Posts by Jim

1) Message boards : Number crunching : Project web page support (Message 81045)
Posted 16 Jan 2017 by Profile Jim
Post:
Do you ever notice that non of the cross-project stats links work. It's been a few years since you could use them.
It's getting harder to support something that doesn't give the number cruncher something back for the effort we give. It would be so nice to not have to go to other boinc sites to find out how I am doing compared to other projects.
2) Message boards : Number crunching : Web Site Updates (Message 71141)
Posted 25 Aug 2011 by Profile Jim
Post:
Over the last 5 years have have bought computers for nothing else than to crunch data here. I believe it is a good cause.

For the last couple years I don't feel the staff is getting very involved here.

For example the newest item present when you look into Top predictions in the Statistics section is FOUR years old.
Now that Rosetta has a following of crunchers they can just set back.
I may be wrong and am now and then but this is my personal option of how I see it.
3) Message boards : Rosetta@home Science : WiFi and Cellphone radiation effects (Message 71140)
Posted 25 Aug 2011 by Profile Jim
Post:
Oh isn't this nice. More junk science.

We all better stop using our key-less entry device for your cars and other remote control devices. WiFi junk and cell phones use a fraction of a watt.

A old CB radio put out about 5 watts.
My Ham Radio can do up to 1000 watts but I find can normally communicate with just a few watts.

They better shut down all the TV and Radio stations. Radio stations can go up to 50,000 watts and TV station will go into the hundreds of thousands of watts.

If you can receive the radio station or TV station then you are getting more RF energy from them than you will from your cell or WiFi.

Besides that, the effects that they are blaming on Cell and Wifi is caused by the Tea Party, everyone knows that.
4) Message boards : Number crunching : which cpu´s are you using for rosetta? (Message 70801)
Posted 29 Jul 2011 by Profile Jim
Post:
i7 920 at 2.4
Q6600 quad core
5) Message boards : Number crunching : Minirosetta v1.32 bug thread (Message 54986)
Posted 7 Aug 2008 by Profile Jim
Post:
Please post bugs/issues with minirosetta v1.32 here.


Had the first one I got fail.
ERROR: Cannot find file 'minirosetta_databasechemical/residue_type_sets/centroid/CSD_ATOM_TYPE_SET fa_standard'
ERROR:: Exit from: ....srccorechemicalresidue_io.cc line: 132
called boinc_finish

It is WU ID 165103113
6) Message boards : Number crunching : Memory Usage in Beta 5.80 (Message 46367)
Posted 16 Sep 2007 by Profile Jim
Post:
There is a recurring problem however in connection with multi-core systems and these "high memory requirement" WUs, which would probably need some co-operation between RAH and the folks at BOINC to resolve by modifying the scheduler logic and/or introducing more WU flags regarding expectable memory use.

I'm talking about the situation where a Rosetta WU runs on one core, and another should be started on the other core, but the combined memory use hits the memory boundary set by user preferences for the project, so it's put into the "Waiting for memory" or simply the "Waiting to run" status, then the scheduler starts another Rosetta WU which happens to be also a high memory use one, it hits the memory use cap too, put into the "Waiting for memory" status, so a third needs to be started, and so on.


I have experienced the same condition you described above on my single core Win OS machines. To solve this problem I have installed a memory management tool and set it to scrub the memory every 15 minutes.
The scrub option frees up unused memory and returns it to the main memory pool so the Win OS can use it. I don't have to run this tool on the Linux box since that OS doesn't leak memory like the Win type OS does.
The utility I use is called Memturbo, (I have no interest or anything else to do with the company or product, I just use it.) I don't know if it will work with a dual or quad core machine. The bottom line is that I have not had this problem or any WU failures since I done this over 24 hours ago.
For example on my Intel based P4 2.8Ghz machine I have about 486 Meg of usable RAM. It would drop to 5 Meg of RAM free in about 30 minutes. With the memory being scrubbed every 15 minutes the free RAM figure now sets at over 100 Meg. That worked, no more "waiting or memory" messages.

