Why are RNA Task so hard to complete?

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bcavnaugh
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Why are RNA Task so hard to complete?

#1 Ungelesener Beitrag von bcavnaugh » 28.02.2016 22:09

It seems that RNA really dose not want anyone completing and tasks.
From what I see and after running more than a week now and most all users get "Error while computing" or "Timed out - no response" and last after days or even weeks they then "Aborted by user"
If the tasks below are so bad and it takes so long to even get an RNA Task are the two below projects or tasks not remove from use and to stop the waste of power for them to run and only fail in the end?


14951045 6330851 43338 22 Feb 2016, 0:07:38 UTC 27 Mar 2016, 0:07:38 UTC In progress --- --- --- cmsearch VM (VirtualBox) 1.0.2 v1.17 (vbox64)
14951020 6330884 43338 17 Feb 2016, 20:00:08 UTC 22 Mar 2016, 20:00:08 UTC In progress --- --- --- cmsearch VM (VirtualBox) 1.0.2 v1.17 (vbox64)

And all this for only 20.06 Credits!

Jacob Klein
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Re: Why are RNA Task so hard to complete?

#2 Ungelesener Beitrag von Jacob Klein » 29.02.2016 02:53

The tasks run a program cmsearch, that doesn't offer any means of checkpointing. So, the program requires the application to run continuously, sometimes for months (or even 1.5 years for the biggest tasks). Also, it doesn't offer any decent estimates on how long the tasks will take to complete, meaning that completion time is usually pretty indeterminate for a given task.

Previously, the "XXL" super-super-large tasks had their own application on the RNA World project, so only users who had machines that could run continuosly for so long, could attempt such tasks, and other users who knew that they restarted their PCs more frequently than a task could be completed, could deselect that application in their RNA World project settings.

Since then, RNA World has implemented VirtualBox's VM support, and so, every 30 minutes the tasks can create a VirtualBox VM snapshot. This provides a means of checkpointing, so that the host PC can be restarted, or BOINC can be restarted, without losing all the work! Even then, though, VirtualBox support isn't completely flawless, and so, it's normal to see tasks fail. It happens.

Also, since there's no good way to estimate how long they'll take, they use a "trickle communication" mechanism, where BOINC relays info like the CPU Time spent on the task. Basically, as long as the PC trickles in a progress update within every 2 weeks, then RNA World will auto-extend the deadline instead of failing it for "No Response.". So, internet connectivity is a must.

Basically, these are MONSTER tasks, that require a lot of dedication and patience. They're best-suited for a BOINC environment that doesn't "change" a whole lot, and the users should attempt them knowing that there's a significant probability that they may fail.

Frankly, I'm just glad to be able to finally attempt some of these monsters, with the VM means of checkpointing. Previously, I had to set my PCs to not attempt these types of tasks, since I restart my PCs every 5 days on average! But now, with VirtualBox VM support, I've actually completed a couple of these VM task, and have 7 more in progress (and I'm VERY careful with those BOINC environments).

If you attempt them, I'd suggest to use the latest released version of BOINC, combined with the latest released version of VirtualBox. And even then, try not to complain if the task fails. We feel your pain. But again, these are MONSTERS, that require care, time, patience, and understanding. Also, for reference, the admins believe that every one of the VM tasks is completeable, given a stable enough environment, which is why they do not consider it a waste of resources. I believe they are correct.

My current CPU time for my 7 tasks are:
212 days, 189 days, 180 days, 139 days, 136 days, 68 days, 38 days

Michael (an admin) just mentioned he completed one that took 160 days of CPU time on his fast processor.
See, it just requires a lot of patience and care! :)

PS: I think I saw that 1 of your tasks failed, using VirtualBox 4.3.6. That's really old, you should update that. There have been many fixes to VirtualBox since that version. I realize the main page suggests 4.3.6, but that should be updated. My testing indicates that the recommendation should be:
For tasks that use "cmsearch VM (VirtualBox) 1.0.2 1.15" or earlier: Use the most-recent 4.3.x version of VirtualBox.
For tasks that use "cmsearch VM (VirtualBox) 1.0.2 1.16" or later: Use the most-recent 5.x or later version of VirtualBox.

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Michael H.W. Weber
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Re: Why are RNA Task so hard to complete?

