Posts by Snagletooth

41) Message boards : RALPH@home bug list : minirosetta 1.80 (Message 4858) Posted 9 Jul 2009 by Snagletooth Post: 2 more quick errors about 12 minutes in: frb_0_8__rnd2_aln_list_mike_chosen_bestaln.alns.combined.csts_hb_t362__IGNORE_THE_REST_1Z54A_2_11448_1_0 frb_0_8__rnd2_aln_list_mike_chosen_bestaln.alns.combined.csts_hb_t362__IGNORE_THE_REST_1NJKA_10_11448_1_0 Hbond tripped: [2009- 7- 9 2:41:29:] interpolate rotamers bin out of range: MET_p:NtermProteinFull 0 nan -60.8264 -60.9057 -68.7799 27 27 10 11 2147483649 22 0 nan ERROR:: Exit from: src/core/scoring/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh line: 590 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish Snags
42) Message boards : RALPH@home bug list : minirosetta 1.80 (Message 4852) Posted 1 Jul 2009 by Snagletooth Post: Couple of quick errors: BOINC_ABRELAX_1itf_CS_DISTEST_SAVE_ALL_OUT_11247_4_0 ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1itf.cs.set1.zip does not exist! ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish BOINC_ABRELAX_1ry3_NN_DISCONTROL_SAVE_ALL_OUT_11248_9_1 ERROR: in::file::boinc_wu_zip /work/rvernon/disulfides/TARGETS/zipfiles/zipfile.1ry3.cs.set1.zip does not exist! ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 114 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish Snags
43) Questions and Answers : Wish list : Different settings for each computer? (Message 4824) Posted 17 May 2009 by Snagletooth Post: Now that I have two computers, I'd like to have different settings for the two on how much weight each project gets, and also different values for a few other settings. Could BOINC be updated to allow this option on all projects? This is already available. You can set separate preferences for up to four different venues (default, home, school, work). Go to your account page and click on "computing preferences". These settings are for the default venue. Scroll to the bottom of the page and you should see three links to add separate preferences for the other venues. Pick one, let's say work, and set the preferences you want for your second computer. Go back to your account page and do the same for ralph@home preferences. Go back to your account page, find the "computers on this account" line and click "view". Click the computer id#(far left column) for the computer in question. Scroll to "location"(near the bottom) and select "work". Hit update. Open BOINC manager, projects tab, select ralph@home, click update. No guarantees , mind you, but I think this should get you what you want. Snags
44) Message boards : RALPH@home bug list : Minirosetta 1.67 (Message 4818) Posted 12 May 2009 by Snagletooth Post: And another process exited with code 193 (0xc1, -63): lb_alnmatrix_thread4_hb_t286__IGNORE_THE_REST_9611_7_0
45) Message boards : RALPH@home bug list : Minirosetta 1.67 (Message 4817) Posted 9 May 2009 by Snagletooth Post: My Mac picked up a resend but broker_lb_test5_hb_t303__IGNORE_THE_REST_9495_5_1 crashed at the end of it's run with exit status 193 # cpu_run_time_pref: 36000 SIGBUS: bus error Crashed executable name: minirosetta_1.67_i686-apple-darwin built using BOINC library version 6.5.0 Machine type Intel 80486 (32-bit executable) System version: Macintosh OS 10.5.6 build 9G55 Sat May 9 04:58:40 2009 sh: /usr/bin/atos: No such file or directory 0 0x006c0345 SIGPIPE: write on a pipe with no reader 1 0x004a3d8e SIGPIPE: write on a pipe with no reader 2 0x90a9e2bb SIGPIPE: write on a pipe with no reader 3 0xffffffff SIGPIPE: write on a pipe with no reader 4 0x0002a4a7 SIGPIPE: write on a pipe with no reader 5 0x000910d0 SIGPIPE: write on a pipe with no reader 6 0x00518bdc SIGPIPE: write