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bayesiancook / phylobayes

PhyloBayes: phylogenetic reconstruction using infinite mixtures (CAT and CAT-GTR) -- serial version (for MPI, see pbmpi.git)
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Memory usage limit? #8

Open morgansobol opened 1 year ago

morgansobol commented 1 year ago

Hi,

I cannot seem to find much information on this, but is there any way to limit the memory usage of PhyloBayes so it doesn't get killed? No matter how much memory I allocate, it will use it all.

Here is the script I tried: pb -d MSNifAlign02.phy -T MSNif02_tree_rooted_2.txt -r bch_chl.outgroup -cal calib -cat -ln -rp 3800 200 MSNifChrono01

Thanks! Morgan

bayesiancook commented 1 year ago

Dear Morgan,

how big is your dataset? Apart from memory issues, phylobayes works well in terms of computational efficiency and inference quality only for datasets of moderate size (a few tens of thousands of aligned positions, for up to 100 / 200 taxa).

best,

Nicolas