Posts by [B^S] sTrey

1) Message boards : Number crunching : Whats up with Ralph website? (Message 49229)
Posted 29 Nov 2007 by [B^S] sTrey
Post:
Ralph site is still unreachable and Rosetta still gives shared memory error, so they both appear to be down as far as getting/returning work is concerned.
2) Message boards : Cafe Rosetta : Moderator contact thread archive (Message 45715)
Posted 3 Sep 2007 by [B^S] sTrey
Post:
There is some SQL syntax error on the RALPH message boards, can you help with that?
1st thread with problem happens to be the 5.78 bug reporting thread.

My attempt to report the problem, which itself has the same problem. The error message implies it is a quote or apostrophe processing issue, but I didn\'t want to clutter up RALPH boards testing. HTH
3) Message boards : Number crunching : Ok... I have a challenge for all of you... (Message 22283)
Posted 11 Aug 2006 by [B^S] sTrey
Post:
I would say the main science is in the model, i.e. the theory being used to predict protein structures, and the software is the testing part (theories being tested as part of the scientific method, right?) so the model can be improved.

4) Message boards : Number crunching : Report Problems With BOINC SERVER UPGRADE (Message 18476)
Posted 11 Jun 2006 by [B^S] sTrey
Post:
Perhaps it\'s coincidence, but the Ralph site\'s no longer allowing result-reports or downloads, and has been reporting \"project down for maintenance\" since about the time of the server update. (& server status shows the feeder is down). Only posting here in case staff might see it sooner, since no one has responded or posted news on the RALPH boards. Meanwhile best of luck on any issues coming from the server update.
5) Message boards : Number crunching : Report Problems with Rosetta Version 5.13 (Message 16430)
Posted 17 May 2006 by [B^S] sTrey
Post:
My box hung during the 5 minutes Rosetta screensaver was allowed to run.
(at 82.93% done, model 8 step 339873, 3 hr 24 min 28 sec cpu). The display was frozen on the Rosetta screensaver image and I had to power-cycle the box. The BOINC Log shows:
5/16/2006 21:52:03 rosetta not responding to screensaver, exiting
5/16/2006 21:52:09 Unrecoverable error for result HOMOLOG_ABRELAX_hom003_t283__505_33632_0 ( - exit code -1 (0xffffffff))

It then went on to crunch CPDN, supposedly.
The above was preceded by a Windows application event log error 1000, timestamp 21:51:57:
Faulting application rosetta_5.13_windows_intelx86.exe, version 0.0.0.0, faulting module rosetta_5.13_windows_intelx86.exe, version 0.0.0.0, fault address 0x0056b66e.

Result link

I do have an ATI graphics card (Radeon 9000, circa 2003 )but I\'ve been running boinc with this hw for over a year without this happening, and drivers are up to date.

Not willing to crunch 5.16 with only 1 GB memory, did it with ralph and it\'s way too greedy. Will wait until more memory arrives but concerned about this error because it effectively crashed my system.
6) Message boards : Number crunching : 5.12 Windows Media Player and ffdshow (Message 15891)
Posted 11 May 2006 by [B^S] sTrey
Post:
It is NOT limited to video applications, because I don\'t use them, and I could repeatably hose my pc after a clean reboot with ralph suspended but other boinc projects running, by running ralph 5.12. Processes as vanilla as notepad took 1 minute to start (and the pc was not memory-starved), and at least one non-media app was badly broken. None of this is happening so far with ralph 5.13, so *big* thanks to Rom.

I hope he will put some details in his blog, because that vendor across the lake from the Rosetta lab will need spoon-feeding to make their app(s) less fragile.
7) Message boards : Number crunching : 5.12 Windows Media Player and ffdshow (Message 15855)
Posted 11 May 2006 by [B^S] sTrey
Post:
There seems to be more discussion here than on ralph boards so I\'ll add my bit.

Dell mb P4 3.2, HT but using only 1/2 of it for boinc, 1GB ram, ati radeon 9800
Started noticing degradation around the time of ralph 5.11 but didn\'t pin it to ralph until 5.12.

I do look at ralph graphics occasionally and use the boinc screensaver limited to 5 minutes, but when I was troubleshooting this I wasn\'t looking at graphics and was too active for the screensaver to kick in. Would hate to see the graphics go, unless they\'re made optional.

Currently task-damager says ralph\'s memory usage is about 72MB with VM size 118MB. And yes, it\'s showing over 2K-4K+ (!) PF every second, which is not wonderful and I\'d really like to know what it\'s doing. This wu has been running 40 cpu minutes and has 2.7 million page faults. Thankfully the memory size is growing only slowly, or this box would be on its lips by now.

