Problems and Technical Issues with Rosetta@home
Message boards : Number crunching : Problems and Technical Issues with Rosetta@home
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P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0 |
Hi SBF-GODS-STONE. You seem to be mixing up cpu cashe with system ram, your system is showing about 3 gigabyte of ram ( Memory 2989.52 MB ). Rosetta can use up to and over 1 gig of ram per task/wu sometimes, there is no way that can fit in the cpu's cashe. You said - This CPU chip has for L2 and L3 cashe storage 1 and 2 gig's of memory on the chip. ==================================================== See spec's for your cpu from CPU-World site. AMD FX-4350 Frequency: 4200 MHz Turbo frequency: 4300 MHz Level 1 cache size: 2 x 64 KB shared instruction caches 4 x 16 KB data caches Level 2 cache size: 2 x 2 MB shared exclusive caches Level 3 cache size: 8 MB shared cache Memory controller: The number of controllers: 1 Memory channels: 2 Supported memory: DDR3-1866 ====================================================== i.m.h.o. - Sorry you need more RAM! 
ID: 76795 · Rating: 0 · rate:
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SBF-GODS-STONE Send message Joined: 6 Nov 05 Posts: 15 Credit: 44,784 RAC: 0 |
Hi SBF-GODS-STONE. This machine has 8 gig's of 1866 (XP can only use 3 gig's). The version of the amd cpu is the FX 4350 Black 12mb cashe for each core (unlocked). At any rate the issue was not how much work the cpu's could do, it was the fragments on the work(boinc) disk which is now 10 gigs and seems to have cleared that problem. thks. ID: 76796 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954 
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Hi SBF-GODS-STONE. I run a different AMD machine, but each task here is using approx 500Mb. On my 8-core machine that's about 4Gb. Fortunately I have a 64-bit OS so I can access all 8Gb of RAM. In my task manager I can see 6Gb RAM is in use in total, including Windows and other applications, so I'm fine. On your 4-core machine you'll be using 2Gb less, but 4Gb is more than the 3Gb RAM your 32-bit OS can access, so it does make sense that a lot of data is getting thrown down to disk. Reserving more space for Boinc does seem to be helping you from what you've said, but your problems may return unless you can find a way of only running 2 Rosetta tasks at a time and letting other projects use your other 2 cores. Ideally, you need to use a 64-bit version of Windows to get the full benefit of the RAM you already have installed. I'm sorry I can't be of more help.  
ID: 76797 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954
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Download files getting truncated 07/07/2014 21:41:01 | rosetta@home | Sending scheduler request: To report completed tasks. This task then displays as "download failed" in the Boinc Tasks window I also have one or two files that are failing to upload after the first 1.71Kb uploaded of 166.19Kb - frxtrimer_5_0979_b5r3_fold_SAVE_ALL_OUT_171800_974_0 - as I checked these numbers I saw an upload going through of over 1Mb without problem. I also seem to have massive problems with downloading Me Anyone else seeing this or only me?
ID: 76970 · Rating: 0 · rate:
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Mod.Sense Volunteer moderator Send message Joined: 22 Aug 06 Posts: 4018 Credit: 0 RAC: 0 |
Sid, have you white-listed R@h in your AV software? Rosetta Moderator: Mod.Sense ID: 76986 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954
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Sid, have you white-listed R@h in your AV software? I did since posting, but with no improvement. I can't see anything in my history indicating an issue since the start of the month either. It also started happening on my laptop shortly after, which may well indicate it's an issue with the AV getting updated later, but I just can't see what. That said, I'm on my travels again and have just opened my laptop and looked to see if there was any improvement. The event log included this excerpt directly on startup: 10/07/2014 01:00:31 | | Resetting file projects/boinc.bakerlab.org_rosetta/ANK12_A.pdb_ANK12_B.pdb_global_docking.xml: wrong size Lo and behold, when I manually retried uploading results they went through first time and I've uploaded results and returned tasks perfectly and downloaded 5 more with complete success. 10/07/2014 01:06:46 | rosetta@home | Started upload of rb_06_20_47426_92932__t000__4_C1_SAVE_ALL_OUT_IGNORE_THE_REST_170261_537_0_0 Whether this is something that's changed at R@H or something to do with me, I can't tell. Whether it's also going to automatically start working on my desktop at home, I won't be able to discover until I return on Sunday. I had updated and rebooted the desktop a few times as well and rebooted the router for good measure. Nothing like the above happened when I did. It's really like something just changed at R@H in the last few hours. That said, no-one else has backed up my report, which points the finger back at me... <confused> Edit: Just to add, occasional tasks (1 in 15?) are downloading ok and the majority (but not all - 9 of 10?) are uploading ok, so it's partial failuresuccess in both directions, not complete failure. I don't know why this is either...
