Closed amkozlov closed 4 years ago
Hi @MaximilianStammnitz, yes there is a test version available here:
https://github.com/amkozlov/raxml-ng/tree/coarse
You can add --workers N
option where N
is the desired number of concurrent tree searches. Please note that not everything works in this version yet, eg. MPI+checkpointing (and MPI support in general is not very well tested). I plan to finalize coarse-grain parallelization support in the next few weeks, but of course early adopters/testers are always welcome! :)
Great, many thanks! Happy to try it out and we don't use MPI, so that shouldn't be a big deal for now.
Could you possibly also make the linux_x86_64 binary available for this fork? (sorry for my lack of experience with this, hope this would not take too much time).
Cheers, Max
sure, here you go:
Thanks, running it now and will report back.
Max
implemented in the coarse branch, to be included in raxml-ng 1.0
Sorry, I'm a little confused with different implementations of multi-threading, like mpi, mpi+pthread, coarse, coarse+mpi and maybe coarse+mpi+pthread (?).
I have seen improvements on coarse version on single node.
I'm currently running mpiexec --host s1,s2 -np 2 raxml-ng-coarse --workers 8 --threads 32 --msa aln.fa --model LG+I+F+G4 --bs-trees 500
on two 32-core machines, is this rational? (version 27.10.2019)
Proper documentation on coarse-grained parallelization is coming soon...
Meanwhile, please read: https://github.com/amkozlov/raxml-ng/wiki/Parallelization and in particular: https://github.com/amkozlov/raxml-ng/wiki/Parallelization#coarse-grained-parallelization-for-short-alignments
This should give you an idea on how many workers to use.
Hi @amkozlov, wanted to ask if there's already a raxml-ng test version for this intended implementation of concurrent tree searches/bootstraps? I'd be keen to give it a try if so.
Many thanks, Max