Fall 2009

10/6 Wai and Rizi

10/13 Myung and Atlal (or Chia-en)

10/20 no group meeting

10/27 Qaiser and Mindy

What to say?

- research updates

- future plans and/or project overview

- open discussion

- lecture about some knowledge in computational chemistry

- lead discussion for an interesting paper

- more...

Remember, always tell me "what", "why", "how" and sometimes "when"

How to quit the terminal after you run a job in biocluster

Please follow the following steps..

• login to the biocluster
• type screen
• sometime you press enter
• qsub -I -l nodes=1:ppn=8
• run your job (for instance, ./run_sander.sh; exit; exit)
• ctrl-a
• d

Now you can safely quit the terminal......cheer up.....

Next time when you login again if still job is not finished (optional)

• type screen -r

you are again there....

Running Sander (Amber10) in Biocluster

Login to biocluster

• Type screen and hit enter (optional)
• Type qsub -I -l nodes=1:ppn=8 (where nodes=1 specifies the number of CPU*2 and ppn=8 defines parts per node i.e. number of cores, so in this case 8 cores are reserved, if you want to use more than 8 cores, for example 16 cores type qsub -I -l nodes=2:ppn=8)
• To run the job just write ./ run_sander.sh; exit; exit, which contains the following commands and arguments;

************************************************************************************************************************************************************

#!/bin/sh

PATH=$PATH:/home/achang/amber10/bin/ INPUT=sander.in

export AMBERHOME=/home/achang/amber10 cat $PBS_NODEFILE

/home/achang/amber10/bin/lamboot -d -v $PBS_NODEFILE

echo "mpirun" 1>&2 /home/achang/amber10/exe/mpirun -np 8 /home/achang/amber10/bin/sander.MPI -O `cat sander.in`

echo "lamclean" 1>&2 /home/achang/amber10/bin/lamclean

echo "lamhalt" 1>&2 /home/achang/amber10/bin/lamhalt

************************************************************************************************************************************************************

• where np 8 indicates 8 cores to be used. If you need more or less than 8 cores do change this option i.e in case of 16 cores write np 16.
• This script reads sander.in file as an input, which describes the input and output file names, a sample sander.in is given below;

************************************************************************************************************************************************************

-i filename.in -o filename.out -p filename.prmtop -c filename.inpcrd -r filename.rst -x filename.traj -v filename.vel -e filename.en

************************************************************************************************************************************************************

• In order to logout the terminal, (optional)

press ctrl-a then d

• If you want to go again to the job, type (optional)

screen -r

Running NAMD in Biocluster

Login to biocluster

• Type namd-start
• Follow the steps

1. screen -S namd-session

2. qsub -I -l nodes=8:ppn=8 && exit

3. namd-start <input-file> --avoid node19,node13,node24 && exit