Posts by Yaroslav Isakov

1) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 60869)
Posted 28 Apr 2009 by Yaroslav Isakov
Post:
Hello, I have a problem: very long pending status in my last WUs:
1 2 3 4 5 6
2) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59878)
Posted 28 Feb 2009 by Yaroslav Isakov
Post:
Very long WU (25000 seconds), probably ended by timeout (intended runtime + 4 hours):

And it's also a Hbond tripped result :(


This one is interesting as it was completed successfully by a second computer in less than half the time and both were run on Linux machines.


Maybe it's because I have a 64-bit Linux?
3) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59874)
Posted 28 Feb 2009 by Yaroslav Isakov
Post:
Very long WU (25000 seconds), probably ended by timeout (intended runtime + 4 hours):
wt_ub_BOINC_ABRELAX_3MERS_NOHOMS_t482_SAVE_ALL_OUT_IGNORE_THE_REST-S25-3-S3-3--wt_ub-_7707_42783_0

It slows down on about 90% and I see in graphics that for about 4 hours it do SmallMoverMoverBase+Minimization stage

And it's also a Hbond tripped result :(
4) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59858)
Posted 27 Feb 2009 by Yaroslav Isakov
Post:
Another bunch of Hbond tripped errors:
hw_mamaln_t290_3_hb_1xyh__IGNORE_THE_REST_1ihg_1_SAVE_ALL_OUT_7736_375_0
hw_mamaln_t290_3_hb_1ihg__IGNORE_THE_REST_1cyn_1_SAVE_ALL_OUT_7729_256_0
hw_mamaln_t290_3_hb_t290__IGNORE_THE_REST_1zkc_1_SAVE_ALL_OUT_7743_255_0
hw_mamaln_t290_3_hb_t290__IGNORE_THE_REST_1xwn_1_SAVE_ALL_OUT_7743_255_0

First three of them have valid status and:
ERROR: dis==0 in pairtermderiv!
ERROR:: Exit from: src/core/scoring/methods/PairEnergy.cc line: 338
called boinc_finish
5) Message boards : Number crunching : Problems with Rosetta version 5.98 (Message 59803)
Posted 25 Feb 2009 by Yaroslav Isakov
Post:
With Rosetta@home, you can configure a runtime preference. This is done via the "[Participants]" link at the top of this forum page. And then click on the Rosetta preferences. The result of increasing the runtime is less bandwidth and scheduler requests on the server, and then the tasks just run more models until the target runtime is approached.

The particular WU you show suffers from the dreaded bug in the BOINC server code where a result if accepted after the deadline is reached but the task has already been reissued. There has been a BOINC trac item open to fix this for over a year.
http://boinc.berkeley.edu/trac/ticket/276


Thank you for explanation!
6) Message boards : Number crunching : Problems with Rosetta version 5.98 (Message 59794)
Posted 25 Feb 2009 by Yaroslav Isakov
Post:
Very strange result:
http://boinc.bakerlab.org/rosetta/result.php?resultid=230979688
and respective WU:
http://boinc.bakerlab.org/rosetta/workunit.php?wuid=208222634
Why canonical result do 108 decoys and mine do 12 decoys? And why I got 'Workunit error - check skipped'? And why there are three results?


The difference is in the:

# cpu_run_time_pref: 86400

yours is 10,800 ...

8 times more runtime gets more decoys ...


Ok, but why more runtime?
7) Message boards : Number crunching : Problems with Rosetta version 5.98 (Message 59789)
Posted 25 Feb 2009 by Yaroslav Isakov
Post:
Very strange result:
http://boinc.bakerlab.org/rosetta/result.php?resultid=230979688
and respective WU:
http://boinc.bakerlab.org/rosetta/workunit.php?wuid=208222634
Why canonical result do 108 decoys and mine do 12 decoys? And why I got 'Workunit error - check skipped'? And why there are three results?
8) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59672)
Posted 19 Feb 2009 by Yaroslav Isakov
Post:
Hey! Very strange one! it's valid, but with Hbond tripped and verys short time, 2380 secs instead of ~10000:
loopbuild_chunk_1_3_B_hb_t357__IGNORE_THE_REST_1VBGA_4_7477_27_0

BTW, I notice that all my wrong results (and this last one) are loopbuild_chunk*.
9) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59657)
Posted 18 Feb 2009 by Yaroslav Isakov
Post:
Another hbond tripped
10) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59631)
Posted 17 Feb 2009 by Yaroslav Isakov
Post:

I notice yours are a bit different though.
The first ones just include the line:
hbond tripped


The other two show:
Starting work on structure: _1JUDA_2_00001
Hbond tripped.

ERROR: dis==0 in pairtermderiv!
ERROR:: Exit from: src/core/scoring/methods/PairEnergy.cc line: 338
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

Not sure if one leads to the other but hbond tripped seems to be coming up in reports more regularly.


Hey, you're right, all my errors are with Hbond tripped in stderr, so I think that it's a source of problems
11) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59596)
Posted 16 Feb 2009 by Yaroslav Isakov
Post:
Hello, I have some problems with Minirosetta 1.54
validate error (about 25,000 seconds of runtime each)

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3

client error

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