Posts by Jim1348
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21)
Message boards :
Number crunching :
Multiattach mode disk images
(Message 106797)
Posted 17 Aug 2022 by Jim1348 Post: <edit> That is my conclusion too. I am trying to get the new CMS on the .dev site. (I know, a bit off topic, but nobody knows what the real topic is here anymore). |
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22)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 106790)
Posted 16 Aug 2022 by Jim1348 Post: I installed the latest Boinc release (7.20.2-1.fc36) for this Fedora and started getting errors. It is because of the security changes in BOINC 7.18.1 and later. Some projects have adapted to it, but not the pythons. https://quchempedia.univ-angers.fr/athome/forum_thread.php?id=166 |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106778)
Posted 12 Aug 2022 by Jim1348 Post: VERR_ALREADY_EXISTS tells you there's a disk registered with this name/UUID But to answer the question, here is what it shows: UUID: ef35dff9-d482-48f8-9519-fef6c1b23a3b I will deal with it later. EDIT: I closed them both, in preparation for a new try later, though this machine is really better on Folding anyway, and I will probably use the 3900X. Thanks loads. |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106777)
Posted 12 Aug 2022 by Jim1348 Post: Very good. I will try it later. I have solved it a different way now. I have put the machine on Folding. But Rosetta will be worth a try again on another machine when I can start up a Ryzen 3900X in a couple of months. You effort is quite remarkable. |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106775)
Posted 12 Aug 2022 by Jim1348 Post: But I did reboot, then a reset, then stopped BOINC and deleted the "AIMNet_vm_v2.vdi" file so that I could try again. I then ran the "sudo vboxmanage clonemedium AIMNet_vm_v2.vdi.bak AIMNet_vm_v2.vdi" command, and got: $ sudo vboxmanage clonemedium AIMNet_vm_v2.vdi.bak AIMNet_vm_v2.vdi So it does think that a hard disk already exists. However, it still does not show up in VirtualBox Manager. There may be something wrong with the VirtualBox installation. That is beyond me for now. |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106774)
Posted 12 Aug 2022 by Jim1348 Post: On Linux you may run "[sudo] systemctl stop boinc-client".Thanks. That is what I needed for that part. On Windows, they have "Exit BOINC" in the GUI, which is probably what you wanted there. Open your VirtualBox GUI -> Media Manager and remove the disk entry there (it shouldn't be connected to a VM).There is no disk (or file) at all in VBox Media Manager. And I am getting the same error messages as before. $ sudo vboxmanage clonemedium AIMNet_vm_v2.vdi.bak AIMNet_vm_v2.vdi It could be a permissions problem. I install BOINC using "sudo apt install boinc", which gets it from Ubuntu I suppose. I don't try to compile it myself, so it is not in the "Home" directory, which may be a difference. I will give it a rest for a while, and try again later. Thanks for you input. |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106771)
Posted 12 Aug 2022 by Jim1348 Post: Pause BOINC's network activity, pause Rosetta or do both before you reset the project and shutdown BOINC. We are getting closer, but the question is how do you shutdown BOINC? There is no command for it in the GUI. The only commands are for pausing BOINC and shutting down the network (no new tasks). (Would a reboot do it?) I get the following error message at Step 5, $ sudo vboxmanage clonemedium AIMNet_vm_v2.vdi.bak AIMNet_vm_v2.vdi So the original .vdi file apparently still exists. But one thing I did learn is that you can't use VirtualBox installed from a downloaded .deb package. You have to use VirtualBox installed via "sudo apt install virtualbox". Otherwise, the "vboxmanage" command will not run at all. |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106767)
Posted 12 Aug 2022 by Jim1348 Post: Files listed in app_info.xml must be present in Rosetta's project dir before the BOINC client starts (including app_info.xml itself). That could be it. But how do you prevent BOINC from starting? There is no option for that in the GUI. You may be referring to a command line option. |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106764)
Posted 11 Aug 2022 by Jim1348 Post: Thanks, but a reset did not fix it. I still get the download errors. I am wondering whether it is because I downloaded the files on a Windows machine, and then transferred them to my Ubuntu machine. Maybe they picked up the wrong permissions or some other attributes? What I am going to do (probably not today) is to totally detach from all BOINC projects, and then download the files again directly onto the Ubuntu machine. It should work. |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106762)
Posted 11 Aug 2022 by Jim1348 Post: I am getting download errors https://boinc.bakerlab.org/rosetta/result.php?resultid=1492609800 and computing errors https://boinc.bakerlab.org/rosetta/result.php?resultid=1492609810 |
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Message boards :
Number crunching :
Not sure what this means
(Message 106740)
Posted 8 Aug 2022 by Jim1348 Post: Go into your motherboard BIOS and ensure that virtualization (VT) is enabled. On a new machine, it is probably disabled by default. |
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Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 106727)
Posted 7 Aug 2022 by Jim1348 Post: I have 7 Rosetta Python tasks, but Rosetta is taking up a whopping 61.77 GB of disk space. Yes. On my Ryzen 3900X for example, when I wanted to run 18 or more Pythons, I had to increase the SSD from 250 GB to 500 GB. So that is what I buy as standard now. |
