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aurora_cluster:running_on_aurora [2016/12/06 10:05] florido [Custom software] |
aurora_cluster:running_on_aurora [2016/12/06 11:17] florido |
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There's only few important things one needs to know: | There's only few important things one needs to know: | ||
- | * HEP nodes are running in a special **partition** (a.k.a. queue) called ''hep''. Whenever in the documentation you're asked to specify a queue, use ''hep'' | ||
* A set of nodes is selected by choosing a **project** and a **reservation**, one for each division. The HEP nodes do not require a special reservation flag to be accessed. The project names and reservation flags are listed in the table below: | * A set of nodes is selected by choosing a **project** and a **reservation**, one for each division. The HEP nodes do not require a special reservation flag to be accessed. The project names and reservation flags are listed in the table below: | ||
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* HEP storage is a bit different from the others and there are a few additional rules to use it. Please read [[aurora_cluster:storage]] | * HEP storage is a bit different from the others and there are a few additional rules to use it. Please read [[aurora_cluster:storage]] | ||
- | A typical direct submission to our nodes looks like: | + | * Basic usage of the batch system is described here: |
+ | * Using the SLURM batch system: http://lunarc-documentation.readthedocs.io/en/latest/batch_system/ | ||
+ | * Batch system rules. Note: these rules might be slightly different for us since we have our own partition. http://lunarc-documentation.readthedocs.io/en/latest/batch_system_rules/ | ||
+ | |||
+ | ===== Batch Scripts Examples ===== | ||
+ | |||
+ | ==== hep partition (Nuclear, Particle and Theoretical Phyisics) ==== | ||
+ | |||
+ | A typical direct submission to ''hep'' nodes looks like: | ||
<code bash>srun -p hep -A HEP2016-1-4 myscript.sh</code> | <code bash>srun -p hep -A HEP2016-1-4 myscript.sh</code> | ||
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</code> | </code> | ||
- | to be run with the command: | + | The script is submitted to the SLURM batch queue with the command: |
<code bash>sbatch slurmexample.sh</code> | <code bash>sbatch slurmexample.sh</code> | ||
- | Basic usage of the batch system is described here: | + | The results will be found in the folder where the above command is ran, in a file named after the slurm job ID. |
- | * Using the SLURM batch system: http://lunarc-documentation.readthedocs.io/en/latest/batch_system/ | + | |
- | * Batch system rules. Note: these rules might be slightly different for us since we have our own partition. http://lunarc-documentation.readthedocs.io/en/latest/batch_system_rules/ | + | |
+ | ==== lu partition (Mathematical Physics) ==== | ||
+ | |||
+ | A typical direct submission to ''lu'' nodes looks like: | ||
+ | <code bash>srun -p lu -A lu2016-2-10 --reservation=lu2016-2-10 myscript.sh</code> | ||
+ | |||
+ | Here is an example of a typical slurm submission script ''slurmexample.sh'' written in bash, that prints the hostname of the node where the job is executed and the PID of the bash process running the script. It will have this prologue: | ||
+ | |||
+ | <code bash> | ||
+ | #!/bin/bash | ||
+ | # | ||
+ | #SBATCH -A lu2016-2-10 | ||
+ | #SBATCH -p lu | ||
+ | #SBATCH --reservation=lu2016-2-10 | ||
+ | # | ||
+ | hostname | ||
+ | srun echo $BASHPID; | ||
+ | </code> | ||
+ | |||
+ | The script is submitted to the SLURM batch queue with the command: | ||
+ | <code bash>sbatch slurmexample.sh</code> | ||
+ | |||
+ | The results will be found in the folder where the above command is ran, in a file named after the slurm job ID. | ||
===== Interactive access to nodes for code testing ===== | ===== Interactive access to nodes for code testing ===== | ||
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<code bash> | <code bash> | ||
- | interactive -t 60 -p hep -A HEP2016-1-1 | + | interactive -t 00:60:00 -p hep -A HEP2016-1-4 |
+ | </code> | ||
+ | <code bash> | ||
+ | interactive -t 00:60:00 -p lu -A lu2016-2-10 --reservation=lu2016-2-10 | ||
</code> | </code> | ||
- | where ''-t 60'' is the time in minutes you want the interactive session to last. You can put as much as you want in the timer. Mind that whatever you're running will be killed after the specified time. | + | where ''-t 00:60:00'' is the time in hours:minutes:seconds you want the interactive session to last. You can put as much as you want in the timer. Mind that whatever you're running will be killed after the specified time. |
//slurm// will select a free node for you and open a bash terminal. From that moment on you can pretty much do the same as you were doing on Iridium testing nodes. | //slurm// will select a free node for you and open a bash terminal. From that moment on you can pretty much do the same as you were doing on Iridium testing nodes. |