Posts by dgnuff

21) Message boards : Cafe Rosetta : Progress Thru Processors (Message 62774)
Posted 5 Aug 2009 by Profile dgnuff
Post:
Interesting.

It will be instructive to watch the flops count over the next weeks and months.

One idea that might be wise, given the following comment on the reviews page:


No Linux support. Epic FAIL!


is to aim Linux users directly at boinc.berkeley.edu and inform them a Linux client for BOINC can be found there. Depending on the support provided by PTP for Mac OS, the same strategy may be necessary for those users.
22) Message boards : Number crunching : Minirosetta 1.90 and 1.91 (Message 62773)
Posted 5 Aug 2009 by Profile dgnuff
Post:
Agreed - I had this guy error out on one of my boxes:

resultid 269800139

Name matches the format noted by Sid, error matches the one posted by Tim.
23) Message boards : Number crunching : Can't upload finished work (Message 62713)
Posted 2 Aug 2009 by Profile dgnuff
Post:
Edit -- Deleted
24) Message boards : Number crunching : Minirosetta 1.90 and 1.91 (Message 62712)
Posted 2 Aug 2009 by Profile dgnuff
Post:

As for Kaspersky, DK contacted the vendor a while ago and it went no where. Maybe it's time to try again.


The other option would be to sign the executable. Depending on the available budget, there are several vendors selling code signing certificates - prices appear to be in the $150 to 200 to 250 per year, with Verisign coming in a little high in the $400 to $500 range.

MSDN article that covers signing executables.

Ignore the under $70 price on Comodo's page, that appears to be a bait and switch. I could not find a way to buy from them at that price when I hit the "Visit our store" link.


Never Mind. I just saw in another thread that there are the necessary files for generating signatures, just that the process had a hiccup.
25) Message boards : Number crunching : Minirosetta 1.90 and 1.91 (Message 62709)
Posted 2 Aug 2009 by Profile dgnuff
Post:
The good news is that 1.90 seems to be stable so far. The network traffic is still heavy, but a lot better than yesterday.


Agreed - I'm now on 1.90 except for a single 1.88 task at about 75% complete. Everything is running smoothly.


As for Kaspersky, DK contacted the vendor a while ago and it went no where. Maybe it's time to try again.


The other option would be to sign the executable. Depending on the available budget, there are several vendors selling code signing certificates - prices appear to be in the $150 to 200 to 250 per year, with Verisign coming in a little high in the $400 to $500 range.

MSDN article that covers signing executables.

Ignore the under $70 price on Comodo's page, that appears to be a bait and switch. I could not find a way to buy from them at that price when I hit the "Visit our store" link.
26) Message boards : Number crunching : Minirosetta 1.90 and 1.91 (Message 62684)
Posted 31 Jul 2009 by Profile dgnuff
Post:
My Kaspersky Internet security is doing the same on ALL my machines. If it cannot be signed or a wildcard fix done soon. I will have to remove rosetta from my project list, which I do not want to have to do. I have been doing them for quite a while, but it is a pain having to go to each machine and add move each to Low Restricted everytime the version changes.


In the case of Rosetta, what Kaspersky need to provide is the ability to say "Don't bother checking for a signature on files that match this wildcard."

The purpose of signatures is twofold:

1. If a file shows up with a virus and a valid signature, you now know where the virus came from.

2. If a file shows up with an invalid signature, it has been tampered with, and therefore should be rejected.

Case 2 is the far more common scenario, and is the main reason why Kaspersky is unwilling to let Rosetta run. It has no signature, and therefore there's no way to determine if it's been tampered with.

That said, in the case of Rosetta the likelihood of tampering is zero, since BOINC itself verifies that the file saved to your disk is what was sent from the server, plus the fact that you always download directly from the project website.

What should be done is to contact Kaspersky and ask them to add this feature. ESET's NOD32 has a very similar feature, which has proven very useful at times.
27) Message boards : Number crunching : How many people are crunching Rosetta? (Message 62675)
Posted 31 Jul 2009 by Profile dgnuff
Post:
...