I set my prefs down to 2 hours to get rid of this last 5.12 wu then will restart boinc and start some ralph 5.13 if there are any left by then, to see if things improve. Any further comments from me will go to the ralph boards.
8) Message boards : Number crunching : Database server unhappy - Jan 29 11:50 UTC (Message 10180)
Posted 29 Jan 2006 by [B^S] sTrey
Post:
This is affecting not only the forums but downloads. Forum pages are now usually getting the error below (though if this post succeeds obviously not always):
Unable to connect to database - please try again later Error: 1040#08004Too many connections


Download attempt gets: Server can\'t open database.
Consistently.
9) Message boards : Number crunching : Report stuck & aborted WU here please (Message 9843)
Posted 25 Jan 2006 by [B^S] sTrey
Post:
Not sure if you want errors reported here, but this is the first errored-out WU I\'ve had in a long time, and I see it wasn\'t just my result.
6543036

2006-01-25 11:48:42 [rosetta@home] Unrecoverable error for result NO_SIM_ANNEAL_BARCODE_30_RLX_NATIVE_1mky_281_29_2 (Incorrect function. (0x1) - exit code 1 (0x1))
10) Message boards : Number crunching : code release and redundancy (Message 4910)
Posted 2 Dec 2005 by [B^S] sTrey
Post:
FWIW, my \"votes\"
I prefer open or at least visible source, and would be in favor of redundancy by two. But I\'ll stay here regardless.

I don\'t get why the idea of rosetta redundancy so outrages some people. Most of the BOINC projects use redundancy --I think of Rosetta as having a temporary advantage in resources by not using it but it doesn\'t seem real world. That said, if the science doesn\'t need it i.e. to weed out bogus (by design or accident) results, and it\'s not needed to avoid a credit or validity \"scandal\" and subsequent mass exodus from Rosetta, then there\'s no point. (I\'d mind non-redundancy less if the benchmarks & credit calcs seemed less flaky, but credit is secondary.)

And for open source -- I have a hard time understanding the driving need behind hacking up the code to get higher numbers on a list, but I\'m cynical/old enough to believe it exists. So opening up the source or making it visible, is only worthwhile if that sort of stupidity can be made ineffective.

11) Message boards : Number crunching : No work from project ... again (5th nov) (Message 2593)
Posted 7 Nov 2005 by [B^S] sTrey
Post:
Larger WUs and reduced quotas are fine, but
Please don\'t shorten the deadline by much, unless you need to for science reasons. At least until the BOINC client stops asking for way too much work given resource share and work estimates and deadlines (on multi-project machines with anything more than a .1 day connection interval). With longer deadlines at least there\'s a chance to keep crunching on the project when the client would otherwise force itself into EDF for no good reason.

p.s. not sure how any of the above is relevant to getting no-work-from-project when there are 60K+ results waiting to be sent. This tends to clear itself up after retries, so is memory constraint the cause?
12) Message boards : Number crunching : Computational Error (Message 1140)
Posted 9 Oct 2005 by [B^S] sTrey
Post:

So it seems the benchmarking issue is isolated to multiple CPU machines, whether logical (HT) or physical (dual core/dual processors)


For what it\'s worth: I\'ve crunched only 17 wu\'s but haven\'t had any problems yet and have gone through a couple of benchmarks. I\'m running it on a HT cpu, but I\'ve told it to limit cpus to one, since that keeps the cpu temp reasonable.
(& it\'s set to keep projects in memory)
Hardware is P4 3.2Ghz, 1G ram, running XP Pro

Just another data point.
13) Message boards : Number crunching : If There Is No Screensaver........ (Message 583)
Posted 27 Sep 2005 by [B^S] sTrey
Post:
Imo: screensavers won't affect project survival, that depends more on good science & good administration. And especially on good feedback, which this project has already demonstrated.

OTOH screensavers do attract people just like stats do, though neither one has anything to do with the science. The original SETI@Home had a screensaver and so do the majority of BOINC projects, so it's hardly surprising that people expect them.

Seems to me that mass computing projects probably need the masses, not just the "elite". And isn't it one of the benefits to involve more people in science in this small way, leading to appreciation and support of same? If some eye-candy is part of the hook, it seems cheap at twice the price...

(And using, say, a 5 minute timeout on the screensaver lets you enjoy it without "wasting" the CPU overmuch.)

So bashing pro and con aside, I'm glad there will be a screensaver eventually; and meanwhile understand it's a lot of work and won't be the highest priority. Maybe this is another area where developer volunteers could be useful.
14) Message boards : Number crunching : Memory leak? (Message 534)
Posted 26 Sep 2005 by [B^S] sTrey
Post:


You shouldn't run rosetta unless you have 512 mb ram. And 108 mb is normal for rosetta though it might fluctuate during the computing. And it progress bar jumps in quite large chunks.

- peter


Well thanks for the warning. I've got a gig of memory but since I leave BOINC projects in memory, and have read that this beta project may have particular difficulties if not left in memory -- I'm not really enthused about the 157 MB it's currently consuming. None of the other 5 projects I run takes as much as 50 MB, but it all adds up, and XP is a hog to begin with. Will keep an eye on it and perhaps run this project only sporadically for a while.


And yes, I see the progress statistic is jumping around. Only cared if that + memory increase indicated a nasty loop, so knowing this is normal for Rosetta is helpful. Thank you.
15) Message boards : Number crunching : Memory leak? (Message 532)
Posted 26 Sep 2005 by [B^S] sTrey
Post:
I don't know if it is a memory leak exactly, but is R@H supposed to take 60MB memory?


It's at 108 MB for me, peak 144. And seems to be stuck at 83.33% done as the to-complete estimate rises. This is my first WU but I might have to abort it if it doesn't decrease memory or start looking like it will finish soon; running over night with increasing memory consumption is not an option.






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