Posts by stewjack

21) Message boards : Number crunching : Is XP Hibernation Function a Long-Setpoint Solution? (Message 30392)
Posted 31 Oct 2006 by stewjack
Post:
There are no problems, but it shuts down and restarts quicker.

But it will not solve the savepoint problem*. ......

* well when i used it it never did, but that was in earlier versions, don't know why it would change now.


I notice that no one is disagreeing with you. That would explain why no one told me to us hibernation to solve my thunderstorm mandated shutdown problems last summer.

I guess I will try it anyway, in a few days. I already have "leave in memory" selected in BOINC preferences.

I usually leave my computer on when I am in the apartment and awake. Since I am retired, that averages about 8 hours a day, 7 day a week. Also Windows update requires me to reboot monthly, and sometime my virus program automatically updates. There just seems to be many reasons to reboot.

Jack

JPL managed to fix the Mars Rovers S2K problem. JPL's Rover Operational Planning software was going to crash at 1000 sol's




22) Message boards : Number crunching : Is XP Hibernation Function a Long-Setpoint Solution? (Message 30380)
Posted 31 Oct 2006 by stewjack
Post:
I am constantly turning my desktop computer on and off. Sometime it seems that Rosetta setpoints rule my life.

I have just discovered the XP hibernation function. I have never seen it mentioned as a solution to long setpoint times. If you leave Rosetta in memory I would think that you should be able to turn off your computer at any time.

Is there any downside to using hibernation constantly? With WIN98SE restarting the system regularly seemed to help reset everything back to normal. Firefox and other programs supposedly "leak" memory.

Do desktop systems running XP home need a "full" restart every so often.

Jack

23) Message boards : Number crunching : Report problems with Rosetta version 5.34 (Message 30374)
Posted 31 Oct 2006 by stewjack
Post:
I may be confused, when I check results it indicates client 5.4.11
Where do I check for the Rosetta version? Or is that the same thing?


Select the task tab in the BOINC manager. Under 'application" you should see rosetta 5.34


(no more hanging up at 1.5% for an hour).

You don't understand that the progress percentage is only updated when rosetta stores a setpoint. If you restart your computer the WU will restart at the last setpoint There is usually an initialization setpoint. That was your 1.5%!

Rosetta does not have fixed setpoints. I once had to wait five and a half hours for my second setpoint! I have my WU set for a completion time of 4 hours, but that was an unusual WU. A Rosetta WU normally setpoints every 10 min to 1.5 hours.

If you get your graphics working, you will discover that Rosetta creates a setpoint before each new model starts.

Jack
24) Message boards : Number crunching : Project encountered internal error: shared memory (Message 29290)
Posted 13 Oct 2006 by stewjack
Post:
Same issue here.

I run XP with AMD CPU, although I doubt that has anything to do with it.

Edit: I did not get a shared memory error. I am on dial-up, and after I made "network activity always available," BOINC requested new work and reported "project is down" although the project was up. I had no results that I could have uploaded or reported.

At least I didn't notice any "shared memory error." I exited and restarted BOINC, so my error messages have been wiped.
25) Message boards : Number crunching : Limiting CPU usage (Message 29278)
Posted 13 Oct 2006 by stewjack
Post:

:-) As you can see the two statments dont exactly match and i had tried the first one. Yes, i had restated the computer every time. Maybe the second statment will work. Should i put it in as it looks exactly?
Yes my system does sound like a turo prop and starts to vibrate. But its not that it is the smell of frying electronics that gets to me.

Either example should work. One would run Rosetta at 60% and the other at 80%

I have run out of ideas.

Jack

26) Message boards : Number crunching : Limiting CPU usage (Message 29277)
Posted 13 Oct 2006 by stewjack
Post:

:-) As you can see the two statments dont exactly match and i had tried the first one. Yes, i had restated the computer every time. Maybe the second statment will work. Should i put it in as it looks exactly?
Yes my system does sound like a turo prop and starts to vibrate. But its not that it is the smell of frying electronics that gets to me.

Either example should work. I have run out of ideas.

Jack
27) Message boards : Number crunching : Limiting CPU usage (Message 29248)
Posted 12 Oct 2006 by stewjack
Post:
Those figure of 40, 60 and 80 i put in place of 80 as i was told to see what would happen and nothing happened.
The rosetta application being run is 5.25.


