Posts by robertmiles

21) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 81576)
Posted 11 Jun 2017 by Profile robertmiles
Post:
Another issue with these overrunning tasks: checkpointing isn\'t working properly. I\'ve got a couple of b21* tasks that have been running for over 12 hours and are stuck on step 7205 having done 52 and 12 tasks respectively. Yet the last checkpoint for each is 18 minutes.

A lot of compute errors lately for workunits with names beginning with b21_ or b22_. For most of them finished by a wingmate, the wingmate gave a compute error also.

Could you check if this series of workunits has built-in errors?

Running under 64-bit Windows 10.

Not overrunning; they hit a compute error when about a quarter done.

Problem not seen for workunits with names beginning with anything else.
22) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 81486)
Posted 18 Apr 2017 by Profile robertmiles
Post:
Could you modify your Server Status web page to show which of the server programs handle uploads and downloads?


I just added some text:

Web servers: boinc, srv1, srv2, srv3, srv4, srv5 (upload and download servers)


boinc is load balanced among the srv web servers. The srv servers handle uploads and downloads.

Looks good so far, but could you also add the status of all those servers to help us tell when to expect upload and download problems?
23) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 81448)
Posted 15 Apr 2017 by Profile robertmiles
Post:
Could you modify your Server Status web page to show which of the server programs handle uploads and downloads?
24) Message boards : Cafe Rosetta : BMAA, Alzheimer\'s, Parkinson\'s, and ALS (Message 81207)
Posted 21 Feb 2017 by Profile robertmiles
Post:
I just found that Brichos is a family of molecules, not just one.

Some articles that may name the most important type:

(title will not copy and paste)
BCJ article

Molecular inhibitor breaks cycle that leads to Alzheimer’s
Molecular inhibitor breaks cycle that leads to Alzheimer’s

High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C.
High-resolution structure of a BRICHOS domain

BRICHOS Domains Efficiently Delay Fibrillation of Amyloid β-Peptide*
BRICHOS Domains Efficiently Delay Fibrillation of Amyloid β-Peptide

Molecule could protect against Alzheimer\'s disease
Molecule could protect against Alzheimer\'s disease

Brichos protein may prevent brain damage in Alzheimer’s
Brichos protein may prevent brain damage in Alzheimer’s
25) Message boards : Cafe Rosetta : BMAA, Alzheimer\'s, Parkinson\'s, and ALS (Message 81206)
Posted 21 Feb 2017 by Profile robertmiles
Post:
Alzheimer\'s researchers find molecule that delays onset of disease
Guardian.article

Could the Rosetta@Home researchers interested in Alzheimer\'s check whether the 3D structure of the Brichos molecule is ready to use, and if not, add it to the list of molecules for structure investigation?
26) Message boards : Cafe Rosetta : BMAA, Alzheimer\'s, Parkinson\'s, and ALS (Message 80996)
Posted 11 Jan 2017 by Profile robertmiles
Post:
Most of the site is accessible only from within Sweden. However, I was able to access enough to use Google Translate to get this summary:

Paul Alan Cox, professor and director of the Institute for ethnomedicine in Wyoming, USA, shows one of the winners of the Earth\'s climate is getting warmer, namely the cyanobacteria. They like the heat, increasing in number and produce a neurotoxin called BMAA. This toxin is now suspected in turn cause including ALS and Alzheimer\'s disease in humans. Preferring Gets Title: Climate change, biodiversity and human health. Moderator: Henrik Ekman. Organizers: King Carl XVI Gustaf\'s 50th årsfond for Science, Technology and Environment, Royal. Agriculture and Forestry Academy, Royal Academy. Sciences, Engineering Sciences and the Confederation of Swedish Enterprise. From the arrangement Faith in the Future held in the Bernadotte Library at the Royal Palace March 22, 2012.


Some articles that seem relevant (some appear to be research papers, some written for the public):

Algae bloom toxin linked to Alzheimer\'s, other diseases
http://www.cbsnews.com/news/algae-bloom-toxin-linked-to-alzheimers-and-other-neurodegenerative-diseases/

Secrets to Alzheimer\'s, ALS and Parkinson\'s Disease: Dr. Paul Alan Cox at TEDxJacksonHole
https://www.youtube.com/watch?v=7jWi6WQQ9wo
You can skip the ad before the video.

