How-to-run-in-jasmin.md

 Configuration file
 ------------------
 
-After installing the environment in JASMIN you need to make sure you specify the corrects paths to the code repository, input and output data at the [configuration file]().
+After installing the environment in JASMIN you need to make sure to specify the correct paths to the code repository, input and output data. Make your own changes to the [configuration file](https://git.noc.ac.uk/brecinosrivas/orchestra-sst/-/blob/master/config.ini).
 
-> **Note** Check with Liz where the lastest version of SST data and drifters is located in JASMIN just to make sure if the paths above are correct.
+> **Note** Check with Liz where the latest path location for the drifting buoys since we use her ICOADS output of data.
 
-Gridding process 
+Griding process 
 ----------------
 
-The re-gridding of SST data and the interpolation of buoy coordinates to the satellite data is done by a single script under:
+The re-gridding of SST data and the interpolation of the data to the buoy's coordinates is done by a single script under:
 ``~/scripts/coarse_cci_sst.py``
 
 The corresponding SLURM script to submit this job in JASMIN can be found under ``~/src/run_gridding.slurm``.
 
+Several things need to be set up before running that script:
+
+1. Make slurm-log output directories: 
+~~~
+cd ~/orchestra-sst/
+mkdir slurm_log_output
+mkdir input_data
+~~~
+
+You should have the following directory configuration under `~/orchestra-sst/`
+
+~~~
+input_data                 
+scripts  
+slurm_log_output
+config.ini             
+src
+sst_tools
+~~~
+
+2. Modify paths and job array set up in the file ``~/orchestra-sst/src/run_gridding.slurm``:
+
+~~~
+#!/bin/bash
+#SBATCH --partition=short-serial-4hr
+#SBATCH --array=3001-6574
+#SBATCH --job-name=sst_buoy_regrid
+#SBATCH --output=../slurm_log_output/sst_buoy_regrid_%A_%a.out
+#SBATCH --error=../slurm_log_output/sst_buoy_regrid_%A_%a.err
+#SBATCH --mem=4000
+#SBATCH --time=01:00:00
+
+source activate ~/miniconda3/envs/sst
+
+start_year=1993
+start_month=1
+start_day=1
+
+echo "Analysing data for $SLURM_ARRAY_TASK_ID days"
+echo "since $start_year $start_month $start_day minus a day"
+
+python ~/orchestra-sst/scripts/coarse_cci_sst.py $start_year $start_month $start_day $SLURM_ARRAY_TASK_ID
+
+echo "Done slurm task ID = $SLURM_ARRAY_TASK_ID"
+
+~~~
+
+Make sure you modify ```#SBATCH --array=1-3000``` at the moment to process the entire time series you need to run it in two parts
+first from day 1 to 3000, and later from 3001 to 6574. So the job can be run in the ``short-serial-4hr`` queue (next part: ``#SBATCH --array=3001-6574``).
+
+3. After configuring the SLURM script you can run it by:
+
+~~~
+cd ~/orchestra-sst/src/
+sbatch run_gridding.slurm
+~~~
+
+For more information on the processing workflow of this script read the following [jupyter notebook](https://git.noc.ac.uk/brecinosrivas/orchestra-sst/-/blob/master/notebooks/cci_at_buoy_coord_results.ipynb)
 
 Computing time series
 ---------------------