Bug reports for Ralph 5.16

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Rhiju
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Message 1622 - Posted: 14 May 2006, 21:24:18 UTC

We\'ve fixed the file input error on Macs for the MAPRELAX jobs. Also, we\'re trying a new feature (COMPTOSERVERS) where at the end of a simulation, Rosetta compares its fold to the predictions made by a dozen other algorithms. (Those predictions are sent to the clients in a compressed format.)

Let us know if you see any bugs. Also, please let us know if the memory requirements for the MAPRELAX jobs are unusually high.
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dainenyu

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Message 1628 - Posted: 15 May 2006, 7:44:52 UTC - in response to Message 1622.  

Some of the MAPRELAX units on my machine are erroring out after 15-20 minutes (normal runtime for me is a little over an hour). stderr out reads:

<core_client_version>5.4.9</core_client_version>
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 3057981
ERROR:: Unable to obtain sequence information.
fasta file must be provided.
ERROR:: Exit at: .\\initialize.cc line:236

</stderr_txt>


Looks ok up till that point. Graphics are good, at least. Upon hitting the error point, the graphics window just disappears.

A successful MAPRELAX
Error result

I\'m on Windows XP SP2, dual Pentium 4 processors.
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Honza

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Message 1629 - Posted: 15 May 2006, 7:49:54 UTC

Got one finished in ~ 45 min, memory usage unknown (finished sooner than I was able to check)
http://ralph.bakerlab.org/result.php?resultid=125948

Another one finished after 55 min, 230MB usage
http://ralph.bakerlab.org/result.php?resultid=125947

3 more to go...

Dumb question: apart from lower traffic of higher \"Target CPU run time\" - does having it set to let\'s say 12 hours brings \"better\" (i.e. more precise) results?
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Message 1630 - Posted: 15 May 2006, 12:07:54 UTC

I also had one of those 5.16\'s with a missing fasta file or whatever:
result
running win xp.
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Message 1631 - Posted: 15 May 2006, 12:35:25 UTC

Hi,

I had big problems with the last rosetta-versions, so I had to stop crunching for RALPH.

Now I tested 5.16 on that machine, where I got the problems; the WU took 3 1/2 hours, the problem didn\'t appear until now.

But, memory-usage has grown up; the actual WU was at 318 MB Main-memory, 339 MB virtuel-memory :-(

BOINC is running as a service, so no rosetta-screensaver ...

The only thing could be, the box uses a normal windows-screensaver: WindowsServer2003 (That is the name of the screensaver !)




Supporting BOINC, a great concept !
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Message 1632 - Posted: 15 May 2006, 13:31:27 UTC - in response to Message 1629.  

Got one finished in ~ 45 min, memory usage unknown (finished sooner than I was able to check)
http://ralph.bakerlab.org/result.php?resultid=125948

Another one finished after 55 min, 230MB usage
http://ralph.bakerlab.org/result.php?resultid=125947

3 more to go...

Dumb question: apart from lower traffic of higher \"Target CPU run time\" - does having it set to let\'s say 12 hours brings \"better\" (i.e. more precise) results?


In a word, No. At least not yet. It simply makes more models. Rosetta is not like a lot of other projects where a particular refined result is sought by a particular machine within a specific work unit. However, the project is starting to experiment with approaches that do sort of \"Learn\" as they go, and refine the work based on each model produced.

The goal here is to provide each work unit with a different starting point, and have each system adjust the work looking for the lowest energy level it can find among the models it can create in the time allotted. So the more models made the better. However, ultimately all of the systems are actually searching for the same result. If we ever get to the point where the project can send out 10,000 work units and they all come back with the same result, and it correctly reflects the actual shape of the protein, then we will have reached part of the goal. If we ever get to the point where a single system can reliable predict a protein shape given the amino acid sequence, we are done.

Since what is being sought is a reliable way to predict the protein shape, at this point the more models returned the better. The hope is that among those returned will be the correct one. If that happens then it is presumed that the technique that was used could repeat the performance.

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Dimitris Hatzopoulos

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Message 1633 - Posted: 15 May 2006, 14:20:54 UTC
Last modified: 15 May 2006, 14:29:16 UTC

Sofar, BOTH ralph 5.16 WUs errored out MAPRELAX_TEST_hom015_1fna__516_1_1, MAPRELAX_TEST_hom025_1fna__516_19_0

with \"Incorrect function (0x1) - exit code 1 (0x1)\"

This is on a very stable PC, which runs Rosetta flawlessly for the past 4 months (apart from 2-3 WUs which were bad).
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Message 1634 - Posted: 15 May 2006, 14:21:40 UTC - in response to Message 1630.  
Last modified: 15 May 2006, 14:26:41 UTC

Hi,

I had big problems with the last rosetta-versions, so I had to stop crunching for RALPH.

Now I tested 5.16 on that machine, where I got the problems; the WU took 3 1/2 hours, the problem didn\'t appear until now.

But, memory-usage has grown up; the actual WU was at 318 MB Main-memory, 339 MB virtuel-memory :-(

BOINC is running as a service, so no rosetta-screensaver ...

The only thing could be, the box uses a normal windows-screensaver: WindowsServer2003 (That is the name of the screensaver !)



Adjust u preferences to \"remove from memory\" when swapping projects,
to free swap space !

Now,
that enough checkpoints are done, this should be OK, for both ralph & rosetta

I had sucessfull run 5.16 on a Linux pc with 256 MB ram.
limited to use 35% of swap at maximum, to not crash the OS
(user of this pc is a heavy user of edonkey)
and its swap space is small ... less than 1MB

that pchttp://ralph.bakerlab.org/show_host_detail.php?hostid=1825

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Message 1635 - Posted: 15 May 2006, 14:36:53 UTC

Carlos,

my machine don\'t swap, I\'m running a cache of 0 days ...

