Editing Resurrection script (section)

== Setting up the calculation==

First, put the three scripts listed here in your ~/bin/ folder in MareNostrum, and do chmod +x to make them executables. 

Now, create the main directory for your dynamics, and the first folder, such as this: 

 you@login1:~> mkdir my_dynamics 
 you@login1:~> mkdir my_dynamics/1
 you@login1:~> cd my_dynamics/1

Now, put in the folder 1 your basic input files (INCAR, KPOINTS, POTCAR and POSCAR). Your first run.sh script should be like this (running in class_c queue):

 #!/bin/bash
 #BSUB -J name_of_job_1
 #BSUB -q class_c 
 #BSUB -n 64 
 #BSUB -W 23:59
 #BSUB -o o_name_of_job_1.%J
 #BSUB -e e_name_of_job_1.%J
 #BSUB -u youremail@iciq.es
 #BSUB -R"span[ptile=16]"
 
 ### Load environment variables ###########
 module load VASP/5.3.3
 
 ### Run job ##############################
 resurrection_timecontrol 23 30 r_name_of_job_1 &
 mpirun vasp.complex ; touch stopflag ; resurrection name_of_job_ 1 16c 64 23 30 ; echo the dynamics has been resurrected >> r_name_of_job_1 ; exit
 

'''Explanation''': 
*In this example, you are running with 64 processors on class_c queue. 
*You have three quickly accesible log files: o_* is the standard output, e_* contains the errors, and r_* contains the information related to the resurrection process.
*Your time limit will be 23:59 hours, the maximum allowed by class_c is 24:00
*Before starting VASP, you will lauch resurrection_timecontrol, which will stop the calculation after 23:30 hours, via STOPCAR (LSTOP = .TRUE.).
*Then the script will execute VASP on your local folder.
*If the VASP calculation ends abruptly before the time limit, it will deliver a signal (stopflag) that will kill "resurrection_timecontrol", avoiding a phantom job to stay on the line for hours.
*Now the calculation will be resurrected with the name name_of_job_2, on folder 2 (see script 1 for more details) on the same queue with the same number of processors and the same time control. This script will call internally to rungen_resurrection, but you can merge them if you prefer.
*This set of scripts is totally self-contained.
*Tested and debugged.

Now that you know how this work, begin to calculate by typing: 
 you@login1:~/my_dynamics/1> bsub < run.sh 

Do not forget to baby-sit your calculations every day, and verify that all your electronic cycles have been converged.