Editing Rungen

go back to [[Main Page]], [[Group Pages]], [[Núria López and Group]], [[Scripts_for_VASP]]

Instructions: 1) Put this script as executable on your ~/bin/ folder (recomended name: rungen). 2) Put your email instead of youremail@iciq.es. 3) Do the same with [[savecalc]].

To generate a run.sh file, write on a terminal:
 $ rungen <''name_of_job''> <''queue''> <''number_of_processors''> <''(optional)vasp_version''> 

Notes:
*<<''name_of_job''>> should start with a letter, not a number or another special character.
*Queues c (or c0) and q (or q0) are part of [[tekla]].
*Queues 4 8 and 12 are interpreted as c4m8... etc, on [[tekla2]].
*Queues 112a are interpreted as ''gp_resa'' on [[MareNostrum]].  
*This script has a security control to avoid sending a calculation with the wrong number of processors.
*Please verify the default version of VASP that you want to use on each queue.
*By default I use Infiniband in the c12m128ib queue, with 24 or more processors.
*I put another security control, named [[savecalc]] that is run before VASP, in case you need to do a long optimization.
*You have two quickly accesible log files: o_* that is the standard output and e_* that contains the errors.


go back to [[Main Page]], [[Group Pages]], [[Núria López and Group]], [[Scripts_for_VASP]]

This script allows you to generate run.sh files for tekla2 and MareNostrum4. It also worked for MareNostrum3. If you make a mistake in the number of processors the script will tell to you, so you'd better use this script (or someone similar) every time you prepare a new calculation. 

= Instructions = 

* Create ~/bin/rungen and put the content below 

* Make it executable 
 chmod +x ~/bin/rungen

* To use it in tekla, put the name, the queue (4, 8, 12, or 24), and the number of processors. If you make a mistake in the number of processors the script will tell to you.  
 rungen nanoparticle 12 60 

* You can change the VASP version using an additional fourth input variable: 
 rungen neb 12 48 5.3.5-IB_VTST_GAMMA

* In MareNostrum, use 112a for gpresa, and debug queues: 
 rungen neb 48 96 

* If you want to change the VASP version, go to this folder to see what versions do you have available. The default is ''vasp_std'': 
 /apps/VASP/5.4.4/INTEL/IMPI/bin/ 
 rungen neb 48 96 vasp_gam_sol

* If you want to use an exotic flavour that is not yet compiled for the version you are using, you can request MareNostrum people to compile it. Ask your boss before doing the request. Otherwise, you can use an older version of VASP. Feel free to explore into these MareNostrum folders: 
 /apps/VASP/

* Remember to adapt your parallelization to the machine and processors you use each time.[http://aliga.iciq.es/wiki/index.php/The_INCAR_file#Improving_Parallelisation]


== rungen ==

 #!/bin/bash

##########################################
# Rodrigo García-Muelas @ iciq-Tgn       #
# Created: Jan 11, 2013                  #
# Edit N : Apr 30, 2024                 #
##########################################

# Input ##################################   
# 1 # name
# 2 # queue id
# 3 # number of processors
# 4 # version
##########################################

# To run in local, write on command line: mpirun -np 2 vasp                                       

# tekla1, tekla2 or marenostrum ##########
tk1=0 ; tk2=0 ; mar=0 ; csc=0 ; 
case $2 in
 c|c0) queue=c0       ; tk1=1 ; procqueue=1  ;;
 q|q0) queue=q0       ; tk1=1 ; procqueue=4  ;;
 4)    queue=c4m8     ; tk2=1 ; procqueue=4  ;;
 8)    queue=c8m24    ; tk2=1 ; procqueue=8  ;;
 12)   queue=c12m48ib ; tk2=1 ; procqueue=12 ;;
 24)   queue=c24m128ib; tk2=1 ; procqueue=24 ;;
 28)   queue=c28m128ib; tk2=1 ; procqueue=28 ;;
 112a) queue=gp_resa  ; mar=5 ; procqueue=112 ; maxhours=24 ;; # maxhours: 71    
 *)    echo "Error in queue name!!! " ; exit ;;
esac

# MOD should be 0 ########################
let AAA=`expr $3 % $procqueue`
#echo $AAA
if [ 0 -ne $AAA ] ; then echo "Error in number of processors" ;  exit ; fi
##########################################

# version

if [ -z $4 ] ; then
  if   [ $mar = 5 ] ; then vaspversion="5.4.4"
  elif [  $2 =  4 ] ; then vaspversion="5.3.5"
  elif [  $2 =  8 ] ; then vaspversion="5.3.5"
  elif [  $2 = 12 ] ; then if [ $3 -gt 12 ] ; then vaspversion="5.3.5-IB" ; else vaspversion="5.4.4" ; fi
  elif [  $2 = 24 ] ; then if [ $3 -gt 24 ] ; then vaspversion="5.3.5-IB" ; else vaspversion="5.4.4" ; fi
elif [  $2 = 28 ] ; then if [ $3 -gt 28 ] ; then vaspversion="5.3.5-IB" ; else vaspversion="5.4.4" ; fi
  elif [ $tk1 = 1 ] ; then vaspversion="4.6"    
  fi 
else vaspversion=$4 ; fi

# queues of tekla1 #######################
if [ $tk1 = 1 ] ; then mpi=_mpi ; 
E=`pwd`; ofile=`echo $E/o_\\$JOB_NAME.\\$JOB_ID` ; efile=`echo $E/e_\\$JOB_NAME.\\$JOB_ID` ; 
cat >run.sh<<!
#!/bin/bash

#$ -N $1

#   pe request
#$ -pe $queue $3
#$ -M rseemakurthi@iciq.es
#$ -o $ofile
#$ -e $efile

cd $E ; /home/rseemakurthi/bin/savecalc  
/usr/bin/mpirun -np $3 -machinefile \$TMPDIR/machines /usr/local/bin/vasp ; rm -f CHG

!
fi
##########################################


# queues of tekla2 #######################
if [ $tk2 = 1 ] ; then mpi=_mpi ; cat >run.sh<<!
#!/bin/bash
### SGE Parameters #######################
#$ -S /bin/bash
#$ -N $1
#$ -cwd
#$ -masterq $queue.q
#$ -pe $queue$mpi $3
#$ -m ae
#$ -M rseemakurthi@iciq.es
#$ -o o_\$JOB_NAME.\$JOB_ID
#$ -e e_\$JOB_NAME.\$JOB_ID
### Load Environment Variables ###########
. /etc/profile.d/modules.sh
module load vasp/$vaspversion
### Run Job ##############################
export OMP_NUM_THREADS=1
echo \$PWD >> o_\$JOB_NAME.\$JOB_ID
echo \$TMP >> o_\$JOB_NAME.\$JOB_ID
~/bin/savecalc ; mpirun -np \$NSLOTS vasp_std ; # rm -f CHG
!
fi
##########################################

# queues of Marenostrum 5 ################
if [ $mar = 5 ] ; then cat >run.sh<<!
#!/bin/bash    
#SBATCH --account=iciq72
#SBATCH --qos=$queue 
#SBATCH --time=$maxhours:00:00   
#SBATCH --job-name=$1  
#SBATCH --cpus-per-task=1  
#SBATCH --tasks-per-node=112  
#SBATCH --ntasks=$3   
#SBATCH --output=o_$1.%j 
#SBATCH --error=e_$1.%j 

module load hdf5
module load vasp/$vaspversion
#module load mkl
~/bin/savecalc ;srun /apps/GPP/VASP/$vaspversion/INTEL/IMPI/bin/vasp_std  

!
fi
##########################################