ID: 76991 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954
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Download files getting truncated Ok, I'm still not home yet, but I note the task quoted above has finally reported back, 5 days after completing along with several others similarly stuck. I also note tasks stopped downloading 4 days ago and none more have come down even after this backlog cleared. I'll report back tomorrow what the Events log showed. I wasn't there to have done anything, unless a reboot was forced somehow. Still completely mystified as it's been my most reliable computer up until now.
ID: 77006 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954
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And here's the relevant excerpt from the Event Log: 12/07/2014 16:02:10 | | Running CPU benchmarks So, just new CPU benchmarks? That makes no sense to me. My AV did an update a few hours before - I suppose it's possible that cleared the blockage. "Not requesting tasks: some task is suspended via Manager" also makes no sense to me. A manual update immediately delivered 6 tasks. Bottom line is everything's back working. Panic over. Now to clear a stack of WCG jobs dl'd in the meantime before I fully get back on track here at Rosetta.
ID: 77007 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954
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I also seem to have massive problems with downloading Happening to me again... :(
ID: 77028 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954
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I also seem to have massive problems with downloading And sorted itself out again 2 days later. Again on a Saturday afternoon, like last week. I wish I had the first clue what was going wrong and how it's righting itself without any intervention along the way. But I don't :(
ID: 77044 · Rating: 0 · rate:
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Murasaki Send message Joined: 20 Apr 06 Posts: 303 Credit: 511,418 RAC: 0 |
And sorted itself out again 2 days later. Again on a Saturday afternoon, like last week. A pattern suggests a setting in BOINC or your system could be causing an issue. Do you have any system maintenance tasks that are scheduled to occur on a Saturday? If your problem is caused by the system being confused about available space in memory or hard disk then one of the maintenance tools may be prompting the system to realise that the space is available. However, as a first step if the issue recurs, I would set the entry in the BOINC Manager Activity menu to "Network activity always available". If the problem resolves itself straight away then it must be an issue with your BOINC preferences. ID: 77047 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954
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And sorted itself out again 2 days later. Again on a Saturday afternoon, like last week. Rather than the problem beginning on Saturday afternoon, that's when it resolves itself. I agree it may be some unknown scheduled task that's putting things right, but it may also be a coincidence. Two occasions is hardly representative. Just stepped through the task scheduler - nothing ran around that time. I've adjusted the Network activity option as you've suggested, just in case it's relevant. There shouldn't be any restrictions, but it's always possible I've missed something. Thanks.
ID: 77050 · Rating: 0 · rate:
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2126 Credit: 41,255,271 RAC: 7,954
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Not that I expect it's of any relevance to anyone except me, but everything ran smoothly this week. None the wiser, mind...
ID: 77069 · Rating: 0 · rate:
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Ananas Send message Joined: 1 Jan 06 Posts: 232 Credit: 752,471 RAC: 0 |
http://srv4.bakerlab.org/rosetta_cgi/cgi gives me timeouts, for BOINC and the same when I try it in the browser. Uploads need several attempts too. Someone standing on the cable? p.s.: no trouble connecting to the Rosetta web site and the database seems to be fast also, so it must be only this one server that is in trouble. ID: 77072 · Rating: 0 · rate:
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P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0 |
I'm not able to upload or download as well.
ID: 77073 · Rating: 0 · rate:
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P . P . L . Send message Joined: 20 Aug 06 Posts: 581 Credit: 4,865,274 RAC: 0 |
This is what boinc is showing in messages now. Tue 29 Jul 2014 15:13:08 EST | rosetta@home | Started upload of tube9_25_A_tube9_25_B_patchdock_split_00_140727_SAVE_ALL_OUT__179884_95_0_0 Tue 29 Jul 2014 15:15:08 EST | | Project communication failed: attempting access to reference site Tue 29 Jul 2014 15:15:08 EST | rosetta@home | Temporarily failed upload of tube9_25_A_tube9_25_B_patchdock_split_00_140727_SAVE_ALL_OUT__179884_95_0_0: transient HTTP error Tue 29 Jul 2014 15:15:08 EST | rosetta@home | Backing off 3 min 7 sec on upload of tube9_25_A_tube9_25_B_patchdock_split_00_140727_SAVE_ALL_OUT__179884_95_0_0 Tue 29 Jul 2014 15:15:10 EST | | Internet access OK - project servers may be temporarily down.
