Posts by mikey

1) Message boards : Rosetta@home Science : RosettaFold3 (and AtomWorks) (Message 113031) Posted 25 Aug 2025 by mikey Post: To this end, we release the AtomWorks framework, together with curated training data, code and model weights for RF3 under a permissive BSD license RF3 Are you saying we need to install AtomWorks to crunch the tasks? If so alot of tasks will come back with errors as people won't do that unless you hold their hands!!
2) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 112655) Posted 9 May 2025 by mikey Post: I just bumped the cache up to 0.5 days. And set the CPU limit (a Pandora parameter) to 300. The polling script is still running. I do have several projects set for "0" resources. So I should have other tasks to process if Rosetta were to burp again. Right now the Epyc system is running 100% Rosetta with a couple of GPU tasks from Einstein at home. I am hoping that yesterdays Free-DC result is a reliable signal of good things to come. Thank you for your discussion and guidance! Respectfully, One problem you may be having is the older versions of Boinc that you are running on the Epyc, if you update it MAY help with the other filling of the cache. BUT you have to be very careful as it's all about the math and if a Project thinks a task will take 30 minutes and your cache is set for 1.5 days be prepared for a boatload of tasks. They keep tweaking things with all the new releases.
3) Message boards : News : Outage notice (Message 111900) Posted 11 Jan 2025 by mikey Post: Hi, I think the whole Boinc system is down and has been so since 2024/12/07. I am running projects Rosetta, SiDock and worldCommunityGrid and all three of them can not get any workunits, so it does not look good. The original notice in December 2024 said that World Community Grid will be back by 2025/01/07, but alas nothing happened yet. Does anyone else know what is happening? Regards Frik Brits Ummm what about Einstein, Prime Grid, GPUGrid, SRBase, GooofyxGrid, wuprop, ODLK2025, Yafu, Yoyo and over half a dozen other Boinc Projects? They are ALL up and running and most have been for YEARS!!
4) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 109492) Posted 30 Jul 2024 by mikey Post: But, if it was true, their sw are VERY old and no longer supported (File system: ZFS on Linux v0.7, OS: Ubuntu Server 16.04) The latest version of Ubuntu Server is 24.04 LTS and ZFS is 2.2.4 (now OpenZFS) I know, i know.....the update/upgrade of the servers are not easy and without worries, but maybe it's the time....[/i] The problem is all the tweaks that most projects put in often get moved around in the newer versions so the notes people left are often pretty useless without a lot of hunting and pecking to find where things are now. And then apparently some things are in multiple places so if you don't change them ALL things don't work like you want them too, In short it's far from smooth especially when some projects run thru Admins like water so putting it off until you can't wait any longer is often better than tackling it little by little over the next 6 months or more.
5) Message boards : Number crunching : New jobs in Rosetta Python projects (Message 108890) Posted 1 Mar 2024 by mikey Post: I added the VM Extension pack, but still having problems. The WUs will now at least run for a while (hours in most cases) but then still error out. Anyone figured out what else to do? How many are you running at a time, I only run 1 at a time
6) Message boards : Number crunching : New jobs in Rosetta Python projects (Message 108845) Posted 15 Feb 2024 by mikey Post: Anyone else running these fine in Vbox under Linux? what config are you running? Don't know if it's needed here but in both LinuxMint and Windows the VBOX Extension Pack is not installed by default, I use both OS's as well and had to install it to get the LHC and LHC-dev tasks to run and get credits. On my Ubuntu Linux box it was installed by default.
