[Bioc-devel] Note on RbowtieCuda and Ubuntu 25.04

[Franck RICHARD]

Hello everyone!

I've recently upgraded my Ubuntu to version 25.04, along with R (4.5) 
and Bioconductor (3.21).

While browsing the "Multiple platform build/check report for BioC 3.21" 
page, I noticed that the netbbiolo1 server redirects to GPU-compatible 
servers biocpgu and kakapo1. It seems the infrastructure isn't fully 
ready yet.

Out of curiosity, I attempted to install the package using:

*BiocManager::install("RbowtieCuda")*

The manager downloaded the source code and initiated compilation. 
However, the process was halted by an error during the CMake phase. 
(What should normally happen? Should the manager download the 
executables directly?)

Upon investigation, the issue stems from a change in the glibc 2.41 
library (provided in Ubuntu 25.04), which introduces new definitions for 
certain trigonometric functions (sinpi, sinpif, cospi, cospif). CUDA 
provides its own version of |math_functions.h| that redefines some 
mathematical functions (cospi, sinpi, etc.). These functions also exist 
in libc but with different signatures, leading to compilation errors.

** Therefore, glibc 2.41 is currently incompatible with all versions of 
CUDA and any software operating under CUDA .​ **

The error is relatively straightforward to fix but requires a bit of 
tweaking:

You need to modify the file:

*/usr/local/cuda-12.8/targets/x86_64-linux/include/crt/math_functions.h*

(for CUDA version 12.8) following the guidance provided here:

https://forums.developer.nvidia.com/t/error-exception-specification-is-incompatible-for-cospi-sinpi-cospif-sinpif-with-glibc-2-41/323591

After this adjustment, compilation becomes possible...

Wouldn't it be prudent to delay the availability of RbowtieCuda until 
NVIDIA releases the necessary patches? Currently, RbowtieCuda only 
functions with BiocManager 3.21 and R 4.5, which necessitates the latest 
version of Ubuntu and the use of glibc 2.41. Any users attempting 
installation will encounter this error...

For your information, it's also possible to compile the package on 
Windows. It was working a few months ago. I can verify and make the 
necessary modifications to ensure it functions again. I think it might 
be interesting to offer the package on Windows as well. No ?

Thank you all!

Franck

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