I was enrolled in an Oxford cancer research program a few years back, but that research ended.

...


That sounds like Find a Drug, run by Keith Davis. If so, welcome aboard from another ex-FaD'er.

I came over for much the same reasons, this project has tremendous potential in several areas: both pute bio-medical research, and the more practical aspects of being able to work on cures for diseases.
28) Message boards : Number crunching : Problems with MiniRosetta 1.87 (Message 62599)
Posted 29 Jul 2009 by Profile dgnuff
Post:
As a followup to my last, this appears to be a fairly major problem with 1.87.

These tasks all have the same problem, in varying degrees. My preferred runtime is 12 hours, 43,200 seconds. They are all significantly shorter.

This isn't a huge problem for me, as I have the bandwidth to support the additional downloads. However for people who need longer runtimes due to being on metered internet access, or dialup, or whatever, this is going to be an increasing problem.

268811488

268817339

268817334

268803610

I am not an expert, but the following looks suspicious to me. In all cases, the task details contain the following line:


This process generated 100 decoys from 100 attempts


It appears to me that these tasks run until one of two conditions are met: the users preferred time, or they've run 100 decoys. Is there any way to increase the number of attempts it will make if it gets through the first 100 too quickly, so that it can keep on working.
29) Message boards : Number crunching : Problems with MiniRosetta 1.87 (Message 62587)
Posted 29 Jul 2009 by Profile dgnuff
Post:
After the problems with 1.86, I flushed all work units from all my systems, and then reset Rosetta on all of them. One system: Host ID 878471 returned its first work unit in about 35 minutes.

Task details are here: Task ID 268817229

Workunit details are here: Workunit ID 245026485

If there's anything else I can do to help track this down, let me know.

For what it's worth, I have my default run time set to 12 hours.
30) Message boards : Number crunching : v 187 very low credit (Message 62586)
Posted 29 Jul 2009 by Profile dgnuff
Post:
Deleted - belongs in the general 1.87 problems thread
31) Message boards : Number crunching : Management all my computers from one of them (Message 62445)
Posted 26 Jul 2009 by Profile dgnuff
Post:
A little bit of a post necromancy here, but .....


If you can find it you can also use BOINC View to control multiple hosts ... there is a replacement for BV being worked on though it is not yet available ... perhaps later this month...


Any news on this?
32) Message boards : Number crunching : Help with Linux Installation (Message 62444)
Posted 26 Jul 2009 by Profile dgnuff
Post:
I did some simple math and 1200 seconds is 20 minutes, 10,000 divided by 20 equals 500. 3 times per hour, times 24 hours, equals 72 times per day, divided into 500 equals about 7 days. Which is how many times you can write before it becomes susceptible to dying, more or less.


Why did you divide 10,000 by 20?

10,000 writes divided by 72 writes per day gives 139 days.


Because 20 is how often it writes, so 10,000 writes divided by a write every 20 minutes gives me the number of writes which can then be translated to hours. I like your math better, but either way you NEED a hard drive. I used to run Seti on a floppy way back when but I do not think you can do it that way anymore. Someone may be able to setup Boinc to use a floppy as the database storage site instead of a USB disk though, but that is beyond me.


It'll go a lot further than that. Flash memory units do all sorts of tricks to shuffle around where they're writing to extend the life. This page on wikipedia covers it in some detail.

http://en.wikipedia.org/wiki/Wear_levelling

Bottom line, your flash drive will last a great deal longer than the hypothetical 139 days
33) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 62410)
Posted 24 Jul 2009 by Profile dgnuff
Post:
Thank you for the pointer to this thread. I just posted an (apologetic) response, and now I will give an update on the work we are doing in my journal page.


The abstract of David Kim's paper that you posted raises the following question for me. He mentions that smaller proteins have been accurately modeled by Rosetta, but it appears there is a size limit, above which we don't yet have the necessary computing power.

