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Message 18102 - Posted: 8 Jun 2006, 10:52:34 UTC

Q: How can I check what the current BOINC version available is?

A: This is shown as the \"recommended version\" for each platform here on the BOINC download site.
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Message 18103 - Posted: 8 Jun 2006, 10:59:19 UTC
Last modified: 8 Jun 2006, 11:58:41 UTC

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

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

Open the BOINC Manager, click \"File\" pulldown menu and 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 18104 - Posted: 8 Jun 2006, 11:01:32 UTC

Q: What are TeraFLOPS?

A: This is a measure of computing power. FLOPS are Floating Point Operations Per Second. A floating point operation is essentially a calculation. And so TeraFLOPS is trillions of calculations per second.
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Message 18105 - Posted: 8 Jun 2006, 11:05:52 UTC

Q: How large is Rosetta compared to other projects?

A: The size is measured in TeraFLOPS and is shown on the Rosetta homepage under the server status.

To get a feel for how large Rosetta is when compared to other computing projects, visit boincstats and click on some of the other projects to see their \"Average floating point operations per second\".

The goal is to grow Rosetta to 150 TeraFLOPS! So keep crunchin\'
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Message 18118 - Posted: 8 Jun 2006, 12:30:02 UTC

Q: My work unit completed, and uploaded, why is it still shown in the work unit list saying \"ready to report\"?

Note: work units are called \"Tasks\" in the current BOINC version.

A: Your results were uploaded, but in your general preferences you have set up how frequently to connect to the project. So, based on that, BOINC will later connect to the project and \"report\" the results. When this happens, you will see a message in the messages tab such as this:
7/8/2005 9:30:05 AM|rosetta@home|Requesting 0 seconds of work, returning 2 results

There is more information on the Ready to report status in the BOINC wiki.

In short, the BOINC manager will take care of itself. You don\'t need to do anything about it. The work unit will later be reported and removed from your tasks list and your computer.

If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
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Message 18166 - Posted: 8 Jun 2006, 18:40:38 UTC
Last modified: 8 Jun 2006, 18:44:19 UTC

Q: Why does BOINC constantly use the internet?

A: It doesn\'t. Any internet use by BOINC is shown in the transfers tab, and the messages tab. Once the transfers are completed and the updates to servers responded to, BOINC doesn\'t need the network again until it has completed crunching a WU. (I take that back, if you are crunching a project like Climate Prediction, it would like a connection periodically to send it\'s \"trickle up\" messages to the server even though the WUs take months to complete.)

But it LOOKS like it \"needs the network\" if you have a product like ZoneAlarm that shows a bar reading on your read and write volume. This is because BOINC spawns off threads that do the crunching, and then it uses a sockets connection (i.e. TCP/IP) to communicate between the crunching thread and the BOINC Manager. This is a connection internal within your PC, not out to the internet. The prior version of BOINC updated the status every 5 seconds, the current version is every 1 second and so ZoneAlarm will blink every 1 or 5 seconds. But this does NOT mean it needs an internet connection.

If BOINC it trying to download something and interfering with your internet access for other applications, you can \"suspend\" the network activity of BOINC in the BOINC Manager \"Commands\" tab (it\'s called \"Activity\" in the new BOINC version). ...don\'t forget to set it back to \"Network activity based on preferences\" when you can allow BOINC to use the internet again.
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Message 18171 - Posted: 8 Jun 2006, 18:50:39 UTC
Last modified: 8 Jun 2006, 18:58:31 UTC

Q: I\'d like to reserve my network bandwidth for my business needs during the business day, and only run BOINC at night. Can I do that?

A: Yes. There are two ways you can control this. One is to control when BOINC projects are running on your PC, and the other is to control the hours of the day that BOINC is allowed to use the network. These are both set in your General preferences. After changing the setting, you must update to the project for the change to take effect. Then set the BOINC client to run based on preferences and network activity based on preferences. These are both in the BOINC Manager \"Commands\" pulldown menu (it\'s called \"activity\" in the new BOINC version).

So you can crunch 24 hours a day, but only use the network from 7PM to 7AM, or crunch only at night (perhaps to save on your air conditioning bill) but use the network anytime. Whatever you want. The more hours of the day you run, the more productive work you do for the projects. And be sure to avoid being too restrictive on the hours for network activity. If you limit access to only one given hour of the day, and the server happens to be offline during that time, then you may be without work to crunch until the next day.

