Posts by Jim Martin

1) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 104010) Posted 3 Jan 2022 by Jim Martin Post: I've been a Rosetta@home participant since the beginning. And, never had I had problems getting new WU's . Now, it appears I have to jump through new hoops? It shouldn't be that difficult. SiDock@home hands out new WU's like candy. Am counting on Dr. Baker to bring back the good old days.
2) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 101338) Posted 16 Apr 2021 by Jim Martin Post: CIA -- Thanks, for the tip. Waited approx. 15 mins., and they ran. Half w/out errors, thus far, the others failed. jm
3) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 101295) Posted 14 Apr 2021 by Jim Martin Post: No WU's will start. Some examples: Pre-helical-bundles TMWFY3V Have tried aborting the first batch, but the second one, of 15 WU's, also did not run. This has happened, once before, a couple of weeks, ago. jm
4) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 101227) Posted 11 Apr 2021 by Jim Martin Post: A reply, here, to Robert, Brian, if I may. Robert -- I, too, wondered if that wasn't an indication of a coding glitch. jm
5) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 101224) Posted 11 Apr 2021 by Jim Martin Post: Brian -- The first Rosetta@home work units have arrived, which appear to be working well. They are: TMWFYIU pre-helical-bundles-round1 (I did not use the underscore, because a red line resulted.) miniprotein-relax8 They are in the mid-40% range of completion. Here's hoping. . . jm
6) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 101145) Posted 8 Apr 2021 by Jim Martin Post: Thanks, for the reply, Brian. I wonder why some have this problem, and others don't. Nothing has changed (computer) on this end of the line. So, will just run SiDock@home, for awhile. Natalia has a cheerful, and informative approach to running things. jm
7) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 101138) Posted 7 Apr 2021 by Jim Martin Post: Hello. After approx. 15 years with Baker Lab, I've experienced an interesting problem, under the general category, computer errors. Sorry to copy the entire err. report, but perhaps it will clarify. Any ideas? The past three downloads gave, basically, the same results. Unless computing requirements have changed, recently, then I'll have to change. Otherwise, perhaps, UW's end is with some new problems? Good luck. Jim Martin Task 1364797245 Name ajzjTxIe_YBAABB_ABYBB_AAAAAAXB_AAY_CGGGGGGCCGGGGGCGGGGGGGGCGGGC_1-4_2-5_3-6.pdb_0001_abinitio_1_abinitio_SAVE_ALL_OUT_1389656_916_1 Workunit 1220204735 Created 7 Apr 2021, 15:30:32 UTC Sent 7 Apr 2021, 15:32:35 UTC Report deadline 10 Apr 2021, 15:32:35 UTC Received 7 Apr 2021, 17:59:51 UTC Server state Over Outcome Computation error Client state Compute error Exit status 1 (0x00000001) Unknown error code Computer ID 1324493 Run time 39 sec CPU time 24 sec Validate state Invalid Credit 0.00 Device peak FLOPS 3.37 GFLOPS Application version Rosetta v4.20 windows_x86_64 Peak working set size 153.00 MB Peak swap size 124.98 MB Peak disk usage 0.01 MB Stderr output <core_client_version>7.16.11</core_client_version> <![CDATA[ <message> Incorrect function. (0x1) - exit code 1 (0x1)</message> <stderr_txt> command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -fragA 00001.500.6mers -fragB 00001.500.4mers -in:file:fasta 00001.fasta -abinitio::increase_cycles 10 -mute all -abinitio::fastrelax -relax::default_repeats 15 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5 -abinitio::use_filters false -ex1 -ex2aro -in:file:boinc_wu_zip cp_ajzjTxIe_YBAABB_ABYBB_AAAAAAXB_AAY_CGGGGGGCCGGGGGCGGGGGGGGCGGGC_1-4_2-5_3-6.pdb_0001_abinitio_1_fold_data.zip -out:file:silent default.out -silent_gz -in:file:native 00001.pdb -out:file:silent_struct_type binary -detect_disulf true -fix_disulf disulf -constraints::cst_file CB_cst -constraints:cst_weight 1 -number_9mer_frags 150 -number_3mer_frags 150 -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 1985841 Using database: database_357d5d93529_n_methylminirosetta_database ERROR: ERROR: FragmentIO: could not open file 00001.500.6mers ERROR:: Exit from: ......srccorefragmentFragmentIO.cc line: 233 BOINC:: Error reading and gzipping output datafile: default.out 11:41:18 (10892): called boinc_finish(1) </stderr_txt> ]]>
8) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 97085) Posted 31 May 2020 by Jim Martin Post: Erich -- A hat-tip to you (and, to Robert, for trying to help/enlighten me). With your suggestion, have now uploaded all the outstanding wu's, with a dozen, downloaded. As in my last previous entry, I still feel that the Boinc software gents need to update Boinc, ASAP, because of Baker Lab's importance. Yes, I'm griping, but -- as a retired hardware engineer (mini-computers, to date myself) -- I know how fast the gents in the corner office want Eco's/Rev's generated. Out the door. . . So, I still can get antsie, at times, when an important Boinc rev. is concerned. Again, hat-tips to you/us all. Let's get a vaccine!
9) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 97039) Posted 31 May 2020 by Jim Martin Post: I'll re-allow more rosetta@home tasks. As for knowledge of normal Microsoft procedures, I don't feel I should have to know all that, to run Baker Lab wu's. After all, "You don't have to be a Scientist to do Science". Well, I'm not a software/IT engineer, either. So, I rely on the experts to make it a simple op. This problem should have never had to be brought to our attention. A fix, before a problem.
10) Message boards : Number crunching : Peer certificate cannot be authenticated with given CA certificates (Message 97038) Posted 31 May 2020 by Jim Martin Post: Erich, et. al. May I suggest that someone with more authority than I have, notify BOINC software engineering, to up-rev BOINC, with our problem. It's certainly impacted some important wu's. Perhaps, this has already been brought to BOINC's attention. If so, I await uploading ops. to commence, with the next BOINC rev.
11) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 97001) Posted 31 May 2020 by Jim Martin Post: Erich -- Thanks, for the info., leading to OneDrive. I installed it, and am now waiting for the uploads It appears there are a lot, ahead of me. Cheers, ps, I installed, w/o (trying) to delete the previous certificate dates. Assume that was ok.
12) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 96989) Posted 31 May 2020 by Jim Martin Post: Robert -- I tried to delete the certificates, after turning off BOINC, but was unsuccessful. Will waiting for BOINC people to address this issue 'be better? No uploading of wu's. It seems it's a BOINC problem, to fix, and not mine (one of 99%). Thanks, for your efforts, however, on ca-bundle.crt ps, I have a Dell E7240, with Windows 7. No problems, until now (Have run rosetta@home, since 2005.)
13) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (5) (Message 77627) Posted 5 Nov 2014 by Jim Martin Post: In folding, can a protein end up in an intermediate state, but not in its lowest energy state? Or, do all proteins manage to arrive at the lowest state?
14) Message boards : Number crunching : minirosetta 2.15 (Message 67998) Posted 9 Oct 2010 by Jim Martin Post: Two enclosures: 1) system boot info. 2) error report. * * * 10/8/2010 11:29:55 PM Starting BOINC client version 6.10.58 for windows_intelx86 10/8/2010 11:29:55 PM log flags: file_xfer, sched_ops, task 10/8/2010 11:29:55 PM Libraries: libcurl/7.19.7 OpenSSL/0.9.8l zlib/1.2.3 10/8/2010 11:29:55 PM Data directory: C:ProgramDataBOINC 10/8/2010 11:29:55 PM Running under account James 10/8/2010 11:29:56 PM Processor: 2 GenuineIntel Intel(R) Core(TM)2 CPU T7200 @ 2.00GHz [Family 6 Model 15 Stepping 6] 10/8/2010 11:29:56 PM Processor: 4.00 MB cache 10/8/2010 11:29:56 PM Processor features: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss htt tm pni ssse3 cx16 nx lm vmx tm2 pbe 10/8/2010 11:29:56 PM OS: Microsoft Windows Vista: Business x86 Edition, Service Pack 2, (06.00.6002.00) 10/8/2010 11:29:56 PM Memory: 2.00 GB physical, 4.23 GB virtual 10/8/2010 11:29:56 PM Disk: 142.71 GB total, 89.40 GB free 10/8/2010 11:29:56 PM Local time is UTC -4 hours 10/8/2010 11:29:56 PM No usable GPUs found 10/8/2010 11:29:57 PM rosetta@home URL http://boinc.bakerlab.org/rosetta/; Computer ID 1324493; resource share 100 10/8/2010 11:29:57 PM climateprediction.net URL http://climateprediction.net/; Computer ID 819110; resource share 100 10/8/2010 11:29:57 PM Einstein@Home URL http://einstein.phys.uwm.edu/; Computer ID 1616831; resource share 50 10/8/2010 11:29:57 PM lhcathome URL http://lhcathome.cern.ch/lhcathome/; Computer ID 9825728; resource share 100 10/8/2010 11:29:57 PM Quake-Catcher Network URL http://qcn.stanford.edu/sensor/; Computer ID 9909; resource share 100 10/8/2010 11:29:57 PM SETI@home URL http://setiathome.berkeley.edu/; Computer ID 5490317; resource share 50 10/8/2010 