Posts by Natronomonas

1) Message boards : Number crunching : RAC graph - time vs credit gained (Message 53665)
Posted 13 Jun 2008 by Natronomonas
How much does overclocking affect credit?

Since most BOINC tasks are CPU bound, increasing the CPU by a certain percentage will usually lead to a similar gain in RAC (usually a fraction less for a variety of factors, but in the main the point is valid).

However, if you're only after credit, you're better off with other projects with optimized apps or 64-bit gains, etc - these will gain you a lot more RAC than overclocking.

Still, Rosetta is a good project, so any increase in crunching power you care to send its way will be appreciated, I'm sure : )
2) Message boards : Number crunching : Crunchers - Who's Got Connections at Sony (PS3) ?! (Message 53611)
Posted 10 Jun 2008 by Natronomonas

Or check out PS3GRID if you would like to get BOINC credit. It is Linux based but the learning curve is not too steep.


This is what I am doing at the moment.

SETI has an ad going for someone to port to PS3... I guess the end goal is to have an app that will run through the GameOS, same as F@H...

I'm not sure on Rosetta's chances, since it's similar enough to F@H that Sony might just ask 'why'? ...Because BOINC is better, of course! : P
3) Message boards : Number crunching : Mac Pro, 8 cores (Message 51462)
Posted 17 Feb 2008 by Natronomonas
The power requirements on Skulltrail are so steep I'd say you're probably better off with Xeons, or a couple of 45nm quads... the chipsets on the Skulltrail board aren't exactly frugal.
4) Message boards : Number crunching : Ubuntu "boinc" user (Message 51460)
Posted 17 Feb 2008 by Natronomonas
Now I can not boot my Win XP. I am not knowlegeable with linux. I hope someone can help. The only way I can boot on my Win XP os is to reconnect the ubuntu sata drive and select from thew dual booting menu Microsft Windows XP. Thank you very much. joseps

GRUB (a bootloader program that Ubuntu installed to allow you to choose which OS to boot) has got your boot record. You can get rid of it by doing a 'repair' install with WinXP. I'd back up your documents first just in case, I've had the "my documents" folder gobbled before.

What failed running BOINC in linux? If you just go to "add/remove programs", select all open source apps, then search for/choose BOINC, it should just install itself easily and properly... even the Synaptic alternative is similarly easy.

5) Questions and Answers : Unix/Linux : Will Rosetta Run on a ps3 Yellow Dog Linux ? (Message 51443)
Posted 17 Feb 2008 by Natronomonas

You will also need to compile BOINC itself, see the BOINC website for that.

I think there are already PS3/PPC versions of BOINC; PS3Grid is a PS3 only BOINC project, for instance, while SETI is looking to build a PS3 version of its application.

I don't think you would need to optimize the actual BOINC app for the SPEs in the Cell; you could just use the PPC core, BOINC doesn't really need heavy duty computation itself. Thus the existence of PS3 versions would be relatively easy, since the PPC was used on Mac for so long (still plenty out there too).
6) Message boards : Number crunching : Good for Rosetta@home? (Message 48213)
Posted 1 Nov 2007 by Natronomonas
that can handle double precision calculations in the 128 bit registers, reaching double precision 100 GFLOPs[/u][/b]

So tell me again, why doesn't Rosie think the PS/3 is worth the effort ???

It may be those double-precision FP units. I know at SETI that was considered an issue, it could be the same here. (The regular Cell only have single-precision).

Now that F@H has got 'the market', as it were, it might be hard for R@H to capture the gains f@h did... perhaps better to aim for xbox or something, especially when to the casual observer the two projects seem quite similar.
7) Questions and Answers : Wish list : I would like to see:: (Message 48212)
Posted 1 Nov 2007 by Natronomonas
I would like to see a regular report on a list of successful accomplishment achieved by the Rosetta@home volunteers. Just to show that the group have done something worthwhile in their effort to help. We have been volunteering for more than a year now. Did we have accomplish something during that period? I hope I am not behind keeping with the news. joseps

On the front page : )


Oct 17, 2007
An article about Rosetta@home is in Nature. Congrats and thank you to all the volunteers that made this possible!

So things are progressing! : )
8) Questions and Answers : Wish list : Why RNA ? (Message 48170)
Posted 30 Oct 2007 by Natronomonas
RNA can be incorporated or involved in protein structure too, of course. Proteins, RNA, DNA etc do not exist in isolation in a cell, and they can affect each other to greater or lesser extents.
9) Message boards : Number crunching : Good for Rosetta@home? (Message 48169)
Posted 30 Oct 2007 by Natronomonas

Don't forget power costs ;)
PS3 takes about 200W while folding, so
24,000 * 200W = 4800 kW, for one year of non stop crunching @ $0.12 / kWh: 4800 * 24 * 365 * 0.12 = $5,045,760

But surely the NEC power costs are also substantial - you'd have to do a 3,5,8 year cost comparison or something to work out which worked out best overall.

