Problems with Rosetta version 5.85 (or 5.86 for linux)

Message boards : Number crunching : Problems with Rosetta version 5.85 (or 5.86 for linux)

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Rhiju
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Message 48876 - Posted: 20 Nov 2007, 19:06:34 UTC

Thanks for continuing to post!
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John Yeatts
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Message 48926 - Posted: 22 Nov 2007, 2:50:23 UTC

I'm sure you've heard this before but. Rossettia version 5.85 is a virtual memory hog. I hope you can find soome ways to fix this problem.

Thank
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Rhiju
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Message 48930 - Posted: 22 Nov 2007, 6:03:29 UTC - in response to Message 48926.  

I have a feeling that this might be due just to the workunits we've sent out in the first couple days of the 5.85 app ("SYMM_FOLD_AND_DOCK_..."). We're working on way to improve the memory usage and the (infrequent) errors with this particular kind of workunit -- if the excess virtual memory issue continues with other kinds of workunits, please do post here. Thanks!

I'm sure you've heard this before but. Rossettia version 5.85 is a virtual memory hog. I hope you can find soome ways to fix this problem.

Thank


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MattDavis
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Message 48932 - Posted: 22 Nov 2007, 6:44:03 UTC

I would love to report a unit that errored out due to virtual memory issues, but I can't link to it because the stupid new spam filter won't let me post it.
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Paulo

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Message 48940 - Posted: 22 Nov 2007, 10:13:37 UTC - in response to Message 48930.  

I have a feeling that this might be due just to the workunits we've sent out in the first couple days of the 5.85 app ("SYMM_FOLD_AND_DOCK_..."). We're working on way to improve the memory usage and the (infrequent) errors with this particular kind of workunit -- if the excess virtual memory issue continues with other kinds of workunits, please do post here. Thanks!

I'm sure you've heard this before but. Rossettia version 5.85 is a virtual memory hog. I hope you can find soome ways to fix this problem.

Thank



Hi.

I am crunching a SYMM_FOLD_AND_DOCK_RELAX-1...
It is using 59 MB RAM, 807 MB VM.

I am running Boinc 5.10.30 on XP sp2 with 512 MB RAM and 1260 MB VM.

Is this respecting my settings of "50% of memory when computer is in use" and "90% of memory when computer is not in use" ?

Thanks,
Paulo
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transient
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Message 48951 - Posted: 22 Nov 2007, 17:04:39 UTC - in response to Message 48932.  
Last modified: 22 Nov 2007, 17:07:54 UTC

I would love to report a unit that errored out due to virtual memory issues, but I can't link to it because the stupid new spam filter won't let me post it.


My first impression is, all links are considered to be spam. I haven't found a workaround, yet. ;)

Edit:
Hmm, breaking the link works, sort of....

http://boinc.bakerlab.org/rosetta/result.php?resultid=122206234

Edit2:

Repairing the link....

So editing your own message to add a link, seems to bypass the spamfilter
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MattDavis
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Message 48970 - Posted: 23 Nov 2007, 6:43:58 UTC
Last modified: 23 Nov 2007, 6:44:06 UTC

This computer of mine is getting lots of virtual memory problems with 5.85


http://boinc.bakerlab.org/rosetta//show_host_detail.php?hostid=582931
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Profile dcdc

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Message 48975 - Posted: 23 Nov 2007, 20:08:06 UTC

VM problems here too - a machine with 256MB RAM and the task is using 180MB RAM and 750MB VM. Rosetta just crashed because the pagefile wasn't set to increase that high (changed it to system managed now).

I'm not sure these tasks be sent out to low memory machines?...
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Scottatron

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Message 48978 - Posted: 23 Nov 2007, 20:34:52 UTC

I am getting constant run time errors for 5.85 WUs

Microsoft Visual C++

It then lists the exe file location (C:\program filesetc|

This application has requested the Runtime to terminate it in an usual way. Please contact the application's support team for more information
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kratko

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Message 48979 - Posted: 23 Nov 2007, 22:10:27 UTC

Another vote for having problems with current version 5.85.
I used one server with two cpus with hyperthreading on.
Currently BOINC client is uninstalled.
I limited use of the memory to 20% for both scenarios, which would be 400 MB. As far as I have seen REAL behaviour of the software, that meant 20% for each of the processors. That gives 800 MB on that server.
In reality, software was using between 180 and 250 MB per task and (virtual) processor, what gives us most of the time over 800 MB of used memory. Sometimes it ran tasks using over 500 MB or even 800 MB of memory per single task. Those tasks I was killing.
And client crashed few times per day and disabled my remote desktop connections. I had to go to console, restart BOINC service and then I could connect remotely. And make up excuses to colleague why he couldn't connect to the server.

Few minutes ago rosetta client crashed on my home pc, after it finished one task and showed on the client some error, client or calculation error. Whatever.