If you would like to do this, you will also want to review your \"connect to network every... days\" setting in the General preferences. If you only allow BOINC to access the network 12 hours of each day, then you want to be sure you have 12-24 hours of work to do (or more if you like). So you would want to change this from the .1 day (i.e. 2.4 hours) default value.
If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
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Message 18172 - Posted: 8 Jun 2006, 18:54:22 UTC

Q: Does it take more electricity to run BOINC than for my computer to sit idle?

A: Yes it does. If you are air conditioning, the primary electricity expense could be cooling the air, because your PC will produce more heat when the CPU is busy crunching for BOINC, then it does when it is on by idle.

Because of this, you may want to limit BOINC to running only during the coolest part of the day.
If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
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Message 18215 - Posted: 9 Jun 2006, 2:55:51 UTC
Last modified: 9 Jun 2006, 2:56:43 UTC

Q: BOINC is running my CPU 100%, I don\'t want to break it, how can I tame it?

A: Firstly, it\'s a computer, not an engine. It\'s not like running a mechanical device at full throttle. So, for most machines, they run a little hotter due to the crunching, and they vary the fan speed accordingly.

However (especially for laptops) some computer designs do not have sufficient cooling to run 24hrs a day. Or become noisey or too hot for your lap. For these situations, there is an add-on called ThreadMaster that allows you to limit the % of CPU time used for crunching. Generally for a PC that is having overheating problems, setting it back to 70 or 80% will resolve the problems and yet still give good crunching for your projects.

A feature is planned for the BOINC Manager that will allow CPU % to be controlled by BOINC rather than adding on a program like ThreadMaster. There is mention in the BOINC forum about this coming in a 5.5.1 BOINC release.
If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
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Message 18225 - Posted: 9 Jun 2006, 4:01:25 UTC
Last modified: 9 Jun 2006, 4:08:16 UTC

Q: Where can I get some help on getting things up and running?

A: Many people seem to think they have to dial an 800 number and talk to someone in Dr. Baker\'s lab to address their question. If the question is about how proteins work, there is probably about a 75% chance another user could answer your question. And if the question is about BOINC, or Rosetta installation or operation, there\'s about a 95% chance another user could answer your question. So... give us a shot! Would you rather your question went out to 1000s of knowledgeble people that know better than to try and post answers to things they don\'t know about? Or... have it go to Dr. Baker\'s team of about a dozen staff and volunteers?

The moderators have to review every post anyway. If they see you getting a wrong answer, they will tell you so.

By the way, if your question should fall in to that low percentage that other users are unable to answer, then the project team WILL step in. But they are all very busy people and it would not be unreasonable to give them a day or two to prepare a reply and post it.

So, you get help by:
1) searching the project FAQs and Message Boards.
2) there is a lot of information in the BOINC wiki.
3) Checking the project notes, perhaps a new issue has cropped up.

...I agree, the search tools are difficult to use. Especially when all the terms are new to you. It\'s almost like looking up how to spell a word in the dictionary, it only really works if you already KNOW the answer. I went through the same frustraition, and that\'s why I created option 4.

4) searching the Q@As (the thread you are reading now).
If you are not able to find an answer elsewhere, then...
5) posting on the message boards. WHICH message board? is discussed elsewhere.

And it is most helpful if you take a moment to make a clear subject line. Things like \"a little help here!\", or \"I\'m deatching Rosetta cuz it doesn\'t work!\" will not be very useful for a future user searching for an answer to the same problem. I mean, give some thought to what you were HOPING the subject would say in your searches. Also, some issues are platform specific, not everyone is running Windows. So a subject line like \"Windows: \'Not requesting new work\', why not?\" creates a long-term asset here on the message boards that others can use in the future in step 1.

Another thing that creates a long-term asset, is if you cast votes as you read through threads. This is done with the little green \"+\" and red \"-\" at the bottom of each post. If people would express an opinion about which threads they found the most useful, then people will be able to sort the list by \"highest rated first\" and actually have all the best stuff come to the top.
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Message 18308 - Posted: 9 Jun 2006, 18:46:41 UTC

Q: What do they mean by \"Should Rosetta@home show your computers on its web site?\"?

