minirosetta 2.15

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Mad_Max

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Message 67872 - Posted: 29 Sep 2010, 11:52:39 UTC
Last modified: 29 Sep 2010, 11:55:23 UTC

+1 to problems with "Txxxx_" tasks on minirosetta 2.15.
Some of them crash and others consume very higt amount of RAM (like 800-1400 Mb per task)
I think crashes was due to lack of memory too - when two such tasks run concurrently (have 2 Gb of RAM on 2 core CPU)
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Message 67881 - Posted: 29 Sep 2010, 22:42:47 UTC

I too have recently seen messages indicating shortage of virtual memory, so have suspended Rosetta.
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Yifan Song
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Message 67892 - Posted: 1 Oct 2010, 4:10:03 UTC

There are quite a few reports here on large memory usage with the latest jobs. Due to the ongoing post-CASP analysis, I think a lot of the jobs are for difficult targets, which means large proteins. And they tend to eat up more memory than normal jobs do. I'll double check with the people submitting these jobs.
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Message 67897 - Posted: 1 Oct 2010, 7:18:40 UTC

I also have been getting daily error messages about lack of virtual memory on all three computers i have running. One machine in particular really bogs down, until i shut off Rosetta.
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Jochen

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Message 67900 - Posted: 1 Oct 2010, 7:27:36 UTC

I had to stop Rosetta as well. My two working rigs (3.4 GB each) got unusable and even my gaming rig (12 GB) was having memory issues.
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Profile John Robert Mallernee
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Message 67915 - Posted: 1 Oct 2010, 14:31:05 UTC
Last modified: 1 Oct 2010, 14:35:06 UTC

Greetings:

I knew something wasn't right when I saw my Rosetta screensaver wasn't displaying the normal graphic.

It showed only the blank chart form, with no activity, even though the displayed work unit numbers indicated that activity had, and was taking place.

I exited BOINC, and then reloaded it, figuring that might solve the problem.

Alas, now the Rosetta screensaver wouldn't display ANY graphic, not even the blank chart form.

So, I aborted Rosetta, and went to another project, which was operating normally.

Up popped an alert notice from the Norton anti-virus program, saying Rosetta had caused a HIGH security risk in my computer.

Here is what Norton detected and quarantined:

c:documents and settingsall usersapplication databoincprojectsboinc.bakerlab.org_rosettaminirosetta_2.15_windows_intelx86.exe

Note the reverse slashes.

Is that normal?

Norton did not specify if this HIGH security risk was a virus, worm, or trojan.

Norton did indicate the threat had been fully removed.

Thank you.
John Robert Mallernee
Armed Forces Retirement Home
Washington, D.C. 20011-8400
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Jochen

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Message 67919 - Posted: 1 Oct 2010, 16:29:49 UTC

Looks like a false alarm. Symantec needs to fix this. There is no virus or any other malware in Rosetta's executable.

But I don't know, whether Rosetta restores the application automatically, once the servers are back online, or whether you have to reset the project.
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Profile John Robert Mallernee
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Message 67923 - Posted: 1 Oct 2010, 20:47:28 UTC - in response to Message 67919.  

Looks like a false alarm. Symantec needs to fix this. There is no virus or any other malware in Rosetta's executable.

But I don't know, whether Rosetta restores the application automatically, once the servers are back online, or whether you have to reset the project.


Greetings:

I took another look at my Norton program's history details (I'm still learning how it works), and I noticed that it had done the same thing with another BOINC project I run, Climate Prediction, over and over and over again.

Norton repeatedly identified Climate Prediction work units as a "HIGH" security threat.

The Rosetta screensaver, which is what got my attention, usually runs as it should.

But, sometimes, the Rosetta screensaver appears either as a blank form graphic, with no activity, or it simply appears as a totally blank screen, without displaying even the blank form.

So, if the problem is a software conflict with Symantec, I don't know how that can be resolved.

I'm wondering if BOINC technicians can't investigate further and maybe coordinate something?

