Problems with Rosetta version 5.54

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Rhiju
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Message 38066 - Posted: 21 Mar 2007, 0:24:27 UTC

Please especially give us some feedback on the graphics -- are you able to display them properly?
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Profile Feet1st
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Message 38068 - Posted: 21 Mar 2007, 1:33:21 UTC

Somehow the date on the home page news item announcing the new release shows the 12th.
If having a DC project with BOINC is of interest to you, with volunteer or cloud computing resources, but have no time for the BOINC learning curve,
use a hosting service that understands BOINC projects: http://DeepSci.com
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Rhiju
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Message 38074 - Posted: 21 Mar 2007, 6:11:37 UTC - in response to Message 38069.  

Hi Angus, your point is well taken -- estimating time to completion for the first decoy is a little difficult due to differences in computer speed and differences in WU complexity. Maybe it does make sense to not show it (instead show \"First decoy not completed\").

Feet1st, thanks fixed the date on the front page. Hey! I see that your icon has changed from a protein beta sandwich to an RNA graphic. Sweet!

1% bug still there in 5.54

Been running a new WU for 23 minutes on a 1 hour CPU crunch time preference. Should be showing about 33% by now.

Estimated run time was 3:46 when the WU started - now up to 4:05, again on a 1 hour WU run time preference. Two problems here - the estimated time should not be almost 4 hours for a 1 hour crunch time WU, and the time to completion is rising, instead of counting down to zero.

No apparent fixes here.


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Profile MM Sihombing
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Message 38087 - Posted: 21 Mar 2007, 14:06:08 UTC

3/21/2007 8:58:43 PM|rosetta@home|Unrecoverable error for result 1fkaA_BOINC_INCREASECYCLES10_RNA_ABINITIO-1fkaA-chunk016__1627_2_0 ( - exit code -1073741819 (0xc0000005))

68718505
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Message 38099 - Posted: 21 Mar 2007, 18:29:35 UTC

Another Compute error:

3/22/2007 1:16:40 AM|rosetta@home|Unrecoverable error for result 1fkaA_BOINC_CORRECTEDXY_INCREASECYCLES10_RNA_ABINITIO-1fkaA-chunk035__1625_77_1 ( - exit code -1073741819 (0xc0000005))

61477863
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Profile Jim

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Message 38102 - Posted: 21 Mar 2007, 20:52:57 UTC - in response to Message 38066.  

Please especially give us some feedback on the graphics -- are you able to display them properly?


The Graphics works just fine on 4 machines.
The time to completion does count UP until the \"model\" changes from 1 to 2.
It also stayed at 1% until the text indicated it had reached model 2. Then the percentage changed to 18% done.
No big deal at all, I don\'t normally use the graphics anyway, looks like it is working well.

No processing errors of any kind.
Windows XP, Win 2000, Linux machines.

Jim

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Mod.Sense
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Message 38106 - Posted: 21 Mar 2007, 22:30:42 UTC
Last modified: 21 Mar 2007, 22:42:00 UTC

Moved all posts mentioning estimated runtime, \"1% bug\", increasing runtime etc. in to this thread. These issues do not pertain specifically to version 5.54. The Project Team has heard your request, you\'ve made the point that this area needs improvement. Please continue to discuss the subject in the other thread.

My apologies for all the EMail that action generated. The project now automatically EMails you whenever you have a post that is effected by a moderator, regardless of whether the moderator adds specific comments to explain why.

...but then I moved them all to thread 2995 rather then 2996, so I had to move them all twice.
Rosetta Moderator: Mod.Sense
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Keith Akins

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Message 38111 - Posted: 22 Mar 2007, 1:51:53 UTC

I\'ve had the screensaver running for five days now with no problems. First time since 5.4x I\'ve been able to do this. Really Nice!
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Keith Akins

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Message 38113 - Posted: 22 Mar 2007, 2:08:29 UTC

Just one thing I\'ve noticed. In 5.51 the WU reported in just over an hour after it uploaded. (Ive never quite understood why the WU doesn\'t report when it\'s uploaded).

However in 5.54, I\'ve had to manually report the WU to clear it from my que some after four hours. Kinda throws the RAC out of wack.

