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Computing a Cure For HIV

Soulskill posted about 4 months ago | from the petaflops-for-science dept.

Supercomputing 89

aarondubrow writes: The tendency of HIV to mutate and resist drugs has made it particularly difficult to eradicate. But in the last decade scientists have begun using a new weapon in the fight against HIV: supercomputers. Using some of the nation's most powerful supercomputers, teams of researchers are pushing the limits of what we know about HIV and how we can treat it. The Huffington Post describes how supercomputers are helping scientists understand and treat the disease.

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Bitcoin mining? (3, Interesting)

Anonymous Coward | about 4 months ago | (#47289207)

Imagen if all that computer power was put to use such as finding the cure of HIV.... We would be done by lunch time.

Re:Bitcoin mining? (-1)

Anonymous Coward | about 4 months ago | (#47289247)

This is brought up all the time. If you don't have a new suggestion for how to have verifiable proof of work that is also useful, then shut up

Re:Bitcoin mining? (5, Insightful)

Anonymous Coward | about 4 months ago | (#47289261)

It isn't lack of computing power that is holding back most theoretical biophysics research.. it's the lack of people who have the rare combination of skills of a programmer, mathematician, chemist, biologist and drug engineer coming up with novel and unique ideas to combat disease who will sacrifice industry paychecks to work in academic fields.

Re:Bitcoin mining? (0)

Anonymous Coward | about 4 months ago | (#47289343)

Exactly this!

Re:Bitcoin mining? (2)

cashman73 (855518) | about 4 months ago | (#47289367)

who will sacrifice industry paychecks to work in academic fields.

Why do researchers have to sacrifice an industry paycheck to do it? In other words, why won't industrial pharma hire more talented scientists. They seem instead to be more interested in hiring salespeople, lawyers and MBAs, then contracting with academia so they can take advantage of "cheap labor" due to the overabundant supply of low-paid graduate students and post-docs. But then they wonder why the amount of NDAs (New Drug Applications) has been declining.

Re:Bitcoin mining? (4, Insightful)

gnupun (752725) | about 3 months ago | (#47289433)

Why do researchers have to sacrifice an industry paycheck to do it? In other words, why won't industrial pharma hire more talented scientists. They seem instead to be more interested in hiring salespeople, lawyers and MBAs...

Perhaps, it has something to do with the high failure rate of such research. Would you pay a salary to 1000 employees, of which only one employee gives you solid results and the remaining fail? That's not very business friendly. This type of research is more feasible under govt. grants.

Re:Bitcoin mining? (5, Insightful)

bmo (77928) | about 3 months ago | (#47289655)

Perhaps, it has something to do with the high failure rate of such research. Would you pay a salary to 1000 employees, of which only one employee gives you solid results and the remaining fail?

>implying that this is bad

Typical bean-counter/MBA attitude.

That's not very business friendly.

Companies like HP, Xerox, etc, built empires on that kind of research.

They declined when they spun off or closed their research divisions because management failed to see the value/use the output of the research labs. The HP example is particularly striking - they went from an advanced technology company to a schlock printer seller, one that is sneered at and loathed, in a handful of years. Xerox is also striking in that PARC laid the foundation for a lot of modern computing but management only saw money to be made in copiers and filing paper and thusly ignored most of PARC's output, ceding the computer revolution to other companies.

It is also part of a larger problem. Because of the emphasis on short-term profits (quarters are too long!) at the expense of everything else, we in the West are so enthusiastic at shoving all our production to the Chinese and others saying "We can't be arsed to get our hands dirty; we want to just do the high-level stuff like design and company management" totally ignoring the fact where the production goes, so does the engineering development, science research, and eventually even upper-management. This was learned by Samuel Slater, Francis Cabot Lowell, and others who founded the "silicon valley" (Blackstone Valley) of the Industrial Revolution. A lesson forgotten through complacency, greed, and snobbery.

Alexander Graham Bell is shouting at you from his grave calling you a moron.

--
BMO

Re:Bitcoin mining? (1)

Anonymous Coward | about 3 months ago | (#47289793)

Typical bean-counter/MBA attitude.

And who do you think makes those decisions?
Research only gives a pay off for the next CEO. Fuck that guy. It's much better to downsize everything, cut down costs and jump with a golden parachute and repeat the formula elsewhere.

Industry doesn't wants theoretical results that might be useful ten years from now. They want results for this quarter. So while they do invest in crazy ideas, small improvements is more their thing. It goes the other way around for academicals: even if it isn't a viable solution right now, you can publish it and in ten years or a century either it will be forgotten or someone will do something incredibly clever with it.

Re:Bitcoin mining? (0)

Anonymous Coward | about 3 months ago | (#47290471)

Surely the short term implication of this borderline sociopathic trend is stagnation, with long term implications of market loss and ultimately business closure.

Re:Bitcoin mining? (1)

pepty (1976012) | about 4 months ago | (#47291061)

Research only gives a pay off for the next CEO. Fuck that guy.

But the stock price moves based on the latest clinical trial results and letters from the FDA. What's a CEO to do?

ILOS: in license, out source. It's much faster to buy a promising drug candidate (in license) then to herd your own to phase II. It may also be less risky. Hence Valeant trying to buy Allergan. For your remaining pipeline outsourcing R &D to contract labs can cut your R&D budget nicely, and it's the investors looking at R&D spending as a black hole into which their money disappears that makes the CEO nervous. Though you will also lose all of the insight and acumen accumulated by the specialists you laid off when you closed that department.

You can also try lots of management tricks: give everyone metrics to measure up to so that they always look busy, the pipeline looks full, the competition creatively destructed. Just don't tell anyone the truth: the candidates you are advancing are actually shit, but you have to advance some to keep your bonus. Hey, that sort of thing worked for the Veterans Administration, should work fine for pharma.

