Alisim mpi

[trongnhanuit]

This pull request includes the following bugs fixed.

• Fix bug #333 - avoid using the same random seed number before and after establishing multiple threads.
• When copying gaps from the real alignments, consider both "-" and "."
• Re-set the minimum version of Cmake (from Thomas)

[trongnhanuit]

Is there any reason why you downgrade cmake requirement from 3.10.2 to 3.0?

It is a fix (by @thomaskf) to avoid compilation errors after someone upgraded cmake requirement to 3.10.2. Is it right, Thomas?

[thomaskf]

yes, We were unable to compile the code into a static binary on Linux until we downgraded the CMake requirement to version 3.0

Thomas

On Sat, Nov 2, 2024 at 7:59 AM Nhan Ly-Trong @.***> wrote:

Is there any reason why you downgrade cmake requirement from 3.10.2 to 3.0?

It is a fix (by @thomaskf https://github.com/thomaskf) to avoid compilation errors after someone upgraded cmake requirement to 3.10.2. Is it right, Thomas?

— Reply to this email directly, view it on GitHub https://github.com/iqtree/iqtree2/pull/334#issuecomment-2452582652, or unsubscribe https://github.com/notifications/unsubscribe-auth/AENQCRUA52BCUWVNYYQGTELZ6PTUPAVCNFSM6AAAAABQFFSSASVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJSGU4DENRVGI . You are receiving this because you were mentioned.Message ID: @.***>

[bqminh]

This is a very big change: you change the random number seed, making AliSim non-reproducible when users run it, compared to the previous version. If they ran AliSim now, the generated alignment will be completely different from the previous version, even if setting the same seed number. We need to discuss more, in what scenarios it will impact users, before releasing it.