Posts by [VENETO] boboviz

1) Message boards : Number crunching : Rosetta 4.0+ (Message 91105)
Posted 4 days ago by Profile [VENETO] boboviz
Post:
Again, out of memory on some wus (1092708763, 1092708790, etc) in a 8gb machine (4 wus running)
<core_client_version>7.14.2</core_client_version>
<![CDATA[
<message>
(unknown error) - exit code -529697949 (0xe06d7363)</message>
<stderr_txt>

Unhandled Exception Detected...
- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x75653442

Engaging BOINC Windows Runtime Debugger...
2) Message boards : News : Another publication in Nature describing the first de novo designed proteins with anti-cancer activity (Message 91099)
Posted 7 days ago by Profile [VENETO] boboviz
Post:
I have recently seen a Ted lecture by an oncologist who says that despite the many billions of dollars spent world-wide on cancer research there has been no real progress in that 50 years.


I don't know who is this oncologist, but he said a lie.
Childhood tumors, for example, now have 5ys survival rate over 80%, when 30 years ago was less than 30%
3) Message boards : Number crunching : Good bye Rosetta !!! (Message 91088)
Posted 9 days ago by Profile [VENETO] boboviz
Post:
One question regarding credits, because I forget. Does the number of credits given vary between machines? E.g. my Ryzen should get tons more credits per WU than, say, the 8350 over a 10 hour period, which is what my cpu runtime is set to, since it's IPC is theoretically much quicker?


Yes, the IPC is very important.
But, in Rosetta, is important also the speed of ram memory and the speed of hd (i saw an increase of rac - with the same cpu, when i changed my hd with an ssd)
4) Message boards : Cafe Rosetta : Linux developers like...Visual Studio! (Message 91085)
Posted 10 days ago by Profile [VENETO] boboviz
Post:
Visual Studio Code

By far the most used development tool was Visual Studio Code at 37.6%! That was quite surprising to see the Microsoft IDE coming out well ahead of Qt Creator at 8% and others like Intellij, Eclipse, Android Studio, GNOME Builder, and others.
5) Message boards : Number crunching : RALPH@Home ? (Message 91071)
Posted 16 days ago by Profile [VENETO] boboviz
Post:
Really? Months without new work, years without new apps and forums abandoned....


Still...
Please, turn off the server, it's a waste of electric current
6) Message boards : Rosetta@home Science : Alphafold visits IPD (Message 91059)
Posted 21 days ago by Profile [VENETO] boboviz
Post:
Remarkable stuff. I wonder how that will affect our work?


Maybe new protocols, new kind of simulations or, simply "to verify" the simulations of AI (like we do with fold.it)
7) Message boards : Rosetta@home Science : Alphafold visits IPD (Message 91057)
Posted 22 days ago by Profile [VENETO] boboviz
Post:
AlphaFold and IPD
8) Message boards : Number crunching : Raspberry Pi4 (Message 91051)
Posted 26 days ago by Profile [VENETO] boboviz
Post:
Great cooling for Pi4
Shim
9) Message boards : Number crunching : Unrealistic expectations (Message 91040)
Posted 28 days ago by Profile [VENETO] boboviz
Post:
There is no way my computer could complete all those tasks in the 5 days allotted for them. It takes almost 9 hours for my computer to crunch one Rosetta task.

What are your project preferences, particulary the "Target cpu runtime"? And the preferences in the boinc manager (store work)??
10) Message boards : Number crunching : Rosetta 4.0+ (Message 91027)
Posted 13 Aug 2019 by Profile [VENETO] boboviz
Post:
1084416855

ERROR: ERROR: FragmentIO: could not open file 00001.200.9mers
ERROR:: Exit from: ..\..\..\src\core\fragment\FragmentIO.cc line: 233
BOINC:: Error reading and gzipping output datafile: default.out
14:35:27 (15216): called boinc_finish(1)



The real problem is that too few admins are reading this thread, seeing the problem reports, and knowing who to contact in order to get them fixed.


Still this error....
11) Message boards : Number crunching : Good bye Rosetta !!! (Message 91024)
Posted 13 Aug 2019 by Profile [VENETO] boboviz
Post:
All are important and make a "global" knownledge. All in paralel, not seperately.
Why to give full priority to proteins, if we are unable to fully decode genome ?

The genome is decoded years ago

Only one "enormous" example : we discover some new proteins, nice. Nobel price.
But later, because we do not know fully genome, we discover that this new protein is toxic...

This is why new proteins are tested not only in silico, but also in wet lab, animal testing, etc
12) Message boards : Number crunching : WU crash after some hours (Message 91008)
Posted 9 Aug 2019 by Profile [VENETO] boboviz
Post:
I want to understand !