Good luck, hope this helps.

Right now I have 3 Rosetta WUs in memory, two using 370MB VM each and a third with 310MB, but only one is able to run because of memory preferences, the other two are just sort of deadlocking each other as they're keeping their committed VM in use without being able to actually run so that one of them could be cleared from memory once finished and then the other one get a chance to get processed too.

I wonder if there would be a way for the project or the scheduler to check the following conditions:
- Does the client asking for new work have any high-memory WUs assigned already?
- Is it a multi-CPU system with more than one CPUs enabled for BOINC?
- Would the combined memory use for "CPUs allowed to be used" x mem requirement of one WU be higher than the allowed memory use?

If they are true, then only low-memory WUs should be sent/requested/accepted as new work to that client for the project as long as it didn't return the current high-memory one to stop the scheduler from keep starting and then suspending high-memory WUs (since it has nothing else to process for this specific project), filling up available memory with "zombie" WUs that can not run because of each other.

7) Message boards : Number crunching : CAPRI14? (Message 46327)
Posted 16 Sep 2007 by Profile Jim
Post:
I am quite curious as to the relative success rate of the Capri14 WUs versus WUs of all other types.

My personal experience is that a Capri14 WU is nearly doomed to failure, no matter the Rosetta version on which it is running, while nearly all other WUs will succeed...

I sincerely hope that the CPU time that (to my layman's perspective) I seem to be wasting on Capri14 is not representative of the experience of the general population of Rosetta crunchers.

Respectfully,
David Emigh


David I believe you are having a bad run of luck on the WUs. I also have had several fail but overall better than 95% have finished with valid results. Like a few others I have had to make adjustments to memory allocations on my old machines but the CAPRI14 project will soon be over and we can get back to the same old boring number crunching.
I also don't like the "client error" result either it does give me a since of loss.

Cheers Jim
8) Message boards : Number crunching : CAPRI14? (Message 46250)
Posted 15 Sep 2007 by Profile Jim
Post:
This is puzzling -- those jobs arent taking long. We'll look into it. In the meanwhile, can your or other post links to the appropriate results that were killed?


I have now done several CAPRI14 WUs with 5.80: Only one has a problem:
http://boinc.bakerlab.org/rosetta/workunit.php?wuid=95775480
with this result:
http://boinc.bakerlab.org/rosetta/result.php?resultid=105522388
I don't have a clue as to why it failed to Validate. It seems to have run the full length of time I have set for processing.

Thanks,
Jim
9) Message boards : Number crunching : CAPRI14? (Message 46107)
Posted 13 Sep 2007 by Profile Jim
Post:
This is puzzling -- those jobs arent taking long. We'll look into it. In the meanwhile, can your or other post links to the appropriate results that were killed?



WU: 95285894
WU: 94876951
WU: 94840468

All 3 are CAPRI14 units and ended by the watchdog timer. My runtime is set for 4 hours (14400 seconds).

cheers . . . jhf
10) Message boards : Number crunching : Problems with Rosetta version 5.78 (Message 46044)
Posted 12 Sep 2007 by Profile Jim
Post:
I'm the second person to get this WU: 94462214
It seems to be missing a file: PROF2.pdb ; will not finish the download
just a error message, "file not found".
11) Message boards : Number crunching : Graphics under Ubuntu Linux 7.04 Fasty Fawn (Message 43168)
Posted 4 Jul 2007 by Profile Jim
Post:
Not support.. Okey, but I not understand this messege:

<core_client_version>5.8.17</core_client_version>
<![CDATA[
<stderr_txt>
Graphics are disabled due to configuration...

I think, rosetta have graphics, but disabled it for something...

Who can answer me: When rosetta have picture in Linux?


