Editing Resurrection script

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== 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.

== Script 1: resurrection ==

 #!/bin/bash
 # Rodrigo García-Muelas
 # 28/03/2013
 # 
 # Input:
 # $1 Name of work
 # $2 Suffix (number id)
 # $3 Queue
 # $4 Number of processors
 # $5 Number of hours of runtime
 # $6 Extra number of minuts of runtime
 #
 # Motivation: I create a directory for the next step.
 # Then, I create the new run.sh, which shall call this script
 # And send
 # run.sh has an internal time control
 
 i=$(($2+1)) 
 
 mkdir ../$i
 cp ./INCAR ../$i/INCAR
 cp ./KPOINTS ../$i/KPOINTS
 cp ./CONTCAR ../$i/POSCAR
 cp ./POTCAR ../$i/POTCAR
 mv ./WAVECAR ../$i/WAVECAR
 mv ./CHGCAR ../$i/CHGCAR
 rm ./CHG
 
 cd ../$i/
 rungen_resurrection $1 $i $3 $4 $5 $6 # generate run.sh
 bsub < run.sh                         # submit run.sh
 exit
 

== Script 2: rungen_resurrection ==

 #!/bin/bash
 # Rodrigo García-Muelas
 # 28/03/2013
 # 
 # Input:
 # $1 Name of work
 # $2 Suffix (number id)
 # $3 Queue
 # $4 Number of processors
 # $5 Runtime hours
 # $6 Runtime minutes (add)
 #
 # Motivation: I create a directory for the next step.
 # Then, I create the new run.sh, which shall call this script
 
 case $3 in
  16a)  queue=class_a  ; mar=1 ; procqueue=16 ; maxhours=47 ;;
  16b)  queue=class_b  ; mar=1 ; procqueue=16 ; maxhours=22 ;; # maybe they give priority to shorter works 
  16c)  queue=class_c  ; mar=1 ; procqueue=16 ; maxhours=22 ;; # idem
  *)    echo "Error in queue name!!! " ; exit ;;
 esac
 
 # Comprobate if the number of processors is correct 
 let AAA=`expr $4 % $procqueue` ; if [ 0 != $AAA ] ; then exit 1 ; fi # number of processars right?
 
 # Generating the run.sh file 
 cat >run.sh<<!
 #!/bin/bash
 #BSUB -J $1$2
 #BSUB -q $queue 
 #BSUB -n $4 
 #BSUB -W $5:59
 #BSUB -o o_$1$2.%J
 #BSUB -e e_$1$2.%J
 #BSUB -u rgarcia@iciq.es
 #BSUB -R"span[ptile=16]"
 
 ### Load environment variables ###########
 module load VASP/5.3.3
 
 ### Run job ##############################
 resurrection_timecontrol $5 $6 r_$1$2 &
 mpirun vasp.complex ; touch stopflag ; resurrection $1 $2 $3 $4 $5 $6 ; echo the dynamics has been resurrected >> r_$1$2 ; exit
 
 !

== Script 3: resurrection_timecontrol ==
 #!/bin/bash
 #
 # Rodrigo García-Muelas
 # Improved on May 17th, 2013
 #
 # INPUT
 #
 # $1 number of hours   +
 # $2 number of minutes
 #    (before generating file STOPCAR)
 # $3 name of file
 # 
 # INTERNAL
 #
 # timeini : The calculus starts
 # timeend : The calculus ends
 # timenow : Current time 
 
 
 timeini=`date +'%s'` 
 timenow=$timeini
 timeend=$(($timeini+3600*$1+60*$2))
 
 echo resurrection flags are timeini $timeini timeend $timeend >> $3
 
 # If VASP finishes before timeend, kill this process
 
 while [ $timenow -lt $timeend ] ;  do 
  if [ -e stopflag ] ; then rm stopflag ; echo resurrection: VASP finished normally at $timenow >> $3 ; exit ; fi 
  sleep 5s  # Verify status each 5 seconds
  timenow=`date +'%s'` 
 done
 
 # If timeend is reached, write STOPCAR 
 
 echo resurrection: writing STOPCAR at $timenow >> $3 
 cat >STOPCAR<<!
  LSTOP = .TRUE.
 
 !
 
 exit