job_ollie

#!/bin/bash
#SBATCH --job-name=present_APRIL
#SBATCH -p mpp
#SBATCH --ntasks=432 #!288
#SBATCH --time=09:00:00
#SBATCH -o slurm-out.out
#SBATCH -e slurm-err.out

set -x

ulimit -s unlimited

###
read -r -d '' AWI_FESOM_YAML << 'EOF_AWI_FESOM_YAML'
---
output_schedules:
  - vars: []
    unit: y
    rate: 1
  - vars: [diags3d01,diags3d02,CO2y,aCO2,CO2,pH,pCO2,HCO3,CO3,OmegaC,kspc,rhoSW,PAR,rDIN,rDON,rDOC,rDSi,NPPn,NPPd,NPPc,GPPn,GPPd,GPPc,NNAn,NNAd,NNAc,GNAn,GNAd,GNAc,ResP,ResD,ResC,benCalc,benSi,benC,benN,denb,aN, aFe, Hp,CO2f,dpCO2s,pCO2s,bgc01,bgc02,bgc03,bgc04,bgc05,bgc06,bgc07,bgc08,bgc09,bgc10,bgc11,bgc12,bgc13,bgc14,bgc15,bgc16,bgc17,bgc18,bgc19,bgc20,bgc21,bgc22,bgc23,bgc24,bgc25,bgc26,bgc27,bgc28,bgc29,bgc30,bgc31,mlotst,omldamax,sic,slp,sithick,sitimefrac,so,sos,tauuo,tauvo,thetao,tos,zos,flice,wnet,evap,runoff,Kw,alphaCO2,O2f,NPPphy3d,NPPdia3d,NPPcoc3d,GPPphy3d,GPPdia3d,GPPcoc3d,NNAsphy3d,NNAsdia3d,NNAscoc3d,GNAsphy3d,GNAsdia3d,GNAscoc3d,TotGraz3d,GRAZphy3d,GRAZdia3d,GRAZcoc3d,RESzoo3d,calcdiss,AGGphy3d,AGGdia3d,AGGcoc3d,EXCphy3d,EXCdia3d,EXCcoc3d,calcif3d,RESphy3d,RESdia3d,REScoc3d,Nutlim_phy,Nutlim_dia,Nutlim_cocco,Tlim_arr,Tlim_cocco,Llim_phy,Llim_dia,Llim_cocco,CO2lim_phy,CO2lim_dia,CO2lim_cocco,PR_phy,PR_dia,PR_cocco,Cal_Tlim,Cal_CO2lim,Cal_Nlim,Cal_pure]
    unit: m
    rate: 1
  - vars: []
    unit: s
    rate: 96
  - vars: [restart]
    unit: y
    first: 1
    rate: 1
  - vars: [tso,lwrd,olat,olwout,osen,relax_salt,shum,tair,uwind,vwind,evs,fsitherm,hfds,opottemptend,pbo,prlq,prsn,rsdo,siarean,siareas,sidmassevapsubl,sidmasssi,sidmassth,sidmasstranx,sidmasstrany,siextentn,siextents,sifllatstop,sisnconc,sisnmass,sisnthick,sispeed,sivol,sivoln,sivols,soga,thetaoga,u2o,uo,uso,uto,v2o,vo,volo,vso,vto,w2o,wfo,wo,wso,wto,zossq,rho,uhice,uhsnow,urho,uv,vhice,vhsnow,virtual_salt,vrho,sistrxdtop,sistrxubot,sistrydtop,sistryubot,siu,siv,thdgr,thdgrsn]
    unit: y
    first: 1000
    rate: 1
EOF_AWI_FESOM_YAML
export AWI_FESOM_YAML
###

# determine JOBID
JOBID=`echo $SLURM_JOB_ID |cut -d"." -f1`

#source ../env.sh
#cp ../build/fesom_cpl/fesom .
cp ./fesom .

date
srun --mpi=pmi2 fesom > "fesom.out"
date
# qstat -f $PBS_JOBID

#export EXITSTATUS=$?
#if [ ${EXITSTATUS} -eq 0 ] || [ ${EXITSTATUS} -eq 127 ] ; then
#sbatch job.ll_ollie
#fi

## exit after 2009
Resultpath='/work/ollie/mseifert/fesom/fesom-1.4-recom/present_APRIL/'
test -e $Resultpath/fesom.1975.oce.nc && exit

IsInFile=$( tail -1 fesom.out | grep -c successfully)
if (( IsInFile > 0 )); then
 ## submit next job                                                                                                                                                                                           
 echo "submitting next job"
 sbatch job_ollie
else
 echo "something is wrong, last line of fesom.out reads"
 echo $( tail -1 fesom.out)
 echo "abnormal termination of job script"
fi