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Message 35843 - Posted: 1 Feb 2007, 1:31:26 UTC
Last modified: 11 Feb 2007, 0:11:21 UTC

Software versions - Rosetta


How do I know what version of Rosetta I am running?

Open the BOINC Manager, go to the "Advanced" view, go to the "Tasks" tab, and the version is shown in the "Application" column. For example "rosetta 5.45" indicates version 5.45.


How do I know what version of Rosetta is currently available?

There is a link on the home page for "applications" (under "Returning Participants").


When a new version of Rosetta comes out, should I abort tasks from the old version?

No. Unless specifically told to do so by the project in the Project Annoucement thread, or unless you are encountering a specific problem that the new version is supposed to correct, do not abort your existing work units.


How to install new Rosetta version without losing work?

When a new version of Rosetta becomes available, the project will begin sending work units that use the new version. When one of these work units is downloaded to your computer, it will check to see if you have the appropriate Rosetta version installed already. If you do not, BOINC will download it for you. You may notice, especially on multi-processor computers, that you can have more then one version of Rosetta running at the same time. This is normal. Once all of the work units that require the older version are completed, BOINC will remove it from your computer for you.


Can I download the new Rosetta version in advance?

Yes. The project team generally will post a few hours before tasks will call for the new release. You can then download it via your internet browser in advance allowing you to schedule the additional internet time for downloading the programs. You might also copy it to multiple machines running BOINC. This could allow you to download it once, rather then once per machine, the way BOINC would by default.

The Rosetta versions available for early download are available here:
https://boinc.bakerlab.org/rosetta/download/next_release/

Once work units calling for the new version are released, the programs can always be downloaded from here:
https://boinc.bakerlab.org/rosetta/download/


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Message 35845 - Posted: 1 Feb 2007, 1:32:04 UTC
Last modified: 10 Feb 2007, 23:47:20 UTC

Software versions - BOINC

How to check currently available BOINC versions

This is shown as the "recommended version" for each platform here on the BOINC download site.


How to check the BOINC version currently installed on my computer?

Right click on the BOINC icon in your task bar, click the "About BOINC Manager..." option.


How do I install a new version of BOINC without losing my existing work?

A new version of BOINC can be installed over the existing version. Here are the steps to follow:

Right click on the BOINC Manager icon in your task bar, select "Exit" to shutdown BOINC and the applications such as Rosetta.

To assure you can recover if there is a problem with the new release you are installing, backup the entire BOINC install directory (in Windows you can do this in Windows Explorer, the default path is /Program Files/BOINC, you can open a second copy of Windows Explorer, create a BOINCBACKUP directory, then just right click on the /Program Files/BOINC directory and drag it to your new BOINCBACKUP folder, then select "Copy").

Download the new version of BOINC from the download site.

Then execute the file you've downloaded and BOINC will install itself. Be sure to select the same installation directory as your existing BOINC programs, and it will replace them.

Now restart BOINC, you will see the version change detected in the messages tab.

If you would prefer more detailed instructions, there is a description in the BOINC wiki.


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Message 35848 - Posted: 1 Feb 2007, 1:33:00 UTC
Last modified: 10 Feb 2007, 22:55:51 UTC

Merging hosts

Click the "[ Participants ]" link at the top of the page you are viewing now.
Click the "view" link beside "Computers on this account".
Click the computer ID in question and go to the bottom of the page.
Click the link "merge this computer".
Select the other machine that is identical with the one shown and click the "Merge hosts" button.

Now you have only one machine left, and it has the credits from both host IDs.

You cannot merge together data from two different user account numbers. Only two different hosts.


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Message 35851 - Posted: 1 Feb 2007, 1:33:36 UTC
Last modified: 2 Feb 2007, 2:30:37 UTC

BOINC Manager use

Meaning of task status "preempted", "ready to report" etc.

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Message 35857 - Posted: 1 Feb 2007, 1:34:50 UTC
Last modified: 23 Sep 2007, 14:37:12 UTC

Workflow
uploads / downloads / getting more tasks

Uploading tasks

Downloading tasks

Getting more tasks

BOINC's use of the internet

How tasks end

Reasons a task ends:

1) it completes it's work and reports back the results.
2) it encounters an error that it cannot recover from, and reports back the failure.
3) the user choses to abort a task from the BOINC manager.

The above apply to any BOINC project. But the following are unique to Rosetta:

4) the task has been restarted 5 times in a row and has not completed a model nor reached a checkpoint.
5) the watchdog determines that the task is not progressing normally, and steps in to end it.

BOINC tasks alternate between actively running, and potentially being suspended for various reasons. Some of those reasons include a system configured to not run while the user is active, or a task that needs more memory then your settings allow, or a transition to do some work from another of your BOINC projects.

When a task is not actively running, if your General Preferences indicate tasks should not stay in memory while suspended, then it will be shutdown. To begin the task again then requires what I'll call a "cold start". This is the same way a task starts up when you restart your computer. The task will retrieve the information stored with the last checkpoint, and begin from that point.

