It would be great if a volunteer or volunteers could extract the most useful (to them) parts of the message board discussions and put it into a "Frequently Asked Questions" format. We could then post this on the home page. the problem now is that questions and answers more than a few days old get totally buried. We'd like to do this ourselves, but are absolutely swamped with keeping things going, the screensaver, analyzing results, etc. thanks in advance! David

---

Ok I'm in, I'll just keep editing this post so anybody notices that I erred give me a yell.

Q. What is BOINC?
A. BOINC is a programme that allows scientific applications to use your computer(s)'s idle time.

Q. What is Rosetta@hHome
A. Rosetta@Homes is a scientific application that is attempting to computationally find the stucture of a portein.

Q. What is the difference between Rosetta@Home and Folding@Home / Predictor@home ?
A.

Q. How do I join Rosetta@Home?
A1. If you do not have BOINC already on your compuer then:
1. Create an account.
2.Download and install BOINC
3.Run BOINC if it isn't already going.
4.Boinc will first ask you to join a project.
5.Copy and paste in the URL https://boinc.bakerlab.org/rosetta
6.Enter your e-mail and password.
7.Change your preferences to leave Rosetta@Home in memory, Rosetta@Home Web site -> Returning Participants -> Your account-> Log in -> View or edit general preferences -> Edit preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

A2. If you already have a BOINC account:
1.Create an account.
1.BOINC Manager-> Pojects (not the tab, but up the top in between commands and options) -> Attach to Project
2.Boinc will now ask you to join a project.
3.Copy and paste in the URL https://boinc.bakerlab.org/rosetta
4.Enter your E-mail and password.
5.Change your preferences to leave Rosetta@Home in memory, Rosetta@Home Web site -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory whil preempted? Check yes and click the update preferences button.


Q. What is the URL of Rosetta@Home?
A. https://boinc.bakerlab.org/rosetta

Q. Why am I getting an error every time BOINC switches tasks?
A. There is a known bug in the Rosetta@Home application. This is just a work around until it can be fixed.

Q. Why am I getting an error every time BOINC runs a benchmark?
A. You need to keep the Rosetta@Home application in memory, unfortunatly BOINC has to clear the deck to get a benckmark. There is nothing that can be done about this until the bug has been tracked down and removed.

Q. Why am I getting a OCOOOOO5 error?
A.This is an error that something somewhere went wrong, it could have been BOINC, or Rosetta@Home 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 occation, in of the BOINC applications. Just ignore this problem.

---

Ok I'm in, I'll just keep editing this post so anybody notices that I erred give me a yell.

No I wont because someone actually turned on the "can't edit after 60min" option :)

Q. What is BOINC?
A. BOINC is a programme that allows scientific applications to use your computer(s)'s idle time.

Q. What is Rosetta@hHome
A. Rosetta@Home is a scientific application that is attempting to improve upon the Rosetta algorithm that computationally finds the structures of proteins.

Q. What is the difference between Rosetta@Home and Folding@Home / Predictor@home ?
A.

Q. What are the minimum system requirements?
A. The only recommendation is that you have at least 512MB of RAM.

Q. How Big is the initial download?
A.

Q. How big are the files?
A.

Q. How big are the results?
A.

Q. How do I join Rosetta@Home?
A1. If you do not have BOINC already on your computer then:
1. Create an account.
2. Download and install BOINC
3. Run BOINC if it isn't already going.
4. BOINC will first ask you to join a project.
5. Copy and paste in the URL https://boinc.bakerlab.org/rosetta
6. Enter your e-mail and password.
7. Change your preferences to leave Rosetta@Home in memory, Rosetta@Home Web site -> Returning Participants -> Your account-> Log in -> View or edit general preferences -> Edit preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

A2. If you already have a BOINC account:
1. Create an account.
2. BOINC Manager-> Projects (not the tab, but up the top in between commands and options) -> Attach to Project
3. BOINC will now ask you to join a project.
4. Copy and paste in the URL https://boinc.bakerlab.org/rosetta
5. Enter your E-mail and password.
6. Change your preferences to leave Rosetta@Home in memory, Rosetta@Home Web site -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.


