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experimental_workflow

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The Experimental workflow

The workflow consists of these steps:

  1. book nodes by submitting a job to the OAR scheduler
  2. submit experimental tasks, with Minus

Book nodes with OAR

To avoid cross interference between multiple experiments, only one person can use the whole CorteXlab testbed at the same time. The OAR scheduler is used to book nodes on the platform. As soon as you book one or more nodes, the CorteXlab room is reserved for your usage.

The role of OAR is to schedule node reservations. It manages jobs associated with users, which has a start time, a duration (walltime), and uses some resources (CorteXlab nodes).

The principle of operation of CorteXlab is that users submit jobs to OAR. When the job starts, the user gets exclusive access to the platform, and inside an OAR job, the user can perform (interactively, or in batch) one or several experiments.

A basic example to submit an OAR interactive job requesting all available nodes, for the default duration (which is 2 hours):

$ oarsub -I -l nodes=BEST

This command will wait for the resources to be available, and as soon as they are, a job is allocated, is started, and a subshell is instanciated where you can work on experiments. As soon as the subshell is closed, the job ends. (It can be usefull to work in a screen session to avoid loosing jobs in case of network disconnection).

By default OAR submissions are scheduled as soon as possible. It is also possible to ask for an OAR reservation where you choose the date at which the job will be scheduled.

Submit experimental tasks

Once inside a running OAR job, you can submit one or several Experimental tasks by using minus:

$ minus task submit <task_file_name>

All submitted minus tasks are enqueued in a simple FIFO and will execute sequentially.

Of course, to be able to schedule experimental tasks, you need to have a running OAR job.

When your OAR job ends, all running and remaining tasks are aborted and removed for the FIFO.

Interactive or batch experiments

When submitting or reserving an OAR job, you have the choice between interactive or batch:

  1. In interactive mode, an interactive subshell is instanciated where you work interactively. The job ends as soon as the interactive shell is closed
  2. In batch mode, you pass to command oarsub the name of an executable file which will be run as soon as the job starts. It is thus possible to write scripts which submit several experimental tasks (for example, to explore the variation of experimental parameters), and to submit OAR jobs which will be run automatically and asynchrously (even during the night).
experimental_workflow.1424959848.txt.gz · Last modified: 2015/02/26 15:10 by lcardoso

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