New research offers hope for Alzheimer’s patients
http://www.jhnewsandguide.com/news/health/new-research-offers-hope-for-alzheimer-s-patients/article_ab9326a2-ddaf-53bf-84cd-9fe814f3fb19.html

The Emerging Science of BMAA: Do Cyanobacteria Contribute to Neurodegenerative Disease?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295368/

Dietary exposure to an environmental toxin triggers neurofibrillary tangles and amyloid deposits in the brain
http://rspb.royalsocietypublishing.org/content/283/1823/20152397

Research points to pond scum connection for ALS, Alzheimer’s diseases
http://www.mypalmbeachpost.com/lifestyles/health/research-points-pond-scum-connection-for-als-alzheimer-diseases/O23lvN1VdNFoxOBPGt86hI/

Could environmental toxins trigger amyloid plaques in the brain? An interview with Dr Paul Alan Cox
http://www.news-medical.net/news/20160314/Could-environmental-toxins-trigger-amyloid-plaques-in-the-brain-An-interview-with-Dr-Paul-Alan-Cox.aspx

Environmental toxin linked to dementia, study shows
https://www.washingtonpost.com/local/social-issues/environmental-toxin-linked-to-dementia-study-shows/2016/01/19/e78b7ac4-bef7-11e5-83d4-42e3bceea902_story.html?utm_term=.907f2b7cabaa

Tangles and Toxins: An interview with Dr Paul Alan Cox
http://www.hurondigitalpathology.com/resource/tangles-toxins-interview-dr-paul-alan-cox/


Mentions vervet monkeys as an animal model for such research.

Does not appear to mention whether l-serine has been tried enough on humans to decide whether it offers humans any help with these conditions.
27) Message boards : Cafe Rosetta : On the way to gene editing without causing cancer (Message 80970)
Posted 2 Jan 2017 by Profile robertmiles
Post:
A simple guide to CRISPR, one of the biggest science stories of 2016

Inserting a new gene at a random point in the old genes is known to give a significant risk of cancer about ten years later. This gives a way to control where it is inserted, and therefore avoid the risk of causing cancer.
28) Message boards : Number crunching : This New Biomarker Can Help Predict Alzheimer's Disease In Patients (Message 80968)
Posted 2 Jan 2017 by Profile robertmiles
Post:
This New Biomarker Can Help Predict Alzheimer's Disease In Patients
29) Message boards : Rosetta@home Science : Rosetta@home Research Updates (Message 80805)
Posted 30 Oct 2016 by Profile robertmiles
Post:
Research Update:

We recently published an article in Nature titled "Accurate de novo design of hyperstable constrained peptides". We would like to thank all Rosetta@Home participants for their help with this work. In the paper, we present computational methods for designing small stapled peptides with exceptional stabilities. These methods and designed peptides provide platform for rational design of new peptide-based therapeutics. Constrained (stapled) peptides combine the stability of conventional small-molecule drugs with the selectivity and potency of antibody therapeutics. Ability to precisely design these peptides in custom shapes and sizes opens up possibilities for "on-demand" design of peptide-based therapeutics.

Other developments describe in the paper:

1) We can now accurately design 18-47 amino acid peptides that incorporate multiple cross-links.
2) We can now design peptides that incorporate unnatural amino acids. Specifically, we designed peptides with a mix of natural L-amino amino acids and D-amino acids (mirror images of L-amino acids). D-amino acids tend to provide better protease resistance and lower immunogenicity; both of which are desired properties in a therapeutic peptide. Unnatural amino acids also let us sample much more diverse shapes and functions.
3) We can now design peptides that are cyclized via a peptide bond between their N- and C-terminus. Cyclic peptides provide increased resistance against exopeptidases as they have no free ends, and thus are ideal candidates for engineering peptide therapeutics.

We are now working to use these computational methods for designing peptides that target therapeutically relevant targets, such as, enzymes that impart antibiotic resistance in pathogenic bacteria.

