• When was the last time the data was saved?
• Timeouts - Is there a time limit set on a Work Unit?
• Why do some work units take longer than others?
• What is a Work Unit?
• Is there a protein archive?
• How To Replace a Bad or Stuck Work Unit

Because there are some long units, suddenly exiting the client or shutting down the computer may cause the loss of some of the work analyzed. If you have one of these long units you can manually check when the last save (or checkpoint) occurred.

Go to the C:\Program Files\United Devices folder and look for the tkst.ud file. Right-click on this file and check the properties. Created: shows when the unit was started and Modified: shows the last update.



UD Monitor allows you to checkpoint more often and also allows you to cache Work Units. More info on UD Monitor is available HERE.

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by Equinox6 edited by KeysCapt
last modified: 2004-01-29 21:57:52

With the latest UD agent processing the Ligandfit client, work units will stop processing (time out) at 264 hours. If this happens, the Agent will contact the server and download a new WU, and begin processing. Full points credit will be received for the CPU time of the stopped WU, but no credit will be received for a completed WU.

There is also a "wallclock" timeout factor ... which means the time that a WU will expire after being downloaded to your computer. This time limit is currently 456 hours.

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by Equinox6 edited by KeysCapt
last modified: 2003-01-11 11:03:01

It takes a variable length of time to finish a work unit. Although many of them can be processed in under an hour on a fast machine, others can run for days if one or more very complex molecules exists within the work unit. The molecules in the Superoxide Dismutase protein target in particular "conform" very well. That's why there are often a lot of hits associated with them and why some of them seem to take so long to crunch. Those that do are considered to be Long Running Molecules (LRM)! If you're processing an LRM (in a Superoxide Dismutase protein or otherwise), stopping the client is generally not advisable if at all possible, because you can lose hours or even days of processing time when restarting it.

If you select the THINK client's information page (the « i » icon on the main screen), you'll see the current molecule name at the top left of the largest section. The name has the following general format: 123-456-xxx, where xxx can either be blank (for the root molecule), or be a number between 1 and 100 (indicating the nth derivative of the molecule being processed).

Each work unit to be processed, that you receive, includes a set number (100/200) of core molecules. Each of the 100/200 core molecules has a name (123-456 in the case above). The client can form up to 100 derivative molecules from each of these 100/200 core molecules. Each molecule plus any of its 100 derivatives can have up to 1,000,000 conformers. The first derivative molecule (represented by the -xx) is -1, the second is -2, and the last is -100. When derivative -100 is processed, the processing for that molecule (123-456 in the case above) is completed, and a checkpoint may be written. Whether a checkpoint is written or not at the end of the processing of a given molecule or molecules is dependent upon how quickly the processing or that molecule or molecules has proceeded. On quickly processed work units (i.e. under one hour) I've seen the client not take a checkpoint for several molecules in a row. You can generally judge when a checkpoint has been taken by the sound of a little disk activity that occurs right around the processing of the -100 derivative.

Regarding de novo structures that you will sometimes see being processed when you're watching the graphical display. Sometimes a molecule may have extra potential if it's slightly altered in some way. The client attempts small variations or substitution of atoms to increase the number of molecules being evaluated. These newly altered molecules are the de novo derivatives, or structures, which are also processed by the client.

The completion percentage is non-linear (i.e. it does not represent wall clock time), but rather indicates the number of completed core molecules within the set of 100/200. This is because the client has no way to determine how complex a core molecule will be until it has been processed. Therefore when you note that the completion percentage has not changed for a while, first check that the time is being updated each second on the main screen and the legend says "Primary task is executing...". If you find these conditions, switch to the information screen to see if the derivative number, the conformer count, the de novo structure count, or the hit count, is increasing. It depends on how fast a machine you have and what else it is doing at the time as to how quickly these numbers will be changing.

If you need to stop and restart the client, try to do so as quickly as possible after the client has written a checkpoint (derivative -100 for the current molecule was processed) so that you'll duplicate as little processing time as possible when you restart the client. When it is restarted, it will not redraw the current molecule, but will wait until it begins processing the next one before updating the display. When this is the case, you'll see a message near the top of the information page that states "Structure not ready for display". This is a normal condition and the message is nothing to be alarmed at.

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by KeysCapt

A Work Unit is the data being processed by the UD program. When that data is done being processed this information is then uploaded to the UD servers and a new work unit is downloaded to replace it. The time needed to finish processing a Work Unit varies with computer speed and is also affected by other applications being run. More info on work units is available HERE.

Note: The UD agent will use only spare CPU cycles. Running other CPU-intensive applications might tend to slow down the UD agent.

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by Equinox6 edited by KeysCapt
last modified: 2005-05-23 13:20:10

Yes! An archive of all the LigandFit Proteins to date can be found here.

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by slash

If a unit is stuck and refuses to complete then you can force the UD agent to download another Unit. There are three ways this can be done.

• The easiest is to bring up the Task Manager (by hitting Ctrl-Alt-Delete), finding UD_******* and then select End Task.

*Please Note: Make sure to not highlight ud.exe.

Also if you have not been running UD for "X" amount of time and you are bringing a box back on line, it would be a good idea to flush the current work unit and replace it

• Or, you can find all the tk*.ud files in the United Devices directory and delete all of them.

• Finally, you can delete the CS.UD file from the United Devices directory. Warning: Deleting CS.UD will cause the agent to re-download the next task and another device profile will be added to your UD home page.

Special thanks to grobinette for updated info

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by Equinox6 edited by lilhurricane
last modified: 2005-09-10 16:54:39