Posts by Murasaki

1) Message boards : Number crunching : Unintended consequences of the new credit system? (Message 80933)
Posted 24 Dec 2016 by Murasaki
Post:

Okay, a second thing. Not sure how I feel about having my personal details broadcast that publicly. So many machines might make me sound like a rich target, when the reality is quite different. Some are just multiple boots and most of them are old machines that I'm skilled at keeping alive for special purposes. I could make things look even worse if I let my VMs run BOINC...


This is entirely in your control.

Go to Your Account > Rosetta@home preferences
You should have an option for, "Should Rosetta@home show your computers on its web site?"
Currently I, and every other public user, can see your computers and work units, so the option must be set to "yes." Switch it to "no" if you would prefer for the data to be hidden from the public but visible to the project scientists.

Feel free to choose the option you are comfortable with but the drawback of hiding the data is that other contributors can't help you identify problems if you start getting errors. Though you could always switch it back on at that time.
2) Message boards : Number crunching : WUs with different deadlines? (Message 79254)
Posted 20 Dec 2015 by Murasaki
Post:
I'm getting some robetta jobs with a 2 day deadline, which I have never seen before. They pop into my work queue and immediately jump to high priority.

I have my tasks set to 6 hours, so it shouldn't be a problem normally. However, would someone with a 1 day runtime also get a 2 day deadline? If so, it would be cutting things a little fine if their system is juggling with some other tasks as well.
3) Message boards : Number crunching : validate errors (Message 78834)
Posted 20 Sep 2015 by Murasaki
Post:
One of your recent errors was on task 756849504 and checking the associated work unit, 685776063, shows that the second user also had an error. In this case it is safe to assume the problem is with the task and not your computer.

This in a "FFD*" task, they all end with validate errors. All his validate errors are from those work units, so no problem on his end.


My advice explains what to do when validate errors occur in the future and I also pointed out the current issue is not with their machine. I don't see what was wrong with my reply...
4) Message boards : Number crunching : validate errors (Message 78832)
Posted 20 Sep 2015 by Murasaki
Post:
If you get any type of errors on your task:

Step 1: Add a quick note on the type of error and the task id number in the Minirosetta 3.62 thread. That will help the scientists to investigate the problem and hopefully speed up finding a solution.

Step 2: Check the work unit details for the invalid task. If one user gets an error the task is sent out to another user to try again. If both users had an error then it is safe to say there is a problem with the work unit. If the other user was successful when you failed then that could suggest a problem with your machine (though I would only make that assumption after several errors that turned out successfully on other machines - one error may just be an isolated glitch).

One of your recent errors was on task 756849504 and checking the associated work unit, 685776063, shows that the second user also had an error. In this case it is safe to assume the problem is with the task and not your computer.


One important point to remember with validate errors is that it is possible for 99% of your data to be useable by the scientists. The system will report a validate error if the final decoy information doesn't come back correctly. In this task you submitted 1,261 decoys so it is possible that 1,260 of them came out fine (unfortunately there is no way for us to tell on the user side whether the data we submit is usable solely on the error message).
5) Questions and Answers : Windows : Can't Upload (Message 78807)
Posted 16 Sep 2015 by Murasaki
Post:
I have the same issue. Unable to upload the result to server in past 3 days. It was okay in for before last week. Now the uploading queue comes longer and longer.
ISP is China Telecom.
Yes, I know how to bypass the "China Firewall" and tried using proxy (both http and socks) and VPN, but it doesn't work.


Network connection has been restored. Please ignore the previous post. :)


The problem was caused by a storm knocking out some of Rosetta's servers. The repair took a few days but all is working normally again.

For these types of issues you may want to check the Number Crunching part of the forum as problems are more likely to be reported there.
6) Questions and Answers : Preferences : 14 days until deadline (Message 78792)
Posted 14 Sep 2015 by Murasaki
Post:
Climate prediction is focused on generating and analysing models of the world's climate with some models calculating up to a few centuries in the future. That type of research lends itself well to giving a big chunk of data to a particular computer and letting it run for several months. At key stages of the process the system can decide if the model is looking reasonable or if it has gone off the rails (like predicting the Earth will become hotter than the Sun). Good models advance the project significantly. Poor models are abandoned with the several months of processing providing little scientific benefit.


