Message boards : RALPH@home bug list : Minirosetta Beta 3.14
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dekim Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 20 Jan 06 Posts: 250 Credit: 543,579 RAC: 0 |
Please post issues and bugs here. We are particularly interested in excessive disk usage and memory errors. We do expect some jobs to use up to 600-700MB of memory and we'll submit these to higher memory clients. We are also interested in a possible dead lock of the main application and the graphics app where the cpu usage goes to zero for both apps. |
BigMike Send message Joined: 23 Feb 06 Posts: 63 Credit: 58,730 RAC: 0 |
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dekim Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 20 Jan 06 Posts: 250 Credit: 543,579 RAC: 0 |
thanks for the info. that's a known issue with that type of job. |
robertmiles Send message Joined: 13 Jan 09 Posts: 103 Credit: 331,865 RAC: 0 |
One where BOINC thinks the workunit is still running, but it's using no CPU time at all now: https://ralph.bakerlab.org/workunit.php?wuid=1802588 Elapsed 07:01:04 48.46% progress and no longer changing To completion 06:27:09 I normally don't have the graphics portion showing, but when I asked for it, it came up solid black. Anything special I need to do to send back useful information on why? |
robertmiles Send message Joined: 13 Jan 09 Posts: 103 Credit: 331,865 RAC: 0 |
A few more details: The workunit not using CPU time had a 530 MB maximum working set size. Was running in 32-bit mode. Any plans to offer a 64-bit version of this application, even if its main advantage is to help computers like mine that seem to have a limit of around 4 GB on the maximum amount of memory that can be assigned to the entire set of 32-bit programs (BOINC or not) that are in memory at once? More memory is installed, but seems useful mainly for 64-bit programs. I haven't found a task name for the graphics app. What should I be looking for? My other computer also has a 3.14 workunit, running in high priority mode but at least still showing an increasing progress. |
robertmiles Send message Joined: 13 Jan 09 Posts: 103 Credit: 331,865 RAC: 0 |
I've now found something that might be the graphics application: Minirosetta Beta 3.14 - Windows Internet Explorer Listed under Applications under Windows Task Manager, not under Processes, and therefore shown without any task name. Have not found any way to show the resource usage of anything listed only as an application. Total disk usage by all programs about 1 MB per minute, and mainly by system programs. Total network usage about 1 MB per minute, mainly by boincmgr.exe and boinc.exe. BOINC 6.10.58 64-bit Vista SP2, with almost all updates offered except Internet Explorer 9 My other computer has already returned its 3.14 workunit hours sooner than its previous estimated time to completion; already marked as a success. Same versions of BOINC and Windows. |
robertmiles Send message Joined: 13 Jan 09 Posts: 103 Credit: 331,865 RAC: 0 |
I've now identified: Minirosetta Beta 3.14 - Windows Internet Explorer It was the browser window under which I entered the last few messages. CPU time at last checkpoint of the faulty workunit: 03:33:00 CPU time for the workunit: 03:33:15 Could this indicate a problem with resuming normal operation after checkpoints? I've forgotten just which BOINC project has often been showing workunits stopping any use of CPU time about that soon after a checkpoint lately. Would a separate thread used mainly for checking for such conditions be useful? I've added up the memory currently reported as in use by 32-bit programs. About 1.7 GB total, so I don't expect any problem from that. |
robertmiles Send message Joined: 13 Jan 09 Posts: 103 Credit: 331,865 RAC: 0 |
I decided to inspect the list of files in the slot for the failed workunit; it appears that the last file modified there was about 6 hours ago. I also inspected the files lists under minirosetta-database and found that the sections for metal ions do not appear to list aluminum, even though it is connected to the brain damage in one of the later stages of Alzheimer's, or copper, even though the human brain's natural defense against Alzheimer's uses a copper-binding protein. I assume that is not important for this workunit, but how important is it for Rosetta@Home workunits aimed at Alzheimer's? |
robertmiles Send message Joined: 13 Jan 09 Posts: 103 Credit: 331,865 RAC: 0 |
Still more: I clicked on the workunit, then Show graphics. Another window, all black inside. I clicked on the X to close that window and got a windows error message for minirosetta_graphics_3.13_windows_x86_64.exe. Details too long to copy, but I used the snipping tool to capture pictures of it. If those details would be useful, how do I send the pictures? Windows Task Manager does not list any program with that name among the programs now running or suspended, and did not when I started this series of messages. |
dekim Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 20 Jan 06 Posts: 250 Credit: 543,579 RAC: 0 |
robertmiles, Sounds like it might be a dead lock issue. You can manually kill the minirosetta process. We'll look into this further. Let us know if it happens again. |
robertmiles Send message Joined: 13 Jan 09 Posts: 103 Credit: 331,865 RAC: 0 |
Thanks for replying. |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 910 Credit: 1,892,541 RAC: 294 |
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svincent Send message Joined: 4 Apr 08 Posts: 34 Credit: 51,768 RAC: 0 |
Failing on Mac also. Slightly different error message ERROR: Cannot open PDB file "2p9hA_suc_0001.pdb" ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 199 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish Task 2056185 |
Rocco Moretti Volunteer moderator Project developer Project scientist Send message Joined: 18 May 10 Posts: 11 Credit: 30,188 RAC: 0 |
ERROR: unrecognized aa LIG Sorry about that - there was a file missing from the input files. It should be corrected in newer submissions. ERROR: Cannot open PDB file "2p9hA_suc_0001.pdb" A different input file issue - also should be corrected with newer submissions. -- (I will double check my input files before submitting. I will double check my input files before submitting. I will double check my input files before submitting. ...) |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 910 Credit: 1,892,541 RAC: 294 |
:-) |
Conan Send message Joined: 16 Feb 06 Posts: 364 Credit: 1,368,421 RAC: 0 |
Had this error on 3 of my last few work units ERROR: unrecognized aa LIG ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 641 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish See 2056632 2056714 2057573 Also had the following error on another 2 work units ERROR: Cannot open PDB file "2p9hA_suc_0001.pdb" ERROR:: Exit from: ......srccoreimport_poseimport_pose.cc line: 199 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish See 2057602 2057618 Conan |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 910 Credit: 1,892,541 RAC: 294 |
2058828 ERROR: ERROR: FragmentIO: could not open file frags_w_cs_wt_200.11mers ERROR:: Exit from: ......srccorefragmentFragmentIO.cc line: 230 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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Pieface Send message Joined: 16 Feb 06 Posts: 64 Credit: 203,513 RAC: 0 |
Same error here 2077145 wingmans unit died also. ERROR: ct == final_atoms ERROR:: Exit from: ......srccorescoringrms_util.cc line: 524 BOINC:: Error reading and gzipping output datafile: default.out called boinc_finish |
Pieface Send message Joined: 16 Feb 06 Posts: 64 Credit: 203,513 RAC: 0 |
Anyone having watchdog problems with the cleft.cyca.CYCA... units? I have three all gone past the 12hr target point and bouncing between 9:59 and 10:00 minutes remaining. Longest one is at about 13 hrs 25 mins. Going to let them run this morning to see if they finish on their own. edit: morning eyes, time for a shower, changed 'deft' to 'cleft' |
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Minirosetta Beta 3.14
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