Bug#1019890: ITP: oxdna-cuda -- coarse-grained simulation software for DNA, RNA, and related systems
Hi Constantine,
On 2022-09-15 19:03, Constantine Evans wrote:
> oxDNA is a simulation code that was initially conceived as an
> implementation of the coarse-grained DNA model introduced by
> T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since
> reworked and it is now an extensible simulation+analysis framework. It
> natively supports DNA, RNA, Lennard-Jones and patchy particle
> simulations of different kinds on both single CPU cores and NVIDIA
> GPUs.
This sounds interesting. oxDNA could be a great addition to DebiChem or
Debian Med teams.
> oxDNA has CUDA and CPU simulation backends. I've only made a package
> so far including CUDA support, which would thus need to go in
> contrib, because I primarily use the CUDA backend, and have mostly
> seen others using it and presenting results with it. It also has two
> python libraries, oxpy and oxDNA_analysis_tools, which I have packaged
> as separate binary packages.>
> I have not made a serious Debian package before, and would need a
> sponsor for this; I'd plan to upload it to mentors. Like much
> research software, it was not built with standard system-wide
> installation as a priority, and has needed some tweaking to its
> build process in that regard, but it is reasonably simple, and the
> upstream authors are responsive to changes to make things easier.
I have never worked with packaging CUDA software. Since it cannot be
built on buildd, I suppose all uploads will have to source+binary. It is
interesting how this works with sponsoring, in particular who (you or
sponsor) will have to build the binaries for upload.
By the way, what would be the binary compatibility of the CUDA package?
I.e., what is the range of CUDA versions that could use the binary
package without rebuilding it from source?
Best,
Andrius
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