update README

README.md

@@ -8,6 +8,17 @@ Teaching material used during the High Performance Computing session of the EMBL
 
 Below are most of the commands used during the practical, so they can be copy/pasted, but I highly recommend typing along if you can.
 
+## Login to the frontend node
+
+```
+ssh <username>@login.cluster.embl.de
+```
+
+## Clone this git repository
+```
+git clone https://git.embl.de/msmith/embl_hpc.git
+```
+
 ## Identifying our computer
 
 ```
@@ -20,35 +31,40 @@ hostname
 srun hostname
 ```
 
-## Exploring our example program
+## Exploring our example program (don't run!)
 
 ```
-cd $HOME/embl_swc_hpc/exercises
-./hpc_example.py -t 10 -l 100
+cd $HOME/embl_hpc/exercises
+./hpc_example -t 10 -m 100
 ```
 
 ## Running example program on on the cluster
 
 ```
-srun ./hpc_example.py -t 10 -l 100
+srun ./hpc_example -t 10 -m 100
+```
+
+## Using our reserved training space
+```
+srun --­­reservation=training ./hpc_example -­t 10 -­m 100
 ```
 
 ## Running in the background
 
 ```
-sbatch ./hpc_example.py -t 10 -l 100
+sbatch ­­--reservation=training ./batch_job.sh
 ```
 
 ## Redirecting output
 
 ```
-sbatch --output=output.txt ./hpc_example.py -t 20 -l 100
+sbatch --output=output.txt --reservation=training ./batch_job.sh
 ```
 
 ## Creating a larger list
-
+You will need to edit batch_jobs.sh to take arguments
 ```
-sbatch --output=output.txt ./hpc_example.py -t 30 -l 5000000
+sbatch --output=output.txt --reservation=training ./batch_job.sh 20 ???
 ```
 
 ## Displaying details of our cluster queue
@@ -60,17 +76,51 @@ scontrol show partition
 ## Requesting more resources
 
 ```
-sbatch --mem=250 \
---output=output.txt \
-./hpc_example.py -t 30 -l 5000000
+sbatch --mem=8200 --reservation=training ./batch_job.sh 30 8000
 ```
 
 ## Requesting a lot more resources
 
 ```
-sbatch --mem=8000 \
---output=output.txt \
-./hpc_example.py -t 120 -l 5000000
+sbatch --mem=100G --reservation=training ./batch_job.sh 30 5000
+```
+
+## Cancel jobs
+```
+scancel <jobID>
+scancel -u <username>
+```
+
+## Defining time limits
+```
+sbatch ­­--time=00­00:00:30  \
+    ­­--reservation=training \
+    batch_job.sh 60 500
+```
+
+## Job efficiency statistics
+```
+seff <jobID>
+```
+
+## Emailing output
+```
+sbatch ­­--mail­user=<first.last>@embl.de \
+    ­­--reservation=training \
+    ./batch_job.sh 20 500
+```
+
+## Finding and using software
+```
+module avail
+module spider samtools
+module load BWA
+```
+
+## BWA example
+```
+nano bwa/bwa_batch.sh
+sbatch ­­­­--reservation=training bwa/bwa_batch.sh
 ```
 
 ## Running interactive jobs