Message boards : Number crunching : Problems and Technical Issues with Rosetta@home
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trevG Send message Joined: 5 Nov 13 Posts: 9 Credit: 687,475 RAC: 0 |
No wonder I struggled but it did 2 WU,s. But for my fault finding glitches it could have completed them all.. The VM box controls were far from intuitive. A warning would have helped, anyway.. Maybe I should stop all RAH work now as this seems the default..? As a by the by- what is the minimum RAM needed for this work? I probably won't upgrade -as other work seems ok, apart from LHC. 17+ hrs of completed work that has been missed from validation, 3 completed units: Rosetta@home 03-12-2021 09:52 03:53:41 (03:47:29) 03-12-2021 09:56 aaas-SAR-VAL_pp-NMVAL-SUGA_pp_12_2559723_1_0 97.35 Reported: OK * 1.03 rosetta python projects (vbox64) DESKTOP-IUPTMBB Rosetta@home 03-12-2021 05:57 07:03:18 (06:52:27) 03-12-2021 05:57 aaap-PIP_pp-mNMPHE_pp-TIC-AMACBEN3_pp_0_2502770_1_0 97.44 Reported: OK + 1.03 rosetta python projects (vbox64) DESKTOP-IUPTMBB (203) 1.03 rosetta python projects (vbox64) DESKTOP-IUPTMBB Rosetta@home 02-12-2021 21:15 06:44:38 (06:22:05) 02-12-2021 21:17 aaas-PHE_pp-mTIC_pp-NMVAL-mSUGA_1_2517870_1_0 94.43 Reported: OK + 1.03 rosetta python projects (vbox64) DESKTOP-IUPTMBB |
Jonathan Send message Joined: 4 Oct 17 Posts: 43 Credit: 1,337,472 RAC: 0 |
The current VM work is using about 3Gb for the work units starting with 'aa'. The 'boinc_cages_IL' is running about 6Gb. You should be able to run camb_boinc2docker VMs from Cosmology at home as those only use 2Gb. You just need to set your preferences to 1 or 2 for Max # CPUs so it only assigns one or two cores to each work unit and VM. It's probably best if you just stick to conventional Boinc work units as they behave better and share resources as they run at a lower priority. Virtual Box task run at a normal priority. |
trevG Send message Joined: 5 Nov 13 Posts: 9 Credit: 687,475 RAC: 0 |
Yes- I did some CAH units ok recently, first time using VM. I am annoyed about what happened on Rosetta though- and I can't be the first. Also, a message to stop trying would be a good idea - whilst wasting effort as even the apparent good units were ignored in the end! |
Jean-David Beyer Send message Joined: 2 Nov 05 Posts: 197 Credit: 6,619,262 RAC: 3,235 |
Jean - I thought you might be on to something. But it was a fluke. Why does it work for me and not for you? |
Grant (SSSF) Send message Joined: 28 Mar 20 Posts: 1734 Credit: 18,532,940 RAC: 17,945 |
Its windblows 7, opteron16 that has gone funkyI still haven't seen any mention of what your BOINC disk settings actually are. Use no more than ? GB Leave at least ? GB free Use no more than ? % of total 11 at once and it is getting the disk space moan again, except even after all that clear out, its got worse !!!??11 Python Tasks will require roughly 88GB of disk space. Grant Darwin NT |
Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
Jean - I thought you might be on to something. But it was a fluke. That is the ultimate question. Talk me through it again...you had all that directory stuff in the text, but I don't have that. Whats the plain text version of all that? I have project name (boinc agrees), project_max_concurrent (no disagreement there), but it ignores those. I just aborted a stuck task and BOINC took 2 pythons to start. |
Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
The current VM work is using about 3Gb for the work units starting with 'aa'. The 'boinc_cages_IL' is running about 6Gb. You should be able to run camb_boinc2docker VMs from Cosmology at home as those only use 2Gb. You just need to set your preferences to 1 or 2 for Max # CPUs so it only assigns one or two cores to each work unit and VM. Correction: Cages is 7,629.39 MB (i've been getting those quite a bit lately) |
.clair. Send message Joined: 2 Jan 07 Posts: 274 Credit: 26,399,595 RAC: 0 |
Its windblows 7, opteron16 that has gone funkyI still haven't seen any mention of what your BOINC disk settings actually are. It was in Message 103670, Posted: 2 Dec 2021, 21:51:18 UTC . I had gone as far to untick all the disk space boxes to give it unlimited use of the disk at the moment I have 89GB free on drive C, and rosetta is using 98GB {greedy hog} And this afternoon I reduced my workunit cash down to 0.1 + 0.1 just to see what happens [it was 1 + 0.5] In the long run , it works , so whatever it is moaning about I can live with it |
