Minor changes to introduction and submitting_jobs. Added hyperlinks

docs/tutorials/introduction.md

@@ -14,8 +14,8 @@ description: Welcome to Spiedie and Binghamton University. Glance through here t
 4. Anything else we can think of? 
 
 
-##<a name="cluster-info"></a> What is a cluster?
-####<a name="node-info"></a> What is a node?
-##<a name="cluster-programs"></a> Running jobs on a cluster?
+## <a name="cluster-info"></a> What is a cluster?
+#### <a name="node-info"></a> What is a node?
+## <a name="cluster-programs"></a> Running jobs on a cluster?
 #### <a name="slurm-info">What is SLURM?</a>
-##<a name="best-practices">Best practices</a>	
+## <a name="best-practices">Best practices</a>	

docs/tutorials/submitting_jobs.md

@@ -14,23 +14,28 @@ description: Documentation for srun and sbatch commands
 ### Table of Contents 
 
 1. [Using srun](#srun)
+    1. [Running a program](#srun-program) 
+    2. [Interactive Session](#interactive-session)
 2. [Using sbatch](#sbatch)
     1. [Writing a run script](#run-script)
+        1. [Directives](#directives)
+        2. [Run commands](#sbatch-program)
+    2. [Job Submission](#sbatch-submit)
 
 ## <a name="srun"></a> Using srun 
 
 Both the srun and sbatch command have similar capabilities and set of parameters. srun is used to submit a job for execution in real time and blocks the terminal. You will not be able to issue other commands while the program executes and must have an open connection while the program runs. It is generally recommended to use srun for quick test runs and for simple workflows. 
 
 
-#### Running simple program
+#### <a name="srun-program"></a>Running simple program
 
 To queue a quick test program use:
 
 ``` bash
-srun -n=1 -c=1 <program run command>
+srun -n=1 -c=4 <program run command>
 ``` 
 
-here we have speciefied to allocate one node (-n=1) and one core (-c=1), and use defaults for other parameters. 
+here we have speciefied to allocate one node (-n=1) and four cores (-c=4), and use defaults for other parameters. 
 
 #### <a name="interactive-session"></a> Interactive Session
 
@@ -45,8 +50,72 @@ srun -n=1 --partition=<partition_name> --pty bash
 This will allow direct access to a single node in a specific partition defined by ***parition_name*** once it is available. 
 
 For more information on partitions, [click here.](spiedie_partitions.html)
-
+For a list of all srun parameters, [click here.](https://slurm.schedmd.com/srun.html)
 
 ## <a name="sbatch"></a> Using sbatch
 
-#### <a name="run-script"></a> Writing a run script 
+The typical way to run a job on a cluster is to write a submission script and run the sbatch command. This allows for greater control and parameter passing. Also sbatch jobs are stored in internal storage awaiting to be executed and the user can log out without affecting the submitted job.
+
+#### <a name="run-script"></a> Writing a run script 
+
+*** Note: Take a look at [example_run_script.sh](code/example_run_script.sh) for a complete run script ** 
+
+The very first line of the script must be the shebang. Such as, 
+
+``` bash 
+#!/bin/bash
+```
+
+##### Directives 
+
+We can include sbatch parameter directives after the shebang to specify the parameters we wish to pass to SLURM. sbatch has the same parameters as srun. For a list of all sbatch parameters [click here](https://slurm.schedmd.com/sbatch.html)
+
+Some example run script directives would be, 
+
+``` bash 
+#SBATCH --job-name=name_of_job
+#SBATCH --output=output_file_name.txt
+#SBATCH --error=error_file_name.log
+#SBATCH --ntasks=1
+```
+
+The above directives specify the job name, standard out, standard error file names and the number of tasks. If output and error are not specified, the output and error will be written to slurm_job_name.out by default. 
+
+##### Shell Commands
+
+Finally, we can simply append the shell command to instruct SLURM to the desired program. 
+
+``` bash
+program_run_command program 
+```
+
+For example to run a python script we would write: 
+
+``` bash
+python python_Script.py
+```
+
+##### Parallel Programs
+
+To run a MPI program, we would write: 
+
+``` bash 
+module load OpenMPI 
+srun MPI_program.mpi 
+```
+It is recommended to use srun inside of the sbatch run script, as srun automatically launches the required processes. 
+
+module load OpenMPI loads the MPI runtime library prior to running the program. [For more information on modules, click here.](spiedie_modules.html)
+
+
+#### <a name="sbatch-submission"></a> Submitting the run script
+
+To use a run script to submit a job use:
+
+``` bash 
+sbatch --partition=partition_name run_script.sh 
+```
+
+
+
+