Welcome to Zhu Group


  1. To learn how to use the cluster, read Introduction to Scyld Clusterware. Paticularly, you should read Reference Guide and Users Guide. You may monitor the system by using Ganglia Web Mornitoring

  2. To remotely access the cluster, install VNC in your Windows system.
    to open a vnc server (e.g., #5), type
    vncserver -geometry 1280x1024 :5 
    
    to kill a vnc server (e.g., #5), type
    cat /home/zhut/.vnc/atom.me.gatech.edu:5.pid
    kill "job id' 
    

  3. To plot on the web
    http://www.wolframalpha.com/input/?i=plot%281%2F%281-c%29+-6c%2C%28c%2C0%2C1%29%29
    

  4. To remotely access the cluster using VNC, but outside Georgia Tech, you may first log into mse-uc01 through VNC viewer, then type
    vncviewer -Shared -via zhut@atom.me.gatech.edu localhost:1
    

  5. To run Abaqus, see demos

  6. To run Abaqus (cae|viewer) through VNC, add the -mesa switch to the command, i.e.,
    abaqus cae -mesa
    

  7. To run Matlab, see demos

  8. To learn how to use various softwares, read Bulletin at mse-uc01

  9. To remotely power on/off any compute node, e.g., node 2 (Note: node 0 needs to powered on/off manually), type
    ipmitool -H 10.54.2.102 -U admin -P admin chassis power reset
    
    if the system is already on, or else:
    ipmitool -H 10.54.2.102 -U admin -P admin chassis power on
    
    if the system is currently off.

  10. The local drives on each nodes are mounted at /scratch. The bpcp command can be used to put or get data from a specific node, e.g.,
    bpcp file 1:/scratch
    

  11. To use atomeye, type
    a ***.cfg & 
    

  12. To securely copy a direcory from, e.g., "mse-uc01", type
    scp -r zhut@mse-uc01.eng.ohio-state.edu:/home/zhut/test . 
    

  13. To find a file, e.g., "index.html", type
    find -name index.html 
    

  14. To estimate the size of a directory, e.g., "abaqus_demo", type
    du -sh abaqus_demo 
    

  15. remote ipmi functions
    Usage:
    # ripmi [last host addr] [ipmi commands]
    
    Examples:
    Check nodes n1/ n4  chassis status and even log
    # ripmi 101 chassis status
    # ripmi 101 sel list
    # ripmi 104 chassis status
    # ripmi 104 sel list
    
    Check power status of all the node .101 - .110
    # for i in 101 102 103 104 105 106 107 108 109 110; do echo -n "Node $i: ";ripmi $i chassis status | grep "System Power"; done
    

  16. add reference to MyBibliography.bib
    When you add reference to MyBibliography.bib, save the references from Web of Science, and then type
    'is /tmp/savedrecs.txt' or 'is ~/savedrecs-4.txt'
    on uc01 or atom.gatech
    

  17. MPI VASP
    MPI VASP (various variants) work now...
    
    atom% ls /usr/local/VASP/exe/
    4.6
    vasp_4.6.28_gamma_HenkelmanVTST_mpich_chain_em64t
    vasp_4.6.28_gamma_HenkelmanVTST_mpich_em64t
    vasp_4.6.28_gamma_HenkelmanVTST_serial_em64t
    vasp_4.6.28_gamma_mpich_em64t
    vasp_4.6.28_gamma_serial_em64t
    vasp_4.6.28_HenkelmanVTST_mpich_chain_em64t
    vasp_4.6.28_HenkelmanVTST_mpich_em64t
    vasp_4.6.28_HenkelmanVTST_serial_em64t
    vasp_4.6.28_mpich_em64t
    vasp_4.6.28_serial_em64t
    
    cd
    rm -rf bench.Hg
    mkdir bench.Hg
    cd bench.Hg
    tar xvfz /home/Beowulf/VASP/4.6/bench.Hg.tar.gz
    set tick = `date +%s`
    mpirun -np 8 /usr/local/VASP/exe/vasp_4.6.28_gamma_mpich_em64t
    @ tock = `date +%s` - $tick
    echo real time spent = $tock seconds
    

Email: ting.zhu@me.gatech.edu, phone: 404-894-6597.