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Message 17972 - Posted: 7 Jun 2006, 18:13:51 UTC
Last modified: 7 Jun 2006, 18:19:55 UTC

I wanted to create a place for all of the new participants to drop their questions and get help in getting started and with running Rosetta. The hope is that we can build a good supplement to the FAQs.

If you are a newbie, welcome to Rosetta!! Post your questions in here. If you are not a newbie, post a question and the answer here that you know the newbies will have. And try to provide links where they can get more details on the issue.

Q: Progress Percent not advancing?
A: Rosetta recomputes the progress percent at the end of each model. The model number is shown in the graphic. As long as the \"steps\" are continuing to progress, it is working. Once it completes the model it is working on, it will recompute the progress. At that point the progress % will be determine by looking at the time it took to complete the first model, as compared to your WU runtime preference. If your WU runtime preference is low (<4hrs) you will frequently see the progress % jump from 1.xx to 100%, or into the 50% range. Basically, each different protein takes a different time to crunch a model. Some proteins will crunch for several hours to complete a single model. Others will crunch a model every 5 or 10 minutes. It is the nature of the science being done with Rosetta.

BOINC and Rosetta have measures in place that will abort work units that aren\'t running properly. So, in general, unless you see some specific advice to the contrary, you should NOT abort work units (WUs).
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 17973 - Posted: 7 Jun 2006, 18:16:47 UTC

Q: \"To completion\" time is going UP!
A: This is normal. The time gets revised when the progress % is recomputed at the end of each model. So at the end of a model the time to completion will drop. Then during the crunching of the next model it will increase again.

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Message 17976 - Posted: 7 Jun 2006, 18:33:31 UTC

Q: I am on a dial-up connection, how can I use less modem time?
A: Rosetta has a flexible work unit runtime setting. It is configured in your Rosetta Preferences. Increasing the setting allows you to crunch more models on each protein you download, and so reduces your download time. MUCH more detail is in the FAQs.

Caution: the BOINC Manager doesn\'t immediately understand any changes in WU runtime preference. So, in general, only change it gradually over time, or when you have few Rosetta WUs in your tasks tab. Once your PC has crunched WUs on the new runtime, and seen they are taking longer to complete, and then updated to the project, it will increase the time estimates accordingly.

This is important if you have set your General perference to connect every few days (i.e. if you have a \"large cache\"). This is because if you only connect every two or three days and start with the default of 3hours, then BOINC Manager will try to download about 20 WUs (40 if you have a dual processor, less if you have <100% resource share allocated to Rosetta) to keep you crunching for 2-3 days. But if you later change your preference to 12hrs or 24hrs, and update to the project, then it will start crunching for that long on each of those existing 20 WUs, and you may miss the deadlines.

So, better to make changes gradually (maybe kick it up one level every 2 days or so). Or reduce your cache size in General Preferences and work through the downloaded WUs before increasing the runtime preference. Crunch until your target runtime is reflected in the \"to completion\" time shown on your WUs. Then increase the cache size to the level you prefer.
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Message 17977 - Posted: 7 Jun 2006, 18:39:43 UTC

Q: Why am I earning less credits per day when I crunch Rosetta?
A: Credits are assigned by each project. Some give more per hour of crunch time than others. It\'s like foreign currency exchange. one U.S. Dollar is not the same as one Euro, or one Yen. Think of it as Rosetta\'s currency is stronger than many other projects.

However, Rosetta does not use a quorum system. So as soon as you report a valid result, you are issued credit for your work. And even if the result is not valid due to some failure in processing, Rosetta awards credit by running a daily job to grant credit to failed results. However, it doesn\'t show that credit on the WU list, you have to look at the WU details to see it has been granted.

Credit isn\'t actually based directly on hours of crunchtime. It\'s also adjusted based on the speed of the computer that is doing the crunching. This way a faster computer earns more credits per hour than a slower one. Because it is doing more computations for the project.
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Message 17979 - Posted: 7 Jun 2006, 18:43:28 UTC

Q: I see many message boards and the Q&A boards, where should I post my question?
A: They are phasing out the Q&A message boards. If you\'d like to start a new thread for a specific question, rather than posting it here, then generally the Number Crunching message board is probably the best place. If your question relates more to the science of how Rosetta works, or the proteins being studied, then the Science board would be appropriate.
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Message 18000 - Posted: 7 Jun 2006, 20:07:10 UTC

Q: Why is my graphic different than the one shown in the explaination of the graphic display?

A: The graphics shown in the description is the format used when they are testing Rosetta against a protein of known structure. The project crunches on structures that are already known to test new ideas about predicting the structure and see how they compare to the known structure.

Most of the work presently being crunched on Rosetta is for the CASP7 test. These proteins do not have a known structure. That is the test, to predict what the structure looks like. Because the structure is not known, the RMSD cannot be computed. This is because RMSD is a measure of how the model your PC is working on compares to the known structure. Because the structure is not known, and RMSD cannot be computed, there is no \"native\" box showing the known structure, and there is no graph along the right-hand side showing the RMSD of each accepted configuration. Instead the \"low energy\" graphic was enlarged to fill those spaces. The lowest energy model we can find is probably the closest to the native structure.
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Message 18001 - Posted: 7 Jun 2006, 20:13:34 UTC

Q: What are credits?