Did you restart the computer??? I seem to recall that nothing takes effect until you restart the computer.

I would like to help, but the Threadmaster program does not seem to be working on your computer the way it does on my computer. I just don't know how to help you.

Can you monitor your cpu temperature? How hot does your CPU get? If your fan isn't going crazy, you probably don't have anything to worry about.

I have a program that displays my cpu temp next to the time in my system tray. The problem is that not all motherboards place the temperature sensors exactly the same place, and the temperature sensors different levels of accuracy. If your fan isn't going crazy you probablt don't have anything to worry about. All moderm computers should regulate the fan speed using the temperature sensor.

If I stop Threadmaster my fan starts sounding like a tubojet!


IF YOU WANT TO RE-INSTALL ThreadMaster

Don't change CPUThresholdPct. Keep it at 15%

Next
Go to Applications in the registry

[HKEY_LOCAL_MACHINESYSTEMCurrentControlSetServicesThreadMasterParametersApplications]

"mfadmin.exe"="5" Note: This is imput automatically. If you see it you are in the right place

Input the following strings and data

"rosetta_5.25_windows_intelx86.exe"="80"
"rosetta_5.32_windows_intelx86.exe"="80"

This is what it should look like after you are finished

[HKEY_LOCAL_MACHINESYSTEMCurrentControlSetServicesThreadMasterParametersApplications]
"mfadmin.exe"="5"
"rosetta_5.25_windows_intelx86.exe"="60"
"rosetta_5.32_windows_intelx86.exe"="60"


Don't forget to restart the computer!!

Jack
28) Message boards : Number crunching : Limiting CPU usage (Message 29240)
Posted 12 Oct 2006 by stewjack
Post:
The biggest boost has come from the second processar comeing on line. With the string value at 80 now, my CPU"s are running at 17% each, system idle at 65 to 70%.
I will increase string value to 90 But i think it wont make much difference. So any thing new that i can do? :-)


Those numbers don't seem right. Something must be wrong. I don't have a dual cpu, but Threadmaster is supposed to work with dual cpu's. On my single cpu, if I had entered 80 my cpu load would be 80 percent or higher, after about two minutes. That would only be true when I was crunching using BOINC of course.

I can only suggest one more action before giving up on Threadmaster. First I need more information.

1. Where those numbers of 60, 80, or 90 that you mentioned entered into the registy key called CPUThresholdPct?

2. Which Rosetta application, is BOINC running at this time? The Rosetta project switched applications yesterday. You may have both applications in the following folder -

Located in Program FilesBOINCprojectsboinc.bakerlab.org_rosetta

rosetta_5.25_windows_intelx86.exe
and / or
rosetta_5.32_windows_intelx86.exe

All new Work Units, as of yesterday, should be using the application - rosetta_5.32_windows_intelx86.exe

Jack

ANOTHER THROTTLE PROGRAM
Warning I have never used this program.
It doesn't say if it works with dual CPU's?
Warning UNINSTALL ThreadMaster and reboot before using this program!

http://mion.faireal.net/BES/

ALSO
A future BOINC version is claimed to have a throttle feature.
29) Message boards : Number crunching : Limiting CPU usage (Message 29196)
Posted 11 Oct 2006 by stewjack
Post:
I am replying to my own post because the last part was confusing. It would probably be better if you just ignored the Correct Method for now.

Jack
30) Message boards : Number crunching : Limiting CPU usage (Message 29191)
Posted 11 Oct 2006 by stewjack
Post:
Thankyou i am going nuts.

Q3. Yes i am familiar with registry but no i have not gone into the registry becuse i am new to XP.


OK I think I can solve your problem now. However it might be a good idea to set
a system restore point, before you start changing registry keys! Have you ever created a system restore point? I think it is new in XP.

Some Background
I will give you more specic instructions later if you need them. Note: The instructions are also included in the readme.txt file that come with threadmaster.

Thread Master was created for use on servers. It was not created for BOINC. Threadmaster really does nothing but create registry keys. Threadmaster is controlled by changing registry values.

By default Threadmaster limits ALL individual computer applications to a maximum CPU load of 15%. Since Rosetta is an individual computer application Threadmaster is limiting it to 15% CPU load. This default value probably works fine for all other application. I increased the value to 30 percent, but that would still too slow for Rosetta. Most people just leave it at 15 percent. Changing this value is not the correct solution to your problem!

