Posts by l_mckeon

1) Message boards : Number crunching : First Skylake CPUs hit the streets (Message 78987)
Posted 26 Oct 2015 by l_mckeon
The i7-5820K lacks a GPU, so unless you're running headerless that's a small extra cost that you'll have to add. Also it has a TDP of 140W which might put some people off.
2) Message boards : Number crunching : SSD (Message 78128)
Posted 17 Apr 2015 by l_mckeon
Yes, but I only started a few weeks ago. There was a large performance gain on ATLAS@home tasks when I installed boinc on my SSD. Apparently my HDD read/write rates weren't fast enough to fully utilize the processor.

Anyone worried about SSD endurance should read this:

Then do the math. Maybe stay away from TLC drives if you're still worried.
3) Message boards : Number crunching : Rosetta on SSD (Message 77537)
Posted 2 Oct 2014 by l_mckeon
How I'm understand rosetta produce a lot of write disk activity and this not very good for ssd. How I can reduce this activity or configure rosetta to use not system disk?

Read this article on SSD life (and the ones leading up to it).

Unless Rosetta's disk writes are truly prodigious, you are unlikely to run into problems with cell wear. All but one or two of the SSDs under test made it past 600 TB of writes, and I think those losers had controller board problems, not cell wear.

Assume 100GB of writes per day, every day -- that's 6000 days or about 16.44 years before the SSD wears out.

4) Message boards : Number crunching : i7 4770K HT ON/OFF results (Message 76640)
Posted 21 Apr 2014 by l_mckeon
I calculated average credit per day as a formula :=

Avg WU per core/day * number of cores(threads) * Avg Granted credit
HT OFF = 8,1509428836 * [b]4[/b] * 144,2326666667
HT ON = 8,3791622648 * [b]8[/b] * 89,5136111111

It was very short period of testing (2 days for each one)
I'll try some long term statistic, and then i will comapre my previous results.

Of course there is some measure error as it was not compared to exactly the same WU's.

I don't have a HT capable CPU myself, but 25% to 30% is a figure I have heard elsewhere, several times.

Incidentally, I think the price difference for a HT vs non-HT capable Intel CPU is somewhere in that area, when you account for other differences.
5) Message boards : Number crunching : Cursor Lag when running Rosetta/BOINC (Message 76263)
Posted 11 Dec 2013 by l_mckeon
Also I think BOINC "hard limits" the CPUs, so it will run all 8 threads at 100% for a while then coast for 3X as long (at 25% CPU setting).

I may be wrong but have a look at Task Manager to see what's happening. I think this feature was designed to limit heat build-up or battery drain in laptops.
6) Message boards : Rosetta@home Science : GPU Computing alternative to RMSD calculation (Message 74113)
Posted 26 Oct 2012 by l_mckeon
From World Community Grid scientists FYI

"Paper Title:

“Accelerated protein structure comparison using TM-score-GPU”

Lay Person Abstract:

As part of the analysis of the computed results of the Nutritious Rice for the World project, the researchers need to be able to compare protein structures and efficiently compute a similarity score. A scoring method based on “Template Modeling”, known as TM-score, provides significantly better results than the “root-mean-square-deviation” method, but requires much more computer processing time. To solve this problem the researchers developed a version of the TM-score algorithm which makes use of Graphics Processing Units (GPU's) which are found in newer video hardware, used particularly on gaming computers to enhance the visual experience. Using GPU's they were able to run millions of protein comparisons about 70 times faster. The paper describes how they accomplished this and they offer the software freely to other scientists, who may be able to use it for their research.

Technical Abstract:

Motivation: Accurate comparisons of different protein structures play important roles in structural biology, structure prediction and functional annotation. The root-mean-square-deviation (RMSD) after optimal superposition is the predominant measure of similarity due to the ease and speed of computation. However, global RMSD is dependent on the length of the protein and can be dominated by divergent loops that can obscure local regions of similarity. A more sophisticated measure of structure similarity, Template Modeling (TM)-score, avoids these problems, and it is one of the measures used by the community-wide experiments of critical assessment of protein structure prediction to compare predicted models with experimental structures. TM-score calculations are, however, much slower than RMSD calculations. We have therefore implemented a very fast version of TM-score for Graphical Processing Units (TM-score-GPU), using a new and novel hybrid Kabsch/quaternion method for calculating the optimal superposition and RMSD that is designed for parallel applications. This acceleration in speed allows TM-score to be used efficiently in computationally intensive applications such as for clustering of protein models and genomewide comparisons of structure.

Results: TM-score-GPU was applied to six sets of models from Nutritious Rice for the World for a total of 3 million comparisons. TM-score-GPU is 68 times faster on an ATI 5870 GPU, on average, than the original CPU single-threaded implementation on an AMD Phenom II 810 quad-core processor. Availability and implementation: The complete source, including the GPU code and the hybrid RMSD subroutine, can be downloaded and used without restriction at The implementation is in C++/OpenCL."

The page also has a link to the original paper.

I wonder if this might be of interest to Rosetta scientists?

7) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 71560)
Posted 1 Nov 2011 by l_mckeon
T0538_boinc_medal_split_medal_cmiles_SAVE_ALL_OUT_IGNORE_THE_REST_34616_13242_0 aborted by user.