7) Message boards : Number crunching : New jobs in Rosetta Python projects (Message 108808) Posted 24 Jan 2024 by mikey Post: I know Rosetta hasn't ever done this but these new Python tasks take 7.45gb of memory for EACH task on my Windows pc's, i have pc's with anything from 6 to 32 cpu cores but not a one of them has enough memory to fill every cpu core with a Python task and not lock up the pc to the point only a reboot and reducing the physical number of tasks I can run at Rosetta. Normally it's not a problem with anything EXCEPT the Python tasks Than limit the amount of concurrent python tasks using an app_confil.xml. This can be even different for each of your computers, depending on the amount of memory. I DO and said that but the problem is as I said when I get the normal or beta tasks I will want to run as many at a time as I can and I can't do that with the current Prefences setup. I know I could use an app_config.xml file to limit this or that type of task but have forgotten how to do that and the settings are all project specific and I don't remember how to that here and besides newbies will have no clue and just give up and go elsewhere and that's NOT what anyone wants. PrimeGrid has an elaborate prefences setup that even includes number of cpu's per task in additionto the type of task and how many of that type of task to run so it IS possible to have more and better choices. Honestly I wish the Developers would just hard code it into the Server coding which would fix places like Gerasim who have totally borked the settings, but that's a whole other problem, as well as help out places like Rosetta. YES Projects should be able to disable the defaults as they do now but sameness can be an advantage for some things.,
8) Message boards : Number crunching : New jobs in Rosetta Python projects (Message 108798) Posted 23 Jan 2024 by mikey Post: We will be releasing new jobs using the Rosetta Python projects application with RoseTTAFold All-Atom, our state-of-the-art deep learning based application that predict the structures of proteins in complex with ligands such as DNA and other biological molecules and also models post-translational modifications. As a reminder, this application will be released in the form of virtual machine. To help us with testing and gathering performance statistics, we ask that you do not abort related work units. I know Rosetta hasn't ever done this but these new Python tasks take 7.45gb of memory for EACH task on my Windows pc's, i have pc's with anything from 6 to 32 cpu cores but not a one of them has enough memory to fill every cpu core with a Python task and not lock up the pc to the point only a reboot and reducing the physical number of tasks I can run at Rosetta. Normally it's not a problem with anything EXCEPT the Python tasks so what I'm asking is you add an optional setting to run the Python tasks, be it thru a choice box or thru a box that says ie 'allow beta tasks' that we can then select. The problem with the 2nd option alone is that people can't choose to not run the regular Rosetta tasks while they wait for any Python tasks to come their way so they could easily end up with the same problem I'm having with lack of memory in my desktops. A simple set of type of tasks choice boxes would make things a whole lot easier on the users end and not really change anything beyond the initial setup for you Admins on your end. This page shows what I am talking about but most Projects have something similar to it: https://escatter11.fullerton.edu/nfs/prefs.php?subset=project In case the link doesn't work, it's to my Preferences page at NFS, here is a copy of one section of it: Home Resource share 1 Use CPU Run only the selected applications 14e Lattice Sieve (lasieved) - uses less than 0.5 GB memory, work may be infrequently available: yes 15e Lattice Sieve for smaller numbers (lasievee_small) - small numbers, uses up to 0.8 GB memory: no 15e Lattice Sieve (lasievee) - medium numbers, uses up to 1 GB memory: no 16e Lattice Sieve for smaller numbers (lasievef_small) - large numbers, uses up to 1 GB memory: no 16e Lattice Sieve V5 (lasieve5f) - largest numbers, uses up to 1.25 GB memory: no If no work for selected applications is available, accept work from other applications? no Thank you for reading this and I hope you can discuss and implement this soon . Thank you for you time mikey
9) Message boards : Number crunching : Rosetta Beta 6.00 (Message 108777) Posted 22 Dec 2023 by mikey Post: I use an APP_CONFIG to run all my projects. I can set to run just 1 beta WU, never tried to set max tasks to 0. Right now i'm running Milky Way until Beta is more stable. <max_concurrent>Zero</max_concurrent> = <max_concurrent>Infinity</max_concurrent> I don't know what your settings are but I'm getting nearly 100% valid tasks here on my both Windows and Linux pc;s. State: All (2097) · In progress (576) · Validation pending (0) · Validation inconclusive (0) · Valid (1514) · Invalid (0) · Error (7) Application: All (2097) · Rosetta (102) · Rosetta Beta (1995) · Rosetta Mini (0) · rosetta python projects (0)
10) Message boards : Rosetta@home Science : Unable to get any work (Message 108734) Posted 2 Dec 2023 by mikey Post: Hi there. Apologies if this is posted in the wrong area, but I am unable to get work. I bought this new computer about a month ago. it has an Intel(R) Arc(TM) A770 Graphics card and a 13th Gen Intel(R) Core(TM) i7-13700F processor. I hope you can help. I've tried attaching to several boinc projects, and I'm not getting any work. Is this just bad luck or is something else wrong? Try PrimeGrid and Einstein, Asteroids also has cpu and gpu tasks but I don't know if they can use your Intel Arc gpu or not
11) Message boards : Number crunching : Ralph test spotted (Message 108654) Posted 1 Nov 2023 by mikey Post: Not really necessary, don't we all have large SSDs? I believe the idea is a Squid thing like LHC crunchers use to download tasks to a single pc then send them out to multiple pc's and then return them from the original pc that downloaded them thereby bypassing one of the security features built into Boinc that is that the pc that downloads a task must be the one that returns it back to the project.