Please go to the the following registry location and just look at it. You don't need to change anything! You can just look!

[HKEY_LOCAL_MACHINESYSTEMCurrentControlSetServicesThreadMasterParameters]

If you can find CPUThresholdPct and Data value 15 You can ignore every thing else. If you feel comfortable you can increase the data value way up to 60 and see what happens. I believe you will have to exit BOINC and restart the computer before you see the increased crunching speed. Remember: Changing this value is not the correct solution to your problem!


The Correct Method

You must go down one more level in the registry beyond Parameters to Applications.

[HKEY_LOCAL_MACHINESYSTEMCurrentControlSetServicesThreadMasterParametersApplications]

Your solution is to to enter the Rosetta or any other applications as an exception to the 15% rule. These are my two exceptions. The second example is the new Rosetta application. It isn't crunching yet. I set them both at 80 percent.

Application Key
String
Value name: Value Data:
rosetta_5.25_windows_intelx86.exe 80

Value name: Value Data:
rosetta_5.32_windows_intelx86.exe 80


This is probably to much information at one time. It depends how familiar you are with Registry Keys. Don't be afraid to ask more questions.

Jack
31) Message boards : Number crunching : Limiting CPU usage (Message 29169)
Posted 11 Oct 2006 by stewjack
Post:
Help i am new to threadmaster. I installed it and now my CPU has started to run at 20% how do i increase it? I am running XP and i cant find the control for thread master, could someone help?


I need a lot more information.

Q1 Are you running XP?

Q2 Does your computer run at 20% when BOINC/Rosetta is actually crunching. The reason I am asking about this because - most computers run at less than 20% during average usage. Everything may be perfect if you are not actually crunching Rosetta. My computer averages about 5% when I am just surfing the web.

Q3 Are you familiar with the registry keys? Have you ever used regedit? And most important - did you modify any of the registry keys created by threadmaster? Threadmaster does provide instructions but they are almost gibberish to people who are unfamilar with the registry keys.


32) Message boards : Number crunching : Limiting CPU usage (Message 29147)
Posted 11 Oct 2006 by stewjack
Post:
How can I remove threadmaster 1.12build128 from my computer once I have installed it?I need a little more control over my cpu usage than what this is able to give me. thanks for any help you might give me.


I have threadmaster installed on my Win XP system and have used the uninstall script available at the web site. I didn't mean to uninstall threadmaster, but I accidentally clicked on the script! It worked. It took me 45 minutes to reinstall it.

http://threadmaster.tripod.com

The uninstall script is found under downloads on the homepage, or the following link.

http://bednorz.uni2.net/anyland/threadmaster/download.htm

Jack
33) Message boards : Rosetta@home Science : Are the results of SIMAP interesting for Rosetta? (Message 18053)
Posted 8 Jun 2006 by stewjack
Post:

@stewjack: I am aware of that but what has this to do with the topic? This thread is of the scientific usefullness of SIMAP for Rosetta.


You are the only other person that has mentioned the same connection of SIMAP to protein folding that I also believe exists.

I guess I was interested in the relationship between SIMAP's data products, and also possibly HMMER's, to the scientific goals of Rosetta - and other folding projects. I was interested in SIMAPS usefulness to any effort to improve our knowledge of protein 3D structure.

If HMMER does not replace SIMAP, then I will be required to consider attaching to HMMER@home as well as SIMAP and Rosetta. It will depend on what I learn about all three projects.

I will not change anything during CASP. I have plenty of time to learn more about HMMER. Heck, I may move on to Einstein at the end of the summer, but right now protein folding, and particularly Rosetta, is much more interesting.


Jack

34) Message boards : Rosetta@home Science : Are the results of SIMAP interesting for Rosetta? (Message 17862)
Posted 6 Jun 2006 by stewjack
Post:
Tralala

Are you aware of the new Windows/x86 application that SIMAP or MIPS is developing?

--------------------------
HMMER@home

http://boinc.bio.wzw.tum.de/boincsimap/apps.php

--------------------------

See SIMAP Message board thread New Application!

http://boinc.bio.wzw.tum.de/boincsimap/forum/viewtopic.php?p=3044

---------------------

Jack
35) Message boards : Number crunching : Is this for real??? (Message 17716)
Posted 5 Jun 2006 by stewjack
Post:
This thread is so long that I don't claim to have read every word, but I have one question that I don't believe has been raised.