on a pipe with no reader 7 0x00b59c20 SIGPIPE: write on a pipe with no reader 8 0x0013b70a SIGPIPE: write on a pipe with no reader 9 0x00005a5b SIGPIPE: write on a pipe with no reader 10 0x0000292e SIGPIPE: write on a pipe with no reader 11 0x00002855 SIGPIPE: write on a pipe with no reader 12 0x00000019 Thread 0 crashed with X86 Thread State (32-bit): eax: 0xffffffe1 ebx: 0x90a66802 ecx: 0xbfffc25c edx: 0x90a321c6 edi: 0x00000000 esi: 0x00000000 ebp: 0xbfffc298 esp: 0xbfffc25c ss: 0x0000001f efl: 0x00000206 eip: 0x90a321c6 cs: 0x00000007 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 It previously failed on a computer using Linux: Exit status -185 (0xffffffffffffff47) Computer ID 17872 Report deadline 11 May 2009 7:55:59 UTC CPU time 0 stderr out <core_client_version>6.2.18</core_client_version> <![CDATA[ <message> Input file minirosetta_database_rev29025.zip missing or invalid: -120 </message> ]]> Mike, you might want to sticky this thread unless we're already giving up on 1.67 and going straight to 1.68 Snags
46) Message boards : RALPH@home bug list : Minirosetta 1.63 (Message 4799) Posted 24 Apr 2009 by Snagletooth Post: My Mac completed Docking_benchmark_natives__1A0O.mppk.pdb.gzdock_score_docking_hi.xml_9362_1 sucessfully but took only 2 hours to hit the 99 model limit. Snags
47) Message boards : RALPH@home bug list : Minirosetta 1.61 (Message 4781) Posted 16 Apr 2009 by Snagletooth Post: DvR115G_BOINC_ABINITIO_RDC_TEST_SAVE_ALL_OUT_IGNORE_THE_REST-S25-15-S3-28--DvR115G-_9225_1 crashed after 14.56 seconds, one second faster than the first attempt with Minirosetta 1.59.
48) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4599) Posted 29 Jan 2009 by Snagletooth Post: Not Paul but just came from Einstein so think I think I remember right where to look It's a long thread so for the short, extremely lucid version go straight to Gary Roberts Hope this helps. Snags
49) Message boards : RALPH@home bug list : minirosetta v1.54 bug thread (Message 4583) Posted 28 Jan 2009 by Snagletooth Post: Just confirming that the 99 model limit works for folks other than Feet1st :) testD_cc_1_8_nocst4_hb_t362__IGNORE_THE_REST_2GF6A_10_7075_3_0 ended after 29642.2 secs with a 36000 sec target runtime. Snags
50) Message boards : RALPH@home bug list : minirosetta v1.48-1.51 bug thread (Message 4506) Posted 23 Jan 2009 by Snagletooth Post: Hi, I'm running RALPH with Ubuntu Jaunty up to date. My BOINC version is 6.2.18. When I click to "show graphic" (or suchs, I'm French), I see a small window, like the screenshot in XP in this Post, but all my memory (1.5 Gio) and all my swap (2.0 Gio) are fullâ€¦ If I do not it (click on "sow graphics"), there isn't any visible problem. Rosetta mini 1.52 http://francois.linkmauve.fr/boinc.png The screenshot show when the window has been killed. If there are questions, ask meâ€¦ I'm showing the same or very similar behavior on the same type of workunit:lr6_D_score12_rlbn_1gu3_IGNORE_THE_REST_NATIVE_6909_1 running Leopard on an Intel Mac. No cpu use but tons of memory and I don't even get the box so nothing to show in a screen capture. Activity Manager says the process has hung and I killed it without trouble from there. Snags
51) Message boards : RALPH@home bug list : minirosetta v1.48-1.51 bug thread (Message 4504) Posted 23 Jan 2009 by Snagletooth Post: Hey, Mike, thanks for all the info you've been giving us lately. It's interesting and certainly provides a bit of extra motivation to keep crunching and reporting what we see at our end. Snags