Q. What is the URL of Rosetta@Home?
A. https://boinc.bakerlab.org/rosetta

Q. How do I set Rosetta@Home to stay in memory?
A. To change your preferences to leave Rosetta@Home in memory, Rosetta@Home Web site -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

Q. Why am I getting an error every time BOINC switches tasks?
A. There is a known bug in the Rosetta@Home application. Till the bug can be found and fixed the work around is to leave Rosetta@Home in memory.

Q. Why am I getting an error every time BOINC runs a benchmark?
A. You need to keep the Rosetta@Home application in memory, unfortunately BOINC has to clear the deck to get a benchmark. There is nothing that can be done about this until the bug has been tracked down and removed.

Q. Why am I getting a Reason: Access Violation (0xc0000005) error?
A. There is one known reason, and that is Rosetta@Home is being swapped out of memory, and the other is: an error occurred somewhere on the computer, it could have been BOINC or Rosetta@Home 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 applications. Keep Rosetta@Home in memory and ignore this problem if it's not getting out of hand.

Q. Why is my computer stuck on 1%?
A1 This could be because Rosetta@Home is being swapped out of memory. Rosetta@Home needs to be left in the memory to change your preferences to leave Rosetta@Home in memory, Rosetta@Home Web site -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory wheel preempted? Check yes and click the update preferences button.

A2. This is another known problem, there are a couple of things you can do about it, they should be done in the order here if the preceding one didn't help:
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 first, if you had another) and see if it's still stuck, give it about 20min.
2. Shutdown BOINC, restart BOINC 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 click the Abort button (on the left hand side).

Q. Can I move work from one computer to another?
A. No.

Q .Master file fetch failed.
A. This means the Rosetta@Home 's server is down. Give it a while then have another go.

Q Exited with zero status but no 'finished' file.
A. It's harmless, just ignore it.

Q. Which ports does Rosetta@Home need open?
A. Port 80 is used for most communications with the project servers. Port 443 is used if the password is being exchanged (happens during the attach wizard).
Ports 1043 and31416 are used for local control as well as for remote control of a BOINC client. 1043 is preferred and 31416 is a fall back.

Q. Should I use Hyper Threading?
A. 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 Rosetta@Home Web site -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) On multiprocessors, use at most y CPUs.

Q. Why can't I get new Work Units from Rosetta@Home ?
A. If your computer is doing more than one science application (Seti@Home and Rosetta@Home for example) BOINC decides how much work you can have, so that that any Work Unit deadlines are not reached. Either allow BOINC to do this or if you are more interested in one of the science applications suspend the other application(s) 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 (to allow BOINC to crunch the Work Units it has on hand but not to get new ones) button, on the left hand side.

---

Q. Why am I getting an error every time BOINC runs a benchmark?
A. You need to keep the Rosetta@Home application in memory, unfortunately BOINC has to clear the deck to get a benchmark. There is nothing that can be done about this until the bug has been tracked down and removed.

V5.2.13 no longer removes applications from memory when doing a benchmark, if the preference is set to leave them in memory...

---

V5.2.13 no longer removes applications from memory when doing a benchmark, if the preference is set to leave them in memory...

Thanks Bill

I'll get around to updating it some more (my) tomorrow :)

---

Q. What is the difference between Rosetta@Home and Folding@Home / Predictor@home ?

A. Rosetta@home and Predictor@home both have similar aims, however they are using very different methods to get there. So although it seems that they duplicate each other, there is little actual overlap. Folding@home is trying to model the actual process of fiolding a protein, rather than simply predicting the final shape

Q. What are the minimum system requirements?
A. The only recommendation is that you have at least 512MB of RAM.

It should be pointed out that Boinc will run one or two projects (except CPDN) quite comfortably in 256 MB of Ram. Another requirement seems to be that you need a fairly large amount of disk space. Boinc appears to err very much on the side of caution when deciding if it can download, so even if your entire BOINC folder is under 50MB Boinc will only often D/L work if there are several GB of free disk space.