#3 Ungelesener Beitrag von Michael H.W. Weber » 29.02.2016 10:28

bcavnaugh hat geschrieben:From what I see and after running more than a week now and most all users get "Error while computing" or "Timed out - no response" and last after days or even weeks they then "Aborted by user".
I don't think so. Most users currently don't get jobs at all, because at present we are just running the very challenging ones and of those only the few that are remaining.
Moreover, our system runs quite rock solid as evidenced by the extremely (!) demanding tasks that are completing successfully. Just check out the last one I returned. Of course, you need to setup your machines according to our suggestions and not use outdated or misconfigured software.
bcavnaugh hat geschrieben:If the tasks below are so bad and it takes so long to even get an RNA Task are the two below projects or tasks not remove from use and to stop the waste of power for them to run and only fail in the end?
First of all these tasks are not bad but just computationally demanding.
Second, they won't fail if you use a properly configured system.
Third, we won't take them off the system unless they are completed because we need the result and consequently their completion is not a waste of power.
And finally, it is your own responsibility to select only those tasks that suit your system capabilities - just use the project settings on our project website and disable the VM tasks if these are taking too long for you to complete. We have users who selectively work only on these tasks, so they make good, good sense.
bcavnaugh hat geschrieben:And all this for only 20.06 Credits!
Certainly not. The VM tasks get special credit.

Besides, the BOINC credit system is generally flawed as there is absolutely no use in comparing credits cross-project or even within a given project that supports both CPUs and GPUs. And then just take a look at Collatz Conjecture's "sieve" application: An AMD R9 290X can easily make around 3 Mio credits a day but then what do you buy with that? Remember, we are in here for the cause / scientific progress and not the points?

Michael.
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sbjnyc
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Re: Why are RNA Task so hard to complete?

#4 Ungelesener Beitrag von sbjnyc » 02.03.2016 11:09

Jacob Klein hat geschrieben:PS: I think I saw that 1 of your tasks failed, using VirtualBox 4.3.6. That's really old, you should update that. There have been many fixes to VirtualBox since that version. I realize the main page suggests 4.3.6, but that should be updated. My testing indicates that the recommendation should be:
For tasks that use "cmsearch VM (VirtualBox) 1.0.2 1.15" or earlier: Use the most-recent 4.3.x version of VirtualBox.
For tasks that use "cmsearch VM (VirtualBox) 1.0.2 1.16" or later: Use the most-recent 5.x or later version of VirtualBox.
Hi. I've had similar problems in the past. Hopefully things will work better with a new laptop. I see that boinc gave me the old 4.3.6 version and rna gave me a 1.0.2.1.17 wu. I tried updating virtual box but am getting a download error noted here. https://www.virtualbox.org/ticket/15054

Jacob Klein
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Re: Why are RNA Task so hard to complete?

#5 Ungelesener Beitrag von Jacob Klein » 02.03.2016 17:59

Did you try the 5.0.15 Test Build, like frank recommended in that ticket? Don't forget to close BOINC (and wait a few seconds for the boinc.exe process to gracefully exit), before attempting it :-p

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bcavnaugh
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Re: Why are RNA Task so hard to complete?

#6 Ungelesener Beitrag von bcavnaugh » 09.03.2016 21:44

Thanks All.

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Re: Why are RNA Task so hard to complete?

#7 Ungelesener Beitrag von bcavnaugh » 06.04.2016 17:21

sbjnyc hat geschrieben:
Jacob Klein hat geschrieben:PS: I think I saw that 1 of your tasks failed, using VirtualBox 4.3.6. That's really old, you should update that. There have been many fixes to VirtualBox since that version. I realize the main page suggests 4.3.6, but that should be updated. My testing indicates that the recommendation should be:
For tasks that use "cmsearch VM (VirtualBox) 1.0.2 1.15" or earlier: Use the most-recent 4.3.x version of VirtualBox.
For tasks that use "cmsearch VM (VirtualBox) 1.0.2 1.16" or later: Use the most-recent 5.x or later version of VirtualBox.
Hi. I've had similar problems in the past. Hopefully things will work better with a new laptop. I see that boinc gave me the old 4.3.6 version and rna gave me a 1.0.2.1.17 wu. I tried updating virtual box but am getting a download error noted here. https://www.virtualbox.org/ticket/15054

I did forget to add this from the Home Page
Important information for users with VirtualBox installed

If you have VirtualBox installed on your computer and participate in this project please note:
•in order to get tasks your CPU needs to have virtualisation capabilities (AMD-v or VT-x)
•those virtualisation capabilities need to be enabled in your BIOS settings or all tasks will error out
•Use the most-recent version of VirtualBox. Note: If you have 1.15-or-earlier tasks, you must use VirtualBox 4.3.x.
•a BOINC client of at least 7.2.33 is recommended
If you don't want to get work for the VM application please disable "cmsearch VM" in your project preferences.

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Re: Why are RNA Task so hard to complete?

#8 Ungelesener Beitrag von johnnymc » 08.04.2016 02:09

Jacob Klein hat geschrieben:Also, since there's no good way to estimate how long they'll take, they use a "trickle communication" mechanism, where BOINC relays info like the CPU Time spent on the task. Basically, as long as the PC trickles in a progress update within every 2 weeks, then RNA World will auto-extend the deadline instead of failing it for "No Response.". So, internet connectivity is a must.
This was the precise information I was seeking.

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