Thank you.

John Robert Mallernee
Armed Forces Retirement Home
Washington, D.C. 20011-8400
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Message 67927 - Posted: 1 Oct 2010, 22:35:19 UTC

One solution is to add Rosetta/Climateprediction to the exceptions, programs which will not be checked. That does require some faith, I suppose.
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Message 67929 - Posted: 1 Oct 2010, 23:55:05 UTC

The T0x series is having troubles.
Getting traceback errors and pointer errors.
T05 and T06 series.
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Message 67931 - Posted: 2 Oct 2010, 4:21:16 UTC

Further to my post of yesterday, on my gaming rig which is a dual core with 4GB of ram, Rosetta was running normally on one core, however, on the second it was not running. The annotation stated Rosetta was "waiting for memory". Definitely an issue with the 2.15 version i would say, if there is not enough memory on a 4GB machine.
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Dale Kirstein

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Message 67934 - Posted: 2 Oct 2010, 17:30:05 UTC

Agreed, something buggy with 2.15 They quickly rise to over 1.5 GB of memory use, at which point they are shut down and wait for memory to free up.
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Message 67935 - Posted: 2 Oct 2010, 18:25:15 UTC

I don't agree. It is not a problem with the application. The problem is a type of WU that needs more memory than your average WU. But since I'm only a cruncher here, I can't be any more certain than you are. :)
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Brian Priebe

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Message 67936 - Posted: 2 Oct 2010, 18:40:40 UTC - in response to Message 67934.  
Last modified: 2 Oct 2010, 19:06:20 UTC

They quickly rise to over 1.5 GB of memory use, at which point they are shut down and wait for memory to free up.
If you haven't already done so, you should review the BOINC memory limits set up in Advanced->Preferences->Disk and Memory Usage. A 4GB machine could be adequate to (barely) run two 1.5GB WU's at once. On a 2GB machine, it might be impossible though.
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Message 67937 - Posted: 3 Oct 2010, 0:05:50 UTC - in response to Message 67935.  

I don't agree. It is not a problem with the application. The problem is a type of WU that needs more memory than your average WU. But since I'm only a cruncher here, I can't be any more certain than you are. :)


As a guess I would say it is a mixture of both. The ones that are using the most memory seem to be reruns of the Casp9 targets. Those ones used up a lot of memory the first time round but didn't seem to get as high as 1.5GB.

It is probably a combination of high-memory targets and new memory-hungry code. Hopefully they can track down the second problem and implement some less hungry code in mini 2.16.
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Message 67939 - Posted: 3 Oct 2010, 13:37:40 UTC

Greetings:

Unfortunately, just like everyone else who's been posting recently, I'm starting to have similar difficulty with the new version of Rosetta.

I'm using a Toshiba Satellite notebook computer with nearly a hundred gigabytes of memory.

Yet, I just now woke up to see the Rosetta screensaver graphic displaying a blank form, and frozen in place.

An alert on my task bar indicated I was out of virtual memory.

Regretfully, I'm going to have to disconnect from the Rosetta project.

Thank you.
John Robert Mallernee
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Michael Gould

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Message 67940 - Posted: 3 Oct 2010, 14:35:51 UTC

I think you should try tweaking your settings before giving up. I'm running on a dual core iMac with only 2 GB of memory installed, and I have had no memory problems at all, including with casp9 units. Every once in a while, I'll get the "Waiting for memory" message in the status column, but it clears up.

Maybe an idiotic suggestion, but if you shortened the runtime per unit, would it use less ram? If the ram usage gradually increases as the unit runs, perhaps this would work?

Also, I would think that running the graphic all the time increases the ram usage. Perhaps shutting off the graphic when memory issues crop up would do the trick.

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Message 67941 - Posted: 3 Oct 2010, 16:04:24 UTC - in response to Message 67940.  

I think you should try tweaking your settings before giving up. I'm running on a dual core iMac with only 2 GB of memory installed, and I have had no memory problems at all, including with casp9 units. Every once in a while, I'll get the "Waiting for memory" message in the status column, but it clears up.