Q. How Big is the initial download?

Depends on your OS and choices. Anywhere from under a meg for linux, up to 3 to 4 for mac or a full Linux D/L to about 10mb for Windows, 15 Mb for Solaris

Q. Can I move work from one computer to another?

A. Yes. If you copy the ENTIRE Boinc folder to a thumb drive, take that to a different system, plug it in and run, it will continue to crunch. The only downside to doing this is that your "view computers" display may get a little confused if you upload a WU from the new system. This can be prevented by running boincmgr from the thumbdrive initially after the copy, and setting network access to never available.

---

I've made this thread sticky... I realize it's a "work in progress", so I'll unsticky it when the work is complete, and we can make a new sticky with just the final result.

---

You may see some of your own comments / fixes (I may of re-worded) in this FAQ I'm stealing most of it from the site, hope no-one minds.
{--- these are comments and reminders or I need some help ---}

{--- maybe change to all Q's first, then jump to the answers. Must check to see if the board has this capability ---}

Q. What is BOINC?
A. BOINC is a programme that allows scientific applications to use your computer(s)'s idle time. More information here.

Q. What is Rosetta@Home
A. Rosetta@Home is a scientific application that is attempting to improve upon the Rosetta algorithm that computationally finds the structures of proteins. More information here.

Q. Is Rosetta@Home is non-profit? / Is someone going to make money out of my donated computer time?
A. The Univerity of Washinton makes available the source code (the actual Rosetta algothim, 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 puplic, when the possible cheating problem on BOINC is addressed. Dr David Baker "Everything will be public domain ... No, I do not believe in patenting naturally ocurring genes, proteins, etc."

Q. What is the difference between Rosetta@Home and Folding@Home / Predictor@home ?
A. Dr David Baker said "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."

Q. What are the minimum system requirements?
A. The only recommendation is that you have at least 512MB of RAM, and a few GB free disk space isn't a bad idea though, around 10 MB for Rosetta@Home and a lot so that BOINC will download Work Units without panicing. A minimum machine should have 256MB RAM and around 500MB free diskspace, depending on the Operating Sysytem how many CPU's etc... .

Q. How Big is the initial download?
A. Depening on your Operatine System and choices. Anywhere from under a meg for linux, up to 3 to 4 for mac or a full Linux D/L to about 10mb for Windows, 15 Mb for Solaris {--- is that BOINC or Rosetta? ---}

Q. How big are the files?
A. {--- forgot to look again :< ---)

Q. How big are the results?
A. {--- forgot to look again :< ---)

/************************ Not sure if I should have these here ? *************************/
Q. How do I join Rosetta@Home with Windows or Mac(?) ? {--- need help, does Mac work this way ---}

A1. If you do not have BOINC already installed on your computer then:
1. Create an account here.
2. Download and install BOINC here.
3. Run BOINC if it isn't already going.
4. BOINC will first ask you to join a project.
5. Copy and paste in the URL https://boinc.bakerlab.org/rosetta
6. Enter your E-mail address and password.
7. Change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account-> Log in -> View or edit general preferences -> Edit preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

A2. If you already have a BOINC installed: {--- need help , does Mac work this way? ---}
1. Create an account.here.
2. BOINC Manager-> Projects (not the tab, but up the top in between commands and options) -> Attach to Project
3. BOINC will now ask you to join a project.
4. Copy and paste in the URL https://boinc.bakerlab.org/rosetta
5. Enter your E-mail address and password.
6. Change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

Q. How do I join Rosetta@Home with Linux?
A1. If you do not have BOINC already on your computer then:
1. Create an account. here.
2. Download the linux version BOINC here.
3. Follow the appropriate instuctions here {--- link to BOINC linux how to ---}
4. --attach_project {--- need to do some reading on the new version of BOINC ---}

A2. If you already have BOINC and are using the BOINC Manager: {--- need some help, is this right with the linux Manager ---}
1. Create an account. here.
2. BOINC Manager-> Projects (not the tab, but up the top in between commands and options) -> Attach to Project
3. BOINC will now ask you to join a project.
4. Copy and paste in the URL https://boinc.bakerlab.org/rosetta
5. Enter your E-mail and password.
6. Change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

