Posts by P . P . L .

1) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 79965) Posted 29 Apr 2016 by P . P . L . Post: You've broken something, I'm getting this message now on all my Ubuntu rigs. Fri 29 Apr 2016 12:13:59 AEST \| rosetta@home \| Sending scheduler request: Requested by user. Fri 29 Apr 2016 12:13:59 AEST \| rosetta@home \| Reporting 6 completed tasks, requesting new tasks for CPU Fri 29 Apr 2016 12:14:04 AEST \| rosetta@home \| Scheduler request completed: got 0 new tasks Fri 29 Apr 2016 12:14:04 AEST \| rosetta@home \| No work sent Fri 29 Apr 2016 12:14:04 AEST \| rosetta@home \| Rosetta Mini for Android is not available for your type of computer.
2) Message boards : Number crunching : Minirosetta 3.73-3.78 (Message 79809) Posted 28 Mar 2016 by P . P . L . Post: Hi krypton. I've had 9 of your tasks fail on one rig just today so far, all with the same error like so. https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=1622019 P76481_PF12034_90-575_300-486_EN_MAP_hyb_cst_v02_i01_t000__krypton_SAVE_ALL_OUT_03_09_341621_123_0 <core_client_version>7.0.27</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63) </message> <stderr_txt> (EDITED OUT THE REST) Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_f513f38.zip Unpacking WU data ... Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/P76481_PF12034_90-575_300-486_EN_MAP_hyb_cst_v02_i01_t000__krypton.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... BOINC:: Worker startup. Starting watchdog... Watchdog active. # cpu_run_time_pref: 14400 SIGSEGV: segmentation violation Stack trace (22 frames): [0xd98d38f] [0xb7766404] [0xb6d9849] [0xb8ef314] [0xb8f1a90] [0xb8f4b33] [0xb90ae55] [0xb7ecda9] [0xb8cebea] [0xc2ff844] [0xc31427f] [0xabe3c0b] [0x8d92b93] [0xb04b065] [0xb05021c] [0xb0f6a35] [0xb0f959e] [0xb1b8bc3] [0xb1b524d] [0x8057071] [0xda24988] [0x8048131] Exiting... </stderr_txt>
3) Message boards : Rosetta@home Science : Zika virus. (Message 79456) Posted 29 Jan 2016 by P . P . L . Post: Hi. So is anyone at your labs working on this one, it seems to becoming a big problem. As there is no treatment or cure as yet.
4) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 79434) Posted 23 Jan 2016 by P . P . L . Post: Hi. Since there is not a tread for app 3.67 I'll put this here, it erred after 48 min this morning it was one of the last for the old app I had left. P75901_PF03239_1-266_REDO_cst_v02_t000__krypton_SAVE_ALL_OUT_03_09_320949_609_2 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=710119997 Starting work on structure: _00001 # cpu_run_time_pref: 14400 ERROR: unknown atom_name: VRT N ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 3187 [35m[0xd0a3b23] [0xcaa8dc9] [0xa2e271f] [0xa2e49d2] [0xa398686] [0xa2a7765] [0xa2aafdd] [0xabc1534] [0xabb9c72] [0x89dcccf] [0x89e0bfd] [0x89f950a] [0x89a4dbe] [0x89aeab5] [0x8049c59] [0xd27d8f8] [0x8048131] [0m* glibc detected * ../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.67_i686-pc-linux-gnu: munmap_chunk(): invalid pointer: 0x12d13f20 *** ======= Backtrace: ========= [0xd2aac45] [0xd26bfe1] [0xc9a1813] [0xc967b46] [0xc036fe7] [0xc037be8] [0x89a7898] [0x89aeab5] [0x8049c59] [0xd27d8f8] [0x8048131] ======= Memory map: ======== 08048000-0dff8000 r-xp 00000000 08:01 133486 /var/lib/boinc-client/projects/boinc.bakerlab.org_rosetta/minirosetta_3.67_i686-pc-linux-gnu 0dff8000-0e001000 rw-p 05faf000 08:01 133486 /var/lib/boinc-client/projects/boinc.bakerlab.org_rosetta/minirosetta_3.67_i686-pc-linux-gnu 0e001000-0e304000 rw-p 00000000 00:00 0 0f98d000-131e1000 rw-p 00000000 00:00 0 [heap] b4500000-b45b5000 rw-p 00000000 00:00 0 b45b5000-b4600000 ---p 00000000 00:00 0 b4600000-b46b6000 rw-p 00000000 00:00 0 b46b6000-b4700000 ---p 00000000 00:00 0 b4700000-b4800000 rw-p 00000000 00:00 0 b4900000-b49d7000 rw-p 00000000 00:00 0 b49d7000-b4a00000 ---p 00000000 00:00 0 b4a00000-b4b00000 rw-p 00000000 00:00 0 b4b00000-b4bfb000 rw-p 00000000 00:00 0 b4bfb000-b4c00000 ---p 00000000 00:00 0 b4c00000-b4d00000 rw-p 00000000 00:00 0 b4d00000-b4e00000 rw-p 00000000 00:00 0 b4f00000-b5000000 rw-p 00000000 00:00 0 b505f000-b5100000 rw-p 00000000 00:00 0 b5100000-b5200000 rw-p 00000000 00:00 0 b5300000-b5400000 rw-p 00000000 00:00 0 b549d000-b5741000 rw-p 00000000 00:00 0 b5741000-b5742000 ---p 00000000 00:00 0 b5742000-b6344000 rw-p 00000000 00:00 0 [stack:15704] b6344000-b7658000 rw-s 00000000 08:01 134834 /var/lib/boinc-client/slots/6/boinc_minirosetta_6 b7658000-b7659000 ---p 00000000 00:00 0 b7659000-b765c000 rw-p 00000000 00:00 0 [stack:15686] b765c000-b765e000 rw-s 00000000 08:01 134716 /var/lib/boinc-client/slots/6/boinc_mmap_file b765e000-b775b000 rw-p 00000000 00:00 0 b775b000-b775c000 r-xp 00000000 00:00 0 [vdso] bfac0000-bfaf1000 rw-p 00000000 00:00 0 [stack] SIGABRT: abort called Stack trace (16 frames): [0xd1d9dff] [0xb775b404] [0xd2c86a0] [0xd285880] [0xd29f2db] [0xd2aac45] [0xd26bfe1] [0xc9a1813] [0xc967b46] [0xc036fe7] [0xc037be8] [0x89a7898] [0x89aeab5] [0x8049c59] [0xd27d8f8] [0x8048131] Exiting... </stderr_txt> ]]> Validate state Invalid Claimed credit 19.6384448376039 Granted credit 0 application version 3.67
5) Message boards : Number crunching : Weird deadline (Message 79215) Posted 13 Dec 2015 by P . P . L . Post: Hi. I've been hit by the same bug, all new rb tasks have a deadline for the 15/12 tomorrow for me. It's to short something needs, unfixing!
6) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 78941) Posted 18 Oct 2015 by P . P . L . Post: Hi. The first w.u. with 3.66 app has run & returned no problems from my xeon, my other rigs have a backlog of 3.65 w.u. as I run a two days cashe they will be on it by tonight my time.
7) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 78918) Posted 16 Oct 2015 by P . P . L . Post: I had to do "sudo apt-get install freeglut3" on three of my Ubuntu rigs to get them working here again. Not good.
8) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 78909) Posted 14 Oct 2015 by P . P . L . Post: Hi. Well it was supposed to be fixed on Ralph already, guess not! http://ralph.bakerlab.org/forum_thread.php?id=567&nowrap=true#5898
9) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 78907) Posted 14 Oct 2015 by P . P . L . Post: Hi. I hope there is a fix for this error on ubuntu rigs, I only have a few 3.62 tasks left on my other rigs( about a days worth ) the rig that got all the errors was the first to get the 3.65 app & I have stopped it getting any new work, no point with all the errors. I'm not going to let my other rigs update to a new app until a fix is out for linux/ubuntu.
10) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 78906) Posted 13 Oct 2015 by P . P . L . Post: Hi. I've had 15 tasks so far error the same, one after the other. The rig is running Ubuntu 14.04lts x64 with Boinc 7.2.42. And it has 32bit libs installed for some other projects that need them. ========================================= <core_client_version>7.2.42</core_client_version> <![CDATA[ <message> process exited with code 127 (0x7f, -129) </message> <stderr_txt> ../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.65_x86_64-pc-linux-gnu: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory </stderr_txt> ]]>
11) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 78700) Posted 5 Sep 2015 by P . P . L . Post: More validate errors this morning. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685225333 FFD__1885c0418f264a32e397ffab4318bbf3_abinitioDocking_15_08_14_27_34_globalDocking_6_SAVE_ALL_OUT_298551_4_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 201 starting structures 14379.4 cpu seconds This process generated 201 decoys from 201 attempts ====================================================== BOINC :: WS_max 1.35666e-166 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ================================================= https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685381286 FFD__7a0bd05235f76b7c212c91d604e6b896_abinitioDocking_15_08_10_13_49_globalDocking_0_SAVE_ALL_OUT_300974_4_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 261 starting structures 14384 cpu seconds This process generated 261 decoys from 261 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ================================================= https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685381283 FFD__7a0bd05235f76b7c212c91d604e6b896_abinitioDocking_15_08_10_13_49_localDocking_8_SAVE_ALL_OUT_300974_4_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 273 starting structures 14369.2 cpu seconds This process generated 273 decoys from 273 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ========================================================= And more FFD validate errors. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685299006 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685330215 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685308187 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685291696 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685378382
12) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 78697) Posted 5 Sep 2015 by P . P . L . Post: You wanted more, enjoy. My rigs got validate error on these.( See below ) https://boinc.bakerlab.org/rosetta/workunit.php?wuid=682557581 1da894305e9a610bd5667cc03eeff6fd_hhhcommon_15_08_20_46_44_globalDocking_4_SAVE_ALL_OUT_292589_6_1 # cpu_run_time_pref: 14400 ====================================================== DONE :: 710 starting structures 14388.2 cpu seconds This process generated 710 decoys from 710 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> -------------------------------------------------- https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685290795 FFD__368f3629c8dc09f0ae4d4402193bd7e0_abinitioDocking_15_08_21_50_55_globalDocking_5_SAVE_ALL_OUT_301979_6_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 425 starting structures 14368.3 cpu seconds This process generated 425 decoys from 425 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> -------------------------------------------------------------- https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685229735 FFD__368f3629c8dc09f0ae4d4402193bd7e0_abinitioDocking_15_08_21_50_55_globalDocking_5_SAVE_ALL_OUT_301979_6_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 425 starting structures 14368.3 cpu seconds This process generated 425 decoys from 425 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ---------------------------------------------------------- https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685229735 FFD__61553d966fba4a94dcf25c2a24befc61_abinitioDocking_15_08_14_11_53_globalDocking_4_SAVE_ALL_OUT_299060_4_0 # cpu_run_time_pref: 14400 ====================================================== DONE :: 253 starting structures 14362.2 cpu seconds This process generated 253 decoys from 253 attempts ====================================================== BOINC :: WS_max 0 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> ]]> ----------------------------------------- More validate errors. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685188207 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=682334661 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181282 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181270 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181239 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181197 ============================================================= These are Compute errors. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685185054 https://boinc.bakerlab.org/rosetta/workunit.php?wuid=685181238
13) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78660) Posted 1 Sep 2015 by P . P . L . Post: Uploads are timing out again. Tue 01 Sep 2015 20:54:29 AEST \| \| Project communication failed: attempting access to reference site Tue 01 Sep 2015 20:54:29 AEST \| rosetta@home \| Temporarily failed upload of FFD__f0bc89e7fe6046579a922ef0133c6fb0_abinitioDocking_15_08_07_25_51_globalDocking_4_SAVE_ALL_OUT_300917_2_0_0: transient HTTP error Tue 01 Sep 2015 20:54:29 AEST \| rosetta@home \| Backing off 2 min 29 sec on upload of FFD__f0bc89e7fe6046579a922ef0133c6fb0_abinitioDocking_15_08_07_25_51_globalDocking_4_SAVE_ALL_OUT_300917_2_0_0 Tue 01 Sep 2015 20:54:31 AEST \| \| Internet access OK - project servers may be temporarily down.
14) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78659) Posted 1 Sep 2015 by P . P . L . Post: Uploads are timing out again. Tue 01 Sep 2015 20:54:29 AEST \| \| Project communication failed: attempting access to reference site Tue 01 Sep 2015 20:54:29 AEST \| rosetta@home \| Temporarily failed upload of FFD__f0bc89e7fe6046579a922ef0133c6fb0_abinitioDocking_15_08_07_25_51_globalDocking_4_SAVE_ALL_OUT_300917_2_0_0: transient HTTP error Tue 01 Sep 2015 20:54:29 AEST \| rosetta@home \| Backing off 2 min 29 sec on upload of FFD__f0bc89e7fe6046579a922ef0133c6fb0_abinitioDocking_15_08_07_25_51_globalDocking_4_SAVE_ALL_OUT_300917_2_0_0 Tue 01 Sep 2015 20:54:31 AEST \| \| Internet access OK - project servers may be temporarily down.
15) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78611) Posted 30 Aug 2015 by P . P . L . Post: Half the server page is now in the RED, No new tasks ready. Still having problems uploading & when they do I'm getting validate errors.?
16) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78609) Posted 29 Aug 2015 by P . P . L . Post: Uploads are timing out for rosetta, all other projects are o.k. Downloads form rosetta are are working for now! Sun 30 Aug 2015 08:21:17 AEST \| \| Project communication failed: attempting access to reference site Sun 30 Aug 2015 08:21:17 AEST \| rosetta@home \| Temporarily failed upload of gr081015_HEEHheeh_go3_nods_new_heeh_12.bp_r3_pass_20150721035246_fragments_fold_SAVE_ALL_OUT_277850_62_1_0: transient HTTP error Sun 30 Aug 2015 08:21:17 AEST \| rosetta@home \| Backing off 6 min 54 sec on upload of gr081015_HEEHheeh_go3_nods_new_heeh_12.bp_r3_pass_20150721035246_fragments_fold_SAVE_ALL_OUT_277850_62_1_0 Sun 30 Aug 2015 08:21:17 AEST \| rosetta@home \| Temporarily failed upload of FFD__8091b9a093b6f6d8e0c04cb95e4c345c_abinitioDocking_15_08_09_29_22_globalDocking_7_SAVE_ALL_OUT_301200_1_0_0: transient HTTP error Sun 30 Aug 2015 08:21:17 AEST \| rosetta@home \| Backing off 4 min 14 sec on upload of FFD__8091b9a093b6f6d8e0c04cb95e4c345c_abinitioDocking_15_08_09_29_22_globalDocking_7_SAVE_ALL_OUT_301200_1_0_0 Sun 30 Aug 2015 08:21:17 AEST \| rosetta@home \| Started upload of fd_t009___robetta_IGNORE_THE_REST_03_09_292878_4889_0_0 Sun 30 Aug 2015 08:21:19 AEST \| \| Internet access OK - project servers may be temporarily down.
17) Message boards : Number crunching : Minirosetta 3.59 (Message 78554) Posted 7 Aug 2015 by P . P . L . Post: Hi natteruw. The problem was that there was a bad kernel update that seemed to cause those errors, a few days later they put out a fix for whatever the problem was. I've put that rig back on Rosetta and it's still going fine now, it was only the one AMD rig for some reason, my other Intel rigs didn't have any problems. Thanks for asking. :)
18) Message boards : Number crunching : Minirosetta 3.59 (Message 78551) Posted 6 Aug 2015 by P . P . L . Post: FFD__5strand14helixWYY_filteredloops_321_0001_dock_PD1CancerImmunotherapy_15_08_07_40_34_globalDocking_4_SAVE_ALL_OUT_277259_19 crashed immediately on Linux (nothing useful in stderr): it also crashed on a Windows machine ------------------------------------------------ I,ve had a few of those error as well.
19) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78515) Posted 30 Jul 2015 by P . P . L . Post: I started getting this message now. Thu 30 Jul 2015 16:08:19 AEST \| rosetta@home \| Scheduler request completed Thu 30 Jul 2015 16:08:19 AEST \| rosetta@home \| Server error: can't attach shared memory I can't report any of your tasks.
20) Message boards : Number crunching : Minirosetta 3.59 (Message 78511) Posted 28 Jul 2015 by P . P . L . Post: Getting a lot of errors on these tasks. Edit // I've taken the rig that started getting all these errors since it got new work this morning off rosetta. C3C3P213xtal_3fuy_3nz2_004017_0005_0001.pdb_150726UN_15_07_09_24_22_globalDocking_2_SAVE_ALL_OUT_276123_35_0 <core_client_version>7.2.42</core_client_version> <![CDATA[ <message> process exited with code 193 (0xc1, -63) SIGSEGV: segmentation violation Stack trace (14 frames): [0xccc64cf] [0xf7736410] [0xcce9213] [0xcce2ade] [0xcce47ec] [0xccebcd4] [0xccec12a] [0xccd3229] [0xccd33c9] [0xccd0144] [0xccd107d] [0x80534f9] [0xcd5e0d8] [0x8048131] Exiting... </stderr_txt>

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