(Obviously, the PS3, you can play super-tournament games on it on the weekend! : P )
10) Message boards : Number crunching : Rosetta CPU optimization - how ? (Message 47742)
Posted 15 Oct 2007 by Natronomonas
Somehow it looks like the whole SSE4/SSE5 "competition"/implementation, on Intel/AMD respectively, isn't going to matter much to Rosetta! : )
11) Message boards : Number crunching : 4000 credit wus? (Message 47667)
Posted 13 Oct 2007 by Natronomonas
The computer isn't claiming many credits, just being granted many... maybe because of the high decoy count, but it doesn't think they're worth that much...??
12) Message boards : Number crunching : I am missing over 1100 credit from Oct 7 (Message 47615)
Posted 11 Oct 2007 by Natronomonas
OK, I didn't realise it was also the status thread; that should be kept relatively up to date; I agree with you there. My apologies.
13) Message boards : Number crunching : I am missing over 1100 credit from Oct 7 (Message 47610)
Posted 10 Oct 2007 by Natronomonas
I do not want to have to watch my information like this and more Importantly I Should not Feel Ignored like this.

The above actions at Folding@Home makes me feel important not ignored. I need to feel that way here too. Why would I want to stay if you make me feel that my contribution is not worth an answer or 2?

Perhaps you're looking in the wrong places for approval. Remember these are volunteer projects; you do not always get the recognition you might want or expect in any volunteer activity; volunteering should by nature be altruistic, not for personal gain, although that isn't always the case. Of course you want to feel that the effort you put in has value, and it does; but I think you'd rather look back and say you helped a good science cause than stressed over a few credits...

I understand that 1100 missing credits is in its way significant, but it's what, 1 day's worth on a q6600 - nothing major. And they usually turn up sooner or later, as it seems reading this thread.

Further, when you're doing real science, you inevitably lose work and effort, through hardware failure, errors, etc; but for these projects, we only ever see a credit total growing steadily upward, never falling back, as can happen in real life, when it's more a case of 2 steps forward, 1 step back.

I'm sure the folks running this project have a long list of tasks to do; getting to forum posts isn't always going to be at the top; there would be a greater fuss if the servers fell over, if they weren't planning future work, etc - it may be a simple matter of the needs of the many than the few.
If worst comes to worst, you could always PM a mod if it was an urgent problem.

I'm glad you're on board doing Rosetta WUs; I'm glad there are thousands of others too. Just remember that the project staff are human too, and we're all in this together.

Also - it's BOINC, not bionic... while we're on the subject of slip-ups.
14) Message boards : Number crunching : Most of my Granted credit is lower than Claimed (Message 47528)
Posted 8 Oct 2007 by Natronomonas
Does Rosetta not use FLOPS counting?
15) Message boards : Number crunching : BOINC server farm idea / survey (Message 47354)
Posted 3 Oct 2007 by Natronomonas
It would be even better if their was a distributed servers for BOINC.

I know when we did FaD (before Rosetta@Home) all results, bandwidth etc where distributed via servers around the globe (three or four iirc). It would normally try the closest one and if that was down thry the others.

It would be nice, but since there is now many BOINC projects, I guess the redundancy is in the project diversity, rather than any one project itself; as long as people are running at least two projects, they should have a pretty high uptime (it's unlikely two of the big projects would go down at once).

I guess the cost/benefit of maintaining the extra servers wasn't worth it.

I'm sure the BOINC project people have looked at options like Amazon, etc. However, they may be getting their power at reduced rates, the equipment tax-free, or any number of other factors that may skew the economics. Still, for the smaller projects especially, it might be a good way to 'test the waters'.
16) Message boards : Number crunching : Merging computers (Message 47353)
Posted 3 Oct 2007 by Natronomonas
17) Message boards : Number crunching : Merging computers (Message 47260)
Posted 1 Oct 2007 by Natronomonas
Just to confirm; if you delete a host, you still keep the credit it earned, right?

18) Message boards : Number crunching : CPU Comparison question (Message 47256)
Posted 1 Oct 2007 by Natronomonas
Perhaps they are attached to multiple projects.

I know my quad is attached to more projects than any of my duals; greater project redundancy (in case one goes down), and also, it's fast enough that the turnaround on all the different WU is still good.
I would imagine many people do this, unless they're aiming for a top 100/1000 computer.
19) Message boards : Number crunching : Best Computer Features for Crunching (Message 47065)
Posted 27 Sep 2007 by Natronomonas

The Penryn is not going to perform any better clock-to-clock wise then the actual core. // in rosetta

Hard to say, right now. Some apps show a few % improvement, others 0%. I think Penryns have some better memory management or something; we'll soon find out, at any rate.

But it's not going to be much, unless the Rosetta coders add SSE4 support (if it's even useful), which seems unlikely for some time.

Still the 12mb cache could come in handy; or would it be better to o/c the 2.5ghz/6mb part...???? : )
20) Message boards : Number crunching : How to stup Rosetta form unnecessary accessing my Drive D: (Message 46611)
Posted 19 Sep 2007 by Natronomonas

Last I knew, not all BOINC applications honored the "write to disk at most every..." general preference. But I believe Rosetta does.

I was just now reading over at Einstein@home forums that Einstein ignores this; at least, the app seems to honour it, but the debug output doesn't, so that the disk is getting written to anyhow. I don't think they'd worked out yet if the debug stuff was BOINC or the worker app though.

I'd like for my disks to power down, but there always seems to be -something- that wants its turn!! : )

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