52) Message boards : RALPH@home bug list : minirosetta v1.48-1.51 bug thread (Message 4501) Posted 23 Jan 2009 by Snagletooth Post: test_cc_1_8_nocst4_hb_t327__IGNORE_THE_REST_2FSWA_6_6888_1 andtest_cc_1_8_nocst4_hb_t327__IGNORE_THE_REST_2F2EA_10_6888_1_1 both ended with: ERROR: unknown model name: 2FRHA_10 ERROR:: Exit from: src/protocols/abinitio/PairingStatistics.hh line: 170 This time they ran a few minutes instead of a few seconds, claimed to be done instead of declaring a compute error and received a validate error instead of a client error. Snags
53) Message boards : RALPH@home bug list : minirosetta v1.48-1.51 bug thread (Message 4492) Posted 22 Jan 2009 by Snagletooth Post: One more with v1.50: test_cc_1_8_nocst4_hb_t367__IGNORE_THE_REST_1UFBA_5_6830_3 <core_client_version>6.2.18</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> Watchdog active. # cpu_run_time_pref: 14400 ERROR: target_strands.size() ERROR:: Exit from: src/protocols/abinitio/TemplateJumpSetup.cc line: 94 called boinc_finish And one with v.1.51: test_cc2_1_8_mammoth_mix_cen_cst_hb_t311__IGNORE_THE_REST_1PERL_6_6852_1 <core_client_version>6.2.18</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> BOINC:: Initializing ... ok. [2009- 1-22 11:56:36:] :: 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. Initializing options.... ok Initializing random generators... ok Initialization complete. Watchdog active. ERROR: unknown model name: 1B0NA_10 ERROR:: Exit from: src/protocols/abinitio/PairingStatistics.hh line: 170 called boinc_finish Snags
54) Message boards : RALPH@home bug list : minirosetta v1.48-1.51 bug thread (Message 4472) Posted 21 Jan 2009 by Snagletooth Post: test_cc_1_8_nocst4_hb_t367__IGNORE_THE_REST_1WOLA_4_6830_2_0 ended with same rare error as Ian D and Paul D Buck. <core_client_version>6.2.18</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> Watchdog active. # cpu_run_time_pref: 14400 ERROR: target_strands.size() ERROR:: Exit from: src/protocols/abinitio/TemplateJumpSetup.cc line: 94 called boinc_finish Snags
55) Message boards : RALPH@home bug list : Bug Reports for Rosetta version 5.98 (Message 4179) Posted 14 Aug 2008 by Snagletooth Post: Well, I assume that one way to cause this to happen would be to abort the transfer from the transfers tab in the advanced view. But, I doubt you did that, and especially since both had the same problem. Have there been any BOINC problems?? I understand there is some handshaking and authorizations that take place to permit your upload while thwarting SPAMers. Perhaps there is a problem with that process? Or, one of the things I think they exchange is the file size. Perhaps the out file for this task grew unexpectedly large? Hopefully Ralph team can shed some light. There have have been no other BOINC problems. I haven't gotten another Ralph wu yet but I have successfully finished, uploaded, and reported results from other projects: wus I received before, during, and after the ralph wu crunched. I was away from the computer while this one was finishing up and returned to find it's status listed as "computation error" instead of "ready to report" as I would have expected if everything finished and uploaded normally. I just went back through the message logs and found this: Wed Aug 13 03:56:13 2008\|ralph@home\|Computation for task MFR_ABRELAX_PICKED_TR5d__4731_6_2 finished Wed Aug 13 03:56:13 2008\|ralph@home\|Output file MFR_ABRELAX_PICKED_TR5d__4731_6_2_0 for task MFR_ABRELAX_PICKED_TR5d__4731_6_2 absent I think -161 may be a bit of a catchall error code as it seems to include problems with the creation of the file to be transferred as well as problems with the transfer itself. Obviously some info is reported as the stderr out for both my co-cruncher and I shows one decoy completed. My co-cruncher has since successfully completed another Ralph WU so I'm inclined to think it the problem is with the wu rather than something on our ends. Of course by now the project may well have discovered the problem, fixed it and moved on. Do you know how to search for this particular protein/app combo as crunched by others, here or on Rosetta, to find out if this is the case? Snags
