SIMONAPreprocessor
How to use the Poempp_Relax script

you need:

  1. xmls with different temperatures
  2. variables.sh http://intfolding/webfiles/variables.sh

what to do?
go to bwgrid, intcool, intfolding,...

  1. install simona (see "How to install...") or update the executable
  2. create a directory for your simulations (e.g. "mkdir simona_simulations")
  3. go to the directory ("cd simona_simulations")
  4. "svn checkout http://intfischer.ka.fzk.de/svn/poempp/trunk/tools/poempp_relax poempp_relax"
  5. change the path in the following files in the poempp_relax folder: qsub_poempp, poempp_vars.sh, restart_broken.sh. Change also "#PBS -q cool" in qsub_poempp.
  6. create a directory for your protein (e.g. mkdir protein_300to500K)
  7. cp the variables.sh and the xmls to your protein-directory
  8. go to the protein-directory and create the following folders: compute incoming failures startup
  9. add the follwing 3 lines to your bashrc with the right path:
    "#POEMPP - relaxskripte
    export PATH=${PATH}:$HOME/simona_simulations/poempp_relax
    export PATH=$PATH:$HOME/programs/poempp/src"
  10. change the settings in the variables.sh:
    • MAXITER: number of iterations..!! If you want to have 20 iterations type MAXITER=21
    • NPOP: number of populations - for every temperature you need an extra population!
    • NUMCOPIES: number of copies for every population
  11. type in your protein-directory
    1 poempp_sorther.sh $PWD
    -> this will generate NPOP POP_# folders!
  12. mv the xmls with the different temperatures to the POP_#/startup/ folders
  13. install a crontab to automatically restart your simulations!

How to restart broken jobs!?

  1. go to the folder with your simulations (e.g. "cd simona_simulations/protein_300to500K/")
  2. type there
    1 bash ~/simona_simulations/poempp_relax/restart_broken.sh
    a) nothing happens -> be happy, nothing crashed
    b) you get something like this:
    "BROKEN JOB FOUND, ID=5992699 \n qsub -vJOBID=5992699,INFILE=5992619_snap.xml /net/inttheorie/home/setzler/POEMDocking/poempp_relax/qsub_poempp"
    -> to restart the job copy the qsub-line and paste this in the shell

How to use cron jobs:

  1. first you need the correct path:
    1 export |grep PATH
  2. 1 crontab -e
  3. modify the file (vi commands..."i" - to insert "Esc :wq!" -to save and close the file...)
    copy the PATH to the first lines of the file, then use a new line for every cron job
  4. Examples:
    1 */10 * * * * command to be exectuted
    will execute the command every 10 min!
    1 59 23 * * 0 commmand to be executed
    will execute the command on Sunday at 23:59
    1 * * * * * = min (00-59) h (0-23) day (1-31) month (1-12) weekday (0-7)