Re:Bitcoin mining? (1)

X0563511 (793323) | about 4 months ago | (#47291973)

They might try not publicly trading. There's no shareholders to yank your leash around. Don't jump into the pool if you don't want to get wet.

Re:Bitcoin mining? (1)

pepty (1976012) | about 4 months ago | (#47293299)

Shareholders are hard to avoid. A new drug approval might cost just $200M (Optimer's Dificid), but on average companies are racking up ~$4B in R&D per new drug. (by new drug I mean new molecule, not new dose/formulation/indication for an old one). If you take venture capital they will be looking for a payout well before a drug is approved, probably by either selling the company or its ideas to a big pharma. Keeping it closely held has worked in the past - but you may need vasty deep (10 figure deep) pockets willing to stay the course for a decade.

Re:Bitcoin mining? (1)

pepty (1976012) | about 4 months ago | (#47290845)

Companies like HP, Xerox, etc, built empires on that kind of research.

Tech research is a lot less risky and has a much shorter wait til revenue then Pharma/Biotech (these days).

Re:Bitcoin mining? (0)

Anonymous Coward | about 4 months ago | (#47291075)

A.G. Bell, second only to Edison, patent dealers. Not inventors...

Re:Bitcoin mining? (1)

Bite The Pillow (3087109) | about 4 months ago | (#47291815)

You rolled all of R&D into one pile, so horseshit.

Drug R&D is way different from tech R&D. Microsoft is sitting on billions of unmonetized discoveries. They could, if they converted 10% of the non-operational Microsoft Research into marketable assets, push Apple off the map.

In comparison, look at the price for a cure for HCV. $100 per pill, or $90,000+ in total. It seems to be a solved problem, and not one of those things where big pharma hides a cure because long-term treatment is financially more beneficial.

If you want to attack big pharma, the number to argue is the advertising to cost, or advertising to research dollar amount. Not arguing unrelated numbers pulled out of your ass.

You accused me of being a troll my first post, because you apparently disagreed with me. After pointing out multiple flaws in your reasoning, you are officially a troll. Maybe unintentionally, out of either ignorance or stupidity, but nevertheless you have a hook upon which you post some faith, and with which you intend to catch respondents. Troll under the bridge, troll on a boat, same same bmo.

Re:Bitcoin mining? (1)

currently_awake (1248758) | about 4 months ago | (#47290723)

This is the reason that most major medical research is done by government grant (historically). Big pharma companies like to tell everyone they are the solution but really they are only the endpoint in the process.

Re:Bitcoin mining? (1)

pepty (1976012) | about 4 months ago | (#47290911)

Year in, year out, 75-80% of new drugs are invented privately in biotechs/pharma. The remainder are invented by academia. In terms of money and sheer manpower required to get from "what causes this disease?" to "new drug approval" the pharma/biotech portion often isn't the short end of the stick either.

Re:Bitcoin mining? (1)

the gnat (153162) | about 4 months ago | (#47291507)

Year in, year out, 75-80% of new drugs are invented privately in biotechs/pharma. The remainder are invented by academia.

Correct; what government grants pay for is the majority of the basic research that informs efforts to find a cure. Naturally, private companies are (mostly) free to use this information when searching for new drugs - this is part of the point of federal funding for basic research. The vast majority of that research won't directly lead to a cure, of course, but it does contribute to our overall knowledge of biomedicine. In contrast, I've heard the drug development process at some companies compared to "piling up stacks of money and setting it on fire", which is why I'm really, really glad the universities and governments don't try to get deeply into the drug development business.

Re:Bitcoin mining? (1)

pepty (1976012) | about 4 months ago | (#47293375)

In contrast, I've heard the drug development process at some companies compared to "piling up stacks of money and setting it on fire", which is why I'm really, really glad the universities and governments don't try to get deeply into the drug development business.

Lots of folks express that exact feeling about the NIH's efforts to get into translational medicine, which is establishing centers to do preclinical and clinical development. I'm pretty sanguine about that too. I could see some payouts happening though even if not many new drugs get made: 1, having publicly funded (and disclosed) research into how to conduct pharma R&D might improve the whole industry; 2, a stable funding source could allow really, really long clinical trials, which could be critical for areas like dementia; 3, an extra carrot for orphan disease drugs in addition to the ones supplied by the FDA.

Re:Bitcoin mining? (1)

SuricouRaven (1897204) | about 3 months ago | (#47289699)

Industry does do a lot of research. There's money to be made in curing HIV, after all. They do shy away from the purely theoretical though, because there's no money to be made if you don't get a patentable drug at the end of it.

Re:Bitcoin mining? (1)

pepty (1976012) | about 4 months ago | (#47290923)

You don't always need a patentable drug, just FDA exclusivity. If you find a new indication for an old generic drug and do the research to back it up you can get market exclusivity for a while and charge out the wazoo for it.

Re:Bitcoin mining? (1)

sillybilly (668960) | about 4 months ago | (#47292843)

The true cure of HIV is a genetic mutation in a human, with HIV resistant genes. The highest likelihood of such a mutation emerging is in an area ravaged by HIV deaths, such as South Africa. If HIV doesn't really cause death (i.e. does not really increase mortality) then it's not really a disease worth mutating against. There are probably a gazillion kinds of bacteria and viruses that live in you, that do nothing special, and these HIV FUD (fear, uncertainty, doubt) spreading people will use one of these standard viruses, and call it the AIDS virus. By the way it's extrememly, extremely difficult, if not impossible, to properly select and filter for a virus - a sodium bloodtest is easy, so is low molecular weight stuff like sugars, etc, but fishing out a virus, staining it with a dye under an electron microscope (because it's too small for optical microscopes, and the electric microscope requires a gold or osmium tetroxide gas layer coating and even then it vaporizes the metal as the electron beam scans, so you can't really dye a metal coating like you can dye the naked virus), then calling it HIV after you stained in with 8 different dies giving you a yes no answer (i.e. 256 bits, as in there are only 256 different viruses out there.) (Notice my recent love of grammatically incomplete/incorrect sentences lacking a verb.) Going for DNA fragment special short chain combination abundance (such as ACTGCTCAACTGACG, a couple of these fingerprint markers specific to each virus) might work, but it's hard to accurately chop DNA to sticks of say 22 units each, and not fully disassemble it to just A, C, T, G, and even then there is a lot of noise, because all life on the planet is based on DNA, and all DNA is made of 2 bit(i.e. 4 variations, 8 bit having 256 variations, and 1 bit 2 variations) A, C, T, G units.