Maybe an idiotic suggestion, but if you shortened the runtime per unit, would it use less ram? If the ram usage gradually increases as the unit runs, perhaps this would work?

Also, I would think that running the graphic all the time increases the ram usage. Perhaps shutting off the graphic when memory issues crop up would do the trick.



Mr. Gould, Et Alii:

The problem with your suggestion is that you exhibit far more knowledge of computer technology than I do.

I'm unable to do what you suggest because I don't understand what you're suggesting.

I'm just an ordinary guy with only an amateur user's ability.

Everything I've learned so far about having a personal computer and using the Internet has been through trial and error "by guess and by gosh!" experimentation.

The really sad thing about all this is that it will have a negative effect on all other BOINC projects.

Up until now, I've been enthusiastically recommending BOINC participation in my e-mails and on my web site.

But, if people suspect problems with any one of the BOINC projects (including Rosetta), then they'll be reluctant to volunteer their personal computers for any scientific research.

I really do want to participate in the Rosetta project, but these technical problems need to be resolved, and any instructions have to be simple enough for an ordinary home computer user to easily comprehend.

Thank you.
John Robert Mallernee
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Message 67942 - Posted: 3 Oct 2010, 17:34:24 UTC - in response to Message 67941.  

I really do want to participate in the Rosetta project, but these technical problems need to be resolved (...)

That are not technical problems, just the information on the Recommended System Requirements Page is not up to date, at least with recent (and even not so recent) WUs in mind.

And that are the minimum system requirements, so system like that maybe still can run rosetta, but doing anything else on that machine gets quite impossible even without those 1GB+ tasks, I know that from my 768MB machine. IMO it's time to update that information and clearly distinguish between minimum and recomended system requirements.
.
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Message 67945 - Posted: 3 Oct 2010, 22:58:54 UTC - in response to Message 67941.  

I think you should try tweaking your settings before giving up. I'm running on a dual core iMac with only 2 GB of memory installed, and I have had no memory problems at all, including with casp9 units. Every once in a while, I'll get the "Waiting for memory" message in the status column, but it clears up.

Maybe an idiotic suggestion, but if you shortened the runtime per unit, would it use less ram? If the ram usage gradually increases as the unit runs, perhaps this would work?

Also, I would think that running the graphic all the time increases the ram usage. Perhaps shutting off the graphic when memory issues crop up would do the trick.



Mr. Gould, Et Alii:

The problem with your suggestion is that you exhibit far more knowledge of computer technology than I do.

I'm unable to do what you suggest because I don't understand what you're suggesting.

I'm just an ordinary guy with only an amateur user's ability.

Everything I've learned so far about having a personal computer and using the Internet has been through trial and error "by guess and by gosh!" experimentation.

The really sad thing about all this is that it will have a negative effect on all other BOINC projects.

Up until now, I've been enthusiastically recommending BOINC participation in my e-mails and on my web site.

But, if people suspect problems with any one of the BOINC projects (including Rosetta), then they'll be reluctant to volunteer their personal computers for any scientific research.

I really do want to participate in the Rosetta project, but these technical problems need to be resolved, and any instructions have to be simple enough for an ordinary home computer user to easily comprehend.

Thank you.



What he is saying is there is a place in your account online here on the project to shorten your run times.

If you goto the top of the screen here and click on participants and then look at preferences and then goto Resource share and graphics section and next to this line you will see on the right in blue text: Rosetta@home preferences
and then modify these settings to like what I have:

Percentage of CPU time used for graphics not selected
Number of frames per second for graphics not selected
Target CPU run time 4 hours

I have no trouble handling 4 tasks with 3.2 GB of ram while running everything else I want on my computer.

Now in the Boinc manager you should click on the projects tab and then highlight via clicking the rosetta@home project and then click on the update tab on the left. This will download your new settings into the Boinc Manager program.

Give this a try and see what happens.
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