Posts by Mod.Sense

1) Message boards : Cafe Rosetta : Moderators Contact Point (Explanations, Assistance etc) Post here! (Message 91359)
Posted 4 days ago by Mod.Sense
Post:
Please delete my account and all associated information from your systems as far as practicable and email me with confirmation.

An option for the users to do this themselves would be appreciated.


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=3291&postid=31231
2) Message boards : Cafe Rosetta : Uploads stuck in 100.00% Upload: active or Upload: pending (Message 91357)
Posted 5 days ago by Mod.Sense
Post:
I would expect that once you come in and reestablish your internet connection, that you should be able to do a retry (or wait for BOINC Manager to do a retry on the send) and have the transfer complete properly.
3) Questions and Answers : Windows : Uploads pending (Message 91302)
Posted 23 days ago by Mod.Sense
Post:
I am not aware of others having upload problems. But the BOINC Manager will automatically perform retries. You just need to make sure your machine has an active internet connection. It is possible to configure BOINC Manager to limit the internet usage by time-of-day or set bandwidth constraints. If you have modified the network settings in the BOINC Manager, you should review them to make sure they allow enough access to the internet.
4) Message boards : Number crunching : I think 6 Million credits is my limit.... (Message 91284)
Posted 29 days ago by Mod.Sense
Post:
I think that rather than trying to wake the computer, the power settings should be changed to not go to sleep when no user is active. As for BOINC running at specific times of day, the preferences allow you to configure the times of day you wish to be running BOINC.
5) Message boards : Number crunching : I think 6 Million credits is my limit.... (Message 91268)
Posted 14 Oct 2019 by Mod.Sense
Post:
I have been looking for a way to only run during the daylight so I would only use the power generated by the panels. If anyone has a solution please post.


BOINC Manager configuration, CPU tab has hours of use entries available by each day of the week.
6) Message boards : Number crunching : I think 6 Million credits is my limit.... (Message 91235)
Posted 9 Oct 2019 by Mod.Sense
Post:
Scooter, thank you so much for all of your crunching. I know it is a bit underwhelming, but, as a research lab, the productive output of BakerLab is generally found in research papers. So, every time you see a post about a new paper or a new article published in Science, this is some of the output of your contribution to the project. The team is not (generally) directly searching for a specific cure to a specific disease, they are learning how proteins work in general, and how to predict whether one protein can disrupt another (i.e. whether a vaccine or immunization can disrupt a disease or build a resistance). They are learning how to model these protein interactions digitally, and how to distinguish a "cure" from a jumbled amino acid strand. And every two years, there are comparisons done with other research labs using other approaches to the problem (CASP), and BakerLab is always a top performer at these events. Showing they can produce meaningful, accurate models very quickly, against a wide variety of protein structures.

Kudos on the solar by-the-way. I lease some panels in a community solar garden myself. Keep in mind that you get a double on your solar credits if you crunch R@h during the cold seasons when you are heating your home anyway.
7) Message boards : Number crunching : Tasks using 4.07 - time remaning clock counting up (Message 91229)
Posted 8 Oct 2019 by Mod.Sense
Post:
...now that I look at it in BOINC tasks, I see its not due until the 11th. So no wonder it is taking so long. Other stuff is before it in due date time.


Due date has no relation on % of CPU used by the task. Any time that Windows task manager shows less than 100%, there is something in the way. Now, it is normal that something is in the way... waiting for page faults, memory fetches, available CPU cores, etc. is all normal, so 100% is not likely to happen. However, you are seeing more like 25%. If task manager shows the same 25% or so, this is an indication that either higher priority (Windows priority, not BOINC priority) tasks are active, or memory to run the task is not available.
8) Message boards : Number crunching : Tasks using 4.07 - time remaning clock counting up (Message 91214)
Posted 4 Oct 2019 by Mod.Sense
Post:

So how do I get Rosie to act like those tasks?


Rosetta does not control the actual dispatch of CPU time. The operating system does this. But we know that the Rosetta application will demand as much CPU as it can get (based on the BOINC settings, and the resource availability in your machine). My guess would be that memory used by the other applications is less, and that R@h is often encountering the situation where the memory pages it requires to run are swapped out, and it has to wait for the operating system to bring them back in to physical memory before it can actually continue running.
9) Message boards : Number crunching : Tasks using 4.07 - time remaning clock counting up (Message 91198)
Posted 2 Oct 2019 by Mod.Sense
Post:
You have now taken my original point. The question of "why is it taking 18 hours to get 6 hours of CPU time?"

The resource shares is really just deciding when to run each project and how much work to request. It is TRYING to run R@h for those 18hrs (or whatever exact number), but during that period of time only actually was able to get 6 hours of CPU time. It basically means that the BOINC Manager is showing the task in a "running" state for 18 hours, but if you were watching the Window tasks manager during that period of time, it would show the task only getting 33% of one core of one CPU.

Do you see BOINC Manager showing tasks "waiting for memory"?

You mentioned vbox, is BOINC running in a vbox? If so, how many cores and how much memory is available in the vbox?