You guys have made it hard to find anything significant to complain about other than the small things. Run\'s Great!!!
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Enricus
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Message 38132 - Posted: 22 Mar 2007, 15:09:08 UTC

Hi! Whenever i open the stderr.log file, i see:
Graphics are disabled due to configuration...
Can\'t open init data file - running in standalone mode
ERROR:: Exit at: options.cc line:498

I had to compile the BOINC client because it won\'t build against the latest wxgtk libraries. Could this be the problem? Do you know any patch to solve this?
Thanks :)

Enric

PS.By the way, this is my first post. woohoo!
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Keith Akins

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Message 38155 - Posted: 23 Mar 2007, 2:38:27 UTC

I looked at your machines giving this stderr\'s you noted. These are Linux machines showing this as the one Win machine does not. If you\'re wondering about graphics display, Rosetta at present I don\'t think has a graphics implementation on their Linux version yet. I could be wrong though.
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ramostol

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Message 38169 - Posted: 23 Mar 2007, 12:19:20 UTC

On my iBook G4 MacOS 10.3.9 Rosetta 5.54 is not happy at all. It is simply unable to keep any WU alive for more than about 16 CPU-seconds. All competing processes are shut down, there are lots of free CPU. I have had to suspend the project for the moment, which has not happened before.

This is the stdoutdae.txt-file from the starting point of Rosetta 5.54:

Errors starting immediately with 5.54:

((Process formerly suspended by user on 00:01 CPU))
2007-03-23 12:16:16 [rosetta@home] Restarting task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 using rosetta version 554
2007-03-23 12:16:19 [rosetta@home] [file_xfer] Started upload of file BENCH_04JUMPING_SAVE_ALL_OUT_-1bm8_-_NATIVE_PAIR_32_74_BARCODE_R17L_filters_1616_960_0_0
2007-03-23 12:16:23 [rosetta@home] [file_xfer] Finished upload of file BENCH_04JUMPING_SAVE_ALL_OUT_-1bm8_-_NATIVE_PAIR_32_74_BARCODE_R17L_filters_1616_960_0_0
2007-03-23 12:16:23 [rosetta@home] [file_xfer] Throughput 5992 bytes/sec
2007-03-23 12:19:40 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 - message timeout
2007-03-23 12:19:40 [rosetta@home] Restarting task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 using rosetta version 554
2007-03-23 12:19:41 [---] [error] Process 22928 not found
2007-03-23 12:23:01 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 - message timeout
2007-03-23 12:23:01 [rosetta@home] Restarting task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 using rosetta version 554
2007-03-23 12:23:02 [---] [error] Process 23155 not found
2007-03-23 12:26:23 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 - message timeout
2007-03-23 12:26:23 [rosetta@home] Restarting task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 using rosetta version 554
2007-03-23 12:26:24 [---] [error] Process 23377 not found
2007-03-23 12:29:45 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 - message timeout
2007-03-23 12:29:45 [rosetta@home] Restarting task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 using rosetta version 554
2007-03-23 12:29:46 [---] [error] Process 23600 not found
2007-03-23 12:33:07 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 - message timeout
2007-03-23 12:33:07 [rosetta@home] Restarting task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 using rosetta version 554
2007-03-23 12:33:08 [---] [error] Process 23826 not found
2007-03-23 12:36:28 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 - message timeout
2007-03-23 12:36:28 [rosetta@home] Restarting task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 using rosetta version 554

Whereupon Rosetta found it necessary to create a new stdoutdae.txt file:
2007-03-23 12:36:29 [---] [error] Process 24048 not found
2007-03-23 12:37:45 [rosetta@home] Sending scheduler request: Requested by user
2007-03-23 12:37:45 [rosetta@home] Reporting 1 tasks
2007-03-23 12:37:50 [rosetta@home] Scheduler RPC succeeded [server version 509]
2007-03-23 12:37:50 [rosetta@home] Deferring communication for 4 min 2 sec
2007-03-23 12:37:50 [rosetta@home] Reason: requested by project
2007-03-23 12:38:40 [rosetta@home] Starting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk005__1621_347_0
2007-03-23 12:38:40 [rosetta@home] Starting task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk005__1621_347_0 using rosetta version 554
2007-03-23 12:39:50 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 - message timeout
2007-03-23 12:39:51 [rosetta@home] Task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk016__1621_347_0 exited with zero status but no \'finished\' file
2007-03-23 12:39:51 [rosetta@home] If this happens repeatedly you may need to reset the project.
2007-03-23 12:42:10 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk005__1621_347_0 - message timeout
2007-03-23 12:42:11 [---] [error] Process 24459 not found
2007-03-23 12:45:51 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk005__1621_347_0 - message timeout
2007-03-23 12:45:52 [---] [error] Process 24689 not found
2007-03-23 12:48:47 [rosetta@home] Starting 2a43__BOINC_INCREASE_CYCLES10_RNA_ABINITIO-2a43_-_1620_399_0
2007-03-23 12:48:48 [rosetta@home] Starting task 2a43__BOINC_INCREASE_CYCLES10_RNA_ABINITIO-2a43_-_1620_399_0 using rosetta version 554
2007-03-23 12:49:51 [---] Restarting 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk005__1621_347_0 - message timeout
2007-03-23 12:49:52 [rosetta@home] Task 1fkaA_BOINC_CORRECTEDXY_RNA_ABINITIO-1fkaA-chunk005__1621_347_0 exited with zero status but no \'finished\' file
2007-03-23 12:49:52 [rosetta@home] If this happens repeatedly you may need to reset the project.