Re:Bitcoin mining? (1)

SuricouRaven (1897204) | about 4 months ago | (#47293997)

I'm trying to figure out what you are saying, but I find your post rambling and self-contradictory.

The test for HIV doesn't use an electron microscope. It's a form of the ELISA test, using specific antibodies that attach only to HIV. Are you trying to claim that HIV is actually harmless, or accusing scientists of fabricating the tests where no virus exists? Because either way, there are about 35 million corpses that disagree with you.

Re:Bitcoin mining? (0)

Anonymous Coward | about 4 months ago | (#47300133)

"specific antibodies that attach only to HIV"

No such antibody exists for any antigen.

Re:Bitcoin mining? (1)

ToddInSF (765534) | about 4 months ago | (#47294125)

You know, I keep hearing that HIV has "ravaged" all these places in Africa, based on WHO estimates of infection, yet when I look at the population growth numbers it just does not add-up.

I remember back in the 90's Oprah saying how HIV would impact straight America profoundly, yet none of that came true either.

If HIV is half the threat we've always been told it is, we should have seen some pretty serious widespread population impact by now. Obviously that never happened, is not going to ever happen, and what we've been told is not true.

But go ahead and keep ignoring the facts and keep repeating the bullshit, people that don't have HIV that draw a paycheck by inflating numbers and misleading the public and diverting resources are relying on it.

Re:Bitcoin mining? (1)

Admiral_Grinder (830562) | about 4 months ago | (#47298519)

So do you have a control group to present to us that didn't buy into the HIV bullshit?

One of the earliest public cases of HIV was a elementary school kid in Indiana that got it through a blood transfusion. That helped push for higher standards in blood donations. It also pushed for higher standards in dealing with spilled bodily fluids. Before all this though the general public thought was only a STD that the gay community passed around.

Remember that real bullshit is pretty green grass before being consumed. Without the widespread focus on preventing these diseases it may have been twice as a bad as predicted. It only looks like bullshit today because of the hidden effort to reduce the damage doesn't get presented to (or ignored by) the public which only remembers the hysteria. Same goes for Y2K bug, global warming, and general pollution

Re:Bitcoin mining? (0)

Anonymous Coward | about 4 months ago | (#47304249)

What do you mean it doesn't add up? HIV infections can lie dormant for years, so people have time to reproduce even if infected. Furthermore, so long as fertility rates are even higher, high death rates in populations will not lead to overall population decreases. Are you defining "ravaging" specifically as a population drop, rather than simply a lot of deaths and the attendant social consequences? You talk about "if HIV is half the threat we've been told," but you don't mention any specific claims, so you aren't really adding anything to the discussion.

Re:Bitcoin mining? (1)

ToddInSF (765534) | about 4 months ago | (#47304261)

I was very specific in stating that none of the estimates and projections are ever accurate.

If you have a problem with that, take it up with the organizations making the inflated estimates and predictions.

I'm not playing the bullshit game of accepting demands to disprove something that's already well documented.

Pull your own head out of your ass, anon.

Re:Bitcoin mining? (1)

dcollins117 (1267462) | about 4 months ago | (#47290973)

Why do researchers have to sacrifice an industry paycheck to do it? In other words, why won't industrial pharma hire more talented scientists.

There is more money in treating a medical condition than in curing it. Once a disease is cured, there is no need to take expensive medications anymore. The financial incentives for both doctors and pharmaceutical companies is to keep a patient in treatment for as long as possible.

Re:Bitcoin mining? (1)

the gnat (153162) | about 4 months ago | (#47291571)

There is more money in treating a medical condition than in curing it.

Not for the insurance companies or government, there isn't. And given the immense cost of long-term treatment for many conditions, pharma companies would be able to charge much more for a drug that completely stopped a disease.* In reality, the reason most medications merely treat rather than cure diseases is that actually eliminating the root cause of a disease without debilitating side effects, for instance death of the patient, is usually really fucking hard.

(* For instance, the common cold is estimated to be a $40 billion per year drain on the US economy. This suggests that if a drug company could come up with a cure, they would be fabulously rich. Every time I get a cold, my employer loses hundreds of dollars in lost productivity; a $100 pill that returned me to work after a day would be a huge savings, far more effective than $10 of Nyquil.)

Re:Bitcoin mining? (1)

Anonymous Coward | about 3 months ago | (#47289753)

And yet, many people do just that - when given a choice between doing good for humanity and making money, they choose to do good.
It's almost weird.

Re:Bitcoin mining? (0)

Anonymous Coward | about 3 months ago | (#47290511)

It's often because they believe their invisible sky fairy is going to reward them for their selfless actions, thus rendering their selfless action as a self-interested one, nullifying their good deeds as they're simply doing it to get a reward.