Rosetta takes a different approach. There are a few different types of work done here, but at a basic level the aim is to find a protein structure with the lowest amount of energy needed to maintain its shape (the less energy needed, the more likely it is that the structure will be the stable shape found in nature). There are billions of potential protein structures for each chemical chain, which would take a single computer centuries or millenia to find the correct answer.

Instead Rosetta asks many computers to do a set of quick and rough models of the protein and return the results in a short time frame. The scientists study the results and find a few rough predictions with low energy levels. A new set of tasks are issued focusing on these key areas and the many computers do a more detailed set of models and return the results. This cycle repeats until the scientists feel that they have a good prediction.
7) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78631)
Posted 31 Aug 2015 by Murasaki
Post:
One day, I believed, that I'm part of something good. 10 years of crunching and I see, I was wrong. I think it's time to leave this project and move resources somewhere, where people do care. You are wasting huge processing power.


You are quitting because a project is taking a bit of time (over a weekend) to recover from a major power failure?

That's your choice of course, but I would value the project more on the results of its research than the amount of processing power they are able to consume.
8) Message boards : Number crunching : rosetta exiting with zero status (Message 78612)
Posted 30 Aug 2015 by Murasaki
Post:
I'm not being negative. I am just saying that you can find your answer in Google if you take 5 minutes to post the error information and the word Rosetta into the search bar and look through the first few entries.

You may find it beneficial to search before posting a question next time as you would have found the answer long ago yourself in this case. If you have tried searching and are still struggling then I would be far more sympathetic. Also, if you take a lesson from this and try searching next time, then my advice is positive - it depends on your perspective.

As I am having to post again anyway, one topic that you can find through searching is this thread where the user managed to fix the problem after trying the advice suggested.

As I said, the issue is a BOINC problem that affects projects at random. For you it has occurred with Rosetta, for others it affects SETI or other projects.
9) Message boards : Number crunching : rosetta exiting with zero status (Message 78608)
Posted 29 Aug 2015 by Murasaki
Post:
This is a common error and there are many threads about this on the forum. It is a BOINC issue that randomly affects all projects and not a Rosetta specific problem.

Just do a Google search for

"exited with zero status but no 'finished' file" rosetta

and you will find all sorts of advice. I could give you the answer now but I do get tired of writing the same thing everytime.
10) Questions and Answers : Web site : Can't set resource share to zero (Message 78584)
Posted 22 Aug 2015 by Murasaki
Post:
I need to set resource share to "0" for awhile, but the Rosetta website won't let me. The lowest that it will let you go is "1". All the rest of my Boinc projects allow you to set them to "0".

Is there a way to make it accept "zero"?


The Rosetta website uses an old version of the BOINC server software due to several customisations made by the project team. As such some of the functionality you find on other BOINC projects isn't available here.

A couple of ways you can get around the problem are:

1) Set the resource share for Rosetta to one and set your BOINC client to "No new tasks" for Rosetta. You will still be building up a small debt to Rosetta over time as your resource share isn't 0 but that won't have an impact until you start accepting tasks again. If the Rosetta share is 1 and your other projects resource shares are set much higher then the debt incurred by Rosetta will be negligible.

2) Detach your BOINC client from Rosetta for a while. No new work will be done for Rosetta by your computer and you won't build up any debt. When you are ready to do more work for Rosetta just reattch to the project.
11) Message boards : Number crunching : show related project ralph@home link on rosetta@home page (Message 78512)
Posted 28 Jul 2015 by Murasaki
Post:
Please, insert a little link to Ralph (with a warning that is a beta project).


This is a little pedantic but...

Rosetta@home is a beta project (a project with constantly changing code that is likely to crash on your system from time to time).

Rosetta Alpha, abbreviated to Ralph, is an alpha project (a project with very early code developments that will frequently crash on your system).

The final release version of the Rosetta software is what is then licensed to the various academic and corporate organisations that participate in the Rosetta research.
12) Questions and Answers : Wish list : Rosetta@Home for Android 5 Lollipop (Message 78485)
Posted 20 Jul 2015 by Murasaki
Post:
You may want to look at the Rosetta and Android thread in the Number Crunching forum.
13) Message boards : Number crunching : Minirosetta 3.59 (Message 78421)
Posted 7 Jul 2015 by Murasaki
Post:
Please report which BOINC version is installed and which host you are making yout observations on.
BOINC 7.4.42 on Windows 8.1/64(4core i3/8GB of RAM).

Task ID 742059437 and Task ID 742059580.

