Accessing QQ cluster

Log in to QQ (qq.meche.rpi.edu):

You need to have your user_id and password ready to login.
ssh user_id@qq.meche.rpi.edu
If you are using windows, you should dowload Putty from here Putty and install it. If this is your first time to login to qq, please use your temperate passcode. Please change your temperate passcode to much longer one for safty issue. For the windows users, I also suggest you to install Oracle VM VirtualBox on your windows and then install the ubuntu on the VM box to reduce the risk of losing your windows data. By the way, both the Oracle VM VirtualBox and Ubuntu are free. You are going to love them.

qq enviroment settings

QQ enviroment settings (.bashrc): /share/apps/shell/bashrc
cp /share/apps/bashrc ~/.bashrc
which ifort

Programs installed on qq

(1) Intel composer_xe_2011_sp1.7.256 was installed in /share/apps/intel
(2) openmpi 1.8.3 was installed in /share/apps/openmpi
(3) fftw-2.15 was installed in /share/apps/fftw/fftw2
(4) fftw-3.3.4 was installed in /share/apps/fftw/fftw3
(5) LAMMPS was installed. The source code is /share/apps/lammps (The lastest stable version lammps-28Jun14) with REAX, MEAM.
The EXE file is /share/apps/bin/lammps
The examples and potentials, etc are in the source code directory.
(6) VASP 5.3.5 was installed in /share/apps/bin.
(7) abinit 7.4.3 was installed /share/apps/bin.
(8) Calypso_3.5
(9) espresso-5.1
(10) PnetCDF
(11) boltztrap-1.2.5

Submitting jobs on qq

All jobs are required to run by SGE job manager.
To submit a parallel job on qq using a script :(example in http://qq.meche.rpi.edu/qpeng/code/job.sge_lammps_qq)
(1) please use wget to download it: wget http://qq.meche.rpi.edu/qpeng/code/job.sge_lammps_qq
(2)Please use : cp /share/apps/bin/job.sge_lammps job.sh
(3)copy the file job.sh to your working directory and modify it.
(4) using qsub command to submit your job to the qq: qsub job.sh
To submit a serial job on qq using a script
qsub job.sh
To echeck the status of your jobs, using qstat
To echeck the status of all jobs on qq, using qst
To delete a job, using qdel
qdel xxx (xxx is the job id)
You can specify your job to run on a single specific host, for example, compute-0-0, using
-l hostname=compute-0-0
So you can use job.sh to run a serial job on qq.

More commands about jobs on qq, please refer to the SGE.
and How to use SGE

Web pages on qq

Please maintain your web sites on qq.
The URL of your website is http://qq.meche.rpi.edu/yourID
To edit/update your website, just upload your files to ~/www on qq.
If you are not familar with build up your webpages, here are templates .

On-going projects on qq

  • Mechanical properties of 2D materials at finite temperature

  • references: Q. Peng, W. Ji and S. De, "Mechanical Properties of the Hexagonal Boron Nitride Monolayer: ab initio Study", Comput. Mater. Sci. 56, 11 (2012) [PDF]
  • Structures, mechanics, and dynamics of nanostructures

  • references: Q. Peng, X. Zhang and G. Lu, "Structure, mechanical and thermodynamic stability of vacancy clusters in Cu", Modelling Simul. Mater. Sci. Eng., 18, 055009 (2010) [PDF]

Tutorials of Science

A full example of running lammps jobs on qq is here:

Tutorials of computers