Poe: I'm Having Issues... [Archive]

Poe

Mar 2nd, 2002, 05:16 AM

wally - here is everything on the UD Message board that relates to your problem

scim through it quick and you might find the cause:

The UD agent has been stuck on the same percentage for ages and it is not saving

There could be a number of reasons for this. One possible reason is the UD agent is not getting very much time to process due to other apps running on your PC or you are running only as a screen saver or have a screen saver running. Remember that UD runs at idle process priority which means it will give up time to any other processes on the system.
- If you are running only as a screen saver (box is ticked in UD agent preferences screen) it is recommended that you don't use this method. This is because the screen saver itself will take away valuable CPU cycles that the UD agent could be using to speed up the processing. Just untick the selection and the UD agent will happily run in the background. Also even if you don't have the box ticked but still run another screen saver this will also slow down UD's processing. Just set Windows screen saver to none and switch off your monitor when not in use.

- If you are not doing the above there may be other apps running that are using up your processsor time resulting in very little idle time being available. Also so other DC programs do not work well with UD - SETI being one of them. With both UD and SETI running on the same system (single processor) SETI will get approx 90% of the idle CPU time and UD 7-8% causing UD to take a long time to process a WU.

The best way to check how much time UD and other apps are using your processor is to use a Windows Task Manager. Some versions of Windows come with one already (Win NT, 2K and XP). Earlier version (Win95/98/Me) don't have one as standard but there are many shareware/freeware task managers available for download e.g. TaskInfo 2002, Another Task Manager 3.0. Just run the task manager and it will show what %age of the CPU each process is using. When your PC is idle, UD will normally expect to get 95->98%. If it is much less than this, find out what process IS using the processor and decide the best way to either stop it or alter its priority (so it is not so much of a process hogger).

You may be surprised what you see when you run the task manager

Here is a post by Rymond H. Earle which I have included in its entirety, since it explains things very well:
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 exist within the work unit.
If you select the THINK client's information page ((i) icon on the main screen), you'll see the current molecule name of 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 for 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 per centage 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 per centage 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.

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.

And finally From UD's FAQ pages: Project FAQ's: Cancer Research Project

Q. My Task Execution Progress bar is frozen at a particular percentage. When I close the United Devices Agent and restart it, it stays at that percentage but I lose some time. Is the Agent frozen?

A. If you look at the top of the THINK screen, you will see a display like SOME-Molecule-E843F-02. The name of the current molecule that the agent is working on is SOME-Molecule-E843F. The -02 indicates a derivative molecule, formed from the original molecule. In this case, the agent is working on the second derivative of the SOME-Molecule-E843F molecule. There can be up to 100 derivatives of each molecule in a work unit.
Currently, the checkpoints in THINK are set after every successfully completed molecule (not its derivatives). If you turn off your PC, or restart the agent, you may be stopping it from completing the current molecule. When you restart it is going back to the beginning of that complex molecule. This is why it seems you are losing time. We are working on a fix, but in the meantime try allowing the agent to run for a longer period, and keep an eye on the conformers to ensure that they are not looping during this run period.

It's likely that THINK task is not stuck. The % indicator is not a linear time indicator; it counts the percentage of molecules in the work unit that have completed processing. The reason that the time on the task bar continues to increment even though the % counter stays the same is that the agent is still doing matches with the protein and the same molecule-the molecule (or one of its derivatives) is just complex. That is why the conformers are still rising - it is still analyzing. We have seen some cases of molecules taking several days to complete!

The time it takes to process a work unit varies depending on the Members' system and the molecules' complexity. All molecules are different. Some molecules may take a few moments to be processed by the agent, while others can take several minutes, or even hours depending on the speed of the machine. Since the % indicator increments by molecule, it will stay the same for long periods as the agent works through these more complex molecules.