Problems and Technical Issues with Rosetta@home

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.clair.

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Message 108073 - Posted: 18 Feb 2023, 21:40:13 UTC
Last modified: 18 Feb 2023, 22:39:16 UTC

I have had my fill with "enter password" again and again this last month ,
In Linux mint 20,2 you can type :-
sudo nemo (enter password)

password is your normal `user` password
You may have to wait a minit or so till the system lets you in ,
nemo is the gui file manager for mint
Or whatever simple file manager for your Linux distro
This will open nemo file manager with a red bar across the top with with the words "Elevated Privaleges" in it
Then you can go screw with your system in a few mouse clicks ;-)
I know this works because I recently built a system using mint and could not place my app_config.xml in the Milkyway project folder "paste" was grayed out , though eventualy remembered how to do it .
To edit a txt/xml file after `search` for it , like cc_config.xml , click on it [enter password] then go play with it , had to do quite a bit of `bang-head-on-screen-till-it-works` stuff lately and its an old CRT , those things are hard ..
unless I have typo`ed what I just wrote :-)
Over 20 years ago when I first found Linux [and found it near impossible to use = still got the Red Hat 5 cd] it was easy to always run as root/administrator , these days it is considered bad practice and `not safe` to do so , spoilsports . . . .

edited several times so not to look like an 1D10T
and for bad spelling
one time my spell casting got so bad I turned a Prince into a musician instead of a frog
I`le let the readers work that one out for them self .
[shop floor humour for witches] with or without pentagram .
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Mr P Hucker
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Message 108074 - Posted: 19 Feb 2023, 0:23:39 UTC - in response to Message 108073.  

I have had my fill with "enter password" again and again this last month ,
In Linux mint 20,2 you can type :-
sudo nemo (enter password)

password is your normal `user` password
You may have to wait a minit or so till the system lets you in ,
nemo is the gui file manager for mint
Or whatever simple file manager for your Linux distro
This will open nemo file manager with a red bar across the top with with the words "Elevated Privaleges" in it
Then you can go screw with your system in a few mouse clicks ;-)
Or just use Windows and not have these problems. If it's a problem of money, did you know 57% of Windows systems worldwide (including 18% in the USA) are pirated?

I know this works because I recently built a system using mint and could not place my app_config.xml in the Milkyway project folder "paste" was grayed out , though eventualy remembered how to do it .
To edit a txt/xml file after `search` for it , like cc_config.xml , click on it [enter password] then go play with it , had to do quite a bit of `bang-head-on-screen-till-it-works` stuff lately and its an old CRT , those things are hard ..
Better than an LCD, which you might damage irrepairably.

unless I have typo`ed what I just wrote :-)
Over 20 years ago when I first found Linux [and found it near impossible to use = still got the Red Hat 5 cd] it was easy to always run as root/administrator , these days it is considered bad practice and `not safe` to do so , spoilsports . . . .
In Windows most of us are admins, and funnily enough the systems don't get destroyed. I found out how to log in as root and always do so. Not sure how to automatically do that though. Do you? I'd like to know. Mine boots up and logs in without asking for a password to "peter", initial account I made when installing it. I can then log out and select "other" as the user, type "root" as the user and enter the password, and that lasts until the next reboot. But I'd rather it auto logged in as root.

edited several times so not to look like an 1D10T
and for bad spelling
one time my spell casting got so bad I turned a Prince into a musician instead of a frog
I`le let the readers work that one out for them self .
[shop floor humour for witches] with or without pentagram .
Isn't a musician more useful than a frog? Or were you trying to punish him?
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Jean-David Beyer

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Message 108075 - Posted: 19 Feb 2023, 0:50:51 UTC - in response to Message 108068.  
Last modified: 19 Feb 2023, 0:58:58 UTC

Jean-David, I see you're using Linux. I've just installed Linux in a virtual machine (the only way I can get CPDN tasks). How on earth do you do a simple task like editing Boinc's cc_config.xml?! It won't let me! I don't have permission to edit a file for an application I installed on my own machine! I eventually had to find a way (which everyone said oh no you'll cause a nuclear war) to log on as root. I've been doing that in Windows for 30 years, and nothing ever broke. Why is Linux such a mess?


I login as myself for my normal use of this machine.