Possibly taking a quote out of context, but approximately how large are the "Larger and more complex proteins" that are spoken of.

As an extension to this, and assuming there is a size limit, does that same size limit come into play for the reverse problem, trying to create a protein chain for a custom shape.

Keeping this in mind, for the proposed flu vaccine, and possibly for your proposed HIV vaccine, do you have any estimates of how many residues these will have, and where that count (again assuming it exists) is in relationship to the above limit.

All of which is a long and convoluted way of asking, "How close are we to having the necessary accuracy in Rosetta, and compute power from all our systems to be able to create the flu vaccine that you spoke of recently?"
34) Message boards : Number crunching : aborting work units (Message 61591)
Posted 6 Jun 2009 by Profile dgnuff
Post:
If you would state your intentions it might help people comment on alternative approaches to achieve your goals.


My intentions are to get as many WU's assigned to my machine as it can process by the required deadline of each WU. Also, I want such WU's to be compliant in quantity and required total crunching time over a given, long period (>= a matter of a few months, at least) with my set %ages for Rosetta et al. Nothing fishy or abusive; just good use of my resources. I know I would finish more discrete WU's with Hydrogen than Rosetta, but I want my PC to run Rosetta more, and it's doing so... thus, good there...


The best thing to do is to determine your long term project percentages, set them up by adjusting the resource share of your chosen projects, set Boinc to keep about three to four days work ahead, and just leave it alone.

The Boinc scheduler is a fairly complex beast, it has to be because of the various projects it deals with. Different work unit durations, different deadlines, things like CPDN with workunits that run for months at a time, etc.

Keeping this in mind, it's really designed to be run in "set and forget" mode. It'll take a week or two to sort everything out, but if you leave it alone, it will respect your resource share choices, and more importantly, leaving it alone and not micromanaging reduces the risk of missed deadlines.

Also, unless you have a very strong reason to do so (intermittent connection, e.g. dial up), there is no benefit whatsoever is maintaining a large work buffer. I run with a three day buffer, and simply don't have any problems.
35) Message boards : Cafe Rosetta : Crunchers, Crunching Gardens, Crunching Farms... (Message 61434)
Posted 28 May 2009 by Profile dgnuff
Post:
Please be gentle, still a "work (very much) in progress", but for me and my S/O Melissa...

This is what keeps our apartment warm in the winter


I like it! Be careful of the amps you are pulling on each circuit though. I had to run a new line just to keep my pc's from blowing the circuit everytime I plugged in the vacuum. I have a house, you say you have an apt, makes thing much more interesting!!


You'd be surprised.

I got a Killawatt meter from Ebay, and found that my crunch boxes are remarkably low power. The two Q6600 quads only take 110 W, or about an amp. So once I get up to eight crunch systems (planned target), that's still only about 8 amps, or sufficiently little that I could pull it from a single outlet.

My solution to the heat problem is to use physics, don't fight it. Crunchers are upstairs, we just move downstairs during the summer. Sure, the upper floor of the house is 15 degrees warmer than downstairs, but who cares if we're not up there.

BTW, with the eight (planned) dedicated crunchers, plus the four others that makes me just a rancher. ;) The four are two desktop machines (my wife's and mine), and our two notebooks. These are not dedicated crunchers, but are still left on 24/7 to crunch.

Currently at 4 crunch systems, but I've got two more in the works now. Gotta get a couple of cases from Ebay, and a couple of hard disks from Weird Stuff, but other than that I'm good to go.

Asus P5KPL-CM mobo, 2 GB ram (overkill), Q8200, and hard disk. That lot just doesn't draw that much power. That's probably more ram than I need, but it's so cheap nowadays, why not?
36) Message boards : Cafe Rosetta : a patent on genes? (Message 61432)
Posted 28 May 2009 by Profile dgnuff
Post:
IANAL, however that being said, I agree that patent must be overturned. I would hope that if the information on this web page is accurate:

http://www.bitlaw.com/patent/requirements.html

then a good patent lawyer should be able to overturn it on the last condition: the non-obvious requirement.

37) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 61431)
Posted 28 May 2009 by Profile dgnuff
Post:

I am very curious how you create a protein structure that presents the multiple tightly binding strands in the proper orientation. This sounds much more difficult then colorizing a couple lengths of string and then figuring out a way to wind the string into a ball that has all of those colors at very specific points in the completed ball.

In other words, once you know the colored bits of string, how do you fill in the rest of the ball in a way that assures the final orientation of the key elements that you've confirmed have good fit with the target? If they bind well enough, is there some wiggle room there? Where the strands in your counter agent will distort upon docking with the viral cell?


I don't know the answer to this, but I am certain that Dr. Baker has mentioned on several occasions that the ability to design a custom protein that has a desired shape is something that Rosetta is capable of doing. And as we improve Rosetta's ability to determine the shape of a given amino acid sequence, we improve it's ability to design custom proteins.

When determining the shape of a protein, Rosetta lets it fold, measures the energy, "shakes it a bit" measures the energy again, and so on. Each shake adjusts the final shape of the protein from the previous test.

This is now a wild guess on my part, I could be totally wrong. Remember, I'm not a biochemist. ;) However it seems like a plausible idea to me. Suppose they do the following. We know exactly what shape we want. So we try a random amino acid sequence, and see how closely it matches. If it's not quite there, change a residue or two, "shake" it, and try again.
38) Message boards : Number crunching : Problems with Minirosetta Version 1.64/1.65 (Message 61077)
Posted 9 May 2009 by Profile dgnuff
Post:
dgnuff, when I've seen that before, it always seems it is with that era of BOINC Manager installed. It seems to lose track of the tasks sometimes and now you probably have an idle CPU. I suggest you suspend and release the task and see if it wakes up. If not, suspend and release it for a minute or so, and after 5 times the watchdog will kick it out for not making progress after 5 restarts and it will report back.


Thanks for the information. Suspending and resuming it a couple of times unlocked it. I'll keep an eye on it for now, since the completion time is totally wrong. However, the "completion percentage" is increasing at a rate that's correct for my standard run time of 12 hours.

-- Edit --

You indicated that a 6.4.? client can cause this. I notice that the current version for Windows is 6.6.20. Do you think it would be worth my time to download and install that to avoid this problem in the future?
39) Message boards : Number crunching : Problems with Minirosetta Version 1.64/1.65 (Message 61066)
Posted 9 May 2009 by Profile dgnuff
Post:
dnuff, what is the current status of the task? "Running"? What platform are you running on? What BOINC version?


Platform: Windows XP SP 3
Boinc client version: 6.4.7
Hardware: Intel Q6600 quad core, 2 GB memory

Link to the host. While I'm at it, Task details and workunit details

According to boincmgr, it's running, high priority.

Keeping that in mind, I ran a VNC session to get to the desktop of the system in question. Task manager shows the process is present, but not using any CPU time.
40) Message boards : Number crunching : Problems with Minirosetta Version 1.64/1.65 (Message 61061)
Posted 8 May 2009 by Profile dgnuff
Post:
A question for all the "error experts". I've got a task running on one of my machines that appears to have stalled.

Here's the line from the messages where it started:

Silver rosetta@home 5/4/2009 18:05:05 Starting abinitio_norelax_homfrag_natfrag_129_B_2hkvA_SAVE_ALL_OUT_6252_7736_0

This is from BoincView, since that program allows me to monitor all my farm machines from one place.

What's a concern is that after almost 4 days, it's still taking a slot up on the machine. CPU efficiency reports as zero (not a good sign), CPU consumed is 1:48:20, however the to completion time is off the scale: 140:06:02.

What I'd like to know is the most useful things I can do to get information about this back to Bakerlab. That includes anything up to and including attaching a debugger to it and poking around inside the process.


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