Posts by Stephen

1) Message boards : Rosetta@home Science : Amyloid diseases, such as Alzheimer's and type 2 diabetes (Message 60446)
Posted 2 Apr 2009 by Stephen
Post:
Some news on nattokinase, known to break up amyloid fibrils.
Extracted from natto, a fermented soy food.


The good thing about nattokinase is that it's safe, at least in the doses obtained from eating natto, since it's a food that's been eaten for years. The vitamin K2 (MK7) it contains has been shown to reduce the rate of fractures in the elderly.

StephenB
2) Message boards : Number crunching : Problems with version 5.96 (Message 53944)
Posted 24 Jun 2008 by Stephen
Post:
I've noticed some "watchdog" processes in ubuntu that have RT priority. Could these be pushing boinc into the background?
3) Message boards : Number crunching : Problems with version 5.96 (Message 53934)
Posted 23 Jun 2008 by Stephen
Post:
I'm experiencing the same issue where the tasks will get to 100% then idle. (Ubuntu 8.04 64 bit on a Intel Q6600).

Just a "me too", using 32 bit Ubuntu 7.10 and a dual core Athlon. I haven't checked today to see if crunching had resumed.

It would be nice to get the answers to these questions:

1. Is there a known issue with crunching stopping after WUs reach 100%?
2. Are we supposed to "wait it out" or take some action?

Stephen
4) Message boards : Rosetta@home Science : First impressions on Fold It game (Message 53540)
Posted 5 Jun 2008 by Stephen
Post:
Is this game cross-platform?

Stephen
5) Message boards : Number crunching : Mac Pro, 8 cores (Message 51729)
Posted 29 Feb 2008 by Stephen
Post:
I hope to do the same once I feel that the price/performance for a quad core is at a sweet spot.

Stephen
6) Message boards : Number crunching : Ubuntu "boinc" user (Message 50855)
Posted 21 Jan 2008 by Stephen
Post:
I uninstalled the ubuntu boinc and downloaded a copy from the website. Not ideal, but it works.

Stephen
7) Message boards : Number crunching : Ubuntu "boinc" user (Message 50848)
Posted 20 Jan 2008 by Stephen
Post:
When I restart my ubuntu computer, two processes are there when I login (one for each core), running as the user "boinc".

As my normal user, I can't run boincmgr because those aren't my processes.

Is this the standard way of running boinc on Linux? Sometimes I get a little frustrated with how ubuntu blindly follows debian practices, though I don't know if this is the case now.

Stephen


Did you install BOINC from the BOINC/SETI download or using one of the Ubuntu software installing methods?


From Ubuntu.

Stephen
8) Message boards : Number crunching : Ubuntu "boinc" user (Message 50837)
Posted 20 Jan 2008 by Stephen
Post:
When I restart my ubuntu computer, two processes are there when I login (one for each core), running as the user "boinc".

As my normal user, I can't run boincmgr because those aren't my processes.

Is this the standard way of running boinc on Linux? Sometimes I get a little frustrated with how ubuntu blindly follows debian practices, though I don't know if this is the case now.

Stephen
9) Questions and Answers : Unix/Linux : Launching a browser from boinc manager (Message 45138)
Posted 18 Aug 2007 by Stephen
Post:
Launching a browser (to view the message boards, for example) fails under the latest ubuntu for me. I get the message:

execvp(epiphany, http://boinc.bakerlab.org/rosetta/forum_index.php) failed with error 2!

Even though I'm using KDE and have this set up:

$ echo $BROWSER
/usr/bin/firefox


Any way to fix? Thanks.

Stephen
10) Message boards : Number crunching : BROWSER variable not being used (Message 43647)
Posted 14 Jul 2007 by Stephen
Post:
I have the following come up when I click on the "message boards" button:

execvp(epiphany, http://boinc.bakerlab.org/rosetta/forum_index.php) failed with error 2!

but $BROWSER does point to /usr/bin/firefox:

$ echo $BROWSER
/usr/bin/firefox
$ which firefox
/usr/bin/firefox

Thanks.

Stephen
11) Message boards : Number crunching : Problems with Rosetta version 5.59 (Message 39998)
Posted 28 Apr 2007 by Stephen
Post:
I have a dual 1.8 GHZ PPC macintosh running the latest OS X.

Using Activity Monitor, I see two rosetta@home processes, both named rosetta_5.59_pow. One is using 94% of a CPU, and the other is using about 75% of the other CPU.

On the BOINC manager window, I see two processes marked as "running". The CPU time, progress, and to completion only increments for one of the two processes. I speculate that the CPU time, progress, and to completion for the process that is not incrementing, which seems to be older, stopped incrementing when the younger process started.