I started programming on an IBM 704 computer in the mid 1960s. I got very proficient at running an IBM 026 card punch. But it had only 32768 words of memory and no operating system. Later on I used the MIT Automatic Operator Program, the FORTRAN MONITOR SYSTEM (FMS) andthen BE-SYS4. And one thing lead to another. When I had to use UNIX for something, I absolutely hated it: It was almost impossible to run it to do real-time process control. Not really Ken Thompson and Dennis Ritchie's fault: they did not design it for that. (So I had to write my own OS, but that's another story.) For the kind of work I do these days UNIX would be just fine, though I happen to use
Red Hat Enterprise Linux release 8.7 (Ootpa)
with the
4.18.0-425.10.1.el8_7.x86_64 kernel.
I do not think it is a mess.

For a simple task like editing one of the cc_config.xml files, I open a Linux terminal (I select it from
Applications->Favorites->Terminal and run like this:


localhost:jeandavid8[~]$ cd /var/lib/boinc/projects/boinc.bakerlab.org_rosetta/
localhost:jeandavid8[/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]$ su
Password: 
localhost:root[/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]# vi app_config.xml 
<app_config>
    <project_max_concurrent>3</project_max_concurrent>
</app_config>
:q
localhost:root[/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]# 


While in the vi editor, I could make any changes I need.
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Mr P Hucker
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Message 108076 - Posted: 19 Feb 2023, 1:11:00 UTC - in response to Message 108075.  
Last modified: 19 Feb 2023, 1:13:54 UTC

I do not think it is a mess.

For a simple task like editing one of the cc_config.xml files, I open a Linux terminal (I select it from
Applications->Favorites->Terminal and run like this:


localhost:jeandavid8[~]$ cd /var/lib/boinc/projects/boinc.bakerlab.org_rosetta/
localhost:jeandavid8[/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]$ su
Password: 
localhost:root[/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]# vi app_config.xml 
<app_config>
    <project_max_concurrent>3</project_max_concurrent>
</app_config>
:q
localhost:root[/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]# 


While in the vi editor, I could make any changes I need.
Wow. In Windows, I just double click the file. Time how long it takes for you to get into that file and make a small change. Now imagine being able to do that in seconds.

What Linux should do (if it insists on protecting a file in an app YOU installed) is let you double click the file in Mousepad or whatever, then when you save it, prompt you for admin permission and require the password. However, since YOU installed it under your usual user account, you should have full permissions on every file in that app under that same account.
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Jean-David Beyer

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Message 108077 - Posted: 19 Feb 2023, 2:01:02 UTC - in response to Message 108076.  

Wow. In Windows, I just double click the file. Time how long it takes for you to get into that file and make a small change. Now imagine being able to do that in seconds.


For something I do only once every few months at most, I do what I said, because it is easier.

I can do it all with a mouse if I insist.

Click on icon at top left of the screen.
Select OtherLocations
Select Computer
Select var
Select lib
Select boinc
Select projects
Select boinc.bakerlab.org_rosetta
Select app_config.xml
Browse to tell it what editor to use. vi is not one of the choices.

That is why I do not do it that way.

In Windows 10 it is so difficult to find the file in question that I find it a mess to use.
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Mr P Hucker
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Message 108078 - Posted: 19 Feb 2023, 3:02:46 UTC - in response to Message 108077.  

For something I do only once every few months at most
I change a Boinc config every other day. Boinc needs constant nursing.

I do what I said, because it is easier.

I can do it all with a mouse if I insist.

Click on icon at top left of the screen.
Select OtherLocations
Select Computer
In Windows all that would just be "press WIN-E"

Select var
Select lib
Select boinc
Select projects
Select boinc.bakerlab.org_rosetta
Select app_config.xml
In windows Boinc is a commonly used folder, automatically. I just click it in the top 10 most recently used.

Browse to tell it what editor to use. vi is not one of the choices.
I just double click it. Notepad is perfectly fine at editing xml. I could have another as default.
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Sid Celery

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Message 108080 - Posted: 19 Feb 2023, 13:56:31 UTC

Oh!
3.2m tasks queued up
Good
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Message 108081 - Posted: 19 Feb 2023, 15:57:12 UTC
Last modified: 19 Feb 2023, 15:57:24 UTC

[Pushes oversized lever to engage processing]
https://youtu.be/27Wzz-2X_v4?t=44
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Jean-David Beyer

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Message 108082 - Posted: 19 Feb 2023, 18:14:02 UTC - in response to Message 108067.  

