Posts by JohnDK

1) Message boards : Number crunching : Rosetta Beta 6.00 (Message 108683) Posted 13 Nov 2023 by JohnDK Post: Out of the 13 WUs I got, 11 of the had computation error within 30 secs. The other 2 have so far run for 2 hours. <core_client_version>7.24.1</core_client_version> <![CDATA[ <message> Forkert funktion. (0x1) - exit code 1 (0x1)</message> <stderr_txt> command: projects/boinc.bakerlab.org_rosetta/rosetta_beta_6.04_windows_x86_64.exe @07aaNewf_af2_7aa_hal_9.flags -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 1920894 Using database: database_0f7f01a1b07database ERROR: Unable to find desired residue 'LEU:N_Methylation' with variant 'LOWER_TERMINUS_VARIANT'. Attempted to add target variant(s) to ResidueType using both ResidueType base name 'LEU' and base ResidueType. Was attempting to add new variant type 'LOWER_TERMINUS_VARIANT' ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 980 BOINC:: Error reading and gzipping output datafile: default.out 19:41:27 (11480): called boinc_finish(1) </stderr_txt> ]]>
2) Message boards : Number crunching : Problen downloading work tasks. (Message 107860) Posted 19 Dec 2022 by JohnDK Post: clair and vdquang, none of you are using BOINC v7.20.2, which, for some reason, seems to work.
3) Message boards : Number crunching : Problen downloading work tasks. (Message 107850) Posted 18 Dec 2022 by JohnDK Post: I had the stuck downloading issue too. On Windows x64. I updated my Bonic manager to 7.20.2 and it cleared up the downloading problem. I had been 7.16.11 Yes. My windows box is running 7.20.2 and it downloads just fine. Same here.
4) Message boards : Number crunching : Rosetta 4.1+ and 4.2+ (Message 105714) Posted 26 Mar 2022 by JohnDK Post: I'm getting computation errors on all Rosetta work from today, anybody else?
5) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 105693) Posted 25 Mar 2022 by JohnDK Post: Problem: WUs often pauses with the VM unmanageable error, no matter if I run 9 or only 5 WUs at a time. It is a long-standing problem, much discussed here (you can search it). It is mainly on Linux that I have seen. If you use Windows, and then the 5.2.44 VirtualBox version (not 6.1.x), you will not have the problem. But there is another problem of tasks using very little CPU and running forever ("0 CPU" problem) that is common to both operating systems. You just abort them as early as you find them. Yes I'm running Linux on that host, on my Windows host I've no problem, even with VirtualBox 6.1. On the Linux host I did have some of those 0 CPU procent WUs and did abort them, again don't think I've had a single one on my Windows host.
6) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 105687) Posted 25 Mar 2022 by JohnDK Post: Problem: WUs often pauses with the VM unmanageable error, no matter if I run 9 or only 5 WUs at a time. Processor: 32 AuthenticAMD AMD Ryzen 9 5950X 16-Core Processor [Family 25 Model 33 Stepping 0] Processor features: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 hw_pstate ssbd mba ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr rdpru wbnoinvd arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif v_spec_ctrl umip pku ospke vaes vpclmulqdq rdpid overflow_recov succor smca fsrm
7) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 105654) Posted 22 Mar 2022 by JohnDK Post: I just can't get the python WUs to work properly on my Linux host, they all too often pauses with the VM unmanageable error. I started with 9 WUs and it has been suggested to lower that and one by one I'm down to 5. Right now I only have 4 left in cache and running, but 3 of them have already pausede with the VM error message after a BOINC restart. So the question of having enough RAM doesn't seem to apply, to my PC anyway.
8) Message boards : News : Thank you! (Message 105599) Posted 20 Mar 2022 by JohnDK Post: The issue I have with restarting BOINC to get the postponed to run, is that you lose time on all running tasks from all projects, due to the checkpoints.
9) Message boards : News : Thank you! (Message 105591) Posted 20 Mar 2022 by JohnDK Post: I've have many Postponed: VM job unmanageable, restarting later WUs on my Linux., seems to getting more worse lately. I'm shutting my PC down for the night so when I startup the next day, the postponed tasks just continue. I'm running 9 python and last night I had 5 tasks postponed, shortly after starting up today I already have 2 tasks postponed. This is very annoying!
10) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 104948) Posted 18 Feb 2022 by JohnDK Post: Don't like those python WUs, but with the movingstub problems, I will have to continue with them.
11) Message boards : Number crunching : Same error on almost all WUs (Message 104947) Posted 18 Feb 2022 by JohnDK Post: Or maybe not. It looks like the same error occurred with that batch of RB Tasks for all those running Linux (yet to find Win system running one of them). Then of course there are all the other Tasks that appear to be erroring out on Win but OK on Linux.... EDIT- looks like some WIn systems had issues with them as well. So i'd leave your system alone. Yes don't think it's my host with the problem, some of those tasks does validate with others but some don't. Also, with the later work I been getting, things runs OK.