Structure prediction runs on Rosetta@Home for these designed peptide models played a key role in selection of good designs that were experimentally synthesized and characterized. So, thanks a lot to all of you for your help in making this work possible.


Gaurav, do any of those new peptides include BMAA? That amino acid is normally found only in blue-green algae and in cyanobacteria, but has also been found in the brains of many Alzheimer's victims. Look for papers on recent Nobel prizes if you need more details.
30) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80783)
Posted 26 Oct 2016 by Profile robertmiles
Post:
[snip]

some of the simulations being run on R@H can complete in just a few days

DAYS? For one work unit? I've never read anywhere if the researchers prefer a long run-time-per-WU over a short run-time-per-WU so I've always (7 years now) had my preferences set to shorter WUs.
Thanks for the input Timo, I appreciate it.

I've read that they wanted longer workunits selected as a way to reduce the load on the server. I haven't seen whether they changed their minds on that, though.
31) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80782)
Posted 26 Oct 2016 by Profile robertmiles
Post:
Please, stop all "2xa0_Xcdp_" wus....


It might be more effective to give a reason why.
32) Message boards : Cafe Rosetta : Researchers identify brain cell 'executioner' (Message 80725)
Posted 9 Oct 2016 by Profile robertmiles
Post:
Researchers identify brain cell 'executioner'
http://www.upi.com/Health_News/2016/10/07/Researchers-identify-brain-cell-executioner/1291475848105/?spt=mps&or=4&sn=hn

Relevant to, for example, Alzheimer's.
33) Message boards : Cafe Rosetta : Breakthrough !? A 1000 cores low power processor are invented (Message 80724)
Posted 9 Oct 2016 by Profile robertmiles
Post:
http://www.zdnet.com/article/say-hello-to-the-worlds-first-1000-core-chip-that-runs-off-an-aa-battery/

Cruwl thing, but where can we will get that, have it disc or something else,
never a x86 architecture i think.

Greets, just spreding the news ;)

Looks suitable for running applications that don\'t require enough memory to need any separate memory chips. The clock speed given in that article is over 100 GHz for each core, and if that is accurate, none of today\'s memory chips are fast enough to avoid leaving most of the cores idle most of the time.

But where are you going to find useful applications small enough to run without any separate memory chips?
34) Message boards : Number crunching : GPU computing (Message 80723)
Posted 9 Oct 2016 by Profile robertmiles
Post:

There is really no way that scientists have to wait hours or even days for their computation results. Personally, I hope BOINC will die because it's a kludge.


I hope not.
If it is "kludge", why you are here?


Because I want to help. That's why.

One of the problems is the heterogeneous architecture of rosetta@home: There are PCs, Macs and tablets/smartphones (seriously?). Why not an internet-connected dual-core toaster?

There are a lot of issues with these devices and this is IMHO a waste of developer resources.

A homogeneous architecture based on AVXx would alleviate all those problems while yielding a higher performance.

The distributed nature of rosetta also introduces latencies: preparing work, zipping it, sending it and collect the results back over a WAN. Being forced to deal with ultra-lame ancient CPUs and the like are another problem.

So you want far fewer processors to be used? None of my computers use a CPU that even has AVXx available, and not enough money is available to replace all the computers available through BOINC with equivalents that have AVXx available. It would be possible, though, to produce separate compiles of the application for computers with AVXx and computers without, and add a shell program that tests what the CPU has available, then starts only the version of the program best for the current CPU.
35) Message boards : Number crunching : GPU computing (Message 80722)
Posted 9 Oct 2016 by Profile robertmiles
Post:
I can't fathom the computing knowledge you need for something like Rosetta. Or anything useful for that matter... I just got into learning Python (I figured an EE should know a good bit of programming) and I'm struggling like mad. MATLAB is the only language I'm proficient at, but it's so user friendly it doesn't count IMO.


If i remember correctly, the public test of rosy on gpu was with and old version of pycl

This is the post one developer wrote about this test. It's a pity that pdfs are not longer available

I've used Fortran for several years, and have taken classes in C++ and CUDA since then. Is any help needed for translating any remaining Fortran code to C++?

I would not be able to travel for this.