On Feb 16, I finally got the following to download. I did not do anything to cause this, but that means that as soon as the server has some tasks for me. I should get some.


I got a bunch overnight and three of them are already running.

    PID    PPID USER      PR  NI S    RES  %MEM  %CPU  P     TIME+ COMMAND                                                            
  85474    4932 boinc     39  19 R 324404   0.5  98.8  3 320:20.08 ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-+ 
  86661    4932 boinc     39  19 R 318656   0.5  99.1  6 303:30.00 ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-+ 
  86815    4932 boinc     39  19 R 317856   0.5  99.2  5 301:23.59 ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-+ 
  97768    4932 boinc     39  19 R 213900   0.3  98.8 11 168:02.96 ../../projects/einstein.phys.uwm.edu/einsteinbinary_BRP4G_1.33_x8+

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Mario W.

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Message 108083 - Posted: 19 Feb 2023, 20:03:10 UTC - in response to Message 108065.  

Yes, i have, i even uninstalled BOINC complete and reinstalled it, still dont get any Tasks sadly.
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Message 108084 - Posted: 19 Feb 2023, 20:04:48 UTC - in response to Message 108083.  

Will i contribute more if i set Target CPU run time to 1 day 12 hours?
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Jean-David Beyer

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Message 108085 - Posted: 19 Feb 2023, 20:26:23 UTC - in response to Message 108084.  

Will i contribute more if i set Target CPU run time to 1 day 12 hours?


What does contribute more mean in this context? Do you think it means you will be assigned more work-units? Or does running 4.4 times longer mean that you will get more credit?

Mine runs with Target CPU run time 8 hours and I have never seen a reason to change it. My current batch is part-way done and the boinc manager predicts they will take slightly over 8 hours.
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Message 108086 - Posted: 19 Feb 2023, 21:33:38 UTC
Last modified: 19 Feb 2023, 21:34:51 UTC

Assuming everyone wants to help the science, and are not being silly and childish with points, I assume it's best to leave it at whatever the programmer chooses. I normally get 8 hour ones, but I've seen a lot of 3 hour ones recently.

Although it may be better for faster computers to have a shorter time, so every task gets the same amount of work done. But David Baker explained a long time ago, they don't mind (or prefer) some tasks to be "more well cooked" than others, as what you're computing is like a single point on a big map. As long as the average work on each point is about right, it's fine.

Steven Rettie probably understands this better than me.
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Message 108087 - Posted: 19 Feb 2023, 21:54:42 UTC - in response to Message 108084.  
Last modified: 19 Feb 2023, 21:58:03 UTC

Will i contribute more if i set Target CPU run time to 1 day 12 hours?
No.
In reality, you'd be contributing less (if work were continually available). The more Tasks you do, the more you contribute to the data being processed.

The project determined years ago that 8 hours was sufficient time with the hardware available back then to do enough work to produce a useful result. Any further time processing a given Task just wasn't worth the extra time required to produce that extra data, better to spend that time processing another Task.
Given how much more powerful systems are now than they were all those years ago, even 8 hours is probably more time than is needed to produce a valid result these days.

The longer it takes you to process a Task, the less work you can do before the deadline is reached, so you actually contribute less to the project. But unless you have the very latest and greatest in x86 or M2 hardware, reducing the Target time from the default 8 hours would most likely result in less useful work being done as older hardware (or phones/tablets) can't do as much work in the same period of time. Hence the Projects' default Target CPU runtime of 8 hours (even though many Tasks these days won't even run for that length of time).
Grant
Darwin NT
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Message 108088 - Posted: 19 Feb 2023, 22:06:42 UTC

So am I right or wrong in thinking in the ideal world a fast CPU would be set to run for 2 hours, and one half the speed for 4 hours? That way every task has the same amount of work done.

I think I'm wrong, there was some reason that wasn't done. If they wanted to, they'd just make each task do x number of (whatever they call the sections inside them), and it would take longer on slower machines, much like almost every other Boinc project.
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.clair.

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Message 108090 - Posted: 20 Feb 2023, 2:11:09 UTC
Last modified: 20 Feb 2023, 2:58:14 UTC

real_fix_S_00078_00011618_af2_SAVE_ALL_OUT_2942332_24_0
======================================================
DONE :: 1 starting structures 10683.5 cpu seconds
This process generated 31 decoys from 31 attempts
======================================================
The test_fix that are now realy_fixed run at about three hours
And the word is "Decoys" for some strange reason only known to rosetta staff .

