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aurora_cluster:running_on_aurora [2016/12/06 10:51]
florido [Nuclear, Theoretical and Mathematical physics: loading libraries and tools]
aurora_cluster:running_on_aurora [2017/02/15 11:53] (current)
florido [Singularity]
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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 **partition**, ​a **project** and a **reservation**,​ one for each division. The HEP nodes do not require a special reservation flag to be accessed. The partitions, ​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:+
  
 ^ Your division ^ SLURM Partition ^ Project String ^ Reservation String ^ call srun with ^ ^ Your division ^ SLURM Partition ^ Project String ^ Reservation String ^ call srun with ^
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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-
 +</​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.
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 The interactive session is terminated when you issue the ''​exit''​ command. The interactive session is terminated when you issue the ''​exit''​ command.
  
 +===== Loading libraries and tools on Aurora =====
 +
 +Aurora allows the user to load specific versions of compilers and tools using the excellent ''​module''​ system.
 +This system configures binary tools and library paths for you in a very flexible way.
 +
 +Read more about it in Lunarc documentation here: http://​lunarc-documentation.readthedocs.io/​en/​latest/​aurora_modules/​
 +
 +If you are in need of a module that is not installed, please check this list:
 +
 +https://​github.com/​hpcugent/​easybuild-easyconfigs/​tree/​master/​easybuild/​easyconfigs
 +
 +If the software you need **is in the list but NOT in Aurora**, report to Florido, and he will coordinate with Lunarc to provide such software. ​
 +
 +If that module **does not exist in the system nor in the above list**, you will have to **build it and configure yourself**. Read more about it in the [[#Custom software]] paragraph.
 +
 +===== Special software for Particle Physics users =====
 +
 +These features are only available on the ''​hep''​ partition. Other users of such partition can use these if they want.
  
-===== Particle Physics users: ​CVMFS =====+==== CVMFS ====
  
 Particle Physics users might want to use CVMFS to configure their own research software. Particle Physics users might want to use CVMFS to configure their own research software.
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 Run them **after** you login to an interactive session or add them in the prologue of your batch job. Run them **after** you login to an interactive session or add them in the prologue of your batch job.
  
-===== Loading libraries and tools on Aurora =====+==== Singularity ​====
  
-Aurora allows the user to load specific versions of compilers and tools using the excellent ''​module''​ system+The old singularity version (1.0) is going to being removed on week 8, year 2017 
-This system configures binary tools and library paths for you in very flexible way.+because of security issuePlease update your scripts to enable singularity using these commands:
  
-Read more about it in Lunarc documentation here: http://lunarc-documentation.readthedocs.io/​en/​latest/​aurora_modules/+<code:bash> 
 +module load GCC/4.9.3-2.25 
 +module load Singularity/​2.2.1 
 +</code>
  
-If you are in need of a module ​that is not installedplease check this list:+It is recommended to **always use the version number** when loading the 
 +module to prevent issues using different versions. ​If you don’t use that 
 +and the default module changesyou will run an unwanted version. 
 + 
  
-https://​github.com/​hpcugent/​easybuild-easyconfigs/​tree/​master/​easybuild/​easyconfigs 
- 
-If the software you need **is in the list but NOT in Aurora**, report to Florido, and he will coordinate with Lunarc to provide such software. ​ 
- 
-If that module **does not exist in the system nor in the above list**, you will have to **build it and configure yourself**. Read more about it in the [[#Custom software]] paragraph. 
  
 ===== Custom software ===== ===== Custom software =====
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 | Particle Physics | ''/​projects/​hep/​nobackup/​software/​pp''​ | | Particle Physics | ''/​projects/​hep/​nobackup/​software/​pp''​ |
 | Theoretical Physics | ''/​projects/​hep/​nobackup/​software/​tp''​ | | Theoretical Physics | ''/​projects/​hep/​nobackup/​software/​tp''​ |
-| Mathematical Phyisics | '''' ​|+| Mathematical Phyisics | Please use your home folder for now. We are negotiating a 10GB project space. ​|
aurora_cluster/running_on_aurora.1481017898.txt.gz · Last modified: 2016/12/06 10:51 by florido