Posts by Odysseus

1) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 72175)
Posted 19 Jan 2012 by Odysseus
Post:
I keep on getting project backoffs from my uploads for a couple days now, and I can\'t download any new workunits for the same reason. Is it working for anyone else?

I’m also having connection problems:
Wed 18 Jan 20:09:36 2012	rosetta@home	Fetching scheduler list
Wed 18 Jan 20:09:41 2012	rosetta@home	Master file download succeeded
Wed 18 Jan 20:09:46 2012	rosetta@home	Sending scheduler request: To fetch work.
Wed 18 Jan 20:09:46 2012	rosetta@home	Requesting new tasks
Wed 18 Jan 20:11:03 2012		Project communication failed: attempting access to reference site
Wed 18 Jan 20:11:05 2012		Internet access OK - project servers may be temporarily down.

Note that “Master file download succeeded” and that I have no problem accessing the website. Could there be a wrong URL in the sched_request_boinc.bakerlab.org_rosetta.xml file? I have tried resetting the project but I still get “Project communication failed” messages.

P.S. From the Statistics panel in BOINC Manager it appears the last time this host successfully updated was about January 3.
2) Message boards : Number crunching : Problems with Rosetta version 5.68 (Message 42057)
Posted 11 Jun 2007 by Odysseus
Post:
My Core2 Duo iMac got an error on 1gidA_BOINC_MG_SASAPAIR_EVENRES_RNA_ABINITIO_SAVE_ALL_OUT_BARCODE_RNA_CONTACT_RNA_LONG_RANGE_CONTACT_RNA_SASA-1gidA-_1760_57723 after just a few seconds of crunching; the salient part of the output appears to be
trouble finding jump_templates_RNA_basepairs_v2.dat
ERROR:: Exit from: read_paths.cc line: 360 
A WinXP/AMD system got a similar error on the WU; one other host appeared to finish it OK but got a Validate error.
3) Message boards : Number crunching : Problems with Rosetta version 5.68 (Message 41902)
Posted 6 Jun 2007 by Odysseus
Post:
Another crash from v5.68 on my G4 Mac, about twenty minutes into 2tif__LARS_ABRELAX_SAVE_ALL_OUT-2tif_-_BARCODE__1775_7010, with exit code 6 (0x6); aside from the crash-dump the output says
SIGBUS: bus error
and finishes with
Exiting...
pure virtual method called
terminate called without an active exception
Caught SIGABRT in graphics thread

4) Message boards : Rosetta@home Science : Investigation into \'Fibonacci\' numbers needed? (Message 41400)
Posted 24 May 2007 by Odysseus
Post:
From what I heard when the ratio is applied to music (frequency of sounds, maybe? I don\'t remember exactly) it also produces something that is commonly found pleasing.

Not in any obvious way: two pitches with frequencies in the golden ratio make a rather unpleasant-sounding chord about halfway between a minor sixth and a major sixth. (In the well-tempered scale those intervals have frequencies respectively 1.5874 and 1.6818 times that of the tonic.)

If you’re as easily amused as I am ;) you might enjoy this calculator exercise:

1. Key 1;
2. Key +, 1, =, √;
3. Repeat step 2 until bored.

For another, try the same thing but replace the ‘main loop’ with:

2. Key 1/x, +, 1, =.
5) Message boards : Rosetta@home Science : Investigation into \'Fibonacci\' numbers needed? (Message 41399)
Posted 24 May 2007 by Odysseus
Post:
Not only do we discover this pattern in leaf arrangements, but it is also commonly found in the arrangement of many flower petals. Examples: a lily has
3 petals, yellow violet 5, delphinium 8, mayweed 13, aster 21, pyrethrum 34, helenium 55, and michaelmas daisy 89. (my addition..these are all fib. numbers)

The spiral arrangements of pinecones, pineapples, and sunflowers display more than one Fibonacci number at a time, depending on which direction you follow the spiral.