And I have finaly been able to reattach my big cruncher to rosetta after pondering "why can this one work without any bother and that one can`t even reattach"
and I have been "try again later" for a month ...........
They are both the same win 7 [sort of]
`Simples`
its a security certificate problem - we knew that .
this one is on IE11 and has loads more security certificates in its store , what a job trying to export them it was , I gave up trying .
than that one which is still on IE8 (raw install from the dvd + SP1) it crunches so I did`nt care , etc .
So , did the upgrade from a heap of win updates I have on backup and now its connected and crunching what a pain in the [bodyparts] that was .
install update - restart , install update - restart , install update - restart , install update - restart , install update - restart ..................
I did`nt want to miss out on my share the of 3,5 million work units that the admin `fixed` up for us ,
so got my act together and did the grind to update the thing
Would anybody else care to search through the Microsoft update catalogue for all the win 7 updates that are needed to get IE11 running with the security certificates that rosetta needs .
I can post a list if anyone wants it :-)
You are as mad as me if you do ,
I was shure there was a way to do it so I did .
I now have the feeling I need to get smashed to recover from todays endeavours .
sad me , I had to look up how to spell "endeavours" in a dikshonery , sigh........ my bwain hurtz .
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Message 108091 - Posted: 20 Feb 2023, 2:20:36 UTC - in response to Message 108090.  

And the word is "Decoys" for some strange reason only known to rosetta staff .
Proteins that distract the virus from attacking your body?

And I have finaly been able to reattach my big cruncher to rosetta
They are both the same win 7 [sort of]
Why would you have a "big cruncher" on that old junk version of Windows? Put 11 on it.

what a pain in the [bodyparts] that was .
I would say "a pain in the gentleman's excuse me" - not sure what the equivalent is for girls.

Would anybody else care to search through the Microsoft update catalogue for all the win 7 updates that are needed to get IE11 running with the security certificates that rosetta needs .
I can post a list if you want :-)
I just let it get everything.

I now have the feeling I need to get smashed to recover from todays endeavours .
That is always a good idea.

I had to look up how to spell "endeavours" in a dikshonery
I just make a best guess and let the browser's spellchecker sort it.

sigh........ my bwain hurtz .
I say "my brain's full".
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.clair.

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Message 108092 - Posted: 20 Feb 2023, 3:02:36 UTC - in response to Message 108091.  
Last modified: 20 Feb 2023, 3:43:45 UTC

Would anybody else care to search through the Microsoft update catalogue for all the win 7 updates that are needed to get IE11 running with the security certificates that rosetta needs .
I can post a list if anyone wants it :-)

I just let it get everything.

R but , MS have dumped win 7 so win update no longer works .
Why would you have a "big cruncher" on that old junk version of Windows? Put 11 on it.

I have bought a `win 10 home` disk and done a test install to see what it`s got , hate the look of the thing .
it would have to be the `pro` or `ultimate` version as its got twin xeon cpu`s so the licence would cost more , hence the new one is on Linux Mint
one interesting thing I saw is that when the installer gets to "input product key"
there is an option to "continue without product key with limited functionality"
low detail graphics and other stuff , and unlike previous versions windblows it still works two months after install and I wunder how long it will last , I installed boinc ok , time will tell .
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Message 108093 - Posted: 20 Feb 2023, 3:14:19 UTC - in response to Message 108092.  

Would anybody else care to search through the Microsoft update catalogue for all the win 7 updates that are needed to get IE11 running with the security certificates that rosetta needs .
I can post a list if anyone wants it :-)

I just let it get everything.

R but , MS have dumped win 7 so win update no longer works .
Why are you still using 7?!
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.clair.

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Message 108094 - Posted: 20 Feb 2023, 3:25:41 UTC
Last modified: 20 Feb 2023, 3:45:48 UTC

Looks like I was editing my previous post while you where replying to it :-)
Why 7 . I hate the look of 10 and 11gui .
I use the basic `windows classic desktop` in 7 , so it looks like win 95/98 :-)
I still have a system that only crunches Moo waper that runs 32 bit XP sp3 with a Q6700 and a AGP HD 4650 gpu coz it works (the motherboard will take a max of only 2GB of memory)
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