Minirosetta 3.73-3.78

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Profile David E K
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Message 79425 - Posted: 20 Jan 2016, 22:42:50 UTC

Please post any issues/bug reports regarding minirosetta and minirosetta_android 3.71 in this thread.
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Message 79426 - Posted: 21 Jan 2016, 1:32:37 UTC
Last modified: 21 Jan 2016, 1:38:58 UTC

New database coming down at 188Mb in size. One of my uploads struggling to upload. I anticipate everyone struggling to upload and download for a few days as the servers take a hit from everyone.

David: what are the fixes\\improvements in this version, please?

Edit: 10mins to upload 2 tasks and download 4 3.71 tasks and the full new database took just 10 minutes here. Hopefully it won\'t be too bad for everyone, but still some patience required, obviously
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Profile David E K
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Message 79427 - Posted: 21 Jan 2016, 4:01:04 UTC

This version uses the latest Rosetta source code which includes an improved score function, new protocols (for example a new cyclic peptide modeling protocol), and some modifications to the graphics application.
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Message 79428 - Posted: 21 Jan 2016, 6:20:51 UTC

One of my hosts is an Android 5 Tablet with 4 CPUs. Just a few moments ago I did an update and BOINC Event Log entry from Rosetta says: Rosetta Mini is not available for your type of computer. Is your server not yet recognizing the qualifications for 3.71? I know this message would be appropriate for earlier Rosetta Mini versions.

Is the delay in sending 3.71 to my device due to overworked server or another reason? Thank you.
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Message 79429 - Posted: 21 Jan 2016, 18:49:28 UTC

We currently are not sending out the android work units yet. We will soon.
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Message 79430 - Posted: 22 Jan 2016, 1:53:31 UTC

Was the blue background intentional? I\'d prefer an all black background like the previous version.
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Profile David E K
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Message 79431 - Posted: 22 Jan 2016, 4:36:59 UTC

Yes it is intentional. Someone in the lab wanted to make it look better but I guess it\'s all a matter of opinion. He also added a nice light source for a spacefill representation which you will see soon once he starts submitting his cyclic peptide modeling jobs.
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Message 79432 - Posted: 22 Jan 2016, 5:52:00 UTC - in response to Message 79431.  

Yes it is intentional. Someone in the lab wanted to make it look better but I guess it\'s all a matter of opinion. He also added a nice light source for a spacefill representation which you will see soon once he starts submitting his cyclic peptide modeling jobs.


Personally I like the new background coloring, though either way is fine really. Looks great in full screen. Will be interesting to see the cyclic peptide jobs.
**38 cores crunching for R@H on behalf of cancercomputer.org - a non-profit supporting High Performance Computing in Cancer Research
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Message 79435 - Posted: 24 Jan 2016, 0:12:17 UTC - in response to Message 79427.  

This version uses the latest Rosetta source code which includes an improved score function, new protocols (for example a new cyclic peptide modeling protocol), and some modifications to the graphics application.


This insinuated itself whilest crunching a v3.65 WU was retained in memory. Currently my machine is crunching WCG WU - both v3.65 & v3.71 Rosetta WU are RAM\'d - prolly to swap space that\'s been striped across two U160 15k SCSI HDD.

Its a pain in the neck - but I do it - when that v3.65 is done, I can gets rid of the old DB zip? And THEN only make symlinks to the newest DB?

I\'ve mentioned this before: I\'d like better control over the DB extract process - so as to automate via script the symlink creation; but I was shouted down, belittled and trivialized by those superior to myself. I understand; that\'s the consequence of progress. :(

That notwithstanding, once I can participate with \'progress\' I\'m certain I\'ll be a happy camper. ;) Imagine crunching on the video card, or even surpassing the 3.5GB memory constraint because of the hardware platform my O/S runs on!

Oh, the future is such halcyion days!

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Message 79436 - Posted: 24 Jan 2016, 6:44:18 UTC - in response to Message 79429.  

We currently are not sending out the android work units yet. We will soon.