11:29:57 PM Einstein@Home General prefs: from Einstein@Home (last modified 08-Jul-2010 11:24:21) 10/8/2010 11:29:57 PM Einstein@Home Computer location: home 10/8/2010 11:29:57 PM General prefs: using separate prefs for home 10/8/2010 11:29:57 PM Preferences: 10/8/2010 11:29:57 PM max memory usage when active: 1022.66MB 10/8/2010 11:29:57 PM max memory usage when idle: 1840.78MB 10/8/2010 11:30:10 PM max disk usage: 50.00GB 10/8/2010 11:30:10 PM don't use GPU while active 10/8/2010 11:30:10 PM (to change preferences, visit the web site of an attached project, or select Preferences in the Manager) 10/8/2010 11:30:10 PM Not using a proxy 10/8/2010 11:30:10 PM Quake-Catcher Network Restarting task qcnk_sc300_sta200_087854_0 using qcnsensor version 562 10/8/2010 11:30:40 PM rosetta@home Restarting task rs_stg0_lrlx_t363__run1_SAVE_ALL_OUT_19372_6575_0 using minirosetta version 215 10/8/2010 11:30:40 PM climateprediction.net Sending scheduler request: To send trickle-up message. 10/8/2010 11:30:40 PM climateprediction.net Not reporting or requesting tasks 10/8/2010 11:30:44 PM climateprediction.net Scheduler request completed 10/8/2010 11:30:44 PM climateprediction.net Message from server: Project is temporarily shut down for maintenance 10/8/2010 11:32:27 PM rosetta@home Restarting task mem_widd_run02_Mevn_A_2ksy_SAVE_ALL_OUT_IGNORE_THE_REST_22157_49662_0 using minirosetta version 215 * * * BoincLogX - History nr / date error_txt project_name domain_name user_total_credit user_expavg_credit CPU error 1596 2010.10.08 13:10:49 rosetta@home james-pc 183398.626579 169.348558 00:00:59 true 1st Entry: result_name rs_stg0_lrlx_t311_run1_SAVE_ALL_OUT_19356_2623_0_0 error_txt The system cannot find the path specified. (0x3) - exit code 3 (0x3);[2010-10-8 12:32:52]::BOINC::Initializing ... ok. [2010-10-8 12:32-52] * * * * * User note: The above error/WU failure appeared to be generated, immediately after an outputted window, "Microsoft Visual C++ Runtime Library", was exited. Prior to deleating it, the system ran slower than normal. Also, after exiting, normal system speed resumed. The failures occurred on three occasions, although only one is listed, above. BoincLogX information was entered, by hand, by this user. Also, approx. 1.29 GB mem was accessed, max. * * * * * 2nd entry, with the following: Rosetta Mini 2.15 Mem_widd_run02_Mevn_A_2key_SAVE_ALL_OUT_IGNORE_THE_REST_22157_49662_0. Used phys mem was in approx. 51%-67% range. No other WU's were run, except QCN@home. After approx. 23+% run-time, with mem. usage varying from an average of 465 MB, to a max of 1.29 GB, a second Rosetta Mini 2.15 WU enabled, even though it had been previously been placed in a "suspended" state: rs_sth0_lrlx_t363_run1_SAVE_ALL_OUT_19372_6575_0. It resulted in Used phys mem to increase to 99% range, with mem usage, by ...Mem_widd..., about 1.934GB, and approx. 393.7MB, for rs_sth0... The system, temporarily, locked up (cursor movement "froze"), until ...Mem_widd... was halted, by the pgrm., and placed in a "Waiting for memory" mode. * * * * * Summary: 1) Rosetta Mini 2.15 WU memory requirements appear to necessitate restricting all other pgrms. from running, to avoid maxing out memory. 2) Successful WU run not possible, because of the entry of a 2nd Rosetta WU (reason unk.). Conclusion: 1) If possible, enable the user the option of allocating memory for Rosetta (ref. Garli, Lattice project). This might free up memory for other projects, for those with multiple CPU's (my system has two); Rosetta@home might lose some users, if this issue cannot be resolved. I had to drop Garli, for this reason. 2) Again, if possible, enable the program to function within the allocated memory. 3) Determine the cause of the activation, from "suspended" state, of another Rosetta WU (If it had not activated, the original WU pbly. would have successfully completed.). * * * Pardon the verbosity; hopefully, it will prove enlightening. JM