A3. If you already have BOINC and are using the BOINC client via RPC: {--- need some help, is this right in the linux Manager ---}
1. Create an account. here.
2. BOINC Manager-> File -> Select computer -> enter the appopriate data to select the RPC controlled computer ->Projects (not the tab, but up the top in between commands and options) -> Attach to Project
3. BOINC will now ask you to join a project.
4. Copy and paste in the URL https://boinc.bakerlab.org/rosetta
5. Enter your E-mail and password.
6. Change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

/********************* not sure I should have these hear ***********************/

Q. What is the URL of Rosetta@Home?
A. https://boinc.bakerlab.org/rosetta

Q. How do I set Rosetta@Home to stay in memory?
A. To change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

Q. Why am I getting an error every time BOINC switches tasks?
A. There is a known bug in the Rosetta@Home application. Till the bug can be found and fixed the work around is to leave Rosetta@Home in memory. To change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button.

Q. Why am I getting an error every time BOINC runs a benchmark?
A1. You need to keep the Rosetta@Home application in memory To change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button

A2. Update your BOINC version to 5.2.13 or higher as it no longer removes applications from memory when doing a benchmark.

Q. Why am I getting a Reason: Access Violation (0xc0000005) error?
A1. There is one known reason, and that is Rosetta@Home is being swapped out of memory. To change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button. {--- should 'known' be in bold? ---}

A2. An error occurred somewhere on the computer, it could have been BOINC or Rosetta@Home 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 applications. Keep Rosetta@Home in memory and ignore this problem if it's not getting out of hand.

A3. If this is happening a great deal, try to find out under what conditions it happens, is it Rosetta@Home ? Is it when Rosetta@Home is running with another science application (Seti@Home for example)? Is it when you run a specific application (A computer game for example)? Post the logs boincdae.txt and boincslots or /BOINC/slots/0 (though it may be another slot) stderr.txt to the Qestions and Answers section of the web site. Someone may be able to help. {--- should this be in FAQ --- }

Q. Why is my computer stuck on 1% ?
A1 This could be because Rosetta@Home is being swapped out of memory. Rosetta@Home needs to be left in the memory. To change your preferences to leave Rosetta@Home in memory, Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> Leave applications in memory wheel preempted? Check yes and click the update preferences button.

A2. 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 one available) and see if it's still stuck, give it about 20min.
2. Shutdown BOINC, restart BOINC 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 click the Abort button (on the left hand side).

Q. Can I move work from one computer to another?
A. Yes. If you copy the ENTIRE Boinc 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 WU from the new system. This can be prevented by running boincmgr from the thumbdrive initially after the copy, and setting network access to never available.

Q. Master file fetch failed?
A1. This means the Rosetta@Home 's server is down. Give it a few hours and then try again.
A2. Your internet connectivity may not be working properly, try to brows the Rosetta@Home web site, have a look at the Server statis{--- staris or statistics need to check ---}, 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).

Q Exited with zero status but no 'finished' file.
A. It's harmless, just ignore it. {--- check does the WU still get credit ---}

Q. Which ports does Rosetta@Home need open?
A. Port 80 (http) is used for most communications with the project servers. Port 443 (https) is used if the password is being exchanged (during the attach wizard) {--- log in? ---}.Ports 1043 and 31416 are used for local control as well as for remote control of a BOINC client. 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 BOINC.

Q. Should I use Hyper Threading?
A. 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 Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) -> On multiprocessors, use at most y CPUs.

Q. How can I limit the number of CPU's BOINC uses?
A. Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit general preferences -> Edit Preferences (down the bottom) On multiprocessors, use at most n CPUs.

Q. Why can't I get new Work Units from Rosetta@Home ?
A. If your computer is doing more than one science application (Seti@Home and Rosetta@Home for example) BOINC decides how much work you can have so that that the Work Unit deadlines are not reached. Either allow BOINC to do this or if you are more interested in one of the science applications you can change the resource share Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit Rosetta@Home preferences->Edit Rosetta@Home preferences and chang e the resource share. Alternatively you can suspend the other application(s), 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 BOINC to finish the Work Units it has on hand but not to get new ones), on the left hand side.

