Rosetta@Home FAQ

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[edit] General

This FAQ was originally created by hugothehermit

[edit] What is the URL of Rosetta@Home?

http://boinc.bakerlab.org/rosetta (http://boinc.bakerlab.org/rosetta)

[edit] Is Rosetta@Home non-profit? / Is someone going to make money out of my donated computer time?

The University of Washington makes the source code (the actual Rosetta algorithm, which our donated computer power is helping improve) available to academics and other universities for free, and will eventually make the source code available to the public, when the possible cheating problem within the BOINC System is addressed. Dr. David Baker said "Everything will be public domain ... No, I do not believe in patenting naturally occurring genes, proteins, etc."

[edit] How do I set Rosetta@Home to stay in memory?

To change your preferences to leave Rosetta@Home in memory, General Preferences Log in (at General Preferences if you're not already) -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button; also, remember to "update" the BOINC Client Software so that the changes are downloaded. Open the BOINC Manager and select the "Projects Tab", left-click on "Rosetta@home" to select the project, and click the "Update" Button.

[edit] Why am I getting an error every time BOINC switches tasks?

Change your preferences to leave Rosetta@Home in memory, General Preferences Log in (at General Preferences if you're not already) -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button; also, remember to "update" the BOINC Client Software so that the changes are downloaded. Open the BOINC Manager and select the "Projects Tab", left-click on "Rosetta@home" to select the project, and click the "Update" Button.

[edit] Why am I getting an error every time BOINC runs a benchmark?

  1. Change your preferences to leave Rosetta@Home in memory, General Preferences Log in (at General Preferences if you're not already) -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button; also, remember to "update" the BOINC Client Software so that the changes are downloaded. Open the BOINC Manager and select the "Projects Tab", left-click on "Rosetta@home" to select the project, and click the "Update" Button.
  2. We suggest that you update your BOINC Client Software to version to 5.2.13 or higher as it no longer removes the Science Applications from memory when doing a Benchmark.

[edit] Why is my computer stuck on 1% ?

  1. Change your preferences to leave Rosetta@Home in memory, General Preferences Log in (at General Preferences if you're not already) -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button; also, remember to "update" the BOINC Client Software so that the changes are downloaded. Open the BOINC Manager and select the "Projects Tab", left-click on "Rosetta@home" to select the project, and click the "Update" Button.
  2. This is another known BOINC and Rosetta@Home issue, there are a couple of things you can do about it, they should be done in the order here:
    1. suspend the Work Unit, BOINC Manager -> Work Tab -> click on the Work Unit click the "Suspend" button (on the left hand side) then "Resume" button, wait for the computer to re-start the Work Unit (it will need to finish the new Work Unit it started, if it had another available) and see if it's still stuck, give it about 20min.
    2. Shutdown the BOINC Client Software, then restart BOINC Client Software see if the Work Unit is still stuck, give it about 20min.
    3. Reboot your computer. See if the Work Unit is still stuck, give it about 20min.
    4. Abort the Work Unit, BOINC Manager -> Work Tab -> click on the Work Unit that's stuck, then click the "Abort" button (on the left hand side).

[edit] Why am I getting a 'Reason: Access Violation (0xc0000005) error'?

  1. Change your preferences to leave Rosetta@Home in memory, General Preferences Log in (at General Preferences if you're not already) -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button; also, remember to "update" the BOINC Client Software so that the changes are downloaded. Open the BOINC Manager and select the "Projects Tab", left-click on "Rosetta@home" to select the project, and click the "Update" Button.
  2. An error occurred somewhere on the computer, it could have been the BOINC Client Software or the Rosetta@Home Science Application or any programme that your computer was doing at the time. This is not a Rosetta@Home specific error, as far as I am aware it happens, on occasion, in all of the BOINC Powered Projects with all of the Science Applications. Keep Rosetta@Home in memory and ignore this problem if it's not getting out of hand.

[edit] What is the difference between Rosetta@Home and Folding@Home / Predictor@home?

Dr. David Baker "The Rosetta@Home Project goals are very different from those of Folding@Home. The goal of Folding@Home, I believe, is to determine how long proteins take to fold, given the sequence of the protein and knowledge of its three dimensional structure. The goal of Rosetta@Home is to predict the three dimensional structure from the amino acid sequence." Dr. David Kim "Our project is similar to Predictor@Home, in that we are trying to improve our methods by conducting research that is only possible with the computing power that a grid computing project can provide."

[edit] Can I move work from one computer to another?

Yes. If you copy the ENTIRE BOINC Directory (folder) to a thumb drive, take that to a different system, plug it in and run, it will continue to work. The only downside to doing this is that your "view computers" display may get a little confused if you upload a Work Unit from the new system. This can be prevented by running the BOINC Manager from the thumb-drive initially after the copy, and setting network access to never available.

[edit] Master file fetch failed?

  1. This means the Rosetta@Home Web Server is down. Give it a few hours and then try again.
  2. Your Internet connectivity may not be working properly, try to brows the Rosetta@Home Web Site, have a look at the Server Status Page, the link is on the Rosetta@Home Home Page. To fix your Internet connectivity (generally shut down everything including your router (if you have one), modem, DHCP server (if you have one) etc... start every thing up in the correct order and and try again).

