Minirosetta 3.73-3.78

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Profile [VENETO] boboviz

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Message 79494 - Posted: 7 Feb 2016, 7:50:20 UTC - in response to Message 79492.  

I am sure, stupid is not the right description. But, for whatever reason was it necessary to change to blue?


There is a scientific reason:
The graphics application was also updated to include new colors and a light source for spacefill rendering used for the new cyclic peptide modeling protocol. Spacefill rendering is only used as default for this protocol since the additional graphics load is minimal due to the small size of the proteins to be modeled.

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Message 79495 - Posted: 7 Feb 2016, 14:14:27 UTC - in response to Message 79494.  

I am sure, stupid is not the right description. But, for whatever reason was it necessary to change to blue?


There is a scientific reason:
The graphics application was also updated to include new colors and a light source for spacefill rendering used for the new cyclic peptide modeling protocol. Spacefill rendering is only used as default for this protocol since the additional graphics load is minimal due to the small size of the proteins to be modeled.


That looks like an adequate reason for making some change, but is there any good reason for making the new colors and the light source mostly blue with no option for any other color instead?
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Profile [VENETO] boboviz

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Message 79497 - Posted: 7 Feb 2016, 19:08:15 UTC - in response to Message 79495.  

That looks like an adequate reason for making some change, but is there any good reason for making the new colors and the light source mostly blue with no option for any other color instead?


Good question, but
- no gpu app
- no 64 bit native app (for windows)
- no optimized app
- no updated server
- no android app (waiting new work)

So, screensaver may be not a priority :-)
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Message 79499 - Posted: 7 Feb 2016, 22:43:42 UTC - in response to Message 79491.  
Last modified: 7 Feb 2016, 22:54:43 UTC

The blue background is stupid and I do not like it at all.


Please, use other terms.


I will use whatever terms I desire to use.


Fine if you then let everyone else use those same terms to describe you.


Apparently the fact that words can have different meanings depending on context escapes you. STUPID can also mean \"ANNOYING\" or \"TROUBLESOME\" and even \"INANE\" or \"IRRITATING\", but I suspect people like you with your limited rational cognitive processes will always have a problem with seeing anything outside your own limited vernacular expression. Thus, keep your droll comments to yourself. I was merely \"EXPRESSING\" how \"IRRITATING\" the color change is, and per the comment about there being a \"scientific reason\" behind the color change...what a banal reason. Black will work just fine. Regardless, I am done with this thread and this topic. The blue is stupid. That is all I have to say; we are done here.
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Message 79500 - Posted: 8 Feb 2016, 16:25:09 UTC - in response to Message 79493.  
Last modified: 8 Feb 2016, 16:35:36 UTC

It\'s high school all over again! Hahaha

If I was still using screensavers, I\'d want an option to choose some main color other than blue. I\'ve read that seeing blue tends to keep people awake for at least half an hour after they see much of it, and I don\'t find much to do in the half hour between the time I turn the monitors of my computers off and the time I go to bed.


Try f.lux (https://justgetflux.com/)
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Profile [VENETO] boboviz

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Message 79502 - Posted: 8 Feb 2016, 18:54:53 UTC - in response to Message 79499.  

Apparently the fact that words can have different meanings depending on context escapes you. STUPID can also mean \"ANNOYING\" or \"TROUBLESOME\" and even \"INANE\" or \"IRRITATING\", but I suspect people like you with your limited rational cognitive processes will always have a problem with seeing anything outside your own limited vernacular expression.

I\'m italian, so my english is very basic and \"stupid\" means \"stupid\".
My rational cognitive processes, on the other hand, are not so bad.

and per the comment about there being a \"scientific reason\" behind the color change...what a banal reason. Black will work just fine.

Are you a scientist? Do you work with Rosetta code? No? So: shut up.

Regardless, I am done with this thread and this topic. The blue is stupid. That is all I have to say; we are done here.