Re:Bitcoin mining? (0)

Anonymous Coward | about 4 months ago | (#47294589)

You do not know any actual scientists. If you did, you would know a very great many are atheists and are working for altruistic reasons

Re:Bitcoin mining? (-1)

Anonymous Coward | about 3 months ago | (#47290017)

BS. That's not the reason. It's because the Republicans won't let them work on that research. Their hero Raygun claimed GRIDS (yes, he constantly spouted that hateful word) didn't exist, and claimed that only gay people got it thus the reason Republicans today still call it GRIDS. They're not smart enough to understand that simultaneously claiming something doesn't exist and claiming only gays get it is illogical, but that is the way of their kind. They claim it doesn't exist then they fight to stop research. They don't want a cure. They're making too much money from treating the symptoms.

Re:Bitcoin mining? (1)

the gnat (153162) | about 4 months ago | (#47291611)

It's because the Republicans won't let them work on that research.

The National Institutes of Health - the single largest government sponsor of biomedical research in the world - spends
approximately $3 billion per year on AIDS research [nih.gov] . That's about 10% of their entire budget. In comparison, they currently spend about $5.5 billion per year on cancer, which affects vastly more Americans than AIDS, and also kills more in wealthy countries (because AIDS patients - or their insurers - can afford the treatments that enable long-term survival with low viral load). Due to federal budget issues, both funding pools have declined since 2010, but AIDS research only slightly - cancer funding is significantly lower.

As for treating the cure versus the symptoms, it is extraordinarily difficult to "cure" viral infections with drugs, and HIV has proven to be incredibly difficult to vaccinate against.

Re:Bitcoin mining? (1)

ToddInSF (765534) | about 4 months ago | (#47294091)

Given the extraordinary amounts of money dumped into HIV/AIDS research every year, for decades, the huge numbers of researchers involved globally, and the simply massive amount of published research, when you take it all in and look at it with a degree of curiosity and attempt to compare all this with other historically similar phenomenon...

Well, that's the problem. It's not really like anything else.

Sometimes what is needed isn't more people or money or research. Sometimes one is compelled to look at the reality and ask what is wrong with this picture, and if there needs to be an entirely new paradigm developed, because the results one would expect given the resources dumped into this one just are not there.

Re:Bitcoin mining? (1)

the gnat (153162) | about 4 months ago | (#47295287)

the results one would expect given the resources dumped into this one just are not there.

I don't know, what kind of results do you expect? HIV is a really tough bug to fight - it's almost the opposite of smallpox where a universal and exceptionally effective vaccine was found early on. Tricking the immune system into killing a virus that is evolved to prey on the immune cells was never going to be easy. But the leading antiviral therapies allow most infected patients to live almost indefinitely while maintaining relatively high quality-of-life, whereas 30 years ago they would nearly all have been doomed (and some of the earlier therapies were debilitating). I consider that a pretty impressive achievement of medical technology.

Now, the fact that millions of Africans (and others) still have AIDS is less impressive, but the reasons for that are entirely social and political, not technological.

Re:Bitcoin mining? (1)

ToddInSF (765534) | about 4 months ago | (#47295499)

"But the leading antiviral therapies allow most infected patients to live almost indefinitely while maintaining relatively high quality-of-life"

That's a pretty neat trick right there, I'm not aware of any drug which makes that possible !

Nothing about HIV makes any sense, outside of the political and financial aspect of it. That's the point.

Re:Bitcoin mining? (1)

pepty (1976012) | about 4 months ago | (#47290895)

Sort of. Basically we need someone to invent a force field (mathematical model) that can simulate proteins, protein-substrate interactions, and protein-protein interactions so well that it can make accurate and useful de novo predictions about drug candidates and disease models. After that we've got plenty of med chemists, structural biologists, etc., ready to make use of it.

Re:Bitcoin mining? (1)

the gnat (153162) | about 4 months ago | (#47291477)

it's the lack of people who have the rare combination of skills of a programmer, mathematician, chemist, biologist and drug engineer coming up with novel and unique ideas to combat disease who will sacrifice industry paychecks to work in academic fields.

Guess what: there are vastly more jobs like this available in academic groups than in industry. (I know this firsthand, because I work in a related field and am basically stuck in academia unless I can change careers somehow.) The bigger problem is that given the limitations of the simulations and our knowledge of human biology, there is still a huge leap from docking results or MD simulations to working drugs. Effective in silico is light years away from effective in vivo.

Re:Bitcoin mining? (-1)

Anonymous Coward | about 4 months ago | (#47289337)

Typical, the big government crowd on on ./ is always so rah-rah about statist solutions. I mine Bitcoin in a network with freedom-loving peers of my choosing because it allows me to support my family, and it provides a form of income that can be hidden from the state, which wants to put a gun to every American's head and take away their hard-earned money in the name of wealth redistribution.

If you want supercomputer or distributed-computing solutions to find a cure for HIV, you need to make a business case for your project like everyone else. Let the free market work this out.

Re:Bitcoin mining? (0)

Anonymous Coward | about 4 months ago | (#47290673)

You mean like how the free market solved Microsoft's abusive monopoly? (Tip: they still have an abusive monopoly.) Or how the free market solved cancer?

The only things the free market seems to be capable of solving is how come the laws don't allow big business to collect data on behalf of the government, and how come the laws don't let business take money from the poor just because they can. It certainly doesn't create freedom, unless you believe "freedom to spend everything you earn just to survive" to be freedom.

Re:Bitcoin mining? (0)

Anonymous Coward | about 3 months ago | (#47289437)

You still have to know what to figure out and that comes from empirical observation and the people who have some ideas.

Re:Bitcoin mining? (0)

Anonymous Coward | about 3 months ago | (#47289465)

My last reply was deleted and/or didn't show up. Strange.

The issue isn't just computing power. There needs to be ways to eliminate it, hinder it, block it, etc and possible solutions. Computing power only comes into play when there is a requirement for solutions that are easily automated.