Credits is a measure of how much computing power you have contributed to the project. You will see them listed in people\'s profiles, and signiture lines. As a newbie, you should use credits as a rough measure of how much experience that user has with Rosetta. And so if you see conflicting answers, you might tend to go with the one from the user with the most credits.

Credits are also used to compare teams. Each participant can join a team and the teams can compete to contribute the most to the project.

Credits have no monetary value, and cannot be traded for a free trip to Seattle. But they help measure the scale of the computing power of the project, and to give you a sense of your personal contribution to the science being done on Rosetta.
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Message 18003 - Posted: 7 Jun 2006, 20:18:08 UTC

Q: What is RAC?

RAC stands for Recent Average Credit. It is basically a measure of the pace at which you are crunching for Rosetta. Since some people report their results infrequently, it isn\'t very useful to just show the credits awarded the last 24hrs or something that simple. BOINC has a process of taking an average over time so the numbers are more comparable to each other. There\'s more details than you wanted to know about how RAC is calculated in the BOINC Wiki.
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Message 18004 - Posted: 7 Jun 2006, 20:24:45 UTC
Last modified: 7 Jun 2006, 20:24:58 UTC

Q: How do I know if Rosetta got installed properly on my PC?

A: If you open the BOINC manager, go to the projects tab and see rosetta@home in the list, and go to the \"work\" tab (it\'s called \"Tasks\" in the newer BOINC version) and see one or more work units with \"rosetta@home\" listed in the first column labeled \"project\", then you\'re in good shape. Your PC will crunch those work units and then report the results back and download more. See the \"How it works\" diagram.
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Message 18007 - Posted: 7 Jun 2006, 20:38:33 UTC
Last modified: 7 Jun 2006, 20:41:34 UTC

Q: Why won\'t BOINC download more Rosetta Work units?

A: It is possible the servers are down for some reason (quite rare). You should check the server status.

But it is more likely you are seeing a message in the BOINC Manager saying \"...not requesting new work\". If so, then your PC is actually not asking for more work.

If you are running multiple BOINC projects, the BOINC manager plans out what will be crunched next, and balances goals like the deadlines of the work units, and your preferences as to resource share to devote to each project. In this balancing act, it sometimes crunches a project more than it\'s normal share in order to meet a deadline. When this occurs, the project being crunched incurs a \"debt\" to the other projects. BOINC will take this debt in to account when requesting new work. It is not uncommon, especially when running 3 or more projects, for BOINC to decide to crunch other projects for a period of a day or two in order to pay back such debts. And so during that time it will not order more work for projects that it does not plan to be crunching for a while.

In the end, if you leave things alone and resist the temptation to try and FORCE BOINC to do work for a specific project, it will work itself back in to balance and again download work for each project.

If you want to increase the resource share for Rosetta, you can increase the value in your Rosetta preferences, and then update to the project. You can view the present resource share in the Projects tab of the BOINC manager. The BOINC Wiki has more discussion of how resource share works.
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Message 18009 - Posted: 7 Jun 2006, 20:52:36 UTC
Last modified: 7 Jun 2006, 20:55:52 UTC

Q: Are there some specific threads I might want to subscribe to in order to keep up to date on any key Rosetta developments?

A: Yes, there are several threads used to deliver information to the Rosetta participants. There is an index of them here. The main ones you would probably want to subscribe to would be:
Dr. Baker\'s science journal,
the project annoucement thread,
and the Rosetta Application Version Release Log.

logon to the Rosetta website. Then click on each of those from the index, and when the thread is displayed click on the \"subscribe to this thread\" link in the upper left. This will send you an EMail with a link directly to the thread when new posts are made to them. As you can see, the three that I mentioned are only posted to when there is news from the project team, so you won\'t fill your EMail inbox with things of lessor importance. But you will stay informed as the project evolves.
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Message 18010 - Posted: 7 Jun 2006, 21:13:40 UTC
Last modified: 7 Jun 2006, 21:14:24 UTC

Q: I find the posts from a given user helpful, how can I see more of their posts?

A: Just display a thread they\'ve posted in, click their user name over on the left, then click the link shown for \"Message board posts\". I find this feature especially useful to keep up to date with posts from:
Dr. Baker - lead scientist.
David Kim - project scientist.
Rhiju - project scientist.
Keith Laidig - Project Admin.
Moderator9 - The most active of the Forum moderators. I don\'t actually try to keep up with Mod9 :) They do a great job keeping the boards organized and help assure every post gets a response. If you get a notification that Mod9 has moved a post of yours or something, take it as a helpful step to bring the proper resources to address your post.