After restarting BOINC 3 or 4 times and shutdown and restart my laptop half a couple times since yesterday, right now both WUs are currently continuing working again, but I have the feeling that they will stop and do the same thing all over again in a while...

Ralf





The first task looks to be completed, the second failed with:

[2015- 7- 3 19:15: 0:] :: BOINC:: Initializing ... ok.
Can't acquire lockfile - exiting
FILE_LOCK::unlock(): close failed.: No error
[2015- 7- 3 19:15:42:] :: BOINC:: Initializing ... ok.
Can't acquire lockfile - exiting


not sure what is causing this. maybe someone else could chime in.




Here is some advice I found on an archive copy of the BOINC wiki:

This Message means that the BOINC Client Software has tried to acquire the "Lock File" but was unable to obtain an exclusive access to this file. This can occur for the following reasons:


  • A previous copy of the BOINC Client Software is still running, or
  • The BOINC Client Software did not exit cleanly and the "Lock File" is still present and is marked as "read only".


The cure for this is to make sure that no copy of the BOINC Manager and BOINC Daemon is running, and then to delete the "Lock File".

You may have to change the permissions on the file to remove it. Restarting your computer after removing the "Lock File" will allow the BOINC Client Software to create a new copy of the "Lock File".

14) Questions and Answers : Macintosh : CUDA (Message 78307)
Posted 15 Jun 2015 by Murasaki
Post:
Rosetta@home doesn't use GPU computations so it isn't an issue for this project. You could revert to the old driver or keep the existing one and there would be no impact.

However, if you are wanting to use your GPU to do computations for a different BOINC project you may want to ask your question again on either their project forum or the central BOINC forum.
15) Message boards : Number crunching : Leadership transfer - I AM GETTING NO REPLY FROM ANYBODY FOR YEARS (Message 78288)
Posted 8 Jun 2015 by Murasaki
Post:
I think I have asked years ago as well, obviously I got nowhere.


But as you are now up to only 2 forum posts you have not asked on the forum before. Unless you have switched accounts?

A few of the project team members keep an eye on the forum and, if they don't see this thread directly, the forum moderator should be able to flag your message for someone to take a look at. I have no idea whether you will get the answer you want but you should at least get a reply within a few days.
16) Message boards : Rosetta@home Science : The real proteins in the WU's (Message 78281)
Posted 6 Jun 2015 by Murasaki
Post:
Some of the task names include references to the protein being studied. For example, your machine currently has task 738033377 with the description "5HTUBE_AB_5HTUBE_AB_043.pdb_15_06_00_14_41_globalDocking_2_SAVE_ALL_OUT_268540_42_0".

Searching Google for 043.pdb brings up this entry from the protein data bank.

I'm not an expert though so there may be other ways to identify a known protein your machine is workin on.
17) Questions and Answers : Windows : Endless tasks with rosetta mini 3.54 (Message 78257)
Posted 3 Jun 2015 by Murasaki
Post:
Not many people read the Q&A section so you will see more replies on your original thread in the Number Crunching section.
18) Questions and Answers : Preferences : How to change selected hard drive for Boinc / Rosetta usage? (Message 78256)
Posted 3 Jun 2015 by Murasaki
Post:
There is some advice on the main BOINC forum (https://boinc.berkeley.edu/dev/forum_thread.php?id=6182).
19) Questions and Answers : Preferences : Rosetta ignores BOINC manager settings (Message 78219)
Posted 19 May 2015 by Murasaki
Post:
Well as the system requirements linked from the Rosetta home page ask for 1 GB of memory, trying to run with 0.4 GB is likely to cause you problems sooner or later.

Rosetta is a memory hungry application (due to the nature of the science) and most tasks will need at least 0.5 GB to complete.

If you were hitting 1.5 GB then you either hit a rare task with a very high memory load or you were running multiple Rosetta tasks at the same time. As your computer and task information is hidden from the public I can't see which of those two occurred.
20) Message boards : Rosetta@home Science : Graphene (Message 78216)
Posted 18 May 2015 by Murasaki
Post:
I've got a task 735267454 I'm intrigued: fascinating material though graphene is, I don't quite see its relevance to protein folding. Could someone please explain?


Doing a google search for "protein folding graphene" brings up several research papers on the effect of graphene on proteins.

Ideas for graphene research include designing nano-scale medical devices (for which you would want to test the material's impact on human proteins) and combining graphene with various proteins to make new super materials.


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