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Message boards :
Number crunching :
High write-rate with Pythons
(Message 106716)
Posted 5 Aug 2022 by Jim1348 Post: But i prefer an officially maintained/optimized/debugged app than 3rd party sw I think what we have is the best they can do. We have to fix up their goofs from there. But I quite agree that it is their job, should they wish to do it. |
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Message boards :
Number crunching :
High write-rate with Pythons
(Message 106713)
Posted 4 Aug 2022 by Jim1348 Post: Adding caching is an interesting idea, but not sure how well it would work on the main system disk. I have a dedicated Win10 machine (Ryzen 3600) where I run 8 pythons at a time, and use PrimoCache on it. It runs great; better than Linux, since you don't get the "Vm job unmanageable" ones on Windows, as least if you use VirtualBox 5.2.44 (not 6.x). However, the problem is that Windows reserves all the memory BOINC allocates for each work unit, even though the pythons do not use it all. And it allocates all the memory that you set for the cache in addition. Therefore, I have to use 128 GB of memory to run only 8 pythons. I could use half that memory (64 GB) in Ubuntu and it would work OK with even more pythons; at least 12 at a time is what I usually run on a Ryzen 3900X or 3950X. On the other hand, I am also running PrimoCache on my main working machine, a Ryzen 5700X running Windows 10. It is also working great, but I am not running the pythons on it, only other BOINC projects. It has 32 GB of memory, and I am allocating 8 GB (4 hours) for the cache. But just because it is a system disk won't be a problem when using PrimoCache; it is only a question of whether you have enough memory. If you run only 2 pythons, that would make the whole process easier, and reduce the write-rate to something more reasonable. I just like to devote an entire machine to them. |
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Message boards :
Number crunching :
High write-rate with Pythons
(Message 106702)
Posted 3 Aug 2022 by Jim1348 Post: My computer is not quite 1 year old, the 500GB SSD has 131TB written. I don't know how much of that is R@H VBox jobs but I'm guessing a lot of it. My Python machine is shut down for an upgrade, but the last time I checked the writes from the operating system were at least 2 TB/day when running 8 to 10 pythons or so. When I included a write-cache (it was 16 GB with a 4 hour latency), the writes to the SSD itself dropped to a negligible amount of less than about 1 GB/day. So the problem is solved for me. Even a 4 GB write-cache with a one hour latency would protect the SSD I think. I managed to kill a 500 GB SSD inadvertently before I learned the correct way to do the write cache as I outlined here: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14871&postid=106343#106343 I was doing the pythons for less than a year; maybe six or eight months. I don't see the point of a second SSD. It would just be killed instead, unless that is OK for you. I can't see your computers. If you are on Windows, there is PrimoCache. https://www.romexsoftware.com/en-us/primo-cache/index.html It is probably no more than the cost of an SSD, and less bother to fix. |
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Message boards :
Number crunching :
Multiattach mode disk images
(Message 106699)
Posted 3 Aug 2022 by Jim1348 Post: Waiting for Rosetta@Home.... There are not that many left. Total queued jobs: 244,472 Given their glacial (or continental drift) rate of progress, I expect they would wait until the next series to introduce any changes. If there is a next series at all. |
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Message boards :
Rosetta@home Science :
AlphaFold reveals the structure of protein universe
(Message 106691)
Posted 1 Aug 2022 by Jim1348 Post: See my post about FoldSeek Yes, it always depends on the size of the data that they have to shuffle around, and the latency. We are ready when they are. |
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38)
Message boards :
Rosetta@home Science :
AlphaFold reveals the structure of protein universe
(Message 106685)
Posted 1 Aug 2022 by Jim1348 Post: Remarkable stuff that will change the world. However, it does not appear that we can contribute to this work directly, since it is mainly done in-house. But they do mention mining: Structural search tools like Foldseek and Dali are allowing users to very quickly search for entries similar to a given protein. This could be a first step toward mining large sequence datasets for practically useful proteins, such as those that break down plastic, and it could provide clues about protein function. The update of the database to include over 200 million predicted structures will further amplify this impact. I really have a very limited idea of how that works, but the LODA project seeks to discover new mining algorithms: https://boinc.loda-lang.org/loda/ I have done a little of it, and think I will do more. |
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39)
Message boards :
Number crunching :
No Work Recieved since June 22, 2022
(Message 106682)
Posted 31 Jul 2022 by Jim1348 Post: What should i do next https://boinc.bakerlab.org/rosetta/forum_thread.php?id=8481&postid=106611#106611 https://www.virtualbox.org/wiki/Downloads |
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40)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 106660)
Posted 26 Jul 2022 by Jim1348 Post: Rosetta blackists computers that fail tasks. Where do you see the failures? His application details show a number of valid completions. |
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