15) Questions and Answers : Windows : Work Units Not Downloading (Message 39451) Posted 15 Apr 2007 by Jim Martin Post: The Tasks tab shows I have workunits downloading, but nothing ever gets downloaded. Under the Transfers tab it shows there are units downloading and pending, but no progress is ever shown on these. Everything seems to be stuck. I have tried reseting the project, I have tried exiting BOINC and restarting the computer. Nothing works. Dead in the water for now. Tom -- Same pblm., with my (Sony VAIO, w/VISTA). The only program running effortlessly is climateprediction.net. Am having to sort the wheat from the chaff. Perhaps one of us, including Baker Lab, can come up with a solution. Cheers, JM Tom -- WU downloads now successful; hat-tip to Baker Lab. Hope you've experienced same. Reguards, JM
16) Questions and Answers : Windows : Work Units Not Downloading (Message 39406) Posted 15 Apr 2007 by Jim Martin Post: The Tasks tab shows I have workunits downloading, but nothing ever gets downloaded. Under the Transfers tab it shows there are units downloading and pending, but no progress is ever shown on these. Everything seems to be stuck. I have tried reseting the project, I have tried exiting BOINC and restarting the computer. Nothing works. Dead in the water for now. Tom -- Same pblm., with my (Sony VAIO, w/VISTA). The only program running effortlessly is climateprediction.net. Am having to sort the wheat from the chaff. Perhaps one of us, including Baker Lab, can come up with a solution. Cheers, JM
17) Questions and Answers : Windows : not enough memory (Message 37553) Posted 6 Mar 2007 by Jim Martin Post: There are a number of tasks which require more then the minimum amount of memory. The minimum is 256MB. A computer with 256MB of memory is able to run most Rosetta work, but larger proteins and some of the simulations being run with HINGE and DOCking tasks require study of two proteins at the same time. These require more memory. So, the version 5.48 of Rosetta is not what resolved your problem getting work. What happened was work units became available on the Rosetta server which can run on systems with 256MB of memory. You're certainly right; the "problem" has resurfaced, today. Will see about upgrading my computer's memory, if possible. Thanks, for the reply. Jim M.
18) Questions and Answers : Windows : not enough memory (Message 37498) Posted 5 Mar 2007 by Jim Martin Post: Problem (#37440) resolved, following download of R@H 5.48. JM
19) Questions and Answers : Windows : not enough memory (Message 37440) Posted 5 Mar 2007 by Jim Martin Post: Until this afternoon, have been able to successfully complete Rosetta@home WU's. Now, server err. mess.' say, "Your computer has 447.48 MB of mem., and a job requires 476 MB. No work will be sent." Have modified my BOINC gen. mem. prefs. from 50% to 60%, plus uninstalling un-needed programs on my system. Note: No major memory demands have been made to my computer, before/after this pblm. as arisen. Pblm. remains, after BOINC 5.8.15 installed. My system (Presario Notebook 3000, w/pentium 4, Windows XP (SP/4), 512 MB tot. phys mem, 155.71 MB avail phys mem., 2.00 GB tot. virt. mem., & 1.96 GB avail. virt. mem. Ques'.: Have the Rosetta@home mem. requirements increased (to 476 MB), or will I have to ax a few more programs (I don't recall what the orig. mem. reqirements for Rosetta were.)? Jim Martin
20) Message boards : Number crunching : Bug Reports for R@h Server Update to BOINC version 5.9.2 (Message 36270) Posted 8 Feb 2007 by Jim Martin Post: Am out of WU's for the first time. Is Baker lab catching its breath, or have I got lost in the upgrade? Thanks, in advance, for any "heads-up". Jim M. Again, a "Reset project" enabled WU downloads. Thank-you, David Kim, for responding to my question. Jim M.

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