This looks like an OS X specific bug, since my dual core Athlon Ubuntu linux client shows updates for two processes. Is there a place to report bugs somewhere? Thanks.

Stephen
12) Message boards : Number crunching : Dual G5 powermac and manager window issue (Message 38084)
Posted 21 Mar 2007 by Stephen
Post:
I'm using a dual G5 powermac. The client does download two work units, but only seems to be working on one at a time, judging from looking at the BOINC manager window -- CPU time is only ticking on one of the two work units.

But, when looked at using activity monitor, both processes are actually running. If I quit out of the manager and restart, both numbers are ticking again.

Is this a known issue for the mac client? It doesn't seem to happen on my dual core AMD linux box.

Stephen
13) Message boards : Rosetta@home Science : Scientists Unveil Piece of HIV Protein that May Be Key to AIDS Vaccine Development (Message 36853)
Posted 15 Feb 2007 by Stephen
Post:
Is the site that the b12 antibody in the NIH press release binds to one of the ones studied with the GP120 work units?

Stephen
14) Message boards : Rosetta@home Science : A possible cure for Cancer (Message 36809)
Posted 15 Feb 2007 by Stephen
Post:


The probelm is DCA has never been tested in humans and is certainly not available to patients. Of course most of the 'implies' comes from the headline (not something NewScientist often do I must say though). don;t forget such a headline will be read by eager cancer patients.


While everything you have written is true, faced with a certain death if nothing were done and given that I am quite capable of making informed consent and doing my own due diligence, I would like to have the choice of trying it.

Stephen
15) Message boards : Rosetta@home Science : Harvard breakthrough in folding prediction? (Message 31097)
Posted 14 Nov 2006 by Stephen
Post:
Here is a link to an article about discussing a new folding technique. It claims to be able to model folding for 10 microseconds, at least "at least a thousand times longer than previous methods":

http://www.physorg.com/news82056528.html

I'm not a biochemist, so I'd be curious to get feedback on how much of a breakthrough this is, and how it relates to the work done with Rosetta@home.

Stephen
16) Message boards : Number crunching : Macintosh, screen saver, and BOINC manager question (Message 26964)
Posted 16 Sep 2006 by Stephen
Post:
Is it ok to run the BOINC manager, and also to activate the screen saver? I can have BOINC run just with the screen saver, or just with the manager.

My concern is what happens when I use the screen saver plus the manager? Would I be starting too many processes?

Thanks.

Stephen
17) Message boards : Number crunching : Linux AMD vs. OS X PPC (Message 22661)
Posted 17 Aug 2006 by Stephen
Post:
The boards were down before I saw any replies, and in the meantime I just installed the linux-686 kernel, without the "smp". Interestingly, I see two processes, each of which is using nearly 100% of a core:

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
12700 stephen 39 19 49060 16m 3624 R 99 1.6 47:42.74 rosetta_5.25_i6...
12571 stephen 39 19 47112 15m 3624 R 93 1.5 57:02.96 rosetta_5.25_i6...

So I have to think that the straight 686 version enables both cores. Can't wait to see my averages go up.

Stephen
18) Message boards : Number crunching : Linux AMD vs. OS X PPC (Message 22541)
Posted 16 Aug 2006 by Stephen
Post:
Great -- I'm off to get the extra core.

There is linux-686 and linux-686-smp. Do I need the smp?

Stephen
19) Message boards : Number crunching : Linux AMD vs. OS X PPC (Message 22512)
Posted 16 Aug 2006 by Stephen
Post:
I have two computers crunching away at rosetta@home. The first is a dual 1.8 GHz powermac, and the second one uses an AMD cpu (Athlon(tm) 64 X2 Dual Core Processor 3800+) on the latest ubuntu with the 2.6.15-26-386 kernel.

So far, I have about 8050 credits on the linux/AMD and 22,500 credits on the mac. There are two processes on the mac and one on the dual core AMD.

The AMD is a newer processor, so I'm suprised that it isn't doing better. Any hints about what makes it slower or ways to make it better would be appreciated.

Stephen
20) Message boards : Rosetta@home Science : Genetic algorithms and rosetta@home (Message 19495)
Posted 29 Jun 2006 by Stephen
Post:
Those are certainly questions to be looked at.

The distributed hardware evolution project (DHEP) I was part of took the approach of having each client be an island on a grid. Each island would evolve its own population of solutions. There was also in place a mechanism that would promote migration among neighboring islands. Over time, the average fitness of the islands' populations would go up. The project generated neat graphics showing the fitness distribution color coded on a map of the "geography".

The whole project, client and server (http://dhep.dbestern.com/), was implemented in java. I wonder if the code is still available (http://freshmeat.net/projects/dhep/) for any of the developers who might want to look at it for ideas. Maybe Miguel Garvie could be reached at his yahoo email.

Stephen


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