The above are all project team members. I follow specific users I like as well simply by clicking their name as I read a post that I found helpful and informative. I often find more posts of interest by scrolling through their recent posts and clicking through to the thread they posted in.
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Message 18012 - Posted: 7 Jun 2006, 21:51:05 UTC

Q: Why doesn\'t BOINC stop when I click the \"X\" to close the window?

A: Basically, it is designed to keep running in the background so that more of those spare CPU cycles go to crunch the work units. If you actually want to end BOINC Manager and the projects that are crunching, then click the \"File\" pulldown menu and select \"Exit\". This will halt the processing immediately, and lose any work done since the last checkpoint. Generally checkpoints are performed every 20 minutes or so to minimize the amount of work that may be lost if you turn off your computer or if you remove the process from memory when BOINC switches to other projects. (remove from memory is a setting in your General preferences).
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Message 18016 - Posted: 7 Jun 2006, 22:15:21 UTC
Last modified: 7 Jun 2006, 22:17:29 UTC

Q: I\'m familiar with SETI and BOINC already, but what should I know about Rosetta?

A: Firstly, know that Rosetta is working to develop the science that will save our lives. As the science behind Rosetta progresses, all of mankind benefits. So, the outcome is much more immediate then hearing a repeating blip from ET... and then not being able to do anything about it. However, you should view Rosetta as the \"10 year plan\" to find cures. 10 years is much more immediate than 100 light years. The work being done on Rosetta will be useful to many areas of medicine and to many many diseases. The actual timeframe to fully develop Rosetta is unknown, (welcome to developmental science!) but the outcome is worth the investment. Crunch more Rosetta!

Secondly, you will notice that your participation in Rosetta is valued. This means your computer, your ideas, your questions, and your concerns, suggestions and problems. So there is no need to cast threats and curses across message boards. It also means the project team wants to keep you informed as they are trying new ideas, and methods to perform the protein structure prediction. And they address your questions about them.

Rosetta has a flexible work unit runtime. You can configure it to suit your computer use. The WUs are larger to download (roughly 3MB). But you can minimize that download time.

You may find you earn less credits per day than with SETI, so it\'s a good thing credits are only compared to users of the same project. Rosetta also grants credit even if your work unit processing fails. They view this as useful information that helps them in developing the science. And they encourage you to report failures and any insight you may have as to their cause so they can correct problems and make things increasingly trouble free.

You will notice that the progress % does not increment steadily the way SETI does. It is really only updated at the end of each model generated. Other fractional adjustments to progress basically represent checkpoints occuring. You can minimize this effect if you set your runtime preference to a larger value. Be sure to study the caution mentioned in the discussion of dial-up.
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Message 18039 - Posted: 8 Jun 2006, 1:56:13 UTC

Q: How do I add a second computer to Rosetta?

A: You follow the same process of installing BOINC and then attaching to the project URL. The question is \"can I use the same Rosetta ID for the second computer?\", yes. Both computers (\"hosts\") will be shown under the same user account and participate in the same term statistics.
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Message 18042 - Posted: 8 Jun 2006, 2:03:08 UTC

Q: I want to split my computer time (resource share) between Rosetta and another project, why don\'t the CPU % shown in the task manager reflect the % resource share I have designated?

A: The way BOINC works is that a given project is either running, or it is not. And since BOINC allows resource share to be very precise (for example, 71% Rosetta, and 29% climate prediction) it achieves this over time by scheduling one project for more time slots than the other.

For example, you have your general preferences set to switch between tasks every hour. BOINC Manager will decide once each hour which project should be running. It may sometimes decide to have two threads running (on a dual core CPU) for the 29% project, so be careful! You probably don\'t want two climate work units at the same time or you may never complete them on time. So for a project with a very long runtime like that, you will want to download your first work unit, and then mark the project for \"no new work\". This is done on the projects tab of the BOINC Manager. That way you won\'t download a second huge WU without specifically allowing it.

Bottom line, look for your resource shares to be implemented over the course of 100 CPU hours... not over 100 minutes. And with that perspective you will find the BOINC manager does an excellant job of meeting the sometimes conflicting goals it is faced with.
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Message 18098 - Posted: 8 Jun 2006, 10:41:27 UTC
Last modified: 8 Jun 2006, 10:45:11 UTC

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

A: Open the BOINC Manager, go to the \"Work\" tab (it\'s called \"Tasks\" in the newer version of BOINC), and the version is shown in the \"Application\" column. For example \"rosetta 5.16\" indicates version 5.16.
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Message 18099 - Posted: 8 Jun 2006, 10:44:54 UTC

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

A: There is a link on the home page for \"applications\" (under \"Returning Participants\").
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Message 18100 - Posted: 8 Jun 2006, 10:48:44 UTC

When a new version of Rosetta comes out, should I abort WUs 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.
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Message 18101 - Posted: 8 Jun 2006, 10:50:33 UTC

Q: How do I know what version of BOINC I am running?

A: Open the BOINC Manager, click the \"Help\" pulldown menu at the top, and select \"About BOINC Manager\".
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