Phyml-mpi stuck before starting bootstraps

[ckallu]

Hi,

I have an alignment file with 455 amino acid sequences. I am running the following command:
mpirun -np 20 ./phyml-mpi -i phyml_analysis/seq_phyml_tree.txt -d aa -q -m LG -a e -o tlr -b 500 > phyml_analysis/seq_phyml_output.txt

It takes ~3hrs to complete the optimization steps but then it gets stuck after this step:
Launch bootstrap analysis on the most likely tree...

The seq_phyml_boot_stats.txt and seq_phyml_boot_trees.txt files are empty. I waited for over 24hrs, yet the bootstrap analysis did not launch. I tried the same approach with fewer input sequences (35 sequences) and fewer bootstraps (40 bootstraps) by running this:
mpirun -np 20 ./phyml-mpi -i phyml_analysis/test_seq_phyml_tree.txt -d aa -q -m LG -a e -o tlr -b 40 > phyml_analysis/test_seq_phyml_output.txt

And for this, the optimization steps complete in 1 min and the bootstrap analysis for 40 bootstraps runs to completion in 5 mins. Unsure why the parallel bootstrapping for 500 replicates run across 20 cores is not launched.

[stephaneguindon]

Are you 100% sure the machine you're using here has enough RAM et CPUs to run 20 analyses in parallel? I would try try -np 10 just to see...