Supercomputers surprisingly link DNA crosses to cancer(deepstuff.org)
deepstuff.org
Supercomputers surprisingly link DNA crosses to cancer
http://www.deepstuff.org/supercomputers-surprisingly-link-dna-crosses-to-cancer/
5 comments
I wonder if there are scientists trying to understand why certain genes are correlated with cancer thinking that it has something to do with proteins being made, but in the end it's the result of those genes affecting the physical stability of the DNA strand. Pretty crazy.
Certainly there are such scientists. There is a very strong incentive for researchers to be novel and make discoveries "out of the box" - how much of these discoveries will be published, and will stand the test of time is a very different thing. Almost every single cancer case we see in our clinical sequencing effort has one or more mutations in a limited set of the "usual suspects" <500 protein coding genes. We are at a stage, where it is more difficult to find a new oncogene or tumor suppressor gene than to suggest an "out of the box" mechanism based on pre-clinical data.
The pursuit of novelty in research drives me crazy. You don't get published as easily with replications and tiny iterative developments. I wish they'd incentivize those kinds of research...
We certainly undervalue replication (or refutation) in the pursuit of novelty.
What is more of a problem is that scientists are being pushed by the system to get their results out as fast as possible so they are not doing the hard work of carefully checking their own work before publication. The incentive is to publish if an experiment works once or twice and hand-wave away the other dozen times it didn’t. Combine that with the enormous pressure PostDocs and PhD students are under to generate results it is amazing anything of value comes out of the lab these days.
What is more of a problem is that scientists are being pushed by the system to get their results out as fast as possible so they are not doing the hard work of carefully checking their own work before publication. The incentive is to publish if an experiment works once or twice and hand-wave away the other dozen times it didn’t. Combine that with the enormous pressure PostDocs and PhD students are under to generate results it is amazing anything of value comes out of the lab these days.
The number of people capable of producing good science, is much less than the number of people in science. The pressures emerge because of it.
Even the people capable of producing good science are pushed into bad situations. The basic problem is we have more good scientists than the funding to support them - when the success rate of grants is less than 15% then the pressure gets extreme and also sorts of bad behaviour results.
As a bit of an aside grant reviews were apparently brought in initially to help scientists avoid working on bad areas. The idea was that everyone would get funded who put up a reasonable grant and they just wanted to help screen out the bad ideas so people didn’t waste their time.
We have since twisted this into the current system where we try to determine which of the top few percent of grants are the best. Of course the whole ranking process is so noisy that it is little better than chance for anyone in the top 25%.
A much better system would be to rank the grants as worth funding or not and then put all those worth funding into a lottery to choose who gets funded. At least this way even the losers would know they were on the right track and they were just unlucky. It would save an enormous amount of grantmanship and other activities that are the antithesis of everything science should be about.
As a bit of an aside grant reviews were apparently brought in initially to help scientists avoid working on bad areas. The idea was that everyone would get funded who put up a reasonable grant and they just wanted to help screen out the bad ideas so people didn’t waste their time.
We have since twisted this into the current system where we try to determine which of the top few percent of grants are the best. Of course the whole ranking process is so noisy that it is little better than chance for anyone in the top 25%.
A much better system would be to rank the grants as worth funding or not and then put all those worth funding into a lottery to choose who gets funded. At least this way even the losers would know they were on the right track and they were just unlucky. It would save an enormous amount of grantmanship and other activities that are the antithesis of everything science should be about.
I think you have the opposite opinion of most of the researchers I know. They go nuts that you can't do anything really out of the box until you have tenure. We agree on replication though. No one cares until there's a crisis, then the Karl Popper quotes never stop.
You are allowed to be as out of the box as you like, but you have to generate results which if very hard to do if you take risks.
Even once you have tenure you are still forced to still play it safe since if you don’t generate the results you don’t get grants and if you don’t bring in the money your university will find ways to get rid of you. Welcome to your new lab - yes we know it was the old broom closet, but you must understand that since you don’t have any grants right now we need to give your lab to research x who has just brought in a $3 million grant.
Even once you have tenure you are still forced to still play it safe since if you don’t generate the results you don’t get grants and if you don’t bring in the money your university will find ways to get rid of you. Welcome to your new lab - yes we know it was the old broom closet, but you must understand that since you don’t have any grants right now we need to give your lab to research x who has just brought in a $3 million grant.
i completely agree. The dna-data metaphor has been a huge, decades-long mistake, and with the state of things today, it's clear we have massive errors in our assumptions.
I'd love to work on the computational side of problems like this.
Subscribe to the right mailing lists; once in a while there are job postings for things like this.