- R. A. Mostol
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kctipton

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Message 38190 - Posted: 23 Mar 2007, 22:46:26 UTC - in response to Message 38169.  

Lots of R@H units not working on my G4 Dual as well with the newest boinc update + 5.54. Same for Predictor@home (involving maybe the same math or same expectations of my system?).

Anyone getting 5.54 to happily run on a G4 Mac with the older boinc client?
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ramostol

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Message 38222 - Posted: 24 Mar 2007, 12:00:16 UTC

I am unable to do much experimenting with error tracing at the moment, but I feel it may be pertinent to mention my last problem with Rosetta 5.51.

I suddenly got 3 WU hanging successively in their first runs (the second processings went normally). I managed to trace this to a very special situation originated in my internat MAMP + WordPress server. When this was corrected Rosetta continued as expected.

I therefore wonder if at least some of the Macintosh errors of Rosetta are connected with the localhost connection.

- R. A. Mostol
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Geoff Roynon

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Message 38247 - Posted: 24 Mar 2007, 18:06:03 UTC - in response to Message 38190.  

Lots of R@H units not working on my G4 Dual as well with the newest boinc update + 5.54. Same for Predictor@home (involving maybe the same math or same expectations of my system?).

Anyone getting 5.54 to happily run on a G4 Mac with the older boinc client?


I\'m running R@H and Seti on a G5 dual 1.8GHz and the work units keep \"stopping\", i.e. the status is \'Running\' but the CPU Time doesn\'t go up. Activity monitor shows zero activity. I guess the work unit will eventually get rolled out to let Seti have a go and maybe it will run for a while when it restarts. It means that my work units are taking much longer to complete.
I\'m running MacOSX 10.4.8.

Geoff
PPC Mac G5 dual 1.8GHz, 3GB Ram, Mac OSX 10.5
BOINC Manager 5.10.28
Rosetta Beta 5.81
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Message 38279 - Posted: 25 Mar 2007, 0:55:42 UTC

Geoff, I see you have two machines. One running BOINC 5.8.15 and the other running 5.8.8. Which is having this problem where Rosetta stops getting CPU time?
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Teppo Nurminen

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Message 38281 - Posted: 25 Mar 2007, 1:20:46 UTC

Hi. The graphics look great, but I found bug in molecule rotation. If graphics are not full screen, you must place the window to top left corner of the desktop in order to rotate the right molecule. Apparently cursor coordinates are from the desktop and not from the window.
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pieface

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Message 38287 - Posted: 25 Mar 2007, 3:40:28 UTC

Been a while since i\'ve seen an error on rosie, but got one here:

RESID 69376321

ERROR:: Exit at: .\\pose.cc line:761

Rosie 5.54, on DOCKING_3rhj_SYMM_13rhj_1_d.hom027_top10.out.1_1628_270_0
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Geoff Roynon

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Message 38319 - Posted: 25 Mar 2007, 10:13:48 UTC - in response to Message 38279.  

Geoff, I see you have two machines. One running BOINC 5.8.15 and the other running 5.8.8. Which is having this problem where Rosetta stops getting CPU time?


I am running BOINC 5.8.15 on my G4 Powerbook - that seems to be running O.K.
The dual G5 is running 5.8.8 and is having the problem. Currently both processors are running Rosetta and nothing is happening. I will probably abort the Rosetta project and let Seti run until this gets resolved.

Should I revert back to BOINC 5.8.15 on the dual G5?

Geoff
PPC Mac G5 dual 1.8GHz, 3GB Ram, Mac OSX 10.5
BOINC Manager 5.10.28
Rosetta Beta 5.81
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David Riese

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Message 38322 - Posted: 25 Mar 2007, 12:03:45 UTC - in response to Message 38247.  

Lots of R@H units not working on my G4 Dual as well with the newest boinc update + 5.54. Same for Predictor@home (involving maybe the same math or same expectations of my system?).

Anyone getting 5.54 to happily run on a G4 Mac with the older boinc client?


For the last 2-3 days I have had problems running 5.54 on most of my Macs, including G4 eMacs, a G4 PowerBook, G4 Mac minis, an Intel Mac Mini, a G5 DP PowerMac, a MacBook Pro, and a Mac Pro. The only machines that have appeared to escape these problems is a G3 iMac and a Toshiba Tablet PC (Pentium III-M).

Regards,

Dave

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Message boards : Number crunching : Problems with Rosetta version 5.54



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