221–230 of 281 posts
Earlier quoted context omitted.
That is not a law.
There are actually laws around such things. You can read about them here: https://www.hhs.gov/ohrp/index.html
Having had the responsibility of providing HPC for a literal buildings full of scientists, I can say that it may be true that you can get computation cheaper with owned hardware, than in a cloud. Certainly pay as you go, individual project at a time processing will look that way to the scientist. But I can also say with confidence that the contest is far closer than they think. Scientists who make this argument almos…
They leave out major costs because they don't pay those costs. Power, Cooling, Real Estate are all significant drivers of AWS costs. Researchers don't pay those costs directly. The university does, sure, but to the researcher, that means those costs are pre-paid. Going to AWS means you're essentially paying for those costs twice. plus all the profit margin and availability that AWS provides that you also don't need.
Earlier quoted context omitted.
There are actually laws around such things. You can read about them here: https://www.hhs.gov/ohrp/index.html
That only applies to government / government sponsored research. That is different from someone doing their own research
Having had the responsibility of providing HPC for a literal buildings full of scientists, I can say that it may be true that you can get computation cheaper with owned hardware, than in a cloud. Certainly pay as you go, individual project at a time processing will look that way to the scientist. But I can also say with confidence that the contest is far closer than they think. Scientists who make this argument almos…
I'd much rather store HIPAA data on a server in my office or closet than worry I got all the IAM settings right. And if I fire someone, security makes sure they can't get in the building. You cannot say the same about the cloud. Yes, I know you can do cloud security right, but on prem security is just harder to mess up.
Having had the responsibility of providing HPC for a literal buildings full of scientists, I can say that it may be true that you can get computation cheaper with owned hardware, than in a cloud. Certainly pay as you go, individual project at a time processing will look that way to the scientist. But I can also say with confidence that the contest is far closer than they think. Scientists who make this argument almos…
Is a postdoc hacking a cluster something you have seen before? I am genuinely curious because I worked on a cluster owned by my university as an undergrad and everyone was kind of assumed to be trusted. If you had shell access on the main node you could run any job you wanted on the cluster. You could enhance security I just wonder about this threat model, that's an interesting one. I am sure it happens to be clear.
I've never worked in this space, but I'm curious about the need for massive egress. What's driving the need to bring all that data back to the institution? Could whatever actions have to be performed on the data also be performed in AWS? Also while briefly looking into this I found that AWS has an egress waiver for researchers and educational instiutions: https://aws.amazon.com/blogs/publicsector/data-egress-waiver..…
You may use AWS yourself, but your collaborators have made their own choices for their own reasons. The data goes where it's needed, often crossing institutional boundaries.
Having had the responsibility of providing HPC for a literal buildings full of scientists, I can say that it may be true that you can get computation cheaper with owned hardware, than in a cloud. Certainly pay as you go, individual project at a time processing will look that way to the scientist. But I can also say with confidence that the contest is far closer than they think. Scientists who make this argument almos…
Perspective from a computational biologist: Campus hosted HPC means the direct cost pressure is seen as IT staff and hardware related costs. Researchers are encouraged to use the available capacity. This is good. Externally-hosted HPC means every single compute job is seen as something that directly costs money. This negatively affects the quality of scientific output (research playfulness / creativity / focus on the…
Earlier quoted context omitted.
Let me echo this as someone who once was responsible for HPC computing in a research intensive public university. Most career academics have NO IDEA how much enterprise computing infrastructure costs. If a 1 terabyte USB hard drive is $40 at Costco we (university IT) must be getting a much better deal than that. Take this argument and apply it to any aspect of HPC computing and that's what you're fighting against. Th…
I remember the first time a server caught fire in the closet we kept the rack in. Backups were kept on a server right below the one on fire. But, y'know, we saved money.
I think this post is identifying scientific computing with simulation studies and legacy workflows, to a fault. Scientific computing includes those things, but it also includes interactive analysis of very large datasets as well as workflows designed around cloud computing. Interactive analysis of large datasets (e.g. genome & exome sequencing studies with 100s of 1000s of samples) is well suited to low-latency, serv…
I've followed Hail and applaud the Broad Institute's work wrt establishing better bioinformatics software and toolkits so I hope this doesn't come as rude, but I can't imagine an instance in a real industry or academic workflow where you need 300ms feedback from an experiment to "maintain flow" considering how long experiments on data that large (especially exome sequencing!) take overall? My (likely lacking) imagina…
Moreover, I think we have differing definitions of “experiment”. In the context of a sequencing study, I think an “experiment” can be as simple as answering the hypothesis: does the missingness of a genotype correlate with any sample metadata (e.g. sequencing platform). You might try to test that hypothesis by looking at a PC1-PC2 plot with points colored by sequencing platform where the PCA is conducted on the 0/1 indicator matrix of missingness.
In the dry lab, that is what I mean by experiment. By that definition, a scientist does many experiments a day. Particularly for sequencing studies, these experiments are data-intensive, I need to run a simple computation on a lot of data to confirm the hypothesis.