Q. How do I change the resource share?
A. Rosetta@Home Home Page -> Returning Participants -> Your account -> Log in -> View or edit Rosetta@Home preferences->Edit Rosetta@Home preferences and chang e the resource share.

Q. I don't receive an E-mail? / My ISP is blocking my E-mail from Rosetta@Home?
A. This is usually caused by your ISP 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 ISP 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.

Q. The programme is using up my disk space in a big way? / The programme is using up more disk space than its allowed?
A. This is because it's writing error messages to the boincslots or BOINC/slots/0 (it could be anther number) stderr.txt or stderrdae.txt file{--- check which file it is ---}. Suspend BOINC if you can catch it before it is too big to open, post the relevant contents so we can have a look and maybe help fix the problem. {--- check did detach and reattach fix this ? ---}.If this contiues stop using Rosetta@Home, as nobody can have there Hard Disk Drive filled with error messages, these error messages mean that no work is being done anyway. Delete the file.

Q. Why is it reported that I have more computers than I actually do? / How do I merge my computers?
A. When you detach and then re-attach to the same project, BOINC assumes that it's a different computer, You can merge these computers so they are one again, Rosetta@Home Home Page -> Returning Participants -> Your Account -> View computers click on the computer you would like merge click Merge this computer (down the bottom of the page).

Q. Why do I have ghost Work Units? / Why do I have Work Units assigned to me that I don't have?
A {--- need to read ---}

Q. Is Rosetta@Home concentrating on a particular disease?
A. 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 mosquitos 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 "

---

The Mac "Standard GUI" is almost completely identical to the Windows Single User install - the CLI or Menubar installs are enough different (but rare enough) that it's not something to worry about for the FAQ.

---

Q. How do I join Rosetta@Home with Windows or Mac(?) ? {--- need help, does Mac work this way ---}

A1. If you do not have BOINC already installed on your computer then:
1. Create an account here.

Step 1 is deprecated, only needed if runs command-line, Mac Menubar, and pre-v5-clients.

Creating accounts is done in step 6.

BTW, the web-page should also be updated to reflect this, see SETI@Home and Einstein@home for possible implementations.

2. Download and install BOINC here.
3. Run BOINC if it isn't already going.
4. BOINC will first ask you to join a project.
5. Copy and paste in the URL https://boinc.bakerlab.org/rosetta
6. Enter your E-mail address and password.

6. Enter your E-mail address, and enter a password of your choise twice to create account.

6a. Your web-browser should now open to finalize creating of new account, select a name, county and so on of your choise to finish creating new account.

7. Select Global Preferences and select Edit preferences (down at the bottom).
Due to a bug in Rosetta@home, set "Leave applications in memory while preempted?" to YES.

While for the other preferences the defaults works in most instances, would also recommend to look-over the other preferences, especially:
Do work while computer is in use?
On multiprocessors, use at most N processors. (Remember, each dual/HT counts as 2 cpu's, and it's no problem to set this to higher than actual #cpus)
Connect to network about every N days. (This is how much work you want to cache, recommended is to use a low setting except if really needed due to dialup or similar non-permanent connection)

When everything is according to your wishes, select "Update preferences" (at bottom of page.

If desired, also generate new preferences for home/work/school.

7a. Last but not least, to get BOINC-client to use the new preferences, go back to the BOINC Manager and select "Projects"-tab, select "Rosetta@home", and click "Update".

8. If also wants to join (or create) a team, goto Teams


Do the similar changes for "A2. If you already have a BOINC installed:"

Thanks Ingleside, it was getting lonly here with only dgnuff and Bill Michael as friends.

I just want to make sure I understand.

Are you saying that Mac doesn't require step 1 that it creates the account step 6, I just want to be sure?

I'll add the rest of your suggestions tomorrow.

Though I think it may be best to put in the FAQ a link to how to join instead of all of that space being used.

Something like
Q. How do I join? / I'm having problems joining.
A. That information is here {--- linked to another thread ---}

---

Bill is it possible to turn on these tags (it's a thing I wrote for another BBCode forum though I think they are HTML tags) so we could have all the Questions up the top and jump to the answers? I would hate to think you would have to do this by hidden threads (lot's of work and no fun).

