xmls with different temperatures
what to do?
go to bwgrid, intcool, intfolding,...
- install simona (see "How to install...") or update the executable
- create a directory for your simulations (e.g. "mkdir simona_simulations")
- go to the directory ("cd simona_simulations")
- "svn checkout http://intfischer.ka.fzk.de/svn/poempp/trunk/tools/poempp_relax poempp_relax"
- 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.
- create a directory for your protein (e.g. mkdir protein_300to500K)
- cp the variables.sh and the xmls to your protein-directory
- go to the protein-directory and create the following folders: compute incoming failures startup
- add the follwing 3 lines to your bashrc with the right path:
"#POEMPP - relaxskripte
- 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
- type in your protein-directory -> this will generate NPOP POP_# folders!
- mv the xmls with the different temperatures to the POP_#/startup/ folders
- install a crontab to automatically restart your simulations!
How to restart broken jobs!?
- go to the folder with your simulations (e.g. "cd simona_simulations/protein_300to500K/")
- type there
a) nothing happens -> be happy, nothing crashed 1
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:
- first you need the correct path:
- 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
will execute the command every 10 min! 1
*/10 * * * * command to be exectuted
will execute the command on Sunday at 23:59 1
59 23 * * 0 commmand to be executed
* * * * * = min (00-59) h (0-23) day (1-31) month (1-12) weekday (0-7)