When we realize that the information to produce these spirals and numbers in living things is stored in the DNA, should we then be surprised to find that the DNA molecule is 21 angstroms in width and the length of one full turn in its spiral is 34 angstroms, both Fibonacci numbers? The DNA molecule is literally one long stack of golden rectangles. (my addition..a \'golden rectangle\' is a rectangle with two sides being = 1 and the other sides = 1.618)

The angstrom is an arbitrary unit (1 Å = 10^–10 m), so looking for significance in the measurements themselves smacks of numerology. However, their ratio is independent of the units chosen. If you were to look down the axis of a DNA double-helix you’d see that it has decagonal symmetry, so it’s not surprising to find golden-section proportions there.
6) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 41369)
Posted 23 May 2007 by Odysseus
Post:
Another crash from my Mac G4/733, on 1gidA_BOINC_UNFOLDED_CHAINBREAK5_ALTSECSTRUCT_RNA_ABINITIO_RNA_CONTACT_RNA_LONG_RANGE_CONTACT_RNA_SASA-1gidA-_1735_46273 with exit status 1 (0x1):
Wed May 23 15:27:02 2007|rosetta@home|Deferring communication for 1 min 0 sec
Wed May 23 15:27:02 2007|rosetta@home|Reason: Unrecoverable error for result 1gidA_BOINC_UNFOLDED_CHAINBREAK5_ALTSECSTRUCT_RNA_ABINITIO_RNA_CONTACT_RNA_LONG_RANGE_CONTACT_RNA_SASA-1gidA-_1735_46273_0 (process exited with code 1 (0x1))
Wed May 23 15:27:02 2007|rosetta@home|Computation for task 1gidA_BOINC_UNFOLDED_CHAINBREAK5_ALTSECSTRUCT_RNA_ABINITIO_RNA_CONTACT_RNA_LONG_RANGE_CONTACT_RNA_SASA-1gidA-_1735_46273_0 finished
Wed May 23 15:27:02 2007|rosetta@home|Output file 1gidA_BOINC_UNFOLDED_CHAINBREAK5_ALTSECSTRUCT_RNA_ABINITIO_RNA_CONTACT_RNA_LONG_RANGE_CONTACT_RNA_SASA-1gidA-_1735_46273_0_0 for task 1gidA_BOINC_UNFOLDED_CHAINBREAK5_ALTSECSTRUCT_RNA_ABINITIO_RNA_CONTACT_RNA_LONG_RANGE_CONTACT_RNA_SASA-1gidA-

This one may have been provoked by interrupting the screensaver.
7) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 40969)
Posted 14 May 2007 by Odysseus
Post:
Another crash on my Mac G4/733, this time with exit status 6 (0x6): 1e6iA_BOINC_CORRECTION2_ABRELAX_SAVE_ALL_OUT_BARCODE-1e6iA-frags83__1714_4852. As before, lots of data that I don’t understand, but that a programmer might, in the output file.
8) Message boards : Number crunching : Coming from SETI and have couple Rosetta questions... (Message 40870)
Posted 13 May 2007 by Odysseus
Post:
I think SETI@Home has too much power for what they need. Don\'t they have 4-5 computers crunch the same data? I would think two would be enough unless you get a discrepancy.

