1)
Message boards :
Rosetta@home Science :
"IGNORE_THE_REST" vs. "SAVE_ALL_OUT" What does it mean?
(Message 101465)
Posted 24 Apr 2021 by svincent Post: See this thread: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=2729 |
2)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 100852)
Posted 28 Mar 2021 by svincent Post: Suggest checking out Foldit. https://fold.it/portal/ |
3)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 96237)
Posted 7 May 2020 by svincent Post: This task failed on Ubuntu 19.10 https://boinc.bakerlab.org/rosetta/result.php?resultid=1172834155 <core_client_version>7.16.3</core_client_version> <![CDATA[ <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_05_07_20646_23758_ab_t000__robetta_FLAGS -in::file::fasta t000_.fasta -jumps:pairing_file t000_.fasta.bbcontacts.jumps -jumps:random_sheets 1 -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_05_07_20646_23758_ab_t000__robetta.zip -frag3 rb_05_07_20646_23758_ab_t000__robetta.200.3mers.index.gz -fragA rb_05_07_20646_23758_ab_t000__robetta.200.11mers.index.gz -fragB rb_05_07_20646_23758_ab_t000__robetta.200.5mers.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 2100616 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 ------------------------ Begin developer's backtrace ------------------------- BACKTRACE: [0x3ce8b7f] [0x62b4e53] [0x408ae82] |
4)
Message boards :
Number crunching :
Rosetta 4.1+ and 4.2+
(Message 95146)
Posted 22 Apr 2020 by svincent Post: I've had a couple of tasks fail on Ubuntu 19.10. They appeared to run for the full 8 hours but the upload failed. <error_code>-131 (file size too big)</error_code> http://boinc.bakerlab.org/rosetta/result.php?resultid=1157342448 </stderr_txt> <message> upload failure: <file_xfer_error> <file_name>Mini_Protein_binds_IL6R_COVID-19_1p9m_3_SAVE_ALL_OUT_IGNORE_THE_REST_3fg6zc0o_924138_1_0_r441246010_0</file_name> <error_code>-131 (file size too big)</error_code> </file_xfer_error> </ and http://boinc.bakerlab.org/rosetta/result.php?resultid=1157317275 </stderr_txt> <message> upload failure: <file_xfer_error> <file_name>Mini_Protein_binds_IL6R_COVID-19_1p9m_2_SAVE_ALL_OUT_IGNORE_THE_REST_2pn8jf2i_924136_1_0_r712855490_0</file_name> <error_code>-131 (file size too big)</error_code> </file_xfer_error> </message> Any settings I need to change? |
5)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 94247)
Posted 12 Apr 2020 by svincent Post: Sorry: I don't seem to be able to find that info: the log didn't go back that far. Anyway its the only task where it happened. |
6)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 94179)
Posted 11 Apr 2020 by svincent Post: I have no antivirus software on my computer. Here's a portion of the event log that I hope may be helpful Sat 11 Apr 2020 12:49:03 AM PDT | Rosetta@home | Starting task 4mc4in7o_Mini_Protein_binds_IL1R_COVID-19_design4_SAVE_ALL_OUT_905389_4_1 Sat 11 Apr 2020 12:49:04 AM PDT | Rosetta@home | Started upload of hgfp_dimer_3x_42_fold_SAVE_ALL_OUT_906263_790_0_r1313969874_0 Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Too old connection (2574 seconds), disconnect it Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Connection 2712 seems to be dead! Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Closing connection 2712 Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Too old connection (2574 seconds), disconnect it Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Connection 2713 seems to be dead! Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Closing connection 2713 Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Trying 128.95.160.157:80... Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: TCP_NODELAY set Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Connected to boinc.bakerlab.org (128.95.160.157) port 80 (#2714) Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: POST /rosetta_cgi/file_upload_handler HTTP/1.1 Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Host: boinc.bakerlab.org Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: User-Agent: BOINC client (x86_64-pc-linux-gnu 7.16.3) Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Accept: */* Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Accept-Encoding: deflate, gzip Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Accept-Language: en_CA Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Content-Length: 314 Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Content-Type: application/x-www-form-urlencoded Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: We are completely uploaded and fine Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Mark bundle as not supporting multiuse Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: HTTP/1.1 200 OK Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Date: Sat, 11 Apr 2020 07:49:05 GMT Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Server: Apache/2.4.18 Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Vary: Accept-Encoding Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Content-Encoding: gzip Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Content-Length: 75 Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Content-Type: text/plain Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | Sat 11 Apr 2020 12:49:05 AM PDT | Rosetta@home | [http] [ID#4338] Info: Connection #2714 to host boinc.bakerlab.org left intact Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Info: Found bundle for host boinc.bakerlab.org: 0x7f9cb4001520 [serially] Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Info: Can not multiplex, even if we wanted to! Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Info: Re-using existing connection! (#2714) with host boinc.bakerlab.org Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Info: Connected to boinc.bakerlab.org (128.95.160.157) port 80 (#2714) Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: POST /rosetta_cgi/file_upload_handler HTTP/1.1 Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Host: boinc.bakerlab.org Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: User-Agent: BOINC client (x86_64-pc-linux-gnu 7.16.3) Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Accept: */* Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Accept-Encoding: deflate, gzip Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Accept-Language: en_CA Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Content-Length: 283230 Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Content-Type: application/x-www-form-urlencoded Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Expect: 100-continue Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Sent header to server: Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Info: Mark bundle as not supporting multiuse Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: HTTP/1.1 100 Continue Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Info: We are completely uploaded and fine Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Info: Mark bundle as not supporting multiuse Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: HTTP/1.1 200 OK Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Date: Sat, 11 Apr 2020 07:49:07 GMT Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Server: Apache/2.4.18 Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Content-Length: 64 Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Content-Type: text/plain Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: <data_server_reply> Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: <status>0</status> Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Received header from server: </data_server_reply> Sat 11 Apr 2020 12:49:07 AM PDT | Rosetta@home | [http] [ID#4338] Info: Connection #2714 to host boinc.bakerlab.org left intact Sat 11 Apr 2020 12:49:08 AM PDT | Rosetta@home | Finished upload of hgfp_dimer_3x_42_fold_SAVE_ALL_OUT_906263_790_0_r1313969874_0 Sat 11 Apr 2020 12:51:24 AM PDT | Rosetta@home | Computation for task 4mc4in7o_Mini_Protein_binds_IL1R_COVID-19_design4_SAVE_ALL_OUT_905389_4_1 finished |
7)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 94165)
Posted 11 Apr 2020 by svincent Post: Problem with this task on Ubuntu http://boinc.bakerlab.org/rosetta/result.php?resultid=1146197010 4mc4in7o_Mini_Protein_binds_IL1R_COVID-19_design4_SAVE_ALL_OUT_905389_4_1 Validate error after a couple of minutes ERROR: [ERROR] Unable to open constraints file: mot_HHH_b1_05627_000000248_0001_1_19_H_._28a7dda1a33635c05f5ab621834c8d3e_0001_0001_0001.MSAcst ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 457 00:51:21 (5035): called boinc_finish(0) |
8)
Message boards :
Rosetta@home Science :
Prioritisation of COVID-19 work units
(Message 92276)
Posted 25 Mar 2020 by svincent Post: COVID-related tasks need not necessarily be identified as such. As an example, there are a number of tasks containing foldit in their names that are testing player designs for proteins that can bind to the coronavirus spike protein. See https://fold.it/portal/blog |
9)
Message boards :
Number crunching :
Stalled downloads
(Message 91927)
Posted 10 Mar 2020 by svincent Post: Several stuck downloads recently. Here's one on on Ubuntu 19.10. The offending file is twc_method_msd_cpp_c3212_9mer_gb_000182_msd.zip (workunit 1014896837) After setting http_debug in the Event Log options and retrying the transfer the following appears in the Event Log: Tue 10 Mar 2020 02:49:18 PM PDT | | log flags: file_xfer, sched_ops, task, http_debug Tue 10 Mar 2020 03:04:06 PM PDT | Rosetta@home | [http] HTTP_OP::init_get(): http://boinc.bakerlab.org/rosetta/download/113/twc_method_msd_cpp_c3212_9mer_gb_000182_msd.zip Tue 10 Mar 2020 03:04:06 PM PDT | Rosetta@home | Started download of twc_method_msd_cpp_c3212_9mer_gb_000182_msd.zip Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Too old connection (2036 seconds), disconnect it Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Connection 354 seems to be dead! Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Closing connection 354 Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Too old connection (2036 seconds), disconnect it Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Connection 355 seems to be dead! Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Closing connection 355 Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Too old connection (2029 seconds), disconnect it Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Connection 356 seems to be dead! Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Closing connection 356 Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Too old connection (2029 seconds), disconnect it Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Connection 357 seems to be dead! Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Closing connection 357 Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Trying 128.95.160.157:80... Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: TCP_NODELAY set Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Connected to boinc.bakerlab.org (128.95.160.157) port 80 (#358) Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Sent header to server: GET /rosetta/download/113/twc_method_msd_cpp_c3212_9mer_gb_000182_msd.zip HTTP/1.1 Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Sent header to server: Host: boinc.bakerlab.org Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Sent header to server: User-Agent: BOINC client (x86_64-pc-linux-gnu 7.16.3) Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Sent header to server: Accept: */* Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Sent header to server: Accept-Encoding: deflate, gzip Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Sent header to server: Accept-Language: en_CA Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Sent header to server: Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Info: Mark bundle as not supporting multiuse Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Received header from server: HTTP/1.1 200 OK Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Received header from server: Date: Tue, 10 Mar 2020 22:04:07 GMT Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Received header from server: Server: Apache/2.4.18 Tue 10 Mar 2020 03:04:07 PM PDT | Rosetta@home | [http] [ID#318] Received header from server: Last-Modified: Fri, 06 Mar 2020 21:55:13 GMT The download is still stuck at the same place (86.50%) |
10)
Message boards :
Rosetta@home Science :
Foldit WU
(Message 91646)
Posted 2 Feb 2020 by svincent Post: These tasks are usually testing promising player designs in Foldit. Before going to the expense of creating the protein and determining its structure, they are run through Rosetta first to see if they are likely to fold/dock in the way predicted. |
11)
Message boards :
Rosetta@home Science :
Alphafold visits IPD
(Message 91645)
Posted 2 Feb 2020 by svincent Post: There's a post on AlphaFold on the Foldit blog here: https://fold.it/portal/blog |
12)
Message boards :
Number crunching :
Computation errors
(Message 91158)
Posted 24 Sep 2019 by svincent Post: rb_09_19_8636_8623_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_03_05_867741_37 failed with invalid chi angle on Windows File: C:cygwin64homeboincRosettamainsourcesrccore/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306 chi angle must be between -180 and 180: -nan(ind) </stderr_txt> [/url] Task 1094602971 http://boinc.bakerlab.org/rosetta/result.php?resultid=109460297 Workunit 985919585 http://boinc.bakerlab.org/rosetta/workunit.php?wuid=985919585 |
13)
Message boards :
Number crunching :
Invalid chi angle
(Message 90613)
Posted 4 Apr 2019 by svincent Post: A couple of tasks have resulted in a computational error with the message File: src/core/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306 chi angle must be between -180 and 180: -nan http://boinc.bakerlab.org/rosetta/result.php?resultid=1066344297 http://boinc.bakerlab.org/rosetta/result.php?resultid=1066337936 From the similarity between the names, it looks as if there might be an issue with that particular batch of tasks. rb_04_03_2488_2617_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_07_07_827676_316_0 rb_04_03_2488_2617_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_08_05_827676_233_0 |
14)
Message boards :
Number crunching :
Rosetta 4.0+
(Message 90350)
Posted 14 Feb 2019 by svincent Post: Graphics in Unix (Ubuntu 18.04) doesn't work in Rosetta 4.08. The graphics window appears as normal with all the appropriate panes and text but no protein is shown. Perhaps relevant is the text "No shared mem" in the lower half of the window. Graphics in Unix works fine however with Rosetta Mini. |
15)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 81574)
Posted 10 Jun 2017 by svincent Post: Another issue with these overrunning tasks: checkpointing isn't working properly. I've got a couple of b21* tasks that have been running for over 12 hours and are stuck on step 7205 having done 52 and 12 tasks respectively. Yet the last checkpoint for each is 18 minutes. |
16)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 81564)
Posted 9 Jun 2017 by svincent Post: I'm seeing problems with these b* tasks also. This one, b21_ncst_s2_0601.108._fold_and_dock_SAVE_ALL_OUT_486796_197, 830463634 , a big all-sheet hexamer, got 'stuck' (although it was clearly doing something) on Model 2 Step 7205 for at least 6 hours before finally expiring with a Validate error. Linux/Boinc 7.6.31 |
17)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 81539)
Posted 27 May 2017 by svincent Post: Why am I having such problems getting work units? The Server Status page is a sea of red: clearly there are problems of some sort. |
18)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 81189)
Posted 15 Feb 2017 by svincent Post: I have a stuck workunit: it's spent several hours at least stuck on Model 6 Step 7205 (Fast Relax). It's an all-sheet hexamer. Is it worth letting it continue? Good advice: it successfully completed and validated. tx. |
19)
Message boards :
Number crunching :
Problems and Technical Issues with Rosetta@home
(Message 81187)
Posted 15 Feb 2017 by svincent Post: I have a stuck workunit: it's spent several hours at least stuck on Model 6 Step 7205 (Fast Relax). It's an all-sheet hexamer. Is it worth letting it continue? 170214.3._fold_and_dock_SAVE_ALL_OUT_468868_40_0 http://boinc.bakerlab.org/rosetta/result.php?resultid=901485891 |
20)
Message boards :
Rosetta@home Science :
CASP12
(Message 81095)
Posted 27 Jan 2017 by svincent Post: It would be nice to hear a little more about the CASP 12 results. Were there any interesting insights into the state of the art in protein folding from the meeting last month? |
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