The message that Graphics are disabled due to configuration is telling us that the graphics is disabled for Linux systems. The reason is that the code for graphics has not yet been done for Linux.
The Questions and Answers section explains that they are working on the code. They are finding that the coding for graphics is fairly large and the resources needed does not allow it to work with systems that have only 256Mbyte of memory.
More detail can be found here:
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1878

I hope this helps answer the question for you.
12) Message boards : Number crunching : Graphics under Ubuntu Linux 7.04 Fasty Fawn (Message 43105)
Posted 3 Jul 2007 by Profile Jim
Post:
My understanding is that the Rosetta client does NOT support graphics on Linux operating systems. I could be wrong of course.

Jim
13) Message boards : Number crunching : Credits/CPU Second (Message 41285)
Posted 22 May 2007 by Profile Jim
Post:
Are you talking about a statistic that is in your host's details page? Or are you talking about the chart on this website: http://boinc.netsoft-online.com/e107_plugins/boinc/get_cpcs.php?


I'm talking about the xml element like " <credit_per_cpu_sec>0.001260</credit_per_cpu_sec>
" found in the host.gz file. Which i believe does power the web page you were refering to.


I use WIN98, 2000, XP and Linux for Rosetta and I don't find a host.gz file on any of them. In what directory are you finding the file? It would be nice to look up credit per cpu sec instead of doing it manually.

14) Message boards : Number crunching : Problems with Rosetta version 5.54 (Message 38102)
Posted 21 Mar 2007 by Profile Jim
Post:
Please especially give us some feedback on the graphics -- are you able to display them properly?


The Graphics works just fine on 4 machines.
The time to completion does count UP until the "model" changes from 1 to 2.
It also stayed at 1% until the text indicated it had reached model 2. Then the percentage changed to 18% done.
No big deal at all, I don't normally use the graphics anyway, looks like it is working well.

No processing errors of any kind.
Windows XP, Win 2000, Linux machines.

Jim
15) Message boards : Number crunching : Problems with Rosetta version 5.43 (Message 35236)
Posted 21 Jan 2007 by Profile Jim
Post:
Has anyone else been having problems opening the BOINC manager from the task bar? I've had this problem at random times for at least the past 4 development releases of BOINC up to the current 5.8.3. Task manager shows both Rosetta threads taking 50/50 CPU share per normal. The only way I can open BOINC manager is if I kill the process and then restart. Anyone else seeing this? Should I consider this strictly a BOINC problem not Rosetta?

Tim


I agree that this is a BOINC problem and not Rosetta problem. I learned early on to open the manager from the task bar by RIGHT clicking the icon then selecting the "Open BOINC manager" option. If I double click the left button to open it then the odds are that I will have to reboot or kill all the boinc tasks to get the manager to run again. This is on Windows machines. On my linux boxs I have learned to minimize the manager and never "close" the manager or I get a simular problem.

Jim
16) Message boards : Number crunching : How much has your RAC Dropped Since 12/6/06 (Message 33809)
Posted 31 Dec 2006 by Profile Jim
Post:
I tend to agree that the RAC has been dropping this month.
I have two machines that run Rosetta and nothing else.

The first is a Inel based laptop with a 1.70Ghz CPU. The first few days of
Dec it had a RAC of 110, the RAC has declined slowly everyday and is at 99 today.
It has not show any recovery around the 20th as some have noticed on their machines. I haven't made a single change to this machine.

The other machine that only runs Rosetta is a AMD 3400+based CPU BUT I didn't
start it until the 12 th of Dec. It is showing an increase everyday but I think this is normal at this point.

The other machines run several other projects in addition to Rosetta and they do
show the RAC decreasing around the first of Dec and increasing around the 20 of Dec. The other projects are SETI and WGC on both Windows and Linux platforms.

I'm not sure what all the results on my machines are telling me. I haven't concluded there is a common factor at his point. Anyway thats my 2 cents worth.