Greetings


Supporting BOINC, a great concept !
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Message 1636 - Posted: 15 May 2006, 14:37:42 UTC

ERROR:: Unable to obtain sequence information.
fasta file must be provided.
ERROR:: Exit at: .\\initialize.cc line:236

http://ralph.bakerlab.org/result.php?resultid=125164
http://ralph.bakerlab.org/result.php?resultid=125315
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Honza

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Message 1638 - Posted: 15 May 2006, 16:11:09 UTC

Thanks for answer, Moderator9.
I\'ve done 5 WUs with no issue, D 820 with 1GB RAM.
...still a bit memory demanding for average machine.

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Message 1640 - Posted: 15 May 2006, 17:38:51 UTC - in response to Message 1638.  
Last modified: 15 May 2006, 17:59:55 UTC

Thanks for answer, Moderator9.
I\'ve done 5 WUs with no issue, D 820 with 1GB RAM.
...still a bit memory demanding for average machine.

While is see many reports of the memory issue, I have not seen this on my machines. Both the Windows and Mac machines look normal and even approximate the memory foot print for einstein. In any case the application always moves out of the way if I use the machines for any other tasks.
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Message 1641 - Posted: 15 May 2006, 18:55:29 UTC
Last modified: 15 May 2006, 19:03:55 UTC

Running a 5.16 wu now for all of 30 minutes (XP Pro SP2, P4, 1 GB mem), and memory usage is already high: 174K memory, 191K VM. These numbers aren\'t intolerable but they\'re higher than I\'m used to seeing from rosetta, and make me think it will climb into the range I reported on earlier. I\'ll be away most of the day,;will report back when the wu has more mileage.

See also this post on the number-crunching thread; it reports 690MB which is higher than I\'ve seen.

p.s. I leave boinc apps in memory when switched. Are these high numbers only happening to machines which leave rosetta in memory when preempted?
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Message 1642 - Posted: 15 May 2006, 20:03:37 UTC

Update before I hit the road: 1 hr 31 minutes into the wu, memory now is 325MB peak 329, Vm size is 341MB. PF ranging from 0-1K/second. Avail memory down to 74K, will see if the box is still functioning when I get home!
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Message 1643 - Posted: 15 May 2006, 23:26:22 UTC - in response to Message 1636.  

ERROR:: Unable to obtain sequence information.
fasta file must be provided.
ERROR:: Exit at: .\\initialize.cc line:236

http://ralph.bakerlab.org/result.php?resultid=125164
http://ralph.bakerlab.org/result.php?resultid=125315

I had a few of these as well. I feel certain they are bad Work Units.
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Message 1644 - Posted: 16 May 2006, 3:18:53 UTC

Ralph 5.16 WU\'s running fine so far, but, they consume a HUGE amount of RAM. The two WU\'s that I have running right now on my dual-core Athlon 64 X2 3800+ are using 664MB and 317MB of RAM respectively. VM usage is slighly higher than that for both.

--- bt
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Message 1645 - Posted: 16 May 2006, 3:29:37 UTC - in response to Message 1643.  

ERROR:: Unable to obtain sequence information.
fasta file must be provided.
ERROR:: Exit at: .\\initialize.cc line:236

http://ralph.bakerlab.org/result.php?resultid=125164
http://ralph.bakerlab.org/result.php?resultid=125315

I had a few of these as well. I feel certain they are bad Work Units.

I noticed a string of 5 of these missing Fasta file errors on my list, as well. Are some of the WUs taking advantage of features in Boinc 5.4.x that aren\'t in the Boinc 5.2.13 client?
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Message 1646 - Posted: 16 May 2006, 3:42:32 UTC - in response to Message 1645.  


I noticed a string of 5 of these missing Fasta file errors on my list, as well. Are some of the WUs taking advantage of features in Boinc 5.4.x that aren\'t in the Boinc 5.2.13 client?


Well I had one to http://ralph.bakerlab.org/result.php?resultid=125195 and I am using Boinc 5.4.9.

Anders n

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Message 1647 - Posted: 16 May 2006, 3:53:36 UTC

I Have a few -

    BOINC 5.4.9, Ralph 5.16
    GenuineIntel Intel(R) Pentium(R) M processor 1.86GHz
    Microsoft Windows XP Professional Edition, Service Pack 2, (05.01.2600.00)
    Memory 2039.37 MB
    cash 76.56 KB
    swap space 932.3 MB
    65.54 GB



resultid=125665 -
ERROR:: Unable to obtain sequence information. fasta file must be provided.
ERROR:: Exit at: .\\initialize.cc line:236
resultid=125589 -
ERROR:: Unable to obtain sequence information. fasta file must be provided.
ERROR:: Exit at: .\\initialize.cc line:236
resultid=125413 -
ERROR:: Unable to obtain sequence information. fasta file must be provided.
ERROR:: Exit at: .\\initialize.cc line:236

The machine is also running Rosetta

Regards
Phil


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Message 1648 - Posted: 16 May 2006, 4:33:26 UTC
Last modified: 16 May 2006, 4:34:53 UTC

http://ralph.bakerlab.org/result.php?resultid=125273

and the next 3 in numerical order all errored out:

<core_client_version>5.4.9</core_client_version>
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 3057874
ERROR:: Unable to obtain sequence information.
fasta file must be provided.
ERROR:: Exit at: .\\initialize.cc line:236

</stderr_txt>

Ran all 4 in a row.

Bill
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