12) Message boards : Number crunching : Same error on almost all WUs (Message 104876) Posted 17 Feb 2022 by JohnDK Post: I'm getting the same error on almost WUs <message> process exited with code 1 (0x1, -255)</message> <stderr_txt> command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu @rb_02_16_213031_208962_ab_t000__robetta_FLAGS -in::file::fasta t000_.fasta -jumps:pairing_file t000_.fasta.bbcontacts.jumps -jumps:random_sheets 3 -constraints::cst_file t000_.fasta.CB.cst -constraints:cst_weight 5.0 -constraints::cst_fa_file t000_.fasta.MIN.cst -constraints:cst_fa_weight 5.0 -in:file:boinc_wu_zip rb_02_16_213031_208962_ab_t000__robetta.zip -frag3 rb_02_16_213031_208962_ab_t000__robetta.200.3mers.index.gz -fragA rb_02_16_213031_208962_ab_t000__robetta.200.8mers.index.gz -fragB rb_02_16_213031_208962_ab_t000__robetta.200.7mers.index.gz -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3475861 Using database: database_357d5d93529_n_methyl/minirosetta_database [ ERROR ]: Caught exception: File: src/core/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306 chi angle must be between -180 and 180: -nan https://boinc.bakerlab.org/rosetta/results.php?hostid=6178331&offset=0&show_names=0&state=6&appid=
13) Message boards : Number crunching : Time estimates seem less than optimal (Message 97447) Posted 18 Jun 2020 by JohnDK Post: So I check the controller before I go to bed, and it's crunching on tasks that had 8 hour estimates. Get up in the morning, they've been running all night, now the estimate is over a day? This will make the later ones, which also think they are 8 hour jobs, report late. All three of my Ubuntu machines are now stuck on 8 hour estimates, even though I run the 18-hour jobs. They no longer correct themselves. It must be the new BOINC version (7.16.6 or 7.16.7, or whatever they have decided to call it today) and how it interacts with the server. The same here, both linux and windows. I had set my 24/7 hosts to 14 hours, but, I think, after the 4.20 app they would only run around 8 hours. My understanding was that longer running tasks would mean less press on the servers, but now I've changed my settings back to the default 8 hours runtime. Things work just as well, it just means more work to do for the servers I guess.
14) Message boards : Number crunching : Peer certificate cannot be authenticated with given CA certificates (Message 97024) Posted 31 May 2020 by JohnDK Post: Greetings, I am running Linux Mint v19.3 which is based on Ubuntu. I have done the following procedure: The procedure that worked for me on Ubuntu 18.04.4: (1) Download this file: https://crt.sh/?d=1720081 (2) Place "1720081.crt" in Home directory (e.g., move from desktop) (3) sudo mv 1720081.crt /usr/local/share/ca-certificates (4) sudo update-ca-certificates I restarted BOINC and am still getting stuck uploads and reports. Is there something else that needs to be done. I have only been using Linux continually for about 8 months, so I'm sorta a noob. ;) Have a great day! :) Siran Are you 100% sure 1720081.crt was moved to /usr/local/share/ca-certificates before doing sudo update-ca-certificates? btw if wasn't necessary to restart BOINC for me, it just worked.
15) Message boards : Number crunching : If You Don't Know Where to Put it, Post it here. (Message 96915) Posted 30 May 2020 by JohnDK Post: Yes I also got the transient HTTP error, it´s only when BOINC contacts the scheduler server you get the certificate error.
16) Message boards : Number crunching : If You Don't Know Where to Put it, Post it here. (Message 96912) Posted 30 May 2020 by JohnDK Post: Even though it says download server is not running it works. Since you have stuck uploads you might have the certificates expired issue I'm guessing.
17) Message boards : Number crunching : 31 second delay (Message 96679) Posted 20 May 2020 by JohnDK Post: Is there an option to disable those "Project requested delay of xx seconds" messages?
18) Message boards : News : Switch to using SSL (Secure Socket Layer) (Message 95840) Posted 2 May 2020 by JohnDK Post: I have just done the following steps in my 2 Linux Laptops managed by BAM. Step 1 - Modify the file account_boinc.bakerlab.org_rosetta.xml <master_url>https://boinc.bakerlab.org/rosetta/</master_url> Step 2 - Modify the file all_projects_list.xml <url>https://boinc.bakerlab.org/rosetta/</url> <web_url>https://boinc.bakerlab.org/rosetta/</web_url> Step 3 - Restart boinc manager systemctl restart boinc-client.service I didn't need to remove the projet and attach it again. Tried that on a win10 host, except I didn't use step 2. BOINC deleted all 5 WUs I had in cache and downloaded 3 new, without any url message, so it works now anyway. Guess I won't try that on my 3 other hosts :)
19) Message boards : News : Switch to using SSL (Secure Socket Layer) (Message 95690) Posted 1 May 2020 by JohnDK Post: Remember to finish all tasks before detaching ;)
20) Message boards : Number crunching : Aborted work and a lot of wasted time - again (Message 95317) Posted 24 Apr 2020 by JohnDK Post: Very annoying, 4 WUs cancelled, all running over 50.000 secs. Is it me or what? https://boinc.bakerlab.org/rosetta/results.php?hostid=4063805&offset=0&show_names=0&state=6&appid=

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