Hello all,
I made a post on this once before for the previous version of RAxML, but was hoping to get some insight on memory allocation for running jobs on the cluster.
I am running a concatenated phylogenomic dataset (UCEs, AHEs, nuclear genes) from the Phyluce pipeline. My dataset contains 169 taxa and 2,706,714 sites, and the nodes in the computer cluster I am using have up to 50 cores (28 cores for nodes that cannot be interrupted by higher priority job submission). A preliminary memory assessment using the RAxML-NG check estimated I use 139 threads and 50 GB of memory.
I have tried running a few different scripts using RAxML-NG, but whether I am running 20 or 50 starting trees, each tree search is taking 6-7 hours, and I only get a 72 hour limit in the cluster. Am I perhaps allocating memory wrong? Do I need to be using thread pinning?
For reference, here is an example of the script I am running (on a node that 25 cores allocated to my job submission, and has up to 182 GB of memory):
raxml-ng --msa mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.phylip --model GTR+G --prefix T25 --threads 25 --seed 2 --tree pars{25},rand{25}
So here I have made the number of threads equal to the number of cores, still using one node. Perhaps I am doing something wrong here? Any recommendations on the script or how I am allocating memory would be extremely helpful. I am happy to provide any other files or info that would be useful.
Best,
Justin