Message boards : RALPH@home bug list : minirosetta 2.03
Author | Message |
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mtyka Volunteer moderator Project developer Project scientist Send message Joined: 19 Mar 08 Posts: 79 Credit: 0 RAC: 0 |
Fixes a stack overflow bug in 2.02. Please report issues here :) |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 912 Credit: 1,892,541 RAC: 294 |
No wu, no debug.... |
ANCHULA-MARK Send message Joined: 2 Mar 08 Posts: 2 Credit: 100,848 RAC: 0 |
11 out of 15 died within 30 secs the other 4 are still running @ 10+mins Task ID 1686211 Name homopt1.t369_.t369_.IGNORE_THE_REST.S_00001_0000857_00042.pdb.JOB_13568_1_0 Workunit 1489861 ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148 ERROR:: Exit from: ....srccoreconformationConformation.cc line: 234 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> |
Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0 |
Have so far had 5 fail and 3 succeed. Result 1686388 had this error ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148 ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234 BOINC:: Error reading and gzipping output datafile: default.out And results 1687361 1687351 1687325 1687296 all had the following error ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 139 fold_tree nres: 140 ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234 BOINC:: Error reading and gzipping output datafile: default.out |
Snagletooth Send message Joined: 4 May 07 Posts: 67 Credit: 134,427 RAC: 0 |
homopt1.t369_.t369_.IGNORE_THE_REST.S_00002_0000860_027.pdb.JOB_13568_1 homopt1.t369_.t369_.IGNORE_THE_REST.S_00002_0000712_020.pdb.JOB_13568_1 after 19-22 seconds ended with: ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148 ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish homopt1.t331_.t331_.IGNORE_THE_REST.S_00002_0000988_00044.pdb.JOB_13563_1 ended after 6 seconds with ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 139 fold_tree nres: 140 ERROR:: Exit from: src/core/conformation/Conformation.cc line: 234 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish homopt1.t368_.t368_.IGNORE_THE_REST.S_00001_0000086_00055.pdb.JOB_13567_1_0 ran successfully completing 11 decoys in 13877 seconds homopt1.t313_.t313_.IGNORE_THE_REST.S_00001_0000429_10056.pdb.JOB_13559_1 appears to be crunching successfully, currently working on Model 1 step 4206 after one hour. |
Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0 |
Have so far had 5 fail and 3 succeed. Have had another 11 fail with a similar error, all exit at the same line (234) only the conformation error varies with a few different numbers. They all error after less than 20 minutes. |
I _ quit Send message Joined: 13 Jan 09 Posts: 44 Credit: 88,562 RAC: 0 |
6 tasks with the same kind of bugs as listed by the others: ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 147 fold_tree nres: 148 ERROR:: Exit from: ....srccoreconformationConformation.cc line: 234 BOINC:: Error reading and gzipping output datafile: default.out https://ralph.bakerlab.org/result.php?resultid=1686083 https://ralph.bakerlab.org/result.php?resultid=1686082 https://ralph.bakerlab.org/result.php?resultid=1686077 and ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 154 fold_tree nres: 155 ERROR:: Exit from: ....srccoreconformationConformation.cc line: 234 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish https://ralph.bakerlab.org/result.php?resultid=1686064 https://ralph.bakerlab.org/result.php?resultid=1686063 https://ralph.bakerlab.org/result.php?resultid=1686062 |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 912 Credit: 1,892,541 RAC: 294 |
https://ralph.bakerlab.org/result.php?resultid=1693258 ERROR: Cannot open PDB file "native.pdb" ERROR:: Exit from: ....srccoreiopdbpose_io.cc line: 170 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish |
Saenger Send message Joined: 28 Feb 06 Posts: 13 Credit: 67,395 RAC: 0 |
I got a bunch of errors, but more valids 'til now. Typical error: stderr out <core_client_version>6.10.17</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> [2010- 1- 5 2:32: 2:] :: BOINC:: Initializing ... ok. [2010- 1- 5 2:32: 2:] :: BOINC :: boinc_init() BOINC:: Setting up shared resources ... ok. BOINC:: Setting up semaphores ... ok. BOINC:: Updating status ... ok. BOINC:: Registering timer callback... ok. BOINC:: Worker initialized successfully. Registering options.. Registered extra options. Initializing broker options ... Registered extra options. Initializing core... Initializing options.... ok Options::initialize() Options::adding_options() Options::initialize() Check specs. Options::initialize() End reached Loaded options.... ok Processed options.... ok Initializing random generators... ok Initialization complete. Setting WU description ... Unpacking zip data: ../../projects/ralph.bakerlab.org/minirosetta_database_rev34260.zip Unpacking WU data ... Unpacking data: ../../projects/ralph.bakerlab.org/job_boinc_t373__loopbuild_threading_tex.boinc.zip Setting database description ... Setting up checkpointing ... Setting up graphics native ... ERROR: Cannot open PDB file "native.pdb" ERROR:: Exit from: src/core/io/pdb/pose_io.cc line: 170 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish </stderr_txt> ]]> Grüße vom Sänger |