I'm still looking for an online OpenCL class aimed at GPUs rather than FPGAs. A CUDA version would work on most Nvidia GPUs, but not on other brands. An OpenCL version should work on other brands of GPUs.

A GPU version REQUIRES that most of the application allows many threads to run in any order, or even at the same time, since they don't use anything produced by the other threads. If this is not satisfied, the GPU version may be as slow as a quarter of the speed of the CPU version.
36) Message boards : Number crunching : GPU computing (Message 80721)
Posted 9 Oct 2016 by Profile robertmiles
Post:
I\'ve just been looking at the performance of the new GTX1080 and for DOUBLE precision calculations it does 4 Tflops!!!! For comparison a relatively high performance chip like an overclocked 5820K will do maybe 350GFlops. So we are talking an order of magnitude difference. In addition the Tesla HPC version will probably be double that at 8 TFlops. (Edit: Looks like it is actually 5.3TFlops) The Volta version of the gtx1080 (next gen on, due in about 18 months time) is rumoured to be 7TFlops FP64 in the consumer version.

There is no way that conventional processors can keep up with that level of calculation. At what point does the gap between serial CPU and parallel GPU have to be before the project leaders decide they can not afford NOT to invest in recoding to parallel processing? Because by 2 years time, HPC GPUs will be around 35 times faster than CPUs. How much will it cost to rewrite the code, $100-150K maybe?? Isn\'t that worth paying for such a huge step up?

With that kind of performance increase, you can make calcs more accurate. You no longer have to use approximations like LJ potentials, you can calculate the energy accurately and get a better answer in a quicker time than now. Whats not to like?

It seems like so many projects, everyone is comfortable with what they are doing now. Revolution has been forsaken for evolution. Understandable, but the best way to do things?

Be bold and take the leap!

More computing performance is not a good answer if the limit comes from available memory limits rather than from computing limits. Rosetta@Home has already looked into GPU versions, and found that they would require about 6 GB of graphics memory per GPU to get the expected 10 times as much performance as for the CPU version. The GPU version would run each workunit at about the same speed as the CPU version, and would therefore need to run 10 workunits at the same time, using 10 times as much memory, to get 10 times as much performance.

Rather few of the high-end graphics boards have that much memory.
37) Message boards : Cafe Rosetta : Another suspected cause for Alzheimer's (Message 80600)
Posted 7 Sep 2016 by Profile robertmiles
Post:
Air Pollution Leaves Significant Traces Of Magnetic Metals In Your Brain

air-pollution-magnetic-particles_us
38) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80587)
Posted 1 Sep 2016 by Profile robertmiles
Post:
This is my second post on this issue. I have two desk top computers. One has 8 processors the other four. For Some reason...you program refuses to send my 4 processor computer any work. So until you can tell me what I\'m doing wrong.. I\'ll just go to another project, which is a shame since I enjoy working with Rosetta@home I\'ll leave it to you to figure out what is going wrong.

John Yeatts


Not enough information to tell much. You need to show more of your settings for those computers, both the settings on the computers and the settings on the server. Be sure to include the amount of memory BOINC is allowed to use on each computer, and the amount of memory that is installed.
39) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80581)
Posted 31 Aug 2016 by Profile robertmiles
Post:
Hello, is it normal to get a couple of tasks with \"Validate Error\"? Is it an issue on my end? I\'ve had 10 of them in the past 4 days or so.

Here\'s a few:
869154381
868770993
868649273

Thanks.


Not a problem I\'ve seen before, on any project. It could mean a problem with the validator, rather than anything on your computer.
40) Message boards : Cafe Rosetta : A protein that might help stroke recovery (Message 80559)
Posted 24 Aug 2016 by Profile robertmiles
Post:
This article names a protein that might help recovery from strokes. Could someone at Rosetta@home check if there has been enough work to determine the 3D structure of this protein?

Mouse Study Suggests Stem Cells May Reverse Stroke Damage
https://consumer.healthday.com/cardiovascular-health-information-20/misc-stroke-related-heart-news-360/mouse-study-suggests-stem-cells-may-reverse-stroke-damage-714075.html

This still needs tests to determine if it also works in humans.
Looks unlikely to help recover memories lost in strokes, but may recover the ability to form those memories.


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