-n does not seem to be honored

[wasade]

I'm running ssu ... -n 8 however, it appears that ssu is using 16 threads

[sfiligoi]

Yes, the semantics of -n has changed.
The documentation has unfortunately not been updated :(

-n now stands for "split the problem in N subproblems to be run in sequence", with the reasoning being that we use less memory during Unifrac compute. This is especially useful for GPU compute.
While it limits the amount of memory saving during the IO phase, it is still beneficial.

The number of threads is fully controlled by the OpenMP threading library, i.e. OMP_NUM_THREADS.

[wasade]

I think we should correctly support the threads parameters from the python interface. Would it suffice to use Python to set OMP_NUM_THREADS?

W/ documentation, I think we should update the ssu usage string to reflect what -n does, I think a new parameter name probably makes sense, and to also note specifically in the usage string the use of OMP_NUM_THREADS

[sfiligoi]

For context:
NumPy typically manages thread parallelism with OMP_NUM_THREADS:
https://numpy.org/devdocs/reference/global_state.html

[wasade]

Ya, good point

…

On Nov 29, 2022, at 9:33 AM, Igor Sfiligoi ***@***.***> wrote: For context: NumPy typically manages thread parallelism with OMP_NUM_THREAD: https://numpy.org/devdocs/reference/global_state.html <https://numpy.org/devdocs/reference/global_state.html> — Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADTZMQLNMCA2WSFM46HYGLWKY45XANCNFSM6AAAAAASEXYCXQ>. You are receiving this because you authored the thread.

[sfiligoi]

Let's deprecate -n and document it accordingly.
I will add a separate flag for the problem splitting.

[wasade]

Thanks!

…

On Nov 29, 2022, at 10:24 AM, Igor Sfiligoi ***@***.***> wrote: Let's deprecate -n and document it accordingly. I will add a separate flag for the problem splitting. — Reply to this email directly, view it on GitHub <#17 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADTZMXWKFKL2TVDYCTIVNDWKZC4XANCNFSM6AAAAAASEXYCXQ>. You are receiving this because you authored the thread.

[sfiligoi]

Released in 1.2.