Moved Slurm docs to existing 40_deploying_ADAM.md and addressed comments

docs/source/40_deploying_ADAM.md

@@ -512,4 +512,81 @@ def _count_child(job, masterHostname):
  
  # and now, count it
  assert rdd.count() == 10000
-```
+```
+
+## Running ADAM on Slurm
+
+For those groups with access to a HPC cluster with [Slurm](https://en.wikipedia.org/wiki/Slurm_Workload_Manager) 
+managing a number of compute nodes with local and/or network attached storage, it is possible to spin up a 
+temporary Spark cluster for use by ADAM.
+
+While the full IO bandwidth benefits of Spark processing are likely best realized through a set of 
+co-located compute/storage nodes, depending on your network setup you may find Spark deployed on HPC 
+to be a workable solution for testing or even production at scale, especially for those applications 
+which perform multiple in-memory transformations and thus benefit from Spark's in-memory processing model.
+
+Follow the primary [instructions](https://github.com/bigdatagenomics/adam/blob/master/docs/source/02_installation.md) 
+for installing ADAM into `$ADAM_HOME`
+
+### Start Spark cluster
+
+A Spark cluster can be started as a muti-node job in Slurm by creating a job file `run.cmd` such as below:
+```
+#!/bin/bash
+
+#SBATCH --partition=multinode
+#SBATCH --job-name=spark-multi-node
+#SBATCH --exclusive
+
+#Number of seperate nodes reserved for Spark cluster
+#SBATCH --nodes=2
+#SBATCH --cpus-per-task=12
+
+#Number of excecution slots
+#SBATCH --ntasks=2
+
+#SBATCH --time=05:00:00
+#SBATCH --mem=248g
+
+# If your sys admin has installed spark as a module
+module load spark
+
+# If spark is not installed as a module, you will need to specifiy absolute path to $SPARK_HOME/bin/spark-start
+start-spark
+
+echo $MASTER
+sleep infinity
+```
+submit the job file to Slurm:
+```
+sbatch run.cmd
+```
+
+This will start a Spark cluster containing 2 nodes that persists for 5 hours, unless you kill it sooner.
+The `slurm.out` file created in the current directory will contain a line produced by `echo $MASTER` 
+above which willindicate the address of the Spark master to which your application or ADAM-shell 
+should connect such as `spark://somehostname:7077`
+
+### Start ADAM Shell
+Your sys admin will probably prefer that you launch your ADAM-shell or start an application from a 
+cluster node rather than the head node you log in to so you may want to do so with:
+```
+sinteractive
+```
+
+Start an adam-shell as so:
+```
+$ADAM_HOME/bin/adam-shell --master spark://hostnamefromslurmdotout:7077
+```
+
+### or Run a batch job with adam-submit
+```
+$ADAM_HOME/bin/adam-submit --master spark://hostnamefromslurmdotout:7077
+```
+
+You should be able to connect to the Spark Web UI at `spark://hostnamefromslurmdotout:4040`, however 
+you may need to ask your local sys admin to open the requried ports.
+
+### Feedback
+We'd love to hear feedback on your experience running ADAM on HPC/Slurm or other deployment architectures, 
+and let us know of any problems you run into via the mailing list or Gitter.