Conclusion: it sucks. I switched off 2x3,6 GHz CPUs. And this is just one machine turned off. How many machines will be turned off?

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AMD_is_logical

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Message 48985 - Posted: 24 Nov 2007, 4:14:01 UTC
Last modified: 24 Nov 2007, 4:14:18 UTC

This WU bombed out after 16 seconds saying: The system cannot find the path specified. (0x3) - exit code 3 (0x3)
http://boinc.bakerlab.org/rosetta/result.php?resultid=122420282
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MattDavis
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Message 48990 - Posted: 24 Nov 2007, 9:16:12 UTC
Last modified: 24 Nov 2007, 9:16:52 UTC

My computer with virtual memory issues has 256 megs of RAM. I upped the VM size to try to preclude more VM errors, and I see that one Rosetta task is using 900 megs of VM. 900.

Wow!
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Evan

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Message 48991 - Posted: 24 Nov 2007, 10:30:12 UTC

And you think that's bad. Normally my computer runs Rosetta using between 400-600mb. It's now running at 1.03gb!
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DexterBelgium

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Message 48993 - Posted: 24 Nov 2007, 11:46:23 UTC

Same problem here, constant C++ and VM errors, and i've got 1GiB of mem!

It even bluescreened my pc just now. There is something serious going on here.
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drghughes

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Message 48994 - Posted: 24 Nov 2007, 13:19:43 UTC

I've had 3 more work units run without checkpointing (2 completed, 1 running). Is this something to do with the high virtual memory usage?

Do these WUs need to run without checkpointing? If you don't run 24/7, it either makes life much harder, or means lots of lost work.

Work units are 122603651, 122657121 and 122729004.


drghughes

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Prom

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Message 48995 - Posted: 24 Nov 2007, 13:38:50 UTC

There is something seriously wrong with the application. It's not a virtual memory hog it's a complete memory hog. I don't have virtual memory, have 2GiB of physical memory. Rosetta now uses 800MB of that for one wu. With the 600MB normally used this is not enough to run two or sometimes even one. I am aborting all version 5.85 tasks until they are disabled.
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The_Bad_Penguin
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Message 48996 - Posted: 24 Nov 2007, 13:47:10 UTC
Last modified: 24 Nov 2007, 13:47:32 UTC

In case you may have missed it in Cafe Rosetta, here's Nick's post.
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MattDavis
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Message 48997 - Posted: 24 Nov 2007, 14:47:32 UTC - in response to Message 48995.  

There is something seriously wrong with the application. It's not a virtual memory hog it's a complete memory hog. I don't have virtual memory, have 2GiB of physical memory. Rosetta now uses 800MB of that for one wu. With the 600MB normally used this is not enough to run two or sometimes even one. I am aborting all version 5.85 tasks until they are disabled.


All Rosetta units are 5.85 now, so please don't abort hundreds of units over and over. Just suspend the project.
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Rhiju
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Message 49019 - Posted: 24 Nov 2007, 21:25:59 UTC - in response to Message 48997.  

There are no more SYMM_FOLD_AND_DOCK_RELAX workunits being sent out -- I want to find out if those particular workunits were the source of the memory hog problem, or whether the application itself has an issue. Is anyone out there noticing bad behavior with other kinds of work? Thanks in advance for the feedback.

There is something seriously wrong with the application. It's not a virtual memory hog it's a complete memory hog. I don't have virtual memory, have 2GiB of physical memory. Rosetta now uses 800MB of that for one wu. With the 600MB normally used this is not enough to run two or sometimes even one. I am aborting all version 5.85 tasks until they are disabled.


All Rosetta units are 5.85 now, so please don't abort hundreds of units over and over. Just suspend the project.


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P . P . L .

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Message 49021 - Posted: 24 Nov 2007, 21:56:20 UTC
Last modified: 24 Nov 2007, 22:35:39 UTC

I did notice the memory use on these was high around 800mb but not a problem.

One on each computer same type / 1uis__BOINC_SYMM_FOLD_AND_DOCK_RELAX-1uis_-crystal_foldanddock__2318_41231_1

This one i did, someone else had an error with.

boinc.bakerlab.org/rosetta/workunit.php?wuid=111041811

-------------------------------------------------------------------

boinc.bakerlab.org/rosetta/workunit.php?wuid=111006442

Other W.U. that have run under 5.85 have haven't used as much memory, yet.

Edit/ had to remove start of url to post. + added W.U. types.
------------------------------------------------------------------
Just noticed these are using a lot of memory also, i have two of these.

w007_1_MolecularRep_1_w007_1_ffas03-1-2b0v_StructuralGenomics_a_2325_37167_0

boinc.bakerlab.org/rosetta/result.php?resultid=122588633

Pete.



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Message boards : Number crunching : Problems with Rosetta version 5.85 (or 5.86 for linux)



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