The validation quorum was recently reduced from three results to two, and the initial replication accordingly from four to three. I don’t think the quorum was ever as high as four.
9) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 40713)
Posted 11 May 2007 by Odysseus
Post:
Another crash, this time with exit status 6 (0x6): 1e6iA_BOINC_CORRECTION2_ABRELAX_SAVE_ALL_OUT_BARCODE-1e6iA-frags83__1714_4852. Instead of failing right away, this one wasted more than three hours of CPU-time.
10) Message boards : Number crunching : Problems with Rosetta version 5.64 (Message 40697)
Posted 11 May 2007 by Odysseus
Post:
I had two tasks crash on my G4/733 (Mac OS 10.3.9) today, during the first few seconds of processing. (I was actually watching the graphics on one of them; it was still “Initializing” when it went down.) Both output files have extensive crash-dumps: 2chf__BOINC_CORRECTION2_ABRELAX_SAVE_ALL_OUT_BARCODE-2chf_-frags83__1714_688 and 1acf__BOINC_CORRECTION2_ABRELAX_SAVE_ALL_OUT_BARCODE-1acf_-frags83__1714_2284. Exit status 1 (0x1) for both.
11) Message boards : Number crunching : Problems with Rosetta version 5.62 (Message 40351)
Posted 5 May 2007 by Odysseus
Post:
My G4 Mac got some RALPH@home work this evening; the first WU had an error (which I’ll post over there), but it appears to have got most of the way through the next one it received because now I see that it’s downloaded a third one.

Please excuse my peevish tone earlier; it hasn’t been a good week. :(
12) Message boards : Number crunching : Problems with Rosetta version 5.62 (Message 40338)
Posted 4 May 2007 by Odysseus
Post:
We always test updates on ralph before releasing on rosetta@home but there are not enough mac participants (particularly w/ 10.3.9) to do thorough tests.

Well, I attached to Ralph to avoid such problems as this. But for a month now (after the public release of 5.59) I have got the message \"No work from project\", and I am simply unable to test your wus if you do not send me the necessary test files...

Having got the impression from Rhiju’s postings that more Macs were wanted there, I attached my G4 as soon as I got the chance today. Evidently I was wrong, because I too am getting “No work from project” messages. Maybe there’s a reason, beyond ‘demographics’, that Mac users aren’t exactly queuing up to help …
Fri May  4 14:07:58 2007|ralph@home|Sending scheduler request to http://ralph.bakerlab.org/ralph_cgi/cgi
Fri May  4 14:07:58 2007|ralph@home|Reason: To fetch work
Fri May  4 14:07:58 2007|ralph@home|Requesting 86400 seconds of new work
Fri May  4 14:08:03 2007|ralph@home|Scheduler request succeeded
[color=red]Fri May  4 14:08:03 2007|ralph@home|No work from project[/color]
Fri May  4 14:08:03 2007|ralph@home|Deferring scheduler requests for 13 minutes and 42 seconds

13) Message boards : Number crunching : Problems with Rosetta version 5.62 (Message 40295)
Posted 4 May 2007 by Odysseus
Post:
If you want to help, please do attach your project to ralph -- there will be an update to 5.63 later tonight that will (hopefully) fix the problem!

Sorry, I don’t know what you mean by “attach your project to ralph”. Is that a library? A repair utility? Where can I download it?

At any rate I’m at home now—the host in question is at work—so I won’t be able to do anything until tomorrow. (I’ll suspend the project first thing, to stop the flow of bad results at least, but I probably won’t have a chance to tinker with anything until mid-afternoon.)

If Mac OS 10.4.x and special libraries or auxiliary programs are needed here, I wish it would say so on the system-requirements page. I’d heard this was a reasonably Mac-friendly project …
14) Message boards : Number crunching : Problems with Rosetta version 5.62 (Message 40290)
Posted 3 May 2007 by Odysseus
Post:
I just started this project today, and it’s not going at all well so far. All three of the tasks I’ve begun errored out immediately: the output in the results says
<message>
process got signal 5
</message>
<stderr_txt>
dyld: rosetta_5.62_powerpc-apple-darwin Undefined symbols:
rosetta_5.62_powerpc-apple-darwin undefined reference to ___cxa_atexit expected to be defined in /usr/lib/libSystem.B.dylib
</stderr_txt>

I’m running several other BOINC projects with no problems on this host. The system is oldish, but appears to meet the posted requirements: Mac G4/733, 1 GB RAM, Mac OS v10.3.9, BOINC v5.4.9. I also have X11, so all the standard Unix libraries should be present—but I’m prepared to install whatever is necessary, within reason …

Any advice on how to get this app to run?






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