Jean-David Beyer Send message Joined: 2 Nov 05 Posts: 197 Credit: 6,619,262 RAC: 3,235 |
Are you putting them in the right app_config.xml file? I.e., the one in the ..../projects/boinc.bakerlab.org_rosetta directory? /var/lib/boinc/projects/boinc.bakerlab.org_rosetta]# cat app_config.xml <app_config> <project_max_concurrent>3</project_max_concurrent> </app_config>
I hope this is what you want. cat /etc/redhat-release: Red Hat Enterprise Linux release 8.5 (Ootpa) uname -r: 4.18.0-348.2.1.el8_5.x86_64 rpm -q boinc-client: boinc-client-7.16.11-3.el8.x86_64 # Two terabyte hard drive. [part of /etc/fstab] UUID=90309ec8-b1d3-4438-b983-f7ab121421a8 /D3P1 ext4 defaults 1 2 UUID=9bea9d6e-2f0d-4636-ac83-7fb9c0b2e108 /D3P2 ext4 defaults 1 2 UUID=8d57a006-8363-4dd0-abe4-d8f77fc15182 /var/lib/boinc ext4 defaults 0 0 <---<<< UUID=840e6522-89ff-4b81-9efa-33d97df3fb1e /home/guest xfs defaults 0 0 UUID=04a403c2-6199-4936-9ab7-1fe2ed25377e /D3P6 xfs defaults 0 0 UUID=c667796a-a283-4db1-9bb9-7f6ef0de9982 /D3P7 xfs defaults 0 0 Disk: Boinc will use the most restrictive of these settings; Use no more than 110 GBytes Leave at least 0.5 GBytes free Use no more than 85% of total. Memory [I have about 64 GBytes RAM] When computer is in use, use at most 80% When computer is not in use, use at most 90% Leave non GPU tasks in memory when tasks are suspended Page swap file: use at most 50% [100% = 16 Gigabytes] [1.5 Megabytes used] [/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]# ls -l total 739232 82 Jul 1 15:29 app_config.xml <---<<< 4096 May 11 2020 database_357d5d93529_n_methyl 507570722 Nov 14 2020 database_357d5d93529_n_methyl.zip 0 Nov 14 2020 database_357d5d93529_n_methyl.zip.is_bad 352308 Nov 14 2020 LiberationSans-Regular.ttf 125232600 Nov 14 2020 rosetta_4.20_x86_64-pc-linux-gnu 123794008 Nov 14 2020 rosetta_graphics_4.20_x86_64-pc-linux-gnu [/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]# cat app_config.xml <app_config> <project_max_concurrent>3</project_max_concurrent> </app_config> top - 23:33:34 up 23:55, 1 user, load average: 8.53, 8.55, 8.62 Tasks: 453 total, 10 running, 442 sleeping, 1 stopped, 0 zombie %Cpu(s): 0.4 us, 0.3 sy, 49.5 ni, 49.7 id, 0.0 wa, 0.1 hi, 0.1 si, 0.0 st MiB Mem : 63902.2 total, 1888.6 free, 9855.8 used, 52157.7 buff/cache MiB Swap: 15992.0 total, 15990.5 free, 1.5 used. 53269.4 avail Mem Boinc processes running; n.b.: I have no Rosetta tasks at the moment PID PPID USER PR NI S RES %MEM %CPU P TIME+ COMMAND 11368 11311 boinc 39 19 T 1.4g 2.2 0.0 2 1260:36 /var/lib/boinc/projects/climateprediction.net/hadam+ 11370 11310 boinc 39 19 R 1.3g 2.1 99.3 6 1334:37 /var/lib/boinc/projects/climateprediction.net/hadam+ 11378 11376 boinc 39 19 R 1.3g 2.1 99.2 7 1343:57 /var/lib/boinc/projects/climateprediction.net/hadam+ 11374 11309 boinc 39 19 R 1.3g 2.1 99.3 2 1268:12 /var/lib/boinc/projects/climateprediction.net/hadam+ 89853 2604 boinc 39 19 R 759984 1.2 99.3 4 68:29.20 ../../projects/www.worldcommunitygrid.org/wcgrid_ar+ 72940 2604 boinc 39 19 R 758500 1.2 99.0 1 350:46.26 ../../projects/www.worldcommunitygrid.org/wcgrid_ar+ 90073 2604 boinc 39 19 R 153240 0.2 99.3 5 64:58.59 ../../projects/www.worldcommunitygrid.org/wcgrid_op+ 93694 2604 boinc 39 19 R 113052 0.2 98.9 0 11:48.64 ../../projects/www.worldcommunitygrid.org/wcgrid_op+ 91188 2604 boinc 39 19 R 73000 0.1 99.2 11 50:54.74 ../../projects/www.worldcommunitygrid.org/wcgrid_mc+ 2604 1 boinc 30 10 S 37876 0.1 0.7 10 5521:29 /usr/bin/boinc 11309 2604 boinc 39 19 S 18564 0.0 0.0 10 1:17.60 ../../projects/climateprediction.net/hadam4_8.52_i6+ 11310 2604 boinc 39 19 S 18468 0.0 0.0 10 1:19.52 ../../projects/climateprediction.net/hadam4_8.52_i6+ 11376 2604 boinc 39 19 S 17536 0.0 0.1 14 0:43.15 ../../projects/climateprediction.net/hadam4_8.52_i6+ 11311 2604 boinc 39 19 S 17084 0.0 0.0 10 0:27.48 ../../projects/climateprediction.net/hadam4_8.52_i6+ |
Grant (SSSF) Send message Joined: 28 Mar 20 Posts: 1734 Credit: 18,532,940 RAC: 17,945 |