Will we be notified, either by post or BOINC notice, when the WUs will be ready for sending? No use keeping space open on devices until work actually can begin flowing. Thanks.
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Message 79437 - Posted: 24 Jan 2016, 15:49:10 UTC
Last modified: 24 Jan 2016, 16:03:37 UTC

updating, i tried this out on ralph actually, 3.71 in ralph seemed to run ok on linux. the blue background looks nicer but it seem somewhat stressful on the eye, i\'d guess preference varies between individuals
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Message 79438 - Posted: 25 Jan 2016, 0:36:57 UTC

no errors for 8 tasks
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Message 79439 - Posted: 25 Jan 2016, 10:19:47 UTC - in response to Message 79437.  

updating, i tried this out on ralph actually, 3.71 in ralph seemed to run ok on linux. the blue background looks nicer but it seem somewhat stressful on the eye, i\'d guess preference varies between individuals

Maybe they could make it configurabe thru Rosetta@Home Preferences, on SETI for example you can configure the screensaver that way.
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Message 79441 - Posted: 25 Jan 2016, 19:12:38 UTC

Krypton\'s works well since your changes and two days of runtime.
Now, i got another WU with the same error (\"exceeded elapsed time limit 141525.53 (500000.00G/3.53G)\"):
https://boinc.bakerlab.org/rosetta/result.php?resultid=788117823

I have about 1300 credits lost with this error, and two days of WU crunching of one core.
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Message 79442 - Posted: 25 Jan 2016, 21:11:08 UTC - in response to Message 79441.  

I have about 1300 credits lost with this error, and two days of WU crunching of one core.


Credit for tasks that have errors is granted via a nightly script and, for whatever reason, is not shown on the task summary web page, only the task details.

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Message 79444 - Posted: 25 Jan 2016, 23:15:04 UTC - in response to Message 79441.  

Krypton\'s works well since your changes and two days of runtime.
Now, i got another WU with the same error (\"exceeded elapsed time limit 141525.53 (500000.00G/3.53G)\"):
https://boinc.bakerlab.org/rosetta/result.php?resultid=788117823

I have about 1300 credits lost with this error, and two days of WU crunching of one core.


Target runtimes of 2 days have been deprecated for a while, to avoid issues I suggest moving your target runtime down to 1 day or less, this will provide enough buffer space between any hard limits like the one your WU hit.
**38 cores crunching for R@H on behalf of cancercomputer.org - a non-profit supporting High Performance Computing in Cancer Research
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Message 79446 - Posted: 26 Jan 2016, 20:02:15 UTC - in response to Message 79442.  
Last modified: 26 Jan 2016, 20:02:41 UTC

Credit for tasks that have errors is granted via a nightly script and, for whatever reason, is not shown on the task summary web page, only the task details.


Oh, good to know! Thanks.

Target runtimes of 2 days have been deprecated for a while, to avoid issues I suggest moving your target runtime down to 1 day or less, this will provide enough buffer space between any hard limits like the one your WU hit.


No, i will not move. I have a weak and unstable internet connection. I do not waste internet traffic with a shorter runtime and disk space as well.

This bug is based on Boinc, not on the server bug that we had before. It seems that it need only a change in the parameters for a WU. I had before the same bug with *Krypton* WUs, since a change at server side there is no bug more.
By the way, two days gives a high chance of getting 99 results per WU. And, wasting less crunching time for finalization of one WU and starting another.
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Message 79448 - Posted: 27 Jan 2016, 8:10:33 UTC - in response to Message 79446.  

Credit for tasks that have errors is granted via a nightly script and, for whatever reason, is not shown on the task summary web page, only the task details.


Oh, good to know! Thanks.

Yes, but the maximum is 300 credits as you can see at the bottom of the result page.



By the way, two days gives a high chance of getting 99 results per WU. And, wasting less crunching time for finalization of one WU and starting another.

This is true, however the chance, that the WU errors out and all that work is lost increases too.
.
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Message 79449 - Posted: 27 Jan 2016, 11:23:21 UTC - in response to Message 79429.  

We currently are not sending out the android work units yet. We will soon.


Will be some limitation, for example more recent than android 4.4??

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Message 79451 - Posted: 27 Jan 2016, 18:32:02 UTC - in response to Message 79446.  


No, i will not move. I have a weak and unstable internet connection. I do not waste internet traffic with a shorter runtime and disk space as well.


@sinspin, I would just point out that if files already exist on your host as you receive new work, then they do not have to be downloaded. However, if the host completes all tasks that need a file, the file is deleted. Any future tasks that might need it would have to download again. So, very difficult to predict your internet bandwidth requirement with much precision. Depends on the mix of tasks you get. But there are cases where having a larger pool of tasks on your host can improve the odds that you already have the needed files downloaded.

If bandwidth and stability are chief concerns, you might consider installing something like squidproxy. It will stash a copy of downloaded files. Then if ever needed again, it already has a copy. Of course that would need some disk space to operate as well. But it (and longer runtimes) is the most effective way to save the network usage.
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