ramostol Send message Joined: 29 Mar 07 Posts: 24 Credit: 31,121 RAC: 0 |
One wu errored out in the recent bunch of tasks: job_boinc_t318__filtered_loopbuild_threading_tex_IGNORE_THE_REST_13730_7_0 ERROR: can't find residue type at pos 11in sequence MTQVLVRNGI QAVGDGLTSL IIVGKKSVLK NVTFEGKFKE VAQKFVTDGD SWNSMISRIP ASGRHPLHYE LAHLITVPDASSRGNTPTNA HSIYKELKPI NYPEDTKNVH FVLFAEYPDV LSHVAAIART FCKFSMKTSG IRELNVNIDV VCDKLTNEDAVFLTDLSESV RETARLIDTP ANILTTDALV DEAVKVGNAT GSKITVIRGE ELLKAGFGGI YHVGKAGPTP PAFVVLSHEVPGSTEHIALV GKGVVYDTGG LQIKTKTGMP NMKRDMGGAA GMLEAYSALV KHGFSQTLHA CLCIVENNVS PIANKPDDIIKMLSGKTVEI NNTDAEGRLI LADGVFYAKE TLKATTIFDM ATLTGAQAWL SGRLHGAAMT NDEQLENEII KAGKASGDLVAPMLFAPDLF FGDLKSSIAD MKNSNLGKMD GPPSAVAGLL IGAHIGFGEG LRWLHLDIAA PAEVGDRGTG YGPALFSTLLGKYTSVPMLK Q ERROR:: Exit from: src/core/chemical/util.cc line: 379 BOINC:: Error reading and gzipping output datafile: default.out |
robertmiles Send message Joined: 13 Jan 09 Posts: 103 Credit: 331,865 RAC: 0 |
One ran about 11 hours instead of the 6 hours I asked for, and produced just one decoy. Appears OK otherwise, though. https://ralph.bakerlab.org/result.php?resultid=1694077 |
Snagletooth Send message Joined: 4 May 07 Posts: 67 Credit: 134,427 RAC: 0 |
ha_notyr_3gbn_1ksk_6Jan2010_13738_2_0 ran for the full 4 hour preferred runtime to complete 567 decoys. It also ran the 4 hours straight through which is quite unexpected. Checking the current short term debts the new Ralph wu I received almost two hours ago won't begin crunching for at about 3 more hours. Every other wu appears to be switching out as expected which also suggests it may indeed be a case of Ralph not giving way when asked rather that BOINC suddenly ignoring its preferences. Earlier a similarly named wu ha_notyr_3gbn_1osh_6Jan2010_13734_2_0 wrapped things up after completing 100 models in 2719.38 seconds. Snags |
[B^S]ABoskovich Send message Joined: 22 Feb 06 Posts: 1 Credit: 37,791 RAC: 0 |
I have a wu running 18+ hours showing 5,4% complete. Should I abort? |
Snagletooth Send message Joined: 4 May 07 Posts: 67 Credit: 134,427 RAC: 0 |
I have a wu running 18+ hours showing 5,4% complete. Should I abort? Is that 18 hours of CPU time or wall clock time? (The newer BOINC managers show both.)If CPU time you could try quitting and restarting BOINC (that's quitting the BOINC client not merely closing the manager). Sometimes this gets a stuck WU moving again, sometimes it errors out immediately upon restart; if neither, nothing left to do but abort. |
coturnix Send message Joined: 5 Jan 10 Posts: 9 Credit: 196,185 RAC: 0 |
Task: 1703705 Workunit: ha_notyr_3gbn_2z84_6Jan2010_13734_1 BOINC:: Worker startup. Starting watchdog... Watchdog active. SIGSEGV: segmentation violation Crashed executable name: minirosetta_2.03_i686-apple-darwin built using BOINC library version 6.5.0 Machine type Intel 80486 (32-bit executable) System version: Macintosh OS 10.5.8 build 9L30 Thu Jan 7 06:48:34 2010 Same workunit segfaults on Windows. |
coturnix Send message Joined: 5 Jan 10 Posts: 9 Credit: 196,185 RAC: 0 |
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coturnix Send message Joined: 5 Jan 10 Posts: 9 Credit: 196,185 RAC: 0 |
Task 1707216 (homopt_cstmc_1.t317_.t317_.IGNORE_THE_REST.S_00006_0000222_090.pdb.JOB_13800_1) Task 1707217 (homopt_cstmc_1.t317_.t317_.IGNORE_THE_REST.S_00006_0000272_00016.pdb.JOB_13800_1) Task 1707218 (homopt_cstmc_1.t317_.t317_.IGNORE_THE_REST.S_00006_0000781_045.pdb.JOB_13800_1) BOINC:: Worker startup. Starting watchdog... Watchdog active. FNAME: native.pdb FNAME: native.pdb ERROR: [ERROR] Unable to open constraints file: /work/tex/projects/cm/benchmark/cross_filt/t317_/t317_.aln_list_mike_chosen_bestaln.alns.combined.csts ERROR:: Exit from: ....srccorescoringconstraintsConstraintIO.cc line: 332 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish |
Snagletooth Send message Joined: 4 May 07 Posts: 67 Credit: 134,427 RAC: 0 |
homopt_cstmc_1.t317_.t317_.IGNORE_THE_REST.S_00001_0000752_10003.pdb.JOB_13800_1_0 process exited with code 1 (0x1, -255) ERROR: [ERROR] Unable to open constraints file: /work/tex/projects/cm/benchmark/cross_filt/t317_/t317_.aln_list_mike_chosen_bestaln.alns.combined.csts ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 332 BOINC:: Error reading and gzipping output datafile: default.out |
Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0 |
Had an error on this work unit 1719676 ERROR: [ERROR] Unable to open constraints file: i2240.dist_csts ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 332 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish |
Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0 |
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minirosetta 2.03
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