You also mentioned "Rosie is using a combined total of about 6%", I was unclear exactly what you meant by this. When the R@h task is running, Windows task manager should show it using close to 100% of one CPU core (at least once passed the first minute or so of initial start-up time for a task, during which time it will not be using 100% of CPU yet).
10) Message boards : Number crunching : Tasks using 4.07 - time remaning clock counting up (Message 91194)
Posted 1 Oct 2019 by Mod.Sense
Post:
...otherwise everything is default.


Does that mean that you do not keep tasks in memory when suspended? When running a mix of projects, tasks often get suspended, but it doesn't have to mean that you lose the work that was in progress. I always suggest that you keep tasks in memory, and point out that it is not physically in memory, memory is virtual.

I'm not positive if any lost CPU seconds would be recorded. The BOINC Manager tries to avoid suspending tasks until after they take a checkpoint, so that helps a lot. But I think a task that is removed from memory and loses the last portion of work since any checkpoint, will also forget about the CPU time of the work it had in progress as well. So, this doesn't really explain what I quoted in the task.
11) Message boards : Number crunching : Tasks using 4.07 - time remaning clock counting up (Message 91182)
Posted 30 Sep 2019 by Mod.Sense
Post:
Tasks like this one:
https://boinc.bakerlab.org/rosetta/result.php?resultid=1096093226

Show a lot of time passing by, but not a lot of actual CPU time. BOINC runs at low priority, is your machine busy running some higher priority work?


Computer ID 3433065
Run time 18 hours 53 min 37 sec
CPU time 5 hours 59 min 25 sec
12) Message boards : Number crunching : Tasks using 4.07 - time remaning clock counting up (Message 91181)
Posted 30 Sep 2019 by Mod.Sense
Post:
Target runtime is configured by the user, default is 6 hours if you have not modified it.
13) Message boards : Cafe Rosetta : Screensaver questions (Message 91165)
Posted 27 Sep 2019 by Mod.Sense
Post:
The screensaver itself is just to make it more interesting. BOINC projects run in the background, and depending on your settings, they can run while the computer is actively doing other things. You can use any screensaver you like (preferably one that does not have a lot of animated objects, those consume resources that could be used to help Rosetta).
14) Message boards : Rosetta@home Science : What is the difference between "Searching..." and "Accepted?" (Message 91136)
Posted 20 Sep 2019 by Mod.Sense
Post:
"Accepted" is the ongoing best answer for this specific model so far... the program then explores around that ("searching...") and if it finds a "better" solution while searching it "accepts" that one.
15) Message boards : Number crunching : Strange work unit. (Message 91129)
Posted 18 Sep 2019 by Mod.Sense
Post:
I presume that there is a safety kill mechanism


Yes, we call it the watch dog. I ensures that tasks that run more than 4 hours longer then their preferred runtime are ended, and any completed models of that WU are returned.
16) Message boards : Number crunching : What is BOINC? I need help explaining to my friends/family. (Message 91107)
Posted 11 Sep 2019 by Mod.Sense
Post:
BOINC is really just a framework for doing distributed computing. The code is shared, so anyone can create a BOINC server. Sometimes people do this as an easy way to coordinate the usage of local campus computer resources. Other times, they place the server on the internet and have hosts running work all over the world.

BOINC is also the client which makes it easy for participants to connect to projects, control their runtime preferences, and monitor the work their machines are performing. If the server behaves the way the server in the shared code behaves, then you can expect any compatible BOINC client will be able to attach to a new project and process work for it. By sharing the server code, it makes it very easy to create a server that behaves in the manner expected by the BOINC client.
17) Questions and Answers : Windows : iPhone 6 not being utilized (Message 91065)
Posted 27 Aug 2019 by Mod.Sense
Post:
Rosetta@home only has work for cell phones occasionally. And, only for Android. link to project apps page
18) Message boards : Number crunching : WU crash after some hours (Message 91022)
Posted 12 Aug 2019 by Mod.Sense
Post:
As I said, the problem seems to be some work units that are consuming more memory than was expected when they were created. Or, at least there are cases where they may consume a lot of memory. As I understand it, you are saying that a machine where BOINC Manager is set to be able to use 16GB of memory cannot complete a specific WU, even when it runs alone. That would be a problem that will need to be fixed in the method the software uses to compute the work unit.

Thank you for fielding the questions of your team. I know English is not easy for many people. When the question is coming from someone else, it is helpful if you can link to the actual host or work unit that is having the problem.
19) Message boards : Number crunching : WU crash after some hours (Message 91014)
Posted 9 Aug 2019 by Mod.Sense
Post:
It sounds like the bottom line here is that there are presently some work units that are using excessive memory. These are reported in several other threads. So this would mean your low-memory system did not happen to get any of these, or perhaps they are flagged to only be sent to systems with large memory.

This sometimes happens when the Project Team is working on new protocols. And it is generally resolved within a few days.
20) Message boards : Number crunching : WU crash after some hours (Message 91006)
Posted 8 Aug 2019 by Mod.Sense
Post:
That would normally be a reasonable match between active WUs and memory. The BOINC Manager allows you to configure values for how much memory BOINC is allowed to use while the machine is idle and while in use. What are you settings there?


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