Why iq-tree not speedup on cluster environment?

[Chang Ye]

I submit iq-tree job to a slurm cluster environment with this command:

#!/bin/bash


#SBATCH --nodes=16

#SBATCH --cpus-per-task=24

#SBATCH --partition=work



srun -n 8 -N 8 -c 24 iqtree -nt AUTO -s file1.fa  -bb 2000 &

srun -n 8 -N 8 -c 24 iqtree -nt AUTO -s file2.fa  -bb 2000 &

The iqtree binary is compiled with omp-mpi option.

I expect iq-tree to use 8*24 = 192 (CPUs), but iqtree show this message in log file.

NOTE: 1665 MB RAM (1 GB) is required!


Measuring multi-threading efficiency up to 24 CPU cores

2 trees examined

Threads: 1 / Time: 38.875 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -602418

Threads: 2 / Time: 62.595 sec / Speedup: 0.910 / Efficiency: 46% / LogL: -708891

BEST NUMBER OF THREADS: 1

After submit the job, I login to the computation node find out the CPU load is ultra low. It seems that iqtree is not speedup on mpi run.

[Minh Bui]

Hi Chang,

The student who initiated the MPI feature left the project, so it’s not well tested. I’m not sure if -nt AUTO option works with MPI… Please specify the number of threads.

Thanks, Minh

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[Chang Ye]

Thanks for the info. 

But I wonder why the speedup fold value is lower than 1 when multiple thread is used.

Speedup: 0.910

[Minh Bui]

Yes it looks weird indeed, but as said the combination of -nt AUTO and MPI might not work.

Cheers, Minh

[Chang Ye]

Ok, I’ll adjust the -nt argument and report the performance here.