[moh_maya]

I don't think it is because no one has tried it as much as the fact that the workloads need the cpu architecture / are not easily parallizable (as far as I understand). Comp bio in genetics is largely sequence alignment & search, which is still largely CPU / memory bound; but I don't understand programming enough to speculate if development in algorithms will allow GPUs to be used because the problem itself is not parallelizable. I think of it as the difference between a super computer & a cluster..

(More than a decade ago, I struggled to / barely succeeded in building a Beowulf cluster; I am just amazed at how far both the hardware & the software tools have come..)

In other areas of comp bio though, GPUs I think are finding use. Protein folding, molecular dynamics. Also, with STORM & such: super resolution microscopy? I think increasingly, gpus will become important.

Also, whole cell simulations?

[timeu]

What you wrote about super computer vs cluster is quite right. Recently I attended a HPC meeting where we were the only DevOps of an HPC for a biological institute and most of the other people were from physics & chemistry. They usually don't consider the biology workloads as High Performance Computing but as big resource/data computing. The physics & chemistry guys run simulation using hundred thousands of cores and are mostly CPU bound. They use MPI and their nodes typically have not more than 64 GB and they consider 120 GB memory usage as a lot. Biologist on the other hand hardly use MPI because they can just parallelize the workload on the data level (i.e. sample or chromosome) and run them independently on each node. For that reason also high memory NUMA machines from SGI can relatively often be found.

You are also right that some of the comp bio areas (CryoEM, protein folding, molecular dynamics) are well suited for GPUs

[noir_lord]

Thank you for your response, it was extremely interesting.

One of the nice things about HN is you get to look outside your own bubble (I mostly do Line of Business/SME stuff so this stuff isn't just outside my wheelhouse it's on the other side of the ocean).