Re:Bitcoin mining? (1)

fuzzyfuzzyfungus (1223518) | about 3 months ago | (#47289951)

Is computational biology really looking to compute a lot of SHA hashes?

/Very/ different hardware (2)

gentryx (759438) | about 3 months ago | (#47290013)

Computational drug design and bitcoin miners have in common that both run best on custom hardware. The crux is, that both require very different types of hardware. As an example, please refer to Anton [wikipedia.org] , designed by DE Shaw Research exactly for molecular dynamics (MD) codes.

Bitcoin mining is classified as a so called embarrassingly parallel algorithm, while MD is a tightly coupled problem. Hence an efficient parallelization for MD codes is much harder to speed up: communication gets in the way, and communication is essentially always bound by the speed of light.

ps: fun fact: bitcoin mining and MD can be carried out (at least somewhat) efficiently on GPUs.

Re:/Very/ different hardware (1)

loufoque (1400831) | about 4 months ago | (#47300061)

It's not that specialized. It's just plenty of DSPs strapped together on a torus.
Unlike what wikipedia claims, you could probably achieve comparable performance using a more classical and general-purpose supercomputer setup with GPU or Xeon Phi accelerators, provided the network topology is well tuned to address this sort of communication scheme (most recent supercomputers don't use tori)

Yesno? (1)

gentryx (759438) | about 4 months ago | (#47300321)

It's not that specialized. It's just plenty of DSPs strapped together on a torus.

Actually Anton uses ASICS, their cores are specially geared at MD codes. This goes way beyond just "strapping together DSPs". They have IIRC ~70 hardware engineers on site. (Source: I've been to DE Shaw Research last year).

Unlike what wikipedia claims, you could probably achieve comparable performance using a more classical and general-purpose supercomputer setup with GPU or Xeon Phi accelerators, provided the network topology is well tuned to address this sort of communication scheme

No, you can't, and here is why: Anton is built for strong scaling of smallish, long running simulations. If you ran the same simulations on a "x86 + accelerator" system (think ORNL's Titan) then you'd observe two effects:

  • The GPU itself might idle a lot as each timestep only involves few computations, leaving many shaders idle or waiting for the DRAM.
  • Anton's network is insanely efficient for this use case. IIRC it's got a mechanism equivalent to Active Messages, so when data arrives, the CPU can immediately forward it to the computation which is waiting for it. That leads to a very low latency compared to a mainstream "InfiniBand + GPU" setup.

(most recent supercomputers don't use tori)

Let's take a look at the current Top 500 [top500.org] :

  • #1 Tianhe-2: Fat Tree
  • #2 Titan: 3D Torus
  • #3 Sequoia: 5D Torus
  • #4 K Computer: 6D Torus
  • #5 Mira: 5D Torus
  • #6 Piz Daint: 3D Torus
  • #7 Stampede: Fat Tree
  • #8 JUQUEEN: 5D Torus
  • #9 Vulcan: 5D Torus
  • #10 nn: 3D Torus

So, torus networks are the predominant topology for current supercomputers.

Re:Yesno? (1)

loufoque (1400831) | about 4 months ago | (#47300361)

Indeed, the GPU constrained programming model is ill-suited for this, but a Xeon Phi isn't. And the next-gen Xeon Phi will have very low latency networking on board, too.

My bad about tori, the supercomputers I have had access to lately were all fat tree.

Re:Bitcoin mining? (0)

Marxist Hacker 42 (638312) | about 4 months ago | (#47290887)

HIV is easy to erradicate. Just use mandatory testing, sterilization, and quarantine, and no mater how it mutates, it will be gone in two generations.

Re:Bitcoin mining? (0)

Anonymous Coward | about 4 months ago | (#47291009)

HIV is easy to erradicate. Just use mandatory testing, sterilization, and quarantine, and no mater how it mutates, it will be gone in two generations.

Works for Jews, too.

Re:Bitcoin mining? (1)

Marxist Hacker 42 (638312) | about 4 months ago | (#47291021)

Jewishness isn't contagious. But Leprosy is, and this is how we practically wiped it out of the Western Hemisphere.

Re:Bitcoin mining? (0)

Anonymous Coward | about 4 months ago | (#47291123)

Jewishness isn't contagious.

That's what they want you to believe, goy.

Re:Bitcoin mining? (1)

godel_56 (1287256) | about 4 months ago | (#47294767)

Imagen if all that computer power was put to use such as finding the cure of HIV.... We would be done by lunch time.

If anyone wants to contribute to computer research on HIV with their own systems then there is a World Community Grid [worldcommunitygrid.org] project called Fight Aids At home (FAAH) that uses your computer's spare cycles to work on AIDS research, using the BOINC platform.

There are versions for Windows, Apple, Linux, and Android software.

Re:Bitcoin mining? (1)

ClintJCL (264898) | about 4 months ago | (#47298647)

No, we would not.

Worst hindrances? (0)

Anonymous Coward | about 4 months ago | (#47289237)

GIGO and the general inability to clean code.

With or without computer involvement.

cure for aids was not a secret a century ago. (-1, Troll)

NemoinSpace (1118137) | about 4 months ago | (#47289333)

Re:cure for aids was not a secret a century ago. (0)

Anonymous Coward | about 3 months ago | (#47290271)

Mod parent funny. If the infected idiots would keep it in their pants and NOT FUCK then we wouldn't have this problem.

Why do they want to destroy something so BEAUTIFUL (-1)

Anonymous Coward | about 3 months ago | (#47289435)

Look at the picture. HI virus is so beautiful.

LOL (-1)

Anonymous Coward | about 3 months ago | (#47289509)

"The tendency of HIV to mutate and resist drugs has made it particularly difficult to eradicate." How convenient.

The only slight problem is that HIV is not the cause of 'AIDS', and I bet that 99% of the idiotic sheep on Slashdot don't even know what 'AIDS' is.

