3.6

SCARFTomoReconstruction v1

../_images/SCARFTomoReconstruction-v1_dlg.png

SCARFTomoReconstruction dialog.

Summary

Perform a control action on jobs running on the SCARF computer cluster at RAL, STFC (http://www.scarf.rl.ac.uk/)

Properties

Name Direction Type Default Description
UserName Input string Mandatory Name of the user to authenticate as
Action Input string LogIn Choose the operation to perform on the compute resource SCARF@STFC. Allowed values: [‘LogIn’, ‘LogOut’, ‘Ping’, ‘Upload’, ‘SubmitJob’, ‘JobStatus’, ‘JobStatusByID’, ‘Download’, ‘CancelJob’]
Password Input string   The password for the user
RunnablePath Input string /work/imat/webservice_test/tomopy/imat_recon_FBP.py The path (on the remote compute resource) of a file to run (example: shell or python script)
JobOptions Input string /work/imat/webservice_test/remote_output/test_ Options for the job command line, application dependent. It can include for example the NXTomo input file when using savu for tomographic reconstruction.
JobName Input string   Optional name for the job, if not given then a name will be generated internally or at the compute resource
FileToUpload Input string   Name of the file (local, full path) to upload to the compute resource/server
DestinationDirectory Input string /work/imat Path where to upload the file on the compute resource/server
RemoteJobsID Output str list   ID strings for the jobs
RemoteJobsNames Output str list   Names of the jobs
RemoteJobsStatus Output str list   Strings describing the current status of the jobs
RemoteJobsCommands Output str list   Strings with the command line run for the jobs
JobID Input number 0 The ID of a job currently running or recently run on the compute resource
RemoteJobName Output string   Name of the remote job
RemoteJobStatus Output string   Current status of the job (running, exited, etc.)
RemoteJobCommand Output string   Command line run remotely for this job
RemoteJobFilename Input string   Name of the job file to download - you can give an empty name to download all the files of this job.
LocalDirectory Input string   Path to a local directory/folder where to download files from the compute resource/server
DownloadJobID Input number 0 ID of the job for which to download files. A job with this ID must be running or have been run on the compute resource.
CancelJobID Input number 0 The ID for a currently running job on SCARF@STFC

Description

Algorithm to control jobs running on the SCARF computer cluster at RAL, STFC (see http://www.scarf.rl.ac.uk/ for more information). This algorithm can be used to log in and out from the cluster, and to initiate, query the status of, or cancel a job. It has been introduced to control tomographic reconstruction jobs but in principle it can be used for any other task.

In a typical use case or session you would use the algorithm a first time to login (for which you need to select the ‘LogIn’ action and set the username and password fields). After this step you can use the algorithm again several times, to submit jobs (setting the action ‘SubmitJob’), query the status of the jobs running on the computer cluster (setting the action to ‘JobStatus’ or ‘JobStatusByID’), cancel jobs (setting the action ‘CancelJob’) and log out from the cluster (action ‘LogOut’). You can also upload and download files. After logging out, subsequent submit or status queries will fail with an informative message. Note that the server will log out users every undetermined amount of time, which depends on server settings.

In principle, in a simple use case, the same username will be used in all the calls to this algorithm. This means that you type in the username only the first time that you use this algorithm, as it will be remembered and filled in automatically in the next calls. But note that it is possible to change the username passed to the algorithm every time you call the algorithm. This means that you can use this algorithm to control jobs for multiple users simultaneously from the same instance of Mantid. You can use for example use the username associated to a particular project or instrument, and in parallel your personal username for different jobs (which can be useful to distinguish quick tests, calibration of parameters, etc.). For this to work, you of course need to perform a ‘LogIn’ action for every username that is used in submit or query status actions.

The ‘JobStatus’ and ‘JobStatusByID’ actions produce an output several output properties with status and general information about the jobs, as retrieved from the compute resource/server.

The algorithm relies on a web service provided by the SCARF computer cluster in order to control jobs on the cluster. If you use this algorithm from its dialog (for example starting it from the algorithm explorer in Mantid) the password will not be shown on the screen. This algorithm can be used interactively. In such case, it is absolutely not recommended to call it from scripts or the Python script interpreter window, as you will be passing passwords as plain text.

The alternative ways to monitor and control your jobs are via shell login and via the web platform at https://portal.scarf.rl.ac.uk/.

This algorithm is used by other components of Mantid, in particular the custom graphical interface for tomography (IMAT instrument).

Usage

Example

try:
    SCARFTomoReconstruction(UserName='foouser', Action='Login')
except ValueError:
    print "ValueError, as expected, because no Password= parameter given"

try:
    SCARFTomoReconstruction(UserName='foouser', Action='Submit')
except ValueError:
    print "ValueError, as expected, as it was not previously logged on"

Output:

ValueError, as expected, because no Password= parameter given
ValueError, as expected, as it was not previously logged on

Categories: Algorithms | Remote