I had gone as far to untick all the disk space boxes to give it unlimited use of the diskThe boxes aren't tickable, they require values. And one value in any one of the options overrides the values in any of the other two when it comes to what disk space is actually available. While people are now able to get & do more Python Tasks, i can see many more people leaving the project anyway. Rosetta 4.20 Tasks weren't exactly high payers with roughly 340 Credits for 8 hours of work (depending on the system). For the same time frame, Python Tasks only pay out around 130, roughly 2.5 times less. Grant Darwin NT |
Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
Are you putting them in the right app_config.xml file? I.e., the one in the ..../projects/boinc.bakerlab.org_rosetta directory? /var/lib/boinc/projects/boinc.bakerlab.org_rosetta]# cat app_config.xml <app_config> <project_max_concurrent>3</project_max_concurrent> </app_config> ------------------------ Yep..for me its in boinc data/projects/boinc.bakerlab.org_rosetta. <name>rosetta python projects</name> <app_config> <project_max_concurrent>1</project_max_concurrent> (it could be 2 but not 3) </app_config> And its back to 3 at a time again. Resource share is at 100%. I'm thinking I will have to bring it back to 50 again. |
Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
Oh man....how dumb can I be. I forgot to change the type from text to xml!!!! SMH Now that it is a xml file it works. Gees That's what happens when your in a rush in the middle of the night. |
Jean-David Beyer Send message Joined: 2 Nov 05 Posts: 197 Credit: 6,619,262 RAC: 3,235 |
Oh man....how dumb can I be. I forgot to change the type from text to xml!!!! That is not dumb. That is just part of being human, and you do not even need to be forgiven for that. There are too many people who seem to have lost their humanity. They seem to me that they end up in government and upper management of large corporations. I do not know your age,. but I am more than three score and ten and I can tell you it gets worse with age. So do not insult yourself. Forgive yourself if you must. |
Jean-David Beyer Send message Joined: 2 Nov 05 Posts: 197 Credit: 6,619,262 RAC: 3,235 |
I do not even have a directory named [b]boinc data/projects/boinc.bakerlab.org_rosetta[/b] ^ ????? >>>-----| I cannot believe this is a space. Filesystem 1K-blocks Used Available Use% Mounted on /dev/sdb3 122908728 18785860 97856396 17% /var/lib/boinc My system is running Red Hat Enterprise Linux release 8.5 (Ootpa) and all its Boinc stuff is in /val/lib/boinc. That is a partition all its own on one of my spinning hard drives. It has only the following directories; [/var/lib/boinc]$ ls -l drwx------. 2 root root 4096 Jul 1 15:22 lost+found drwxrwx--x. 2 boinc boinc 4096 Dec 5 09:46 notices drwxrwx--x. 6 boinc boinc 4096 Nov 27 2020 projects drwxrwx--x. 12 boinc boinc 4096 Dec 4 11:56 slots |
Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
but I am more than three score and ten and I can tell you it gets worse with age. - I am more than XLV and less than LV |
Jim1348 Send message Joined: 19 Jan 06 Posts: 881 Credit: 52,257,545 RAC: 0 |
For the "Vm job unmanageable errors", you can try this fix: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14839&postid=103729#103729 It will probably work as well as going back to VirtualBox 5.2.44, which is easy in Windows, but not so easy in Ubuntu. |
trevG Send message Joined: 5 Nov 13 Posts: 9 Credit: 687,475 RAC: 0 |
I'm LXXVIII and feeling it a little on here atm..:/ |
Jonathan Send message Joined: 4 Oct 17 Posts: 43 Credit: 1,337,472 RAC: 0 |
Rosetta is already using that wrapper version, vboxwrapper_26203_windows_x86_64.exe on windows. |
Jim1348 Send message Joined: 19 Jan 06 Posts: 881 Credit: 52,257,545 RAC: 0 |
Rosetta is already using that wrapper version, vboxwrapper_26203_windows_x86_64.exe on windows. I haven't tried it on Windows yet. But maybe you could check the file size to see if they are the same? (Or maybe Rosetta fixed it themselves? That would be the best fix.) And they don't seem to have a fixed version for Linux on that website, so I will be using the one from LHC, which is different than the Rosetta one. PS - The ones you have finished state: <stderr_txt> So maybe they just changed it? |
Jim1348 Send message Joined: 19 Jan 06 Posts: 881 Credit: 52,257,545 RAC: 0 |
I'm LXXVIII and feeling it a little on here atm..:/ That is an outstanding age. You have acquired a lot of experience by then. |
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Problems and Technical Issues with Rosetta@home
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