Indicator disease + HIV = AIDS
Indicator disease - HIV = Indicator disease.

It is a laughable, circular definition. Also, the 'CDC' have added numerous diseases to the definition of 'AIDS' so that they can falsely inflate the number of 'AIDS' deaths. Also, the 'AIDS' deaths are measured CUMULATIVELY, unlike any other disease.

What happened to the millions of people who were going to die from 'AIDS' that Oprah warned us about? It must be those magical drugs that saved everybody's lives! Even the hundreds of thousands who don't know they are 'HIV positive' (LOL) and are therefore spreading the 'deadly' virus with all the people who don't use condoms - which would be the majority...

So why aren't millions of people dying in the U.S.A. each year?

Try reading 'The trouble with Nevirapine' to see who is actually behind this massive and sickening scam - the pharmaceutical industry, and the 'research' industry, both criminal.
http://www.tig.org.za/pdf-files/trouble_nevirapine.pdf

Also, read the book 'Science sold out', which explains in very simple terms why HIV cannot be the cause of 'AIDS'.

Re:LOL (-1)

Anonymous Coward | about 3 months ago | (#47289585)

Nice to see you branching out from your usual "Jooz did 9/11" posts.

Re: LOL (0)

Anonymous Coward | about 3 months ago | (#47289589)

Just coming back from an HIV meeting in D.C. at the NIH... Dude, you made my day! Thank $DIVINITY, they keep shrinking Science funding, so nobody is going to keep with these scams you so cleverly discovered.

Re: LOL (-1)

Anonymous Coward | about 3 months ago | (#47289593)

Just coming back from an HIV meeting in D.C. at the NIH... Dude, you made my day! Thank $DIVINITY, they keep shrinking Science funding, so nobody is going to keep with these scams you so cleverly discovered.
Oh my, let me pass the enlightment to all my colleagues...
(posting anonymously for obvious reasons [I'm in the conspiracy, alright])

LOL (0)

Anonymous Coward | about 4 months ago | (#47304283)

Um, actually the syndrome is defined specifically as a white cell count below a certain level in someone infected with the virus. How is that circular? I know that you are denying the premise that the virus is the cause of the syndrome (go infect yourself, then!), but your assertion that what you don't accept doesn't even make logical sense seems entirely baseless. To put it in perspective, I could imagine a hypothetical universe in which the influenza virus existed but something else actually caused the flu, and yet the statement "the flu is a disease characterized by fever, chills, and coughing, and it is caused by the influenza virus" would remain logically self-consistent and non-circularly defined but (in this hypothetical universe) false.

Your shaky grasp of logic doesn't exactly lend credence to your claim that the entire scientific community is wrong.

All this for the most difficult disease to catch (-1)

Anonymous Coward | about 3 months ago | (#47289533)

venereal diseases such as HIV are possibly the most difficult diseases there is to catch.
It could be entirely eliminated in a generation if people stopped being stupid
It's one things to have multiple partners such as serial monogamists, but quite another to have multiple every month.
If. If only ...

colds, flu, respiratory viruses - just walk through a space where infected people were earlier.
measles, chicken pox? same as the cold
cancer? just be alive long enough
malaria? sleep outdoors in Africa
cholera and diarrheal diseases? fail to boil your water or cook your food

HIV? stick a needle in another person, draw their blood and inject it in yourself, or let infected people repeatedly insert their body parts into your body where soft tissues are exposed.

Society already went through this with syphilis (also fatal in the long-term and only recently curable) although syphilis is somewhat more easily transmitted than HIV. Some societies largely got rid of it solely by education and societal pressure.

Many states had to pass laws making it illegal for HIV positive people to have sex without informed consent of the partner. They had to because so very many HIV positive people were knowingly infecting others.

What aer we going to have to do? mandatory testing and tattoos for the infected?

At first, I was horrified. All these poor people dying, and what about the children?
My sympathy for all veneral disease victims went away about 10 years ago. At some point, it really is time to blame the victim.

Also, I absolutely do not care about the concept of sexual morality.
If you could have 10,000 sex partners in a disease-free situation, you should go for it. But on planet earth, you try that and you will get sick and you will spread it.

Norton Anti Virus? (0)

Anonymous Coward | about 3 months ago | (#47289569)

Just saying.

It may be wiser... (1)

amightywind (691887) | about 3 months ago | (#47289701)

To let this disease run its socially useful course.

Re:It may be wiser... (1)

fuzzyfuzzyfungus (1223518) | about 3 months ago | (#47289991)

The 'meh, it's just homos and drug addicts' theory of epidemiology often leads to some...fascinating...discoveries concerning unexpected transmission paths between the filthy expendables and the good, decent, people who we assumed were safe.

As a social experiment, it's actually pretty interesting. not so much with the 'advisable'; but interesting.

Re:It may be wiser... (0)

Anonymous Coward | about 4 months ago | (#47294617)

The 'meh, it's just homos and drug addicts' theory of epidemiology often leads to some...fascinating...discoveries concerning unexpected transmission paths between the filthy expendables and the good, decent, people who we assumed were safe.

As a social experiment, it's actually pretty interesting. not so much with the 'advisable'; but interesting.

It is interesting Because the people who we assumed were pretty much safe, I.e. non-promiscuous, turned out to be pretty much safe. HIV is not a threat to any reasonably intelligent and educated person because it is extremely difficult to transmit

Re:It may be wiser... (1)

Admiral_Grinder (830562) | about 4 months ago | (#47298603)

"non-promiscuous, turned out to be pretty much safe"

Some how I bet this kid wouldn't agree with you:

http://en.wikipedia.org/wiki/R... [wikipedia.org]

Re:It may be wiser... (0)

Anonymous Coward | about 3 months ago | (#47290567)

(To those who voted this to -1) This idiotic thinking needs to be addressed.