There is nothing to understand.
The "not enough memory" it's only a repetitive excuse.
I had this problem even when i had 60% of ram in use.
It's a sw problem, not an hw problem
But, as i say in the other thread, nobody is interested in solving problems.....
13) Message boards : Number crunching : Rosetta 4.0+ (Message 90998)
Posted 7 Aug 2019 by Profile [VENETO] boboviz
Post:
1084416855

ERROR: ERROR: FragmentIO: could not open file 00001.200.9mers
ERROR:: Exit from: ..\..\..\src\core\fragment\FragmentIO.cc line: 233
BOINC:: Error reading and gzipping output datafile: default.out
14:35:27 (15216): called boinc_finish(1)


For this task, it looks like input file 00001.200.9mers was not sent along with the task and therefore could not be opened.
The other recently reported errors look more like the program found an error in one of the input files, and therefore could not continue properly past that point.


And, still....1086460738
No one can send the correct input file?
14) Message boards : Number crunching : Rosetta 4.0+ (Message 90997)
Posted 7 Aug 2019 by Profile [VENETO] boboviz
Post:
My post implies there are no errors or bugs in the application as I crunch quite a few workunits.

Again. I don't care if the problem is the application or the data.
If the problem is the application, debug the app.
If the problem is the data, work on data.

but you don't report the work unit

I report always if i have problems Message 90975, 08/05/2019
And this morning 1086416267
You can see also my reports on Ralph@Home during these years of volunteer in beta project.

The final BOINC error is probably because the job failed to start, and therefore did not create an output file.

Why i have NO problems with other projects (WCG, Tn-Grid, LHC, etc)?
15) Message boards : Number crunching : Rosetta 4.0+ (Message 90994)
Posted 7 Aug 2019 by Profile [VENETO] boboviz
Post:
I just looked at my results and have nothing odd, no errors.

Good for you. But in this thread (and in others) people report errors/bugs, without any answer.
For example, me this morning the same error of 4 days ago:
ERROR: Unrecognized residue: DRH
ERROR:: Exit from: ..\..\..\src\core\io\pose_from_sfr\PoseFromSFRBuilder.cc line: 1258
BOINC:: Error reading and gzipping output datafile: default.out
07:23:08 (13816): called boinc_finish(1)
16) Message boards : Number crunching : Rosetta 4.0+ (Message 90988)
Posted 6 Aug 2019 by Profile [VENETO] boboviz
Post:
In this thread we don't see admins since....i don't remember. I don't know even if they are reading this thread.

They hang out over here:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1000


Mod.Sense is a great, but he is not an admin or a developer of the project.
17) Message boards : Number crunching : Rosetta 4.0+ (Message 90984)
Posted 6 Aug 2019 by Profile [VENETO] boboviz
Post:
The last few errors reported all look like there was an error in the input files, not an error in the application program or an error specific to your computer......
The other recently reported errors look more like the program found an error in one of the input files, and therefore could not continue properly past that point.


Uh, interesting.
But i don't care if the problem is the exe or the input files. I think that, if there are problems, it's better to resolve these.
In this thread we don't see admins since....i don't remember. I don't know even if they are reading this thread.
A message like "Ok, guys, we release soon a new kind of input files to resolve your errors" or even if simple "we are working on it", it's not difficult to write.
Or, maybe, they are not interesting in our "wasting cpu's time".
18) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 90979)
Posted 5 Aug 2019 by Profile [VENETO] boboviz
Post:
Anybody minding the store ???


Maybe all the people is here: RosettaCon 2019
19) Message boards : Number crunching : Rosetta 4.0+ (Message 90978)
Posted 5 Aug 2019 by Profile [VENETO] boboviz
Post:
1084416855

ERROR: ERROR: FragmentIO: could not open file 00001.200.9mers
ERROR:: Exit from: ..\..\..\src\core\fragment\FragmentIO.cc line: 233
BOINC:: Error reading and gzipping output datafile: default.out
14:35:27 (15216): called boinc_finish(1)


Again.
Please there is no one who can debug this amount of errors (cannot open files, out of memory, etc)??
20) Message boards : Number crunching : Rosetta 4.0+ (Message 90975)
Posted 5 Aug 2019 by Profile [VENETO] boboviz
Post:
1086028567
1085948412
and others...

ERROR: Unrecognized residue: DRH
ERROR:: Exit from: ..\..\..\src\core\io\pose_from_sfr\PoseFromSFRBuilder.cc line: 1258
BOINC:: Error reading and gzipping output datafile: default.out
06:32:13 (4848): called boinc_finish(1)


Next 20



©2019 University of Washington
http://www.bakerlab.org