12) Message boards : Cafe Rosetta : Happy 2023 (Message 107909) Posted 1 Jan 2023 by mikey Post: Happy new year. A lot of wus to everyone!! Let's do science Well said!! I certainly hope so too!!
13) Message boards : Cafe Rosetta : Antibody That Can Take Out All COVID-19 Variants (Message 106877) Posted 7 Sep 2022 by mikey Post: https://www.prevention.com/health/a41092334/antibody-neutralize-covid-variants/ This is in a mice test ONLY so far so it's VERY early days but it may help cut down on all the boosters they are putting out
14) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 106673) Posted 29 Jul 2022 by mikey Post: I'm a bit mystified why my RAC keeps diving despite 9 validated tasks in the last whatever time period it is allowed to show. That means that you are not returning validated tasks as fast as you were earlier in the month the RAC is for. If you can't download tasks, you can't complete and return them. The tasks that are shown is usually for a shorter period, such as a week. I see the problem now, LHC had a big batch of use all (15 in my case)cpu tasks. Correction: It's Milkyway with 15 out 16 CPUs for 3-4 minutes per task. 83 tasks in queue. But I switch applications every few hours so everyone has their turn. Try an app_config.xml file in each Project folder that looks like this: <app_config> <project_max_concurrent>2</project_max_concurrent> </app_config> Then change the number, 2 in this case, to reflect how many tasks you want that project to run at a time. Keep the cache settings in mind as you do this and you can run 2 tasks from this project, 1 from that project and 12 from that project over there all at the same time day after day after day.
15) Message boards : Number crunching : Not getting any python work (Message 103368) Posted 17 Nov 2021 by mikey Post: The standard Rosetta tasks also reserve 8gb of ram for each task, No they don't. They request & release RAM as required- none is reserved. And apart from a batch of faulty Tasks some time back, the most i have seen used by a single Task was around 4GB. Generally the highest is around 1.3GB. The current batch of work are using between 700MB & 1GB each. Please stop making thing up, it's not helpful. I didn't 'make it up' it was my misunderstanding that the 4.20 tasks 'request & release ram as required'. I have only ever looked in the properties of a running task and see what it says so was going by that.
16) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 103367) Posted 17 Nov 2021 by mikey Post: I am out, until someone can confirm that the pythons are working correctly, and I can select them. Part one of that is no problem. I returned at least two proper results before the one I was complaining about. Unfortunately I can't show them off anymore, as the db seems to have taken them out by now. vbox can be a hassle on every project, and I encountered similar problems elsewhere. Dealing with projects that have nothing except vbox apps is one thing, but Rosetta isn't one of those. So the possibility to unselect those monsters should obviously and absolutely be existing! I can confirm that the Python tasks work just fine on my Windows 11 beta testing laptop, I am running ver 6.1.26 of VBox and ver 7.16.20 of Boinc: 1450357706 1293408677 4767328 17 Nov 2021, 0:09:28 UTC 20 Nov 2021, 0:09:28 UTC In progress --- --- --- rosetta python projects v1.03 (vbox64) windows_x86_64 1450297317 1293408267 4767328 17 Nov 2021, 0:09:28 UTC 20 Nov 2021, 0:09:28 UTC In progress --- --- --- rosetta python projects v1.03 (vbox64) windows_x86_64 1450357611 1293408634 4767328 17 Nov 2021, 0:08:51 UTC 17 Nov 2021, 12:13:59 UTC Cancelled by server 0.00 0.00 --- rosetta python projects v1.03 (vbox64) windows_x86_64 1450286960 1293407997 4767328 17 Nov 2021, 0:08:03 UTC 20 Nov 2021, 0:08:03 UTC In progress --- --- --- rosetta python projects v1.03 (vbox64) windows_x86_64 1450357628 1293408478 4767328 17 Nov 2021, 0:08:03 UTC 20 Nov 2021, 0:08:03 UTC In progress --- --- --- rosetta python projects v1.03 (vbox64) windows_x86_64 1449564483 1293454887 4767328 15 Nov 2021, 23:25:48 UTC 17 Nov 2021, 12:12:47 UTC Completed and validated 22,488.82 20,606.27 185.74 rosetta python projects v1.03 (vbox64) windows_x86_64 1449564347 1293454813 4767328 15 Nov 2021, 23:25:48 UTC 18 Nov 2021, 23:25:48 UTC In progress --- --- --- rosetta python projects v1.03 (vbox64) windows_x86_64 1449486504 1293416591 4767328 14 Nov 2021, 3:21:18 UTC 17 Nov 2021, 5:45:55 UTC Completed and validated 34,804.85 31,782.95 441.35 rosetta python projects v1.03 (vbox64) windows_x86_64 1449487643 1293416839 4767328 14 Nov 2021, 3:20:38 UTC 16 Nov 2021, 13:32:46 UTC Completed and validated 40,661.08 40,217.94 515.61 rosetta python projects v1.03 (vbox64) windows_x86_64 1449487583 1293416824 4767328 14 Nov 2021, 3:20:38 UTC 16 Nov 2021, 19:56:35 UTC Completed and validated 22,768.22 20,693.41 186.15 rosetta python projects v1.03 (vbox64) windows_x86_64