If you think the disease should run its socially useful course, then check out what happened to the Chimpanzee population when SIV struck them (I think it was 250,000 years ago). Something like 98% of the population died out, and the survivors were either SIV-immune, or SIV-resistant.

Now, what would happen if 98% of humanity died out? For a start, the bulk of the corpses would rot in public. You'd die from related diseases. Of couse, the natural world would prosper without humans to chop or burn it all down. Shame about the nuclear reactors that would have nobody to watch over them.

Of course, there are many people out there who contracted HIV because of others. For example, in New Zealand a while ago, a woman was deliberately infected by her partner (he was regularly injecting her with his blood until she caught it just so she would have sex with him again and wouldn't leave). How many people have caught HIV from blood transfusions?

Their suffering is fine, because it suits your eugenic beliefs?

You should head back to the 30s, I'm pretty sure at least one country shared your views.

Re: It may be wiser... (0)

Anonymous Coward | about 4 months ago | (#47294913)

Yes your idiotic thinking needs to be addressed:
1. Monkeys didn't know they had aids.
2. If 98% of aids victims died of their illness so would the disease. That is what run it's course means.
3. All people get aids from other people. Nobody injects themselves with the aids virus. You are a dope.
I don't want you to die of aids. That is why I also don't want you to be a homo. But it's not up to me. Like Ãll liberals you want me to pay for your really stupid choices. Fuck off.

Computing also prevents HIV (2)

Rashdot (845549) | about 3 months ago | (#47289765)

Because we don't get out much.

How (1)

Kerstyun (832278) | about 3 months ago | (#47289945)

> cure aids
killniggers? Y/n
> Y
niggers killed
killfaggets? Y/n
> Y
faggets killed

Re:How (0)

Anonymous Coward | about 4 months ago | (#47291165)

killfuckers? Y/n
> Y
fuckers killed

There ye go. When nobody fucks anymore, the problem solves itself. Even better: all human problems solve themselves. Because we'll all die of old age (the only fucking happening in the basement involves a palm and xhamster) and have no children to continue our folly.

Misleading headline (0)

Anonymous Coward | about 3 months ago | (#47290327)

Humans have never found a "cure" for a virus. We've been able to find cures for bacterial infections, and we've been able to find immunizations for SOME viruses (NOT a cure, just a stimulation of the body's own immune capabilities) but NEVER a cure for a virus. The now 30-year old lie that we're going to cure HIV/AIDS "any day now" if only we throw many more $BILLIONS at the problem, has mislead many people to think they could go-on living dangerous and dysfunctional lifestyles, refusing to even moderate their activities, while millions of people died from the disease. Oh, and when the death toll is mentioned, "Blame Bush" or "Blame Reagan" is the fall-back idiocy.

Will there EVER be a cure? Hopefully, yes. I sincerely hope people eventually develop a full understanding of viruses and the ability to easily cure ANY of them... but there is currently NO proof this is even possible - no proof we CAN find a cure, and no proof we can administer such a "cure" without killing the patient. I hate articles like this one because they seem specifically-designed to mislead the general public into bad decisions and bad policies based on false promises by unaccountable people who are often pushing political agendas without regard for the human wreckage that results when people take them seriously and are then harmed by believing this stuff.

Re:Misleading headline (2)

pepty (1976012) | about 4 months ago | (#47290943)

Humans have never found a "cure" for a virus. We've been able to find cures for bacterial infections, and we've been able to find immunizations for SOME viruses (NOT a cure, just a stimulation of the body's own immune capabilities) but NEVER a cure for a virus.

Hepatitis C.

Re:Misleading headline (1)

KingOfBLASH (620432) | about 4 months ago | (#47292045)

As I understand it, the key problem is rate of mutation. We can easily develop a cure for the common cold, for instance, but any cure we develop will be strain based, and the virus just mutates too fast for any "cure" to be effective for more than a few percentage of the population.

The same holds for HIV. If you give the right person a blood sample, he can come back with a cure for your particular virus. However by the time he comes back, your virus has mutated to something different.

Hasn't this already been cured? (0)

Anonymous Coward | about 4 months ago | (#47290611)

Hasn't this already pretty much been cured?

I'm pretty damn sure there were extremely successful trials of a new treatment that actually resulted in curing the people since there hasn't been any remission of any HIV since the medication was stopped.
It was based on a very smart researcher saying "Well, wait, why aren't these people getting HIV?" and they figured out the difference and supposedly found a trivially simple way to target something common to all forms.
Or does it still need to go through that "trial phase" before we can officially say "yayifications we gotta cure!"?

Either that or it was AIDS, but it don't think it was that, AIDS is far more complicated than a virus. (and isn't only caused by HIV)

Very much confused.

It was easy after all (1)

manu0601 (2221348) | about 4 months ago | (#47291015)

We bothered about HIV for decades while we just had to run supercomputers to get rid of it. I wonder why nobody thought about it before.

OR... (2)

Peter Kowalchuk-Reid (3484611) | about 4 months ago | (#47291295)

Condoms. Cheap, plentiful, and 99% effective.

Re:OR... (1)

As_I_Please (471684) | about 4 months ago | (#47291961)

Those aren't much help to the people already infected.

Re:OR... (1)

DigiShaman (671371) | about 4 months ago | (#47293457)

Or don't have casual sex with people you know little about. AKA don't go fucking around.

Re:OR... (0)

Anonymous Coward | about 4 months ago | (#47299339)

Or don't have casual sex with people you know little about. AKA don't go fucking around.

But.. this is exactly what is fun... sex with people you know little about.. Do you really want your fuck buddy to tell you about his/her day/coworkers/mother ?

took alot of mating to figure out (0)

Anonymous Coward | about 4 months ago | (#47291899)

invention of supercomputer: 1980
discovery of HIV virus: 1980
coincidence?
then again maybe HIV was a mutation of a harmless virus living on the bikini atoll -or- was brought back from the moon?