A: You have the choice of hiding or showing your computer information. It SOUNDS like it might be opening some way for people to get to my computer from the website, but this is not at all what they mean.

And when YOU look at your own computers, you see much more detail than others will be able to see. Take a look at mine... click my \"Feet1st\" user name at the left, and then click the link called \"view\" shown after \"Computers\". This is the type of information you are deciding to show or not.

Basically it shows your operating system, your CPU speed, the amount of memory, and some other basic performance information about your network speeds. If you specify \"yes\" for the setting, then others can see information about your systems, just as you saw mine. If you specify \"no\" then after the \"Computers\" label, it will say \"hidden\" and there won\'t a link there.

So, what to set it to? In general, set it to YES. This will allow people to better understand any posts you make requesting help, because it let\'s people see \"oh, they are on an old version of Linux\" or \"they don\'t have enough memory, that\'s probably why things are slowing down\".

Setting this to YES ALSO let\'s others see the work units your computer(s) have crunched, and any errors that were reported in them, credits issued, your average runtime etc. So, it can really help you to get help when you need it.
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Message 18431 - Posted: 11 Jun 2006, 2:03:27 UTC - in response to Message 18397.  

Q: What settings should I be aware of to provide the most usefulness to the science of Rosetta? (cal)

A: There are many of us trying to figure out why specific users and machines seem to claim so many credits.

In a nutshell, either their system made an error in the CPU benchmarks that BOINC performs periodically... they are going to extra measures to funnel work through one machine to feed several behind it... or, they are flat out cheating the system to get credits (which have no value and do not help the science per se).

I think your credits look reasonable. My RAC is 400+ now, but I\'m using 3 machines and also crunch a few other projects a portion of the time.

So far as settings... I see all but your last work unit seemed to take the 3hr default runtime. So perhaps you are already working to step it up, but you might consider increasing your WU runtime. That way your PC will spend less time managing internet traffic to download more WUs, and stay focused on crunching more models on each WU you already have (it\'s really a negligeble difference).

You want to set your General Preference to \"Leave applications in memory while preempted?...YES\". If Rosetta is your only project, this would only make a difference if you suspend BOINC from time to time to work on a really intense application. But with 3ghz, and 2GB, I doubt you ever have the need.

You want to set your General Preference for \"Connect to network about every... days\" to at least .5 or so, to assure that you have something to crunch through any server downtime as we had this week during the upgrade. This would only make a difference if you find yourself without work, and access to the server from time to time (ISP outage, or Rosetta server outage).

Since you have a dual core CPU, you also want to check your general preference for \"On multiprocessors, use at most...\" and be sure it says \"2\" (or more). I suspect it already is, based on your 200+RAC. But for future readers, if this is set to \"1\" and your PC is a dual core, then you\'re only really using half of it.

Keep in mind that screen savers consume a little CPU time as well. So, ideally set your screen saver to \"none\" and turn off the monitor when it is not in use. And only display the graphic when you actually want to study what Rosetta is working on, and then close it when you are through.

Beyond that, you just want to assure your PC is up and running as many hours as possible; keeping your air conditioning and electricity expense reality in mind.

The only other thing I can think of would be for you to try and bring friends and family to crunch Rosetta as well. If you bring on 3 friends, and each of them brings on 2 more, and each of them brings on 1 more, then you\'ve arranged for a contribution to Rosetta\'s science that\'s 15 times more than you can do by yourself.

Thanks for posting, I\'m sure others have the same question as well. And thanks for breaking the ice here. I did not intend for this thread to be one directional.
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Message 26632 - Posted: 11 Sep 2006, 22:03:42 UTC
Last modified: 11 Sep 2006, 22:03:55 UTC

Q: What are the little red dots in the graphic for? (PUDDIN TAME)

A: These indicate the best predictions of your previous models. As the work unit progresses, you will see the model number increment once it completes a model. That completed model becomes a red dot on subsequent runs.
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Message 26634 - Posted: 11 Sep 2006, 22:06:35 UTC

Q: Why don\'t I see the red dots from my prior runs in the graphic?