17) Message boards : Number crunching : Not getting any python work (Message 103342) Posted 16 Nov 2021 by mikey Post: I see I'm not the only one who wished there was an option in the preferences as to which work units I want! I have a Virtual Box installed but even when it's closed, BOINC downloads Python wu's. These are MASSIVE memory hogs at around 7.6gig each. As a result, I have both standard & Python running but w/u's queued up due to insufficient memory. (I have 32gig) If I had a choice, I'd only enable the standard wu's instead of the Python one's but there's no way to toggle one or the other. To be honest, I aborted the work and moved onto another project. That's not a win for Rosetta@Home. I guess I could just let my pc's crunch as much as possible and leave it be. I'd still like to see an option in the preferences. The standard Rosetta tasks also reserve 8gb of ram for each task, one way around this is a simple app_config file that limits the number of tasks running per project, like this: <app_config> <project_max_concurrent>1</project_max_concurrent> </app_config> Put it in the Project folder and then tell Boinc to reread the config files and you are good to go. It's also useful for running 3 tasks of this project and 5 of that project on an 8 core cpu. You do need to be careful as each Project will download work thinking it's for all 8 cores so it's best to limit the cache size accordingly otherwise you could easily run into task deadline issues. But it does not do anything about not getting Python over regular Rosetta tasks, that's a Project issue and they haven't done anything yet.
18) Message boards : Number crunching : High number of invalid tasks (Message 103341) Posted 16 Nov 2021 by mikey Post: An update: After switching back to running RAH on just one core, all invalids are gone. I now have 27 Consecutive valid tasks. @mikey, it looks like you're spot on with the memory requirements. The other 7 cores now run FAH and WCG and because i only have 16gb on this system, just 1 runs RAH. And that's exactly why I also limit Rosetta tasks to one at a time on all my machines, most only have 16gb of ram anyway.
19) Message boards : Number crunching : Excessive workunit fetch (Message 103340) Posted 16 Nov 2021 by mikey Post: On macOS those python VB tasks take much much less than 8 Gb (I would 13 Gb free when it was running) + as I explained, I had limited them and only 1 was running at a time (the rest was regular rosetta). The regular Rosetta tasks also reserve 8gb of ram per task, so if you are trying to run 20 tasks total, or near that and all of them are Rosetta tasks your machine doesn't have enough memory. Yes I know Mac's use less memory but I don't remember how much, you can check by clicking on a running task in the Boinc Manager and then in the left hand panel click on Properties and it will tell you how much the Virtual Memory Size is and the Working set size is, you care about the one that shows the most memory.
20) Message boards : Number crunching : Excessive workunit fetch (Message 103325) Posted 16 Nov 2021 by mikey Post: I'm not sure if you mean "don't bother too much and change project for now" or "there are useful tips in that other thread" ? I had a (very) quick look and it's long and complicated, not even sure if the problems they mention are similar ? In any case it'll have to wait, for now I have dropped all those many tasks I had (running or not) and I'm focusing on other projects for the moment. Thanks ! Since each task here at Rosetta takes 8gb of ram and you only have 40gb of ram in that pc you need to limit the cache and extra cache settings on this pc and limit the total number of task you run at one time to no more than 4 at one time and depending on what else you do with that pc fewer than that. It seems to me with 20 cpu's in that pc and a cache size of even 1 day could mean 120 tasks if it used all the cpu cores at once. Of course you can't use 20 cores at once as your pc would be swapping memory like crazy and destroying your hard drives and pushing your memory to it's limit in the process. One key thing, to me you said. it that it was only advancing at 0.01% even after 48 hours of crunching, that means you are trying to run to many tasks at the same time, again at 8gb of ram per task you can only 4 at a time max because the pc itself uses some overhead with Windows using more than most Linux versions.

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