Could Dr DB give a

Q. Is Rosetta@Home is non-profit? / Is someone going to make money out of my donated computer time?

And maybe a better

Q. What is the difference between Rosetta@Home and Folding@Home / Predictor@home ?

than I could find, I know he did at the start of the project, but is has been all been cropped.

---

Bill is it possible to turn on these tags

You assume I have way more power than I have... I can "sticky" a thread. Delete a thread or a posting. Move a posting to another thread. That's it! _Anything_ else, gonna have to be "staff"...

---

You assume I have way more power than I have... I can "sticky" a thread. Delete a thread or a posting. Move a posting to another thread. That's it! _Anything_ else, gonna have to be "staff"...

Fair enough, hopefully an admin will take a look...

What I should of also posted at the time was a link to the working code it's http://here Warning this site contains profanity and adult themes, please don't go there if your not an adult or easily offended

Edit: Just found out it doesn't work if your not logged in, oh well the best laid plans and all that, I also removed the link and fixed a bit of spelling

---

Are you saying that Mac doesn't require step 1 that it creates the account step 6, I just want to be sure?

Don't having a Mac can't be sure, but it should be the same across all v5-versions if users runs the BOINC Manager...

Are you saying that Mac doesn't require step 1 that it creates the account step 6, I just want to be sure?

Still getting way too in-depth on the Mac stuff... forget Menubar and CLI. The standard Mac GUI client is 99% identical to the Windows one. The very-rare person who uses Menubar or CLI hopefully knows enough to translate the requirements for themselves - if not, it's better to have them get the Standard GUI.

What he was saying is that Step 1 is no longer needed _except_ for the odd cases.

---

When dealing with the initial download I would not explain BOINC as in my opinion, just point them to the Boinc download page and they can see quite clearly what the size is of the current program.

By initial downlaod I would assum they actualy mean the Rosetta program and other bits that come down.

For windows the initial download is about 13MB
the larger files being (until Rosetta get around to some decent compressing!)
rosetta_x.xx_windows_intelx86.exe ~4.5MB
bbdep02.May.sortlib.gz ~6.5MB
DunbrackBBDepRots12.dat.gz ~1.5MB

Jobs seem to up to 2MB dominated by the
aa1hz6A09_05.200_v1_3.gz type files

(again until decent compression is used)





Q. What do the graphics mean ?
A. See here Quick guide to Rosetta and its graphics




Also for some of the other FAQ's mentioned, a quick brief and a link to the already written page should be sufficiant. This is Rosetta FAQ, not Boinc or other projects.



Q. What's the association with the HPF using Rosetta @ World Community Grid
A. (it's somewhere in the forum... HPF are using a cut down version of rosetta to do ......)

---

Team mauisun.org

Still getting way too in-depth on the Mac stuff... forget Menubar and CLI. The standard Mac GUI client is 99% identical to the Windows one. The very-rare person who uses Menubar or CLI hopefully knows enough to translate the requirements for themselves - if not, it's better to have them get the Standard GUI.

Yep we're losing focus here, I'm splitting the how to join off on different platfroms off the FAQ, that's what we'll work on next, and have a link in the FAQ to a new thread.


{--- we also need some input as to the frequency of question, or what are most important questions so we can get them in order ---}

{--- I noticed that I forgot to say update BOINC to get your new pref's ta Ingleside will do that on the document should have that by tomorrow, I didn't get as much done as I would of liked, I'll see if I can squeze in an hour on two tonight ---}





Q. What is BOINC?
A. BOINC is a programme that allows scientific applications to use your computer(s)'s idle time. More information here.

Q. What is Rosetta@Home
A. Rosetta@Home is a scientific application that is attempting to improve upon the Rosetta algorithm that computationally finds the structures of proteins. More information here.

Q. Is Rosetta@Home non-profit? / Is someone going to make money out of my donated computer time?
A. The Univerity of Washinton makes available the source code (the actual Rosetta algothim, 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 puplic, when the possible cheating problem on BOINC is addressed. Dr David Baker "Everything will be public domain ... No, I do not believe in patenting naturally ocurring genes, proteins, etc."