By contrast, if the task does remain in memory, it will be able to do a warm start and pick up right where it left off. Providing BOINC has not been completely shutdown, and the computer has remained powered on.

Each time a cold start is performed on a task, Rosetta checks to see how many times it has previously started from this same exact point. If we are now on our 5th start, the task is aborted for you with an error shown in the result to the effect of "too many restarts, keep job in memory". Removing tasks from memory while suspended is the most frequent cause of this type of task end.

Other likely causes:
- the computer or BOINC was restarted several times in a row, without being active long enough to reach a checkpoint each time.
- the task is one that takes significant time to reach a checkpoint, perhaps because it is running on a slower machine, or that the task is too complex to be able to checkpoint more frequently.

In most all cases, if 5 cold starts have occured on a task and it has not been able to preserve any work done via a model completion or a checkpoint, it is a reliable indication that this task is not running well on your machine and so it is ended for you. When another task is downloaded, it may have different characteristics that make it able to run better on your machine.

Rosetta watchdog

Dr. Baker has compared the 100,000 computers running Rosetta@home to an exploration team surveying a large planet and searching for the lowest elevation on that new planet. So, each of the 100,000 surveyers has a lot of ground to cover. If they happen to land in the middle of a mountain range, they will likely have to climb one or more times to see if lower elevation points exist on the other side of the mountain peaks in their area.

The Rosetta program is constantly trying to assess whether it would be the best use of time to go climb that next mountain to look over the other side. This is why you sometimes see the accepted energy levels increasing as a model progresses.

As with any exploration effort, it is possible to climb over to the other side and then reassess your situation and decide that the route most likely to succeed would be to backtrack. Rosetta backtracks all the time as it creates it's predictions. You follow a given river valley to the ocean, and then you go back to the last major branch and check the other direction to see if it can produce an even better result (i.e. lower elevation in the analogy, or lower energy level in Rosetta's model).

As with exploration of a planet's surface, it is possible to find yourself back where you started, and not realize it. If you proceed from that point again, using the same logic you applied the first time to decide which direction to proceed in, you will retrace more of your steps. If you are, for any reason, unable to find your bread crumbs and understand you've already tried going in that direction, then you can find yourself going in circles, and consistently making the same decisions as the last time you went around.

Rosetta incorporates a sort of breadcrumb trail that enables it to realize, in most cases, when a given path in the model has already been explored. But it's not always possible, given the complexity of the underlaying atoms, to conclude you are running in circles.

And so the watchdog was created to watch over each explorer. Think of the watchdog as an observer from up in an airplane watching you. He can more clearly see when you are going in circles, and radio this information to you. This is done by reviewing the energy score of the model in progress.

In the case of Rosetta, the watchdog uses the following criteria to determine that your current path is getting you nowhere, and that you should wrap up your search:

- If the task has run for more then 4 times your runtime preference.
A message in the reported task will indicate something to the effect of "CPU time xxx greater than 4 x prefered time xxx seconds".

- If the energy score of the model has not changed in a given amount of time.
When the task is sent out by the project, a watchdog time is established. Usually 15 minutes. If the watchdog determines that the model has not advanced in that time, it will end the task. A message in the reported task will indicate
"Rosetta score is stuck or going too long. Watchdog is ending the run!
Stuck at score -xxx.xxx for 1800 seconds"

A watchdog termination is treated as partial success and all the models made before it happens will be returned back to server and credits granted for the valid models returned, plus an additional 20 credits will be awarded for the time spent on the final, uncompleted model.


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Message 35862 - Posted: 1 Feb 2007, 1:35:49 UTC
Last modified: 2 Feb 2007, 2:28:15 UTC

Terminology:

models, vs proteins
tasks vs WU vs result
Amino acids
Boinc vs Rosetta
Ralph vs Rosetta
host vs user
TFlops

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Message 35866 - Posted: 1 Feb 2007, 1:36:56 UTC
Last modified: 2 Feb 2007, 2:29:27 UTC

time to completion

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Message 35871 - Posted: 1 Feb 2007, 1:38:06 UTC
Last modified: 2 Feb 2007, 2:29:47 UTC

describe the graphic

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Message 35962 - Posted: 2 Feb 2007, 1:42:02 UTC - in response to Message 35883.  
Last modified: 23 Sep 2007, 14:18:44 UTC

This FAQ will soon have posts describing:

-- describe the graphic/screensaver

-- time to completion

-- Terminology:
models, vs proteins
tasks, WUs & results
Boinc vs Rosetta
Ralph vs Rosetta
host vs user
TFlops

-- Workflow
download tasks
upload tasks
getting more tasks
BOINC's use of the internet
reasons tasks end

-- BOINC Manager usage
Meaning of task status "preempted", "ready to report" etc.
BOINC doesn't stop when I click the X to close.
BOINC benchmarks

-- Merging hosts

-- Software versions - BOINC
How to check currently available
How to check currently installed
How to install new version without losing work

-- Software versions - Rosetta
How to check currently available
How to check currently installed
How to install new version without losing work


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Message boards : Number crunching : FAQ - Normal Operations (Read Only)



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