Bye bye, you don\'t miss.
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Profile David E K
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Message 79503 - Posted: 8 Feb 2016, 20:53:19 UTC

We\'ll try to put a color option in the next update. It should be simple.
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Message 79505 - Posted: 9 Feb 2016, 6:00:42 UTC

Two workunits each gave Compute error after about 48 minutes.

http://boinc.bakerlab.org/rosetta/result.php?resultid=792069698
http://boinc.bakerlab.org/rosetta/result.php?resultid=792073059

Both reported out of memory. Is that accurate enough that I\'ll have to set No new tasks? The motherboard won\'t take any more memory.
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Message 79507 - Posted: 9 Feb 2016, 19:39:46 UTC - in response to Message 79505.  

Two workunits each gave Compute error after about 48 minutes.

http://boinc.bakerlab.org/rosetta/result.php?resultid=792069698
http://boinc.bakerlab.org/rosetta/result.php?resultid=792073059

Both reported out of memory. Is that accurate enough that I\'ll have to set No new tasks? The motherboard won\'t take any more memory.


There is a batch of workunits that may contain some high memory jobs. These should be done soon so I wouldn\'t change anything.
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Message 79510 - Posted: 11 Feb 2016, 9:54:37 UTC

Had the same issue with https://boinc.bakerlab.org/rosetta/workunit.php?wuid=718197115

What is the problem with high memory wu? I suppose 64 GB RAM should be sufficient.
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Message 79513 - Posted: 11 Feb 2016, 15:45:00 UTC - in response to Message 79510.  
Last modified: 11 Feb 2016, 15:45:26 UTC

Had the same issue with https://boinc.bakerlab.org/rosetta/workunit.php?wuid=718197115

What is the problem with high memory wu? I suppose 64 GB RAM should be sufficient.


It always depends on the BOINC Manager settings as to how much of that memory BOINC is allowed to use, and how much memory is available per CPU core that is running BOINC tasks. But yes, the primary area where high memory tasks will likely turn up issues is on machines with relatively less memory for CPU core.
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Message 79523 - Posted: 12 Feb 2016, 11:41:24 UTC - in response to Message 79513.  
Last modified: 12 Feb 2016, 11:44:07 UTC


It always depends on the BOINC Manager settings as to how much of that memory BOINC is allowed to use, and how much memory is available per CPU core that is running BOINC tasks. But yes, the primary area where high memory tasks will likely turn up issues is on machines with relatively less memory for CPU core.

Boinc is allowed to use up to 90% of memory independant from usage. Both settings have 90% applied. HDD Usage is set to 500 GB. I\'m running 10 simultanous tasks.

CPU type GenuineIntel
Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz [Family 6 Model 45 Stepping 7]
Number of CPUs 12
Operating System Microsoft Windows 10
Professional x64 Edition, (10.00.10586.00)
Memory 65449.89 MB
Cache 256 KB
Swap space 65465.89 MB
Total disk space 3725.9 GB
Free Disk Space 1974.17 GB
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Message 79526 - Posted: 12 Feb 2016, 14:58:11 UTC

@Eric_Kaiser
I\'d say that essentially proves that memory is not the only cause of these tasks ending abnormally. Nice rig!
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Message 79527 - Posted: 12 Feb 2016, 21:52:12 UTC

Today on my WIN10 with 16GB (6GB in use) I have 5 WU which terminated successfull, but 6 WU with \"Compute error\":

Task-ID: 792931235 + 792931236 + 792931184
02_2016_3mfj_backrub_design_327089_231_1
02_2016_3ork_backrub_design_327089_310_1
02_2016_1q06_backrub_design_327089_220_1

Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x763DD928
---------

Task-ID: 792839120 Name: 02_2016_1vhs_backrub_design_327089_236_1
Task-ID: 792839114 Name: 02_2016_3bl5_backrub_design_327089_216_1

Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x74F95B68
---------

Task-ID: 792931217
02_2016_2ozz_backrub_design_327089_321_0

Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x015BF87E write attempt to address 0x00000024
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Message 79548 - Posted: 15 Feb 2016, 9:28:33 UTC - in response to Message 79527.  

Today on my WIN10 with 16GB (6GB in use) I have 5 WU which terminated successfull, but 6 WU with \"Compute error\":

Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x763DD928
---------


Same here with 16gb and win10....
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Message 79549 - Posted: 15 Feb 2016, 15:37:47 UTC - in response to Message 79526.  

@Eric_Kaiser
I\'d say that essentially proves that memory is not the only cause of these tasks ending abnormally. Nice rig!


