on the x86 architecture. So I volunteered to do some building. The following is an account of it.

Here is my experience while compiling NAMD and Cham++ on Solaris 10 x86

Machine info: Ultra 20 - AMD Opteron Solaris 10 x86 with mpich 1.1.2

Expectation:

• We will learn how to compile NAMD2 with tcl on Solaris 10 x86. Compiling namd2 with fftw is still in the works.

Things to download:

• NAMD2 source code from CVS - Jim Philips was nice enough to give me access.
• Charm-5.9 source code from here
• Tcl sol-x86 binaries from here

Notes:

• Do take a look at the notes.txt under the namd2 directory.
• Desist from using relative paths while setting the environment variables.

Steps

1. untar charm-5.9, tcl and namd2

I. Compile charm++ for Solaris 10 x86

1. cd charm-5.9/src
2. mkdir arch/mpi-sol-x86
3. cp mpi-sol/* mpi-sol-x86/
4. vi mpi-sol-x86/conv-mach.sh;
   1. set CMK_QT to 'generic'
   2. append ' -lrt' to the value of CMK_LIBS
5. Since I have mpich installed I give the following command in the charm-5.9 directory
   1. $ ./build charm++ mpi-sol-x86 gcc --incdir=/export/home/mpich/include --libdir=/export/home/mpich/lib
6. This command creates a directory called 'mpi-sol-x86-gcc' under the 'charm-5.9' directory.
   1. mpi-sol-x86-gcc is your CHARMARCH
   
   

II. Compile NAMD on Solaris 10 x86

1. cd namd2; chmod +x config
2. vi Make.charm; and set the CHARMBASE to the top-level 'charm-5.9' directory.
3. vi arch/Solaris-i686-g++.arch; and set the CHARMARCH to mpi-sol-x86-gcc.
4. vi arch/Solaris-i686.tcl; and set the TCLDIR appropriately.
5. ./config tcl Solaris-i686-g++
6. cd Solaris-i686-g++;
7. vi Makefile; go to the target 'psfgen' and append '-lsocket -lnsl' to the line starting with '$(CC)'
8. make;
9. Please check the compilation by running some examples. I haven't yet got time to run tests. I seem to have messed up my ip, machine, automount-config ( I am prone to such unfortunate events.. Sigh!)

Posted at 08:13PM Sep 28, 2006 by jeevan in Sun Grid  |  Comments[0]

A beginning

It has been almost a year since I joined Sun. It is about time I started a blog about Sun, its techologies, its people and me.

There are many reasons I love working for Sun. One of them is the amount of freedom one is given to work. I personally feel that brings the best out in people and that is how a innovation centered company should function.

Now, there is another reason why I have admired Sun for a long time (much before I even joined Sun), it is the ground breaking innovations that come out of Sun. Java is already more than 10 years old. More recently the shipping of UltraSparc T1 processor-that has 8 cores with 4 threads each, when the industry has just started making dual core processors. Now that is called 'leading the pack'.

The Sun Grid Compute Utility is another such innovation, which opened early this year. The Sun Grid compute server is a utility computing service that Sun has pioneered. It is much like your electricity usage. You plug-in your application and pay for the compute time it uses.
Simple..eh? More details here. Get youself an account and get rolling.

I am super-happy to be a part of this initiave and proud to contribute to it.

Posted at 07:34PM Sep 28, 2006 by jeevan in Sun  |  Comments[0]