Q. What is the difference between Rosetta@Home and Folding@Home / Predictor@home ?
A. 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."

Q. What are the minimum system requirements?
A. The only recommendation is that you have at least 512MB of RAM, and a few GB free disk space isn't a bad idea though, around 10 MB for Rosetta@Home and a lot so that BOINC will download Work Units without panicing. A minimum machine should have 256MB RAM and around 500MB free diskspace, depending on the Operating Sysytem how many CPU's etc... .

Q. How big are the file sizes?
A. At the moment the intial download is around 13MB, the results are around 30K {--- need to know about WU size rough is good enough as they will be different and this stuff does matter to dial-up users ---}

Q. What do the graphics mean ?
A. See here Quick guide to Rosetta and its graphics

Q. What is the URL of Rosetta@Home?
A. https://boinc.bakerlab.org/rosetta

Q. What's the association with the HPF using Rosetta @ World Community Grid
A. (it's somewhere in the forum... HPF are using a cut down version of rosetta to do ......)

Q. How do I set Rosetta@Home to stay in memory?
A. To change your preferences to leave Rosetta@Home in memory, General Preferences Log in (if your 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 BOINC. BOINC Manager and select "Projects"(tab) , select "Rosetta@home", and click "Update"

Q. Why am I getting an error every time BOINC switches tasks?
A. There is a known bug in the Rosetta@Home application. Till the bug can be found and fixed the work around is to leave Rosetta@Home in memory. To change your preferences to leave Rosetta@Home in memory, General Preferences Log in (if your 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 BOINC. BOINC Manager and select "Projects"(tab) , select "Rosetta@home", and click "Update"

Q. Why am I getting an error every time BOINC runs a benchmark?
A1. To change your preferences to leave Rosetta@Home in memory, General Preferences Log in (if your 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 BOINC. BOINC Manager and select "Projects"(tab) , select "Rosetta@home", and click "Update"

A2. Update your BOINC version to 5.2.13 or higher as it no longer removes applications from memory when doing a benchmark.

Q. Why am I getting a 'Reason: Access Violation (0xc0000005) error'?
A1. There is one known reason, and that is Rosetta@Home is being swapped out of memory. To change your preferences to leave Rosetta@Home in memory, General Preferences Log in (if your 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 BOINC. BOINC Manager and select "Projects"(tab) , select "Rosetta@home", and click "Update"

A2. An error occurred somewhere on the computer, it could have been BOINC or Rosetta@Home 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 applications. Keep Rosetta@Home in memory and ignore this problem if it's not getting out of hand.

A3. If this is happening a great deal, try to find out under what conditions it happens, is it Rosetta@Home ? Is it when Rosetta@Home is running with another science application (Seti@Home for example)? Is it when you run a specific application (a computer game for example)? Post the logs boincdae.txt and boincslots or /BOINC/slots/0 (though it may be another slot) stderr.txt to the Questions and Answers section of the web site. Someone may be able to help. {--- should this be in FAQ --- }

Q. Why is my computer stuck on 1% ?
A1 This could be because Rosetta@Home is being swapped out of memory. Rosetta@Home needs to be left in the memory. To change your preferences to leave Rosetta@Home in memory, General Preferences Log in (if your 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 BOINC. BOINC Manager and select "Projects"(tab) , select "Rosetta@home", and click "Update"

A2. 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 BOINC, restart BOINC 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 click the Abort button (on the left hand side).

Q. Can I move work from one computer to another?
A. Yes. If you copy the ENTIRE Boinc 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 WU from the new system. This can be prevented by running BOINC Manager from the thumbdrive initially after the copy, and setting network access to never available.

Q. Master file fetch failed?
A1. This means the Rosetta@Home 's server is down. Give it a few hours and then try again.
A2. Your internet connectivity may not be working properly, try to brows the Rosetta@Home web site, have a look at the Server statis{--- staris or statistics need to check ---}, 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).