(e.g. this one: http://listserv.uni-heidelberg.de/science-jobs-de/sjd-e.html , and subscribe for IT and biology/medicine - I'm sure there are tons more of these lists out there.)
(e.g. this one: http://listserv.uni-heidelberg.de/science-jobs-de/sjd-e.html , and subscribe for IT and biology/medicine - I'm sure there are tons more of these lists out there.)
This would really work better implemented in an FPGA. You could construct a circuit that exhaustively searches for all repeats within a maximum distance rather than just checking a relatively small number of random sequences.
Hm. Surprise is not really my response, but "huh. Neat. Makes sense."
I wish people would stop using the term 'supercomputer' for large scale batch processing on clusters. This seems like just the sort of problem that could be run more cheaply using EC2 spot instances.
I work for a supercomputer company. There is almost no way you'll get anywhere near the performance you need on EC2.
Supercomputers today are built to transfer data between nodes using locality of the node as well as its physical location. Ok EC2 could do the same thing or similar sure, but, it won't have fibre optic links that allow direct DMA of memory from one node to another.
The interconnects and the overall use of a supercomputer is drastically different than what you have on EC2. Additionally, your process is just that, another process running on a bare metal system. No hypervisor to get in the way.
Keep in mind that some compiled code can care about if an avx instruction is used or not. A tiny detail like that means things like a 5% reduction in cpu cost. When your job/process overall takes months to run, this is a significant reduction.
Supercomputers exist because they're more economical than regular hardware. No really, it is true. These things can generate terabytes of data a second and shunt it around efficiently. Until you can demonstrate the same on EC2 you might want to read up on the architectures of modern supercomputers.
As a fun note, today cpu power is mostly a gimme, now most simulations care more about memory. For the memory you need you effectively get the cpu for free.
Supercomputers today are built to transfer data between nodes using locality of the node as well as its physical location. Ok EC2 could do the same thing or similar sure, but, it won't have fibre optic links that allow direct DMA of memory from one node to another.
The interconnects and the overall use of a supercomputer is drastically different than what you have on EC2. Additionally, your process is just that, another process running on a bare metal system. No hypervisor to get in the way.
Keep in mind that some compiled code can care about if an avx instruction is used or not. A tiny detail like that means things like a 5% reduction in cpu cost. When your job/process overall takes months to run, this is a significant reduction.
Supercomputers exist because they're more economical than regular hardware. No really, it is true. These things can generate terabytes of data a second and shunt it around efficiently. Until you can demonstrate the same on EC2 you might want to read up on the architectures of modern supercomputers.
As a fun note, today cpu power is mostly a gimme, now most simulations care more about memory. For the memory you need you effectively get the cpu for free.
For simulation problems where each iteration of an algorithm depends on calculated world state from the previous iterations, then interconnect speed is all. You can't start the next iteration until all jobs in the current iteration are complete. This is what you need a supercomputer for!
Most bioinformatics workloads are simply nothing like that. There are very large amounts of data to process, but it is not a supercomputing problem because the jobs are independent and can be completed in any order.
> ‘We had 20,000 translocations from human cancers from the COSMIC database; 200 bases of DNA for each translocation; and about 200-400 iterations at each position,’ Bacolla said. The number of iterations totaled about two billion.
Here we don't even have a big-data problem (200 * 20K = 4M), just a huge number of combinations to test.
Most bioinformatics workloads are simply nothing like that. There are very large amounts of data to process, but it is not a supercomputing problem because the jobs are independent and can be completed in any order.
> ‘We had 20,000 translocations from human cancers from the COSMIC database; 200 bases of DNA for each translocation; and about 200-400 iterations at each position,’ Bacolla said. The number of iterations totaled about two billion.
Here we don't even have a big-data problem (200 * 20K = 4M), just a huge number of combinations to test.
You can roughly mimic the Oakridge Titan cluster (#2 in the world) by using AWS: 4 GPUs / node, 10 GE across nodes, and you can spin up a lot of them. Best of all, you don't need $60 mil.
This is what we're pushing towards at graphistry ;-)
Edit: link: https://en.wikipedia.org/wiki/Titan_(supercomputer)
This is what we're pushing towards at graphistry ;-)
Edit: link: https://en.wikipedia.org/wiki/Titan_(supercomputer)
Mimic sure, but it won't be quite the same. I won't deny you can't do a one off job possibly cheaper on aws. The thing is, these simulations run for weeks or months on end and these clusters are run and setup to run at 100% at all times.
They really are efficient power wise, which is the true test for things like this. I'm hitting towards nda things but needless to say keep an eye out for gpu technology in supercomputers. As well as what that top 500 chinese supercomputer has.