FUNDING
How will these projects justify their funding if the can't document the computing power they are generating. Isn't that directly, or indirectly, related to accurate points, benchmarking, etc.

Jack
36) Message boards : Number crunching : limiting cpu usage to less than 90%? (Message 17712)
Posted 5 Jun 2006 by stewjack
Post:
In the interests of prolonging the life of my cpu, I would like to limit the amount of cpu BOINC uses to less than 90%. Is such possible?


I currently use ThreadMaster to limit my CPU. ThreadMaster can be confusing. If you need to use ThreadMaster I will attempt to help you.

Jack
37) Message boards : Rosetta@home Science : Are the results of SIMAP interesting for Rosetta? (Message 17708)
Posted 5 Jun 2006 by stewjack
Post:
I wonder, whether the BOINC-SIMAP project produces valuable results for Rosetta. SIMAP is a database of protein similarities. Provide those similiarities useful informations about the shape of a protein?

http://boinc.bio.wzw.tum.de/boincsimap/


I just noticed your post. I also run Rosetta@home (75%) and boincsimap (25%).

I don't know if the Rosetta project has ever used the SIMAP database, because it is so new, but I am quite certain that the Rosetta@home project makes use of protein similarities.


What is SIMAP?

SIMAP is a database of protein similarities. It contains about all currently published protein sequences and is continuously updated. Protein similarities are computed using the FASTA algorithm which provides optimal speed and sensitivity. SIMAP is to our knowledge the only project that combines comprehensive coverage with respect to all known proteins and incremental update capabilities.

http://boinc.bio.wzw.tum.de/boincsimap/project.php

What is SIMAP used for?

Because of the huge amount of known protein sequences in public databases it became clear that most of them will not be experimentally characterized in the near future. Nevertheless, proteins that have evolved from a common ancestor often share same functions (so-called orthologs). So it is possible to infer the function of a non-characterized protein from an ortholog with known function. A well-known example are the investigations about mouse genes and proteins. Their results are also beeing true for orthologous human genes and proteins in many cases. Protein similarities provide information about relations between proteins and are necessary for the prediction of orthologs.

Note:
I have noticed that Rosetta@home often mentions Homologs and simap talks about Orthologs, but I think that an Ortholog is just a subset of a Homolog. I don't fully understand if the difference in terminology is significant.

Homolog: Any member of a set of genes, DNA sequences or protein sequences whose nucleotide sequences show a high degree of one-to-one correspondence.

Ortholog: homologous sequence found in different species and derived from a common ancestor.

Jack
38) Message boards : Number crunching : As aThread Master user I wonder how many new application versions I must be enter into the registry. (Message 15119)
Posted 1 May 2006 by stewjack
Post:

If you really wanted to, you can see what's coming be reviewing the website for Ralph apps.


Thanks for the link. I have spent the last week learning about Thread Master. It is an old program used by SETI@HOME crunchers to limit the amount of overheating caused by the constant 100 percent load on the cpu. It can limit the percentage of cpu resources that any single process can control.

A modern cpu allows limiting clock rates by software control, but my computer has been sitting in a closet since 2002! It was given to me about two weeks ago, and while it has very respectable speed at 1.7 GHZ, (AMD Athlon) - it has very poor heat tolerance!

The fan sounded like a turbo jet when I would run BOINC.

Jack



39) Message boards : Number crunching : As aThread Master user I wonder how many new application versions I must be enter into the registry. (Message 15108)
Posted 30 Apr 2006 by stewjack
Post:
I attached to this project less than 10 days ago. I wasn't prepared for all these new executables.

Actually, I guess the worst thing that could happen is rosetta would be clamped at 30% of my cpu speed rather than 80%.

I guess I could also pre-enter new versions into the registry.
rosetta_5.08_windows_intelx86.exe
rosetta_5.09_windows_intelx86.exe
rosetta_5.10_windows_intelx86.exe
rosetta_5.11_windows_intelx86.exe

It's not really a serious problem, but I had never thought about this particular situation. I need a more modern cpu.

On a positive note, I haven't had any problems with my many 5.01 workunits. I haven't reached my single 5.06 or 5.07 workunits yet.

Jack
Tampa, Florida



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