Dear astral-Team,
Thanks for this great software package.
Describe the bug
I am trying to run a moderately large dataset with ~1500 gene trees and ~140 species using the astral-MP. Surprisingly, I am not able to run it on my university's HPC cluster. I run out of memory even with 60 threads and the option -Xmx1300g (the maximum possible on my cluster). I thought this option would set a memory limit for astral and it just runs longer but actually it stops with OOM error when calculating distance matrix.
To Reproduce
java -Xmx1300g -D"java.library.path=/path/to/Astral.5.15.5/lib/" -jar /path/to/Astral.5.15.5/astral.5.15.5.jar -T 60 -i genes.treefile -o genes_astral.tre -t 2 2>genes_astral.log
Log file
last 4 lines of the log before it stopped:
...
Using polytree-based weight calculation.
Number of gene trees: 15079
15079 trees have missing taxa
Calculating distance matrix (for completion of X) ....with 4 distance matrices for parallellism
slurm error file:
slurmstepd: error: Detected 1 oom_kill event in StepId=702545.batch. Some of the step tasks have been OOM Killed.
** Version
5.15.5
Thanks in advance and all the best
Patrick
Dear astral-Team,
Thanks for this great software package.
Describe the bug
I am trying to run a moderately large dataset with ~1500 gene trees and ~140 species using the astral-MP. Surprisingly, I am not able to run it on my university's HPC cluster. I run out of memory even with 60 threads and the option -Xmx1300g (the maximum possible on my cluster). I thought this option would set a memory limit for astral and it just runs longer but actually it stops with OOM error when calculating distance matrix.
To Reproduce
java -Xmx1300g -D"java.library.path=/path/to/Astral.5.15.5/lib/" -jar /path/to/Astral.5.15.5/astral.5.15.5.jar -T 60 -i genes.treefile -o genes_astral.tre -t 2 2>genes_astral.log
Log file
last 4 lines of the log before it stopped:
...
Using polytree-based weight calculation.
Number of gene trees: 15079
15079 trees have missing taxa
Calculating distance matrix (for completion of X) ....with 4 distance matrices for parallellism
slurm error file:
slurmstepd: error: Detected 1 oom_kill event in StepId=702545.batch. Some of the step tasks have been OOM Killed.
** Version
5.15.5
Thanks in advance and all the best
Patrick