Note, its at the top mostly due to its accelerator cards. Most simulations don't need those.
I know 60 mill seems like a lot but when it runs for 5 years it really isn't that expensive. For a one off job sure go with aws, it'll take longer, but i'm not kidding when you get down to the detail of the cpu architecture and keep track of things like how cache misses affect a program.
It really is night and day difference in how things run. The avx comment is not a joke, reducing even cpu cost by 5% over months is a huge deal. These are just a few of the differences in how supercomputers operate. It is far less to do with the cpu and memory and more how they communicate amongst themselves. One node may compute a value, but another adjacent node then takes on that output to calculate more. This is the key differentiator, and if you aren't compiling fortran (not joking), its likely its not a very great simulation.
If you'd like to know more, i'd recommend getting a job at a supercomputer company. They've solved a lot of the overall cluster problems aws has many years ago. And it is really fun stuff where details matter. Something I can't say about most aws deployments. PS: I'm working on something that will make Titan look like a kid. :) Every 2-3 years this stuff gets pushed aside its fun.
They really are efficient power wise, which is the true test for things like this. I'm hitting towards nda things but needless to say keep an eye out for gpu technology in supercomputers. As well as what that top 500 chinese supercomputer has.
Note, its at the top mostly due to its accelerator cards. Most simulations don't need those.
I know 60 mill seems like a lot but when it runs for 5 years it really isn't that expensive. For a one off job sure go with aws, it'll take longer, but i'm not kidding when you get down to the detail of the cpu architecture and keep track of things like how cache misses affect a program.
It really is night and day difference in how things run. The avx comment is not a joke, reducing even cpu cost by 5% over months is a huge deal. These are just a few of the differences in how supercomputers operate. It is far less to do with the cpu and memory and more how they communicate amongst themselves. One node may compute a value, but another adjacent node then takes on that output to calculate more. This is the key differentiator, and if you aren't compiling fortran (not joking), its likely its not a very great simulation.
If you'd like to know more, i'd recommend getting a job at a supercomputer company. They've solved a lot of the overall cluster problems aws has many years ago. And it is really fun stuff where details matter. Something I can't say about most aws deployments. PS: I'm working on something that will make Titan look like a kid. :) Every 2-3 years this stuff gets pushed aside its fun.
We handwrite PTX ;-)
Cost-wise, public cloud destroys traditional supercomputers, and the gap will just keep increasing. However, the economics enabling it, e.g., sufficiently non-interfering multitenancy, are only now reaching the needs of HPC. Likewise, only recently did public clouds embrace non-wimpy hardware: SSDs, multiGPU, starting to have FPGAs, etc. Exposed interconnects are 10 gige, so not the best, but like you said, scale requires designing for minimizing communication to beginwith.
RE:long jobs, we focus on interactive exploration (< 100ms). Spark etc. give up latency to ensure resiliency on long jobs.
Cost-wise, public cloud destroys traditional supercomputers, and the gap will just keep increasing. However, the economics enabling it, e.g., sufficiently non-interfering multitenancy, are only now reaching the needs of HPC. Likewise, only recently did public clouds embrace non-wimpy hardware: SSDs, multiGPU, starting to have FPGAs, etc. Exposed interconnects are 10 gige, so not the best, but like you said, scale requires designing for minimizing communication to beginwith.
RE:long jobs, we focus on interactive exploration (< 100ms). Spark etc. give up latency to ensure resiliency on long jobs.
They used Stampede for this project, most recently #7 on the Top500 list of supercomputers.
http://www.top500.org/lists/2014/11/
http://www.top500.org/lists/2014/11/
Unless you have all the details and you have compared the price of both options, you don't know that it's cheaper.
That seems unlikely to me, for an entity of the size of UT Austin. They probably have enough jobs to run to keep their clusters busy.
That seems unlikely to me, for an entity of the size of UT Austin. They probably have enough jobs to run to keep their clusters busy.
Stampede actually serves the entire U.S. research community. Any researcher at a U.S. institution can apply for a resource allocation.
Yes, and IIRC (from the presentation I went to, and for those that don't know) the resource allocation doesn't have to be the whole cluster, they can split it up and run smaller less scalable jobs across just a portion of the hardware. In fact I think they said the vast majority of the jobs are unable to consume the entire cluster.
AKA its AWS for HPC.
Also AFAIK, that has been the model at TACC for at least a decade, maybe longer.
AKA its AWS for HPC.
Also AFAIK, that has been the model at TACC for at least a decade, maybe longer.
That's a perfectly good use of the term these days.