A: Because your current model hasn\'t made it down that far. The scaling factor used for the display only includes the high and low of your current model. Often you catch it near the beginning of the model and the energy value and RMSD values aren\'t very good yet, that\'s why it is continuing to refine the model. With any luck, this model will find better energy values and drop the lower end of the scale, and then you will see your prior predictions down there indicated with the red dots.
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Message 28275 - Posted: 23 Sep 2006, 16:12:09 UTC

Q: Are there any guidelines for when to abort a task?

A: Use your judgement, and experience level as a guide. If you are inexperienced with the Rosetta application, keep in mind that it is running on 1,000s of other machines without requiring work to be aborted. So, when in doubt, let it run for at least 4 hours before you consider aborting.

If your computer is turned off and back on, you sometimes lose significant amounts of work. This is a fact of life. There are \"checkpoints\" made periodically to preserve the work up to a given point, but for some proteins these are few and far between.

Rosetta has a \"watch dog\" in place which helps assure that a given task is crunching properly, and to abort it for you if it is not progressing. So, again, when in doubt, let it run.

There have been some issues recently, apparently with the current BOINC versions, where the status shown on BOINC Manager may not match what is going on in your computer. Specifically, BOINC may show a task running, but your Windows task manager may show your machine is idle. Until this glitch is resolved, ending the BOINC manager (from the menu bar File -> Exit) and restarting generally seems to get things running properly again.
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Message 32020 - Posted: 3 Dec 2006, 18:44:44 UTC
Last modified: 3 Dec 2006, 18:45:32 UTC

Q: How to merge together credits from two machines?

A: 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 32774 - Posted: 17 Dec 2006, 0:58:14 UTC

Q: Should I run with the screensaver active?

A: If you are looking for performance, then no. A screensaver of \"none\" will save your machine the compute time of drawing all the graphics. If you are looking to better understand what Rosetta is doing with these proteins, or perhaps hoping others around you will get curious and join Rosetta, then yes. The screensaver really shows you what the program is thinking about.

At Rosetta version 5.41, using the screensaver has presented problems for some machines. These problems have, for the most part, been resolved in the Rosetta 5.43 version which addresses these concerns by turning off some of the graphic features which were causing the problems. These will be reintroduced at a later date once the problems with these features are addressed.

If you have problems with the screensaver freezing, or with the watchdog stepping in to end hung tasks when the screensaver is running, then the suggestion is to set your screensaver to \"none\" until a new Rosetta version addresses the problem you have.

If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
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Message 32775 - Posted: 17 Dec 2006, 0:59:03 UTC

Q: What are the benchmarks that BOINC runs periodically? Do I need to calibrate anything?

A: Benchmarks are run for 60 seconds when you first install BOINC. They also happen whenever you change boinc versions, and every 5 days. These benchmarks give the servers a feel for the capacity of your computer to process work. The benchmarks however are general to BOINC and are not calibrated to Rosetta, so you might find two machines where one has double the benchmark ratings of the other, but it falls short of crunching twice the number of Rosetta models.

You do not need to set or calibrate anything. For the most part, the benchmark figures are no longer used by Rosetta. Credits are issued based on the number of models you complete. When you look at your reported work, you will see \"credit claimed\" and \"credit granted\"
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Message 32777 - Posted: 17 Dec 2006, 1:18:08 UTC

Q: How can I change my Rosetta handle shown on my message posts?

A: Unfortuantely the default when you set things up is to take your Windows user name and place that in the blanks. And this leads to many many accounts being called \"administrator\".

You can change your account UserID. If you\'ve signed on to Rosetta to view this message board, then just click the link on top of this message board page for \"participants\". Then click on the link \"other account info\", you can change your username there. It is shown on the screen simply as \"Name (real name or nickname)\".
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Message 32778 - Posted: 17 Dec 2006, 1:18:38 UTC
Last modified: 17 Dec 2006, 1:19:00 UTC

Q: My PC requested 1,345 seconds of work, but I received work for 3 hours. Why didn\'t it send what I asked for?

A: BOINC just knows work was needed and requested some. The number of tasks sent to you is based on the amount of time BOINC thinks it will take you to complete a task (see the flexible work unit runtime discussion) and the amount of work you requested.

In your case, a single work unit was the smallest amount of work that could be sent to answer your request for more work. And BOINC estimates (based only on the last Rosetta tasks it has completed, NOT based on the current setting for work unit runtime) that task will take 3 hours to complete.
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