56) Message boards : RALPH@home bug list : Bug Reports for Rosetta version 5.98 (Message 4177) Posted 14 Aug 2008 by Snagletooth Post: Snagletooth, a file transfer error, but only after you completed a model. And given the file name, it looks like your machine finally gave up on trying to upload the result file. Have you had any other upload problems? No but since the other cruncher who attempted this wu before me reported the same error I assumed the problem is with the wu. I've noticed other folks have occasionally reported this error for different types of wus and I have become curious about the cause. Can you offer any enlightenment? Snags
57) Message boards : RALPH@home bug list : Bug Reports for Rosetta version 5.98 (Message 4175) Posted 13 Aug 2008 by Snagletooth Post: Both computers attempting this one failed with the same error: MFR_ABRELAX_PICKED_TR5d__4731_6_2 stderr out <core_client_version>5.10.45</core_client_version> <![CDATA[ <stderr_txt> Rosetta@home Macintosh Stack Size checker. Original size: 0. Maximum size: 8388608. RLIM_INFINITY 0 # cpu_run_time_pref: 14400 # random seed: 1052640 ====================================================== DONE :: 1 starting structures 15594.9 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down... </stderr_txt> <message> <file_xfer_error> <file_name>MFR_ABRELAX_PICKED_TR5d__4731_6_2_0</file_name> <error_code>-161</error_code> </file_xfer_error> </message> ]]>
58) Message boards : RALPH@home bug list : Bug reports for 5.96 (Message 3907) Posted 15 Apr 2008 by Snagletooth Post: Another two time failure 1r69__BOINC_GEOSOL_ABRELAX-1r69_-_3497_1 Same error messages From my log file: \|ralph@home\|Output file 1r69__BOINC_GEOSOL_ABRELAX-1r69_-_3497_1_1_0 for task 1r69__BOINC_GEOSOL_ABRELAX-1r69_-_3497_1_1 absent I also had another 1n0u__BOINC_GESOL_LKSOL_MIX_ABRELAX-1n0u_-_3497_19 which my ppc mac handled just fine but the first attempt, by an intel machine running windows XP, crashed within a few seconds of starting.
59) Message boards : RALPH@home bug list : Bug reports for 5.96 (Message 3899) Posted 13 Apr 2008 by Snagletooth Post: This time my ppc mac was able to complete a model but I notice that the first computer to try it, a intel mac , ended with another exit status 193(0xc1). I was able to open and view the graphics window without causing a problem. 1di2__BOINC_GESOL_LKSOL_MIX_ABRELAX-1di2_-_3497_13 I do realize it's not exactly the same type of wu but thought it might be sufficiently similar that a report could be helpful. edit/ And another bites the dust. 1dcj__BOINC_GEOSOL_ABRELAX-1dcj_-_3497_18. Both attempts, one ppc mac, one windows, same errors as before. No attempt to look at graphics this time, at least by me.
60) Message boards : RALPH@home bug list : Bug reports for 5.96 (Message 3897) Posted 13 Apr 2008 by Snagletooth Post: 2tif__BOINC_GEOSOL_ABRELAX-2tif_-_3497_18 and 1dtj__BOINC_GEOSOL_ABRELAX-1dtj_-_3497_4 ended with Exit status 193 (0xc1) on my ppc Mac. There is a long stderr out for both mentioning a segmentation violation. The second wu also errored out on a windows machine, this time with Exit status -1073741819 (0xffffffffc0000005) Unhandled Exception Detected... - Unhandled Exception Record - Reason: Access Violation (0xc0000005) at address 0x00737A21 read attempt to address 0x3DFF41FC

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