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Commit db8c0aef authored by Mike Smith's avatar Mike Smith
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update README

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...@@ -8,6 +8,17 @@ Teaching material used during the High Performance Computing session of the EMBL ...@@ -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. 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 ## Identifying our computer
``` ```
...@@ -20,35 +31,40 @@ hostname ...@@ -20,35 +31,40 @@ hostname
srun hostname srun hostname
``` ```
## Exploring our example program ## Exploring our example program (don't run!)
``` ```
cd $HOME/embl_swc_hpc/exercises cd $HOME/embl_hpc/exercises
./hpc_example.py -t 10 -l 100 ./hpc_example -t 10 -m 100
``` ```
## Running example program on on the cluster ## 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 ## Running in the background
``` ```
sbatch ./hpc_example.py -t 10 -l 100 sbatch ­­--reservation=training ./batch_job.sh
``` ```
## Redirecting output ## 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 ## 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 ## Displaying details of our cluster queue
...@@ -60,17 +76,51 @@ scontrol show partition ...@@ -60,17 +76,51 @@ scontrol show partition
## Requesting more resources ## Requesting more resources
``` ```
sbatch --mem=250 \ sbatch --mem=8200 --reservation=training ./batch_job.sh 30 8000
--output=output.txt \
./hpc_example.py -t 30 -l 5000000
``` ```
## Requesting a lot more resources ## Requesting a lot more resources
``` ```
sbatch --mem=8000 \ sbatch --mem=100G --reservation=training ./batch_job.sh 30 5000
--output=output.txt \ ```
./hpc_example.py -t 120 -l 5000000
## 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 ## Running interactive jobs
......
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