[edit] Exited with zero status but no 'finished' file.

This is a benign problem with the BOINC Daemon and the communication with the Science Application, it's harmless, just ignore it.

[edit] Which ports does Rosetta@Home need open?

Port 80 (HTTP) is used for most communications with the project servers. Port 443 (HTTPS) is used if the password is being exchanged . Ports 1043 and 31416 are used for local control as well as for remote control of an instance of the BOINC Client Software. Port 1043 is preferred and 31416 is a fall back. Unless you are RPC'ing over the Internet don't open 1043 and 31416 in your non-local firewall specifically for the BOINC Client Software.

[edit] Should I use Hyper Threading?

Yes, it gets you a small gain over not using it. If you are very low on memory and don't want to use more than x CPUs then Log in (at General Preferences if you're not already) -> Edit Preferences (down the bottom) -> On multiprocessors, use at most "N" CPUs.

[edit] Why can't I get new Work Units from Rosetta@Home?

If your computer is doing more than one BOINC Powered Project (SETI@Home and Rosetta@Home for example) the BOINC Daemon decides how much work you can have so that that the Work Unit Deadlines are not reached. Either allow the BOINC Daemon to do this or if you are more interested in one of the BOINC Powered Projects you can change the Resource Share in the Rosetta@Home preferences ->Edit Rosetta@Home preferences and change the resource share. Alternatively you can suspend the other application(s), open the BOINC Manager -> Projects Tab click on the application you would like to suspend and either click on the "Suspend" button or the "No New Work" button (to allow the BOINC Client Software to finish the Work Units it has on hand but not to get new ones), on the left hand side.

[edit] I don't receive an E-mail? / My ISP is blocking my E-mail from Rosetta@Home?

This is usually caused by your Internet Service Provider blocking the E-mail as spam, Even though you can join up without it I would suggest that you get a free E-mail account and use that, remembering that if you don't log on to these free E-mail accounts every so often then some of them will delete your account. I also as a general suggestion that I give to everybody (no inference that Rosetta@home could or would contribute to this should be taken) that you never use you Internet Service Provider E-mail account for anything else than talking to your ISP as it's not funny being spammed on an account that you actually need.

[edit] Why is it reported that I have more computers than I actually do? / How do I merge my computers?

When you detach and then re-attach to the same project, the BOINC Scheduler assumes that it's a different computer, You can merge these computers so they are one again, on the "Your Computers" Page click on the computer you would like to merge, then click the "Merge this computer" link (down the bottom of the page).

[edit] Why do I have ghost Work Units? / Why do I have Work Units assigned to me that I don't have?

This seems to be caused by the BOINC Client Software and the Rosetta@Home Scheduling Server losing the ability to communicate properly, and it can safely be ignored.

[edit] Is Rosetta@Home concentrating on a particular disease?

Dr. David Baker "My research group is involved both in fundamental methods development research and in trying to fight disease more directly...

Malaria: We are part of a collaborative project headed by Austin Burt at Imperial College in London that is one of the Gates Foundation "Grand Challenge Projects in Global Health". Malaria is caused by a parasite that spends part of its life cycle inside the mosquito, and is passed along to humans by mosquito bites. The idea behind the project is to make mosquitoes resistant to the parasite by eliminating genes required in the mosquito for the parasite to live. Our part of the project is to use our computer based design methods (Rosetta) to engineer new enzymes that will specifically target and inactivate these genes.

Anthrax: We are helping a research group at Harvard build models of anthrax toxin that should contribute to the development of treatments. You can read the abstract of a paper describing some of this work at http://www.pnas.org/cgi/content/abstract/102/45/16409

HIV: One of the reasons that HIV is such a deadly virus is that it has evolved to trick the immune system. We are collaborating with researchers in Seattle and at the NIH to try to develop a vaccine for HIV. Our role in this project is central--we are using Rosetta to design small proteins that display the small number of critical regions of the HIV coat protein in a way that the immune system can easily recognize and generate antibodies to. Our goal is to create small stable protein vaccines that can be made very cheaply and shipped all over the world "


[edit] Rosetta generates an error telling me that I must free xxx.x MB. I don't understand, there's gigs of free space on this system....

Example from message log - 

Fri 20 Jan 2006 10:05:32 AM EST|rosetta@home|Message from server: No work sent
Fri 20 Jan 2006 10:05:32 AM EST|rosetta@home|Message from server: (there was work but you don't have enough disk space allocated)
Fri 20 Jan 2006 10:05:32 AM EST|rosetta@home|Message from server: No disk space (YOU must free xxx.x MB before BOINC gets space). Review preferences for minimum disk free space allowed.
Fri 20 Jan 2006 10:05:32 AM EST|rosetta@home|No work from project

Your issue is not the actual hard drive space on your disk, but the amount of space that is allowed to be used on your hard drive for Rosetta@Home, which is specified by your online account settings.

  • Once logged in, go to edit General Preferences, and once there, adjust the settings for the disk and memory usage.
  • Once you save the settings, open the BOINC Manager, and on the Projects Tab, click the update button. This will load your saved preferences onto the PC, and this should solve the issue.

Solution by: JDHalter; XPC Team - Rosetta@Home

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