slurm_opt.jcf

#!/bin/bash                                                                     
#SBATCH --qos=short                                                             
#SBATCH --partition=broadwell                                                    
#SBATCH --ntasks=5                                                              
#SBATCH --cpus-per-task=2 # for 64GB total                                                                                             
#SBATCH --job-name=LPJmLmdi                                              
#SBATCH --workdir=/p/projects/biodiversity/drueke/LPJmLmdi/LPJmLmdi                    
##SBATCH --output=outfile.%j.out                                                 
##SBATCH --error=outfile.%j.err                                                  
#SBATCH --mail-type=end                                                         

module purge
module load R
module load intel/2018.1
module load netcdf
module load netcdf-c/4.2.1.1/serial
module list
module load udunits
module load json-c/0.13
module load intel/2018.1
module load mpi/intel/5.1.3
module load R
#unset I_MPI_DAPL_UD_PROVIDER
export I_MPI_PMI_LIBRARY=/p/system/slurm/lib/libpmi.so
export R_LIBS_USER=/p/projects/biodiversity/R

# call R                                                                        
#R --no-save --file=.R --silent --slave
R CMD BATCH --vanilla inst_gldas/LPJmL-MDI_example_gldas.R ./optim_experiment.Rout