ID: 77074 · Rating: 0 · rate:
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Dougb Send message Joined: 29 Nov 07 Posts: 1 Credit: 5,175,908 RAC: 0 |
My PCs can't upload or report either; I get this error: 29/07/2014 5:26:25 PM | rosetta@home | Started upload of rb_07_27_48552_95186_ab_stage0_t000___robetta_IGNORE_THE_REST_12_13_179905_3_0_0 29/07/2014 5:26:25 PM | rosetta@home | Started upload of rb_07_27_48552_95186_ab_stage0_h002___robetta_IGNORE_THE_REST_09_15_179904_3_0_0 29/07/2014 5:26:47 PM | rosetta@home | Temporarily failed upload of rb_07_27_48552_95186_ab_stage0_h002___robetta_IGNORE_THE_REST_09_15_179904_3_0_0: connect() failed 29/07/2014 5:26:47 PM | rosetta@home | Backing off 00:13:42 on upload of rb_07_27_48552_95186_ab_stage0_h002___robetta_IGNORE_THE_REST_09_15_179904_3_0_0 29/07/2014 5:26:47 PM | rosetta@home | Started upload of tj_7_11_2helix_highRadius_X18_GB_16_DDD_3_e_fb_fragments_abinitio_SAVE_ALL_OUT_174854_765_0_0 29/07/2014 5:26:48 PM | rosetta@home | Temporarily failed upload of rb_07_27_48552_95186_ab_stage0_t000___robetta_IGNORE_THE_REST_12_13_179905_3_0_0: connect() failed 29/07/2014 5:26:48 PM | rosetta@home | Backing off 00:11:34 on upload of rb_07_27_48552_95186_ab_stage0_t000___robetta_IGNORE_THE_REST_12_13_179905_3_0_0 29/07/2014 5:26:48 PM | rosetta@home | Started upload of HELFOLD1376_5_fold_SAVE_ALL_OUT_179896_257_0_0 29/07/2014 5:26:52 PM | | Project communication failed: attempting access to reference site 29/07/2014 5:26:53 PM | | Internet access OK - project servers may be temporarily down. ID: 77077 · Rating: 0 · rate:
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JohnH Send message Joined: 25 Mar 13 Posts: 43 Credit: 2,319,355 RAC: 0 |
Copy that ... no up/download this morning. Typical event log. 7/29/2014 11:10:14 AM | | Project communication failed: attempting access to reference site 7/29/2014 11:10:14 AM | rosetta@home | Temporarily failed upload of HELFOLD1376_6_fold_SAVE_ALL_OUT_179898_984_0_0: connect() failed 7/29/2014 11:10:14 AM | rosetta@home | Backing off 01:10:18 on upload of HELFOLD1376_6_fold_SAVE_ALL_OUT_179898_984_0_0 7/29/2014 11:10:14 AM | rosetta@home | Temporarily failed upload of HELFOLD1376_7_fold_SAVE_ALL_OUT_179899_1090_0_0: connect() failed 7/29/2014 11:10:14 AM | rosetta@home | Backing off 00:56:15 on upload of HELFOLD1376_7_fold_SAVE_ALL_OUT_179899_1090_0_0 7/29/2014 11:10:16 AM | | Internet access OK - project servers may be temporarily down. ID: 77078 · Rating: 0 · rate:
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Eric Detheridge Send message Joined: 26 Aug 12 Posts: 2 Credit: 1,975,060 RAC: 0 |
No uploads for me either, with similar errors. Tue 29 Jul 2014 06:14:55 AM CDT | | Project communication failed: attempting access to reference site Tue 29 Jul 2014 06:14:55 AM CDT | rosetta@home | Temporarily failed upload of rb_07_28_48577_95038_ab_stage0_h001___robetta_IGNORE_THE_REST_11_13_179916_5_0_0: connect() failed Tue 29 Jul 2014 06:14:55 AM CDT | rosetta@home | Backing off 24 min 40 sec on upload of rb_07_28_48577_95038_ab_stage0_h001___robetta_IGNORE_THE_REST_11_13_179916_5_0_0 Tue 29 Jul 2014 06:14:55 AM CDT | rosetta@home | Temporarily failed upload of rb_07_28_48577_95038_ab_stage0_h002___robetta_IGNORE_THE_REST_11_11_179917_4_0_0: connect() failed Tue 29 Jul 2014 06:14:55 AM CDT | rosetta@home | Backing off 12 min 9 sec on upload of rb_07_28_48577_95038_ab_stage0_h002___robetta_IGNORE_THE_REST_11_11_179917_4_0_0 Tue 29 Jul 2014 06:14:56 AM CDT | | Internet access OK - project servers may be temporarily down. ID: 77079 · Rating: 0 · rate:
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 Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
Same here, thought it might be a bug in my system for uploading, but even task requests hit a wall. (Times are CET (GMT+2)) 7/29/2014 3:04:23 PM | rosetta@home | Requesting new tasks for CPU and NVIDIA 7/29/2014 3:04:45 PM | rosetta@home | Scheduler request failed: Couldn't connect to server 7/29/2014 3:04:46 PM | | Project communication failed: attempting access to reference site 7/29/2014 3:04:47 PM | | Internet access OK - project servers may be temporarily down. ID: 77081 · Rating: 0 · rate:
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