Q Exited with zero status but no 'finished' file.
A. This is a BOINC problem, it's harmless, just ignore it. {--- check does the WU still get credit ---}

Q. Which ports does Rosetta@Home need open?
A. Port 80 (http) is used for most communications with the project servers. Port 443 (https) is used if the password is being exchanged (during the attach wizard) {--- log in? ---}.Ports 1043 and 31416 are used for local control as well as for remote control of a BOINC client. 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 BOINC.

Q. Should I use Hyper Threading?
A. 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 (if your not already) -> Edit Preferences (down the bottom) -> On multiprocessors, use at most N CPUs.

Q. How can I limit the number of CPU's BOINC uses?
A. [url=https://boinc.bakerlab.org/rosetta/prefs.php?subset=global]General Preferences Log in (if your not already) -> Edit Preferences (down the bottom) -> On multiprocessors, use at most N CPUs.

Q. Why can't I get new Work Units from Rosetta@Home ?
A. If your computer is doing more than one science application (Seti@Home and Rosetta@Home for example) BOINC decides how much work you can have so that that the Work Unit deadlines are not reached. Either allow BOINC to do this or if you are more interested in one of the science applications you can change the resource share Rosetta@Home preferences ->Edit Rosetta@Home preferences and change the resource share. Alternatively you can suspend the other application(s), 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 BOINC to finish the Work Units it has on hand but not to get new ones), on the left hand side.

Q. How do I change the resource share?
A. Rosetta@Home preferences ->Edit Rosetta@Home preferences and change the resource share.

Q. I don't receive an E-mail? / My ISP is blocking my E-mail from Rosetta@Home?
A. This is usually caused by your ISP 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 ISP 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.

Q. The programme is using up a massive amount of disk space? / The programme is using up more disk space than its allowed?
A. This is because it's writing error messages to the boincslots or BOINC/slots/0 (it could be anther number) stderr.txt or stderrdae.txt file{--- check which file it is ---}. Suspend BOINC if you can catch it before it is too big to open, post the relevant contents so we can have a look and maybe help fix the problem. {--- check did detach and reattach fix this ? ---}.If this contiues stop using Rosetta@Home, as nobody can have there Hard Disk Drive filled with error messages, these error messages mean that no work is being done anyway. Delete the file.

Q. Why is it reported that I have more computers than I actually do? / How do I merge my computers?
A. When you detach and then re-attach to the same project, BOINC assumes that it's a different computer, You can merge these computers so they are one again, Your computers click on the computer you would like merge click Merge this computer (down the bottom of the page).

Q. Why do I have ghost Work Units? / Why do I have Work Units assigned to me that I don't have?
A This seems to be caused by BOINC and the Rosetta@Home server losing the ability to communicate properly, and it can safely be ignored.

Q. Is Rosetta@Home concentrating on a particular disease?
A. 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 mosquitos 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 "

---

I would reorganize all the "set it to leave in memory" questions and make them just say "set it to leave it in memory", then at the bottom of the string of those, have the "how do I set it to stay in memory" question. As it is, you're saying the same thing over and over.

You might look at 10 Frequently Asked Questions / Common Problems just to get an idea of another FAQ-in-progress.

Otherwise, I think you've got a lot of great info, but it needs to be shorter; eliminate or move the _less_ frequent ones elsewhere.

---

I would reorganize all the "set it to leave in memory" questions and make them just say "set it to leave it in memory", then at the bottom of the string of those, have the "how do I set it to stay in memory" question. As it is, you're saying the same thing over and over.

You might look at 10 Frequently Asked Questions / Common Problems just to get an idea of another FAQ-in-progress.

Otherwise, I think you've got a lot of great info, but it needs to be shorter; eliminate or move the _less_ frequent ones elsewhere.

My thoughts exactly, I was looking into how to organise the Q. in that format, it's too big and too repeditive.

Yep we're losing focus here, I'm splitting the how to join off on different platfroms off the FAQ, that's what we'll work on next, and have a link in the FAQ to a new thread.

I just thought I may be being silly here, if someone else wants to work on this problem independantly that would be great, as the code tags don't work on the board I can't give you access to all the URL stuff unless I upload it so here is the txt version I didn't zip (the site dosn't like Mozilla, and I don't know how to FTP and am a bit busy / lazy to find out) .


Edit: for some fomatting

---