Since Eric\'s rig is Windows, even though its the 64 bit OS, the Windows rosetta app is still only 32 bit and thus can only address up to 4GB per instance (if memory serves). Still, he definitely has enough to allow the entire 4GB allocation to be filled.. With that said, I work with database applications on a daily basis that take many more gigabytes of memory per instance, so it\'s in the realm of possibility that this particular Rosetta task has a bit more of an appetite... to put it lightly :D
**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 79550 - Posted: 15 Feb 2016, 22:24:52 UTC - in response to Message 79549.  

@Eric_Kaiser
I\'d say that essentially proves that memory is not the only cause of these tasks ending abnormally. Nice rig!


Since Eric\'s rig is Windows, even though its the 64 bit OS, the Windows rosetta app is still only 32 bit and thus can only address up to 4GB per instance (if memory serves). Still, he definitely has enough to allow the entire 4GB allocation to be filled.. With that said, I work with database applications on a daily basis that take many more gigabytes of memory per instance, so it\'s in the realm of possibility that this particular Rosetta task has a bit more of an appetite... to put it lightly :D


Does this mean that minirosetta needs to be recompiled in 64-bit mode so it can handle workunits that need more than 4 GB of memory?
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Message 79552 - Posted: 16 Feb 2016, 4:19:00 UTC - in response to Message 79550.  
Last modified: 16 Feb 2016, 4:19:08 UTC

@Eric_Kaiser
I\'d say that essentially proves that memory is not the only cause of these tasks ending abnormally. Nice rig!


Since Eric\'s rig is Windows, even though its the 64 bit OS, the Windows rosetta app is still only 32 bit and thus can only address up to 4GB per instance (if memory serves). Still, he definitely has enough to allow the entire 4GB allocation to be filled.. With that said, I work with database applications on a daily basis that take many more gigabytes of memory per instance, so it\'s in the realm of possibility that this particular Rosetta task has a bit more of an appetite... to put it lightly :D


Does this mean that minirosetta needs to be recompiled in 64-bit mode so it can handle workunits that need more than 4 GB of memory?


Bingo!
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Message 79553 - Posted: 16 Feb 2016, 5:22:17 UTC - in response to Message 79552.  

@Eric_Kaiser
I\'d say that essentially proves that memory is not the only cause of these tasks ending abnormally. Nice rig!


Since Eric\'s rig is Windows, even though its the 64 bit OS, the Windows rosetta app is still only 32 bit and thus can only address up to 4GB per instance (if memory serves). Still, he definitely has enough to allow the entire 4GB allocation to be filled.. With that said, I work with database applications on a daily basis that take many more gigabytes of memory per instance, so it\'s in the realm of possibility that this particular Rosetta task has a bit more of an appetite... to put it lightly :D


Does this mean that minirosetta needs to be recompiled in 64-bit mode so it can handle workunits that need more than 4 GB of memory?


Bingo!


I think that the Windows version should be 64-bit BUT it will not fix this problem. IMO, it is a memory leak bug. Code is allocating memory but not freeing it.

Rosetta typically takes about 400mb - 450mb of memory to run. There is no way that a new Rosetta version should require 10x as much memory. It has to be a bug. It is a memory leak or a problem with the code that scans command line arguments for proper combinations.

IF 4gb is not enough memory to run Rosetta, then how much memory should a system have to successfully run 1 copy of Rosetta. My 8-core/16-thread system has 32gb of memory. Is 2gb per Rosetta workload enough? So far it has been.

When a system runs low on memory, it will start paging and performance will slow by 100x and choke your machine.


I compiled Rosetta source to build the default gcc 64-bit Linux version AND THEN added the -m32 option to build an identical 32-bit Linux version. The 64-bit version was 10% to 15% faster than the 32-bit version.








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Message 79554 - Posted: 16 Feb 2016, 10:34:47 UTC - in response to Message 79553.  

I compiled Rosetta source to build the default gcc 64-bit Linux version AND THEN added the -m32 option to build an identical 32-bit Linux version. The 64-bit version was 10% to 15% faster than the 32-bit version.


In Italy, we say \"buttali via\" (means approximately \"better than nothing\"). :-P
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