The general guideline for Anaconda is: Please do not use it on the clusters. It is meant for easy installations on a single-user laptop and is not well suited for multi-user clusters. It sometimes makes wrong assumptions about the OS configuration, generates a huge number of files (~100.000), etc. Conda is great to easily test the latest versions of some packages. Still, it’s not meant to keep several versions of the same package on the system, which is needed for scientific reproducibility/provenance. But, more importantly, Anaconda distributes pre-compiled binaries in many cases, and otherwise uses pre-configured compilation options which are often not optimal for the CPUs we have on the clusters. Even if the situation is not as bad now that Conda ships with MKL, very few wheels are optimised. Furhtermore, pre-compiled binaries might need versions of the system libraries more recent than what the clusters can offer, which can lead to the typical ‘Symbol not found’ error at runtime.

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