This document will explain how to dowload, configure, and run a parameter space search for ShelfMC on a computing cluster. 
These scripts explore the ShelfMC parameter space by varying ATTEN_UP, REFLECT_RATE, ICETHICK, FIRNDEPTH, and STATION_DEPTH for certain rages. 
The ranges and increments can be found in setup.sh. 

In order to vary STATION_DEPTH, some changes were made to the ShelfMC code. Follow these steps to allow STATION_DEPTH to be an input parameter.
1.cd to ShelfMC directory
2.Do $sed -i -e 's/ATDepth/STATION_DEPTH/g' *.cc
3.Open declaration.hh. Replace line 87 "const double ATDepth = 0.;" with "double STATION_DEPTH;"
4.In functions.cc go to line 1829. This is the ReadInput() method. Add the lines below to the end of this method. 
   GetNextNumber(inputfile, number); // new line for station Depth
   STATION_DEPTH  = (double) atof(number.c_str()); //new line
5.Do $make clean all

#######Script Descriptions########
setup.sh -> This script sets up the necessary directories and setup files for all the runs
scheduler.sh -> This script submits and monitors all jobs. 


#######DOWNLOAD########
1.Download setup.sh and scheduler.sh
2.Move both files into your ShelfMC directory
3.Do $chmod u+x setup.sh and $chmod u+x scheduler.sh

######CONFIGURE#######
1.Open setup.sh
2.On line 4, modify the job name
3.On line 6, modify group name
4.On line 10, specify your ShelfMC directory
5.On line 13, modify your run name
6.On line 14, specify the NNU per run
7.On line 15, specify the starting seed
8.On line 17, specify the number of processors per node on your cluster
9.On lines 19-56, edit the input.txt parameters that you want to keep constant for every run
10.On line 57, specify the location of the LP_gain_manual.txt
11.On line 126, change walltime depending on total NNU. Remember this wall time will be 20x shorter than a single processor run.
12.On line 127, change job prefix
13.On line 129, change the group name if needed 
14.Save file
15.Open scheduler.sh
16.On line 4, specify your ShelfMC directory
17.On line 5, modify run name. Make sure it is the same runName as you have in setup.sh
18.On lines 35 and 39, replace cond0091 with your username for the cluster
19.On line 42, you can pick how many nodes you want to use at any given time. It is set to 6 intially. 
20.Save file 

#######RUN#######
1.Do $qsub setup.sh
2.Wait for setup.sh to finish. This script is creating the setup files for all runs. This may take about an hour.
3.When setup.sh is done, there should be a new directory in your home directory. Move this directory to your ShelfMC directory.
4.Do $screen to start a new screen that the scheduler can run on. This is incase you lose connection to the cluster mid run. 
5.Do $./scheduler.sh to start script. This script automatically submits jobs and lets you see the status of the runs. This will run for several hours.
5.The scheduler makes a text file of all jobs called jobList.txt in the ShelfMC dir. Make sure to delete jobList.txt before starting a whole new run.


######RESULT#######
1.When Completed, there will be a great amount of data in the run files, about 460GB.  
2.The run directory is organized in tree, results for particular runs can be found by cd'ing deeper into the tree.
3.In each run directory, there will be a resulting root file, all the setup files, and a log file for the run.