The task time to completion was increasing at 1 second per second. I think it went wrong when I tried to look at the graphics.
8) Message boards : Number crunching : which cpu´s are you using for rosetta? (Message 70795)
Posted 28 Jul 2011 by l_mckeon
Tom's Hardware has just done an excellent piece on the relative merits of different CPU architectures.

They tested the efficiency of single cores at a standard 3 GHz speed.

Moral: if you're still using a Pentium 4 for crunching, dump it now.,2974.html
9) Message boards : Cafe Rosetta : Moderators Contact Point (Explanations, Assistance etc) Post here! (Message 70772)
Posted 23 Jul 2011 by l_mckeon
According the the Message Boards' top page, the most recent posting on Rosetta@Home Science is 6 days old. Where the hell is the message?

I can't see it on any variety of sort option, at least 2 pages deep.

I've run into this invisible message problem before on Rosetta. Why isn't "Most Recent Post" one of the sort options?
10) Message boards : Rosetta@home Science : WiFi and Cellphone radiation effects (Message 70424)
Posted 28 May 2011 by l_mckeon

I am fine with more ridicules from you guys since whole study is being hugely ridiculed everywhere. (sponsored with high tech industry and supporters I guess)

11) Message boards : Rosetta@home Science : Design of protein-protein interfaces (Message 70334)
Posted 14 May 2011 by l_mckeon
[quote]I am running a couple of these tasks and need to reboot my computer and do not want to lose hours of core time when there is some way of avoiding this.

Ditto on complaint. Four hours between checkpoints is a bit much!

Thanks for the feedback, we're looking into this!

Also, have you been having problems with one particular set of jobs, or is it a more general problem with many different Rosetta@home jobs?

I'm fairly sure it was one of the Measles Protein interface design tasks - MVH etc. Most tasks update ok.
12) Message boards : Rosetta@home Science : Design of protein-protein interfaces (Message 70321)
Posted 11 May 2011 by l_mckeon
I am running a couple of these tasks and need to reboot my computer and do not want to lose hours of core time when there is some way of avoiding this. I cannot sit for ages checking on the task properties.

Ditto on complaint. Four hours between checkpoints is a bit much!

BTW, I have a program manager that I use solely for watching when tasks checkpoint. I have EF Commander Free permanently pointed at the "...Application DataBOINCslots" folder.

This program updates dynamically whereas the Properties window is a snapshot.
13) Message boards : Rosetta@home Science : MS-Disease (Multiple Sclerosis) (Message 69885)
Posted 24 Mar 2011 by l_mckeon
Transcript on new and controversial theory of cause of MS.

Easy to check out via CT scan.
14) Message boards : Rosetta@home Science : Young Blood Reverses Signs of Aging in Old Mice (Message 69757)
Posted 8 Mar 2011 by l_mckeon

So once a year we all go in and get younger! Oh it would be soooo nice to be young and dumb again!!

If this works, I wonder how long before people start harvesting blood from children in third world countries for supply to the rich.

15) Message boards : Number crunching : Communication during recent downtime (Message 69595)
Posted 4 Feb 2011 by l_mckeon
The BOINC home page is the obvious place for official announcements of outages, with Twitter, FB etc. available as extras.
16) Message boards : Rosetta@home Science : Shrink wrapped molecules. (Message 67612)
Posted 6 Sep 2010 by l_mckeon
Here is a new and different approach to determining the shape of molecules. They shrink wrap them in graphene and examine the resulting shape with scanning atomic microscopes.

Nano Tech Wire
17) Message boards : Number crunching : Long Time no Checkpoints (Message 67258)
Posted 18 Aug 2010 by l_mckeon
intSpin1_1f0s_2ew0_ProteinInterfaceDesign_13Aug2010_21746_168_0 went 4.5 hours between checkpoints at one stage, and its companions (..._166_0 and ...167_0) both ran towards 1.5 hours between checkpoints at some point.

Also, intSpin1_1f0s_2ew0_ProteinInterfaceDesign_13Aug2010_21746_166_0 finished after 7:10 hours, but its status was then changed to "ready to start" with no results data present or uploaded. I aborted the task.
18) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 66967)
Posted 21 Jul 2010 by l_mckeon
What are the implications of the new enzyme?

Briefly, what are the time and energy improvements over the standard reaction??
19) Message boards : Rosetta@home Science : CASP9 (Message 66430)
Posted 3 Jun 2010 by l_mckeon
I just spotted that the graphics of a casp 9 task I have is showing both energy levels and RMSD. As CASP9 targets are unknown I had thought the RMSD comparison was impossible.

Ditto, I've been wondering that as well.

Aren't CASP targets supposed to be blind?
20) Message boards : Rosetta@home Science : Possible cancer cure found in plant (Message 65336)
Posted 15 Feb 2010 by l_mckeon

Regarding the health care in US - AFAIR it asks for some tweakings and it's not only the "treat all the people" issue. One example: AFAIK still in US, Australia etc. if the branded medicine is prescribed, it cannot be changed by a patient/pharmacist even if a proper generic (and far cheaper) drug is available. This is an outrageous waste and invitation to corruption (sponsoring practicioners to win their prescriptions). In EU any patient has a right to ask in a pharma for the cheapest generic equivalent.

Not true in Australia unless the doctor specifically ticks a box on the prescription, which they will rarely do, and mostly in the
case of special circumstances (allergies etc.)

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