Drs.William Lyman and Steven Kaali create cures (0)

Anonymous Coward | about 4 months ago | (#47293049)

In the Fall of 1990, two medical researchers, Drs.William Lyman and Steven Kaali, working at Albert Einstein College of Medicine in New York City made an important discovery. They found that they could inactivate the HIV virus by applying a low voltage direct current electrical potential with an extremely small current flow to AIDS infected blood in a test tube. Initially, they discovered this in the lab by inserting two platinum electrodes into a glass tube filled with HIV-1 (type 1) infected blood. They applied a direct current to the electrodes and found that a current flow in the range of 50-100 microamperes (uA) produced the most effective results. Practically all of the HIV viral particles were adversely affected while normal blood cells remained unharmed. The viral particles were not directly destroyed by the electric current, but rather the outer protein coating of the virus was affected in such a way as to prevent the virus from producing reverse transcriptase, a necessary enzyme needed by the virus to invade human cells. Reverse transcriptase allows the virus to enter a human T cell line (called CEM-SS) and commandeer the DNA reproduction machinery. After using the host cell to reproduce itself into thousands of new virii, the swollen host cell (now called syncytia or giant cell) will burst and spew the contents into the bloodstream or lymph system. This is how the virus spreads, but lacking reverse transcriptase, the HIV virus can't invade the host cell and it becomes vulnerable to destruction by the body's immune system. (The details of this experiment can be read from Kaali's patent application.)

Getting the Word Out?

A brief announcement of this discovery appeared in The Houston Post (Mar 20, 1991), then in Science News (Mar. 30, 1991 pg. 207) and later in Longevitymagazine: (Dec.1992 pg. 14). Following their work in the Fall of 1990, Kaali and Lyman presented their findings at the First International Symposium on Combination Therapies (an AIDS conference) in Washington DC on March 14th, 1991. Kaali outlined two methods for treating an AIDS patient with this new therapy: One method involved removing a small amount of blood, electrifying it and then returning it to the patient's body. The second method involved sewing a miniature electrifying power supply along with two tiny electrodes directly into the lumen of an artery. For long term treatment, the mini electrifying unit needed to be removed and relocated to a new artery site after 30-45 days since scar tissue and calcification forming around the implant unit would lead to artery blockage. Kaali (along with co-inventorPeter Schwolsky) filed for a patent on this implantable electrifying device on Nov 16, 1990 and nine months later was granted patent #5,139,684 on August 18, 1992. It's interesting to note two things here:

1. In order to obtain a patent from the United States Patent Office, Kaali and Schwolsky had to prove that the device works as claimed. Lacking solid proof, US patents are simply not granted.

2. Very often it takes years to obtain a patent, yet this patent was granted in only nine months; a further indication to me of the strength of their demonstrated claims

It's also interesting to note that other than the 3 publications mentioned above and the March '91 AIDS conference, nothing again appeared in print, radio, or TV about this important discovery as a potential treatment and cure for AIDS from Kaali and company. Most knowledgeable observers feel that Kaali and Lyman's discovery was intentionally suppressed following the March '91 AIDS conference presentation. If AIDS research was on the level and not the sham that it actually is, this should have made front page news around the world. (Around 1999, I was contacted by a woman with AIDS who had managed to reach Dr. William Lyman over the phone. She asked him about his experiments with Kaali regarding blood electrification and if she could obtain the treatment through them. Lyman denied any knowledge of any AIDS treatment or cure. He said he never heard of Dr. Kaali and he had no idea what she was talking about concerning blood electrification and then hung up on her. What does that tell about the power of the people behind the suppression of this discovery?

Blood Electrification (0)

Anonymous Coward | about 4 months ago | (#47293097)

Kaali and Lyman presented their findings at the First International Symposium on Combination Therapies (an AIDS conference) in Washington DC on March 14th, 1991. Kaali outlined two methods for treating an AIDS patient with this new therapy: One method involved removing a small amount of blood, electrifying it and then returning it to the patient's body. The second method involved sewing a miniature electrifying power supply along with two tiny electrodes directly into the lumen of an artery. For long term treatment, the mini electrifying unit needed to be removed and relocated to a new artery site after 30-45 days since scar tissue and calcification forming around the implant unit would lead to artery blockage. Kaali (along with co-inventorPeter Schwolsky) filed for a patent on this implantable electrifying device on Nov 16, 1990 and nine months later was granted patent #5,139,684 on August 18, 1992.

New paradigm (0)

Anonymous Coward | about 4 months ago | (#47295113)

Females are equipped with a sense of smell which detects the immune system state of any potential mate. This allows them to create progeny with two different immune systems, evolving defenses against pathogens evolving (mutating) to evade our immune defenses. The use of oral contraceptives causes the mating choices of the females using them to be opposite to the usual mating choices, and the females mate with males with similar immune systems, depriving their progeny of the enhanced protection. Nature protects the species from being at risk from this by making some of these progeny effectively sterile e.g. homosexual. This prevents the behavior from being passed on. This protection evolved against eugenic practices by religious and political organizations. The widespread use of oral contraceptives has overwhelmed the natural defenses provided by nature and led to an upping of natures protection of our species - HIV.

IÃ(TM)m Mercy Tebogo (0)

Anonymous Coward | about 4 months ago | (#47373949)

IÃ(TM)m Mercy Tebogo, IÃ(TM)m from South-Africa, I was tested HIV positive, Dr. Ozalla cured me from HIV, so I will advise you people that have it too, to contact him now, so that you will be cured by him okay.. Contact him via his email on ozalla.the.great.healer@gmail.com

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