17) Message boards : Number crunching : Problems with Rosetta version 5.43 (Message 33040)
Posted 21 Dec 2006 by Profile Jim
Post:
RebelRex
It appears I wasn't clear in describing the problem. We are talking the same
problem with "unfinished" WU and switching task/projects. Upgrading my Linux DID
solve the "unfinished" WU problem for me. It's now been over 24 hours of
crunching with no problems.


Swithching task/project works fine.. Its when bonic switches back to the "unfinished" WU is where mine hangs (says its running but its not)... Not sure its a Rosetta issue more than Boinc..

Chu

Concerning the problem with Linux machines not processing after switching
tasks/projects.

I upgraded my Linspire Linux (Debian 3.0 [2.6.10]) to Freespire Linux (2.6.14)
At this point the system has completed 3 WUs without any problems.

I am also running SETI and WCG (Genome Comparsion) on that machine.

So it appears at this point (to me) that if a user has this problem they need to
upgrade or change to a different Linux OS.

I will post IF this problem reappears.

Jim


18) Message boards : Number crunching : Problems with Rosetta version 5.43 (Message 32982)
Posted 20 Dec 2006 by Profile Jim
Post:
Chu

Concerning the problem with Linux machines not processing after switching
tasks/projects.

I upgraded my Linspire Linux (Debian 3.0 [2.6.10]) to Freespire Linux (2.6.14)
At this point the system has completed 3 WUs without any problems.

I am also running SETI and WCG (Genome Comparsion) on that machine.

So it appears at this point (to me) that if a user has this problem they need to
upgrade or change to a different Linux OS.

I will post IF this problem reappears.

Jim
19) Message boards : Number crunching : Problems with Rosetta version 5.43 (Message 32948)
Posted 20 Dec 2006 by Profile Jim
Post:
Chu
No this problem has been happening on my Linux machines since around the
13th or 15th of November. At first I figured it was just my machines.

I run two different "flavors" of Linux, Linspire and Mandriva. It has happened
on both OS's but mainly on the Linspire machine.

I have tried:
1- Turning OFF the "leave in memory" option when switching to another project.
Didn't help
2- Extended the processing time from the default 60 min to a longer period.
Didn't help
3- Reboot the computer.
That works
4- Suspend and Resume task.
Didn't help
5- Tonight I installed a newer version of Linux on machine 1.
(Will watch and see what happens over night.)

Machine 1: 1.3Ghz AMD processor (Linspire-Linux)
377 meg of ram
(has only finished about 1/2 dozen Rosetta WUs in the last month)
Machine 2: 475 Mhz AMD K6 processor (Mandriva 2007 - Linux)
256 meg of RAM
(doesn't process once in a while, but when it doesn't it is after
switching projects/tasks)

As the other folks have noticed the project says it is RUNNING but CPU time,
To Completion time, Progress percentage never changes. (The first time it was "hung" 5 days before I noticed it.

Boinc 5.4.9
Rosetta 5.4.x on seems to be a problem

Good luck, Jim
20) Message boards : Number crunching : Problems with Rosetta version 5.43 (Message 32827)
Posted 17 Dec 2006 by Profile Jim
Post:
I moved daniels' post here, as he's got Linux problems with 5.43 as well as having seen them on 5.41.

process exited with code 131 (0x83)
process got signal 11


I am seeing the same thing on both of my Linux machines.
I can make the WU finish by shutting down the computer and restarting it.
I tried to suspend the project and let WCG run for a while then resume the
Rosetta WU but that didn't work.
The Rosetta projects get to about 58.71% done then just set there for hours doing nothing.
I did see this before "once" that I remember with 5.41 but 5.43 has become a brick
wall. Both machines have 256 meg of RAM. One has Linspire Linux and the other has Mandriva 2007.

http://boinc.bakerlab.org/rosetta/result.php?resultid=51996472
http://boinc.bakerlab.org/rosetta/result.php?resultid=51738512

Jim


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