> Azure does have some better HPC infrastructure than AWS

That's somewhat surprising to hear, I just assumed AWS has equivalent products. My customer is 80% AWS and 20% Azure, so it's a useful data point to know that some HPC workloads are better off in Azure.

> large CPU/RAM instances have availability issues, especially for spot instances.

I've had two different ~128 vCPU instances running for days and days in my lab environment, but that's probably because my region tends not to have a lot of HPC workloads that would compete for spot instances. I've noticed that "popular" sizes in Azure such as D4, D8, E4, and E8 are pre-empted regularly, but the "special" sizes like HPC not so much.

> surprising large charge for sufficiently large files.

Both Azure and AWS use this as a "roach motel" to encourage vendors and partners to co-locate in the same cloud. It's unfortunate that they charge on the order of $100 per terabyte, but it is what it is. However, bioinformatics files compress well, and compared to getting something out of an on-prem traditional network, the egress fees are a bargain.

My customer has a rural site with a "WAN" link. Their non-cloud option is to buy a NAS, replicate it to another NAS in a data center, and then build a permanent "file sharing solution". This is going to cost tens of thousands of dollars. They might share a few terabytes annually, which makes cloud egress fees look practically free in comparison.

> A new Illumina NovaSeq sequencer (about the size of a copy machine) with dual S4 flow cells produces 6Tb every couple days.

The scientists I talked to raised this, and to be honest I'm also concerned, especially as some of the groups I deal with are in rural areas "far from the cloud." (They analyse samples from cattle ranchers to try and prevent foot and mouth disease.)

Let's say the machine generates 6 terabytes in 2 days, so 3 TB daily. Assuming that's the uncompressed data, it'll be about 1 TB after compression. The location I'm thinking of has a 500 Mbps link, but that can transfer that data volume in just 4 hours: https://www.wolframalpha.com/input?i=%28+1+TB+%29+%2F+500+Mb...

One trick I discovered recently is that both the s3cmd and azcopy tools can take pipeline input. Combine that with a parallel compression tool like 'pigz' that can output to the pipeline, and you can have a workflow where the "raw" input files are compressed and streamed to the cloud storage at the same time. That alone can cut hours off the transfer time!

> If you have 100 TB of data, that increases the cost of re-running data – especially if it's in cold storage or archived.

Not necessarily. Azure Cold storage access has no special charges associated with it. It's a bit slower, but streaming reads were quite fast in my experience. Archive tier of course has some additional costs, but it's not a drama in most cases. For example, "high priority" retrieval costs extra, but normal priority appears to be free.

> what software are they using in bioinformatics that uses a GPU

From: https://developer.nvidia.com/blog/nvidia-hopper-architecture...

"An example is the Smith-Waterman algorithm for genomics processing".

Admittedly, GPU usage for genomics is still rare, but it is becoming more common.

> If you want instant scalability, the math is different.

In my example, think of 10-20 scientists doing semi-regular gene sequencing workloads and running related analyses. Sometimes needing a single machine with 2TB of memory, other times running 10,000 trivial jobs.

In principle, the flexibility of the cloud is nearly optimal for a scenario like this.