How to run iqtree in a slurm parallel system?

[Chang Ye]

The lastest version of iq-tree is MPI inplanted. 

But when trying to start a iq-tree job in slurm system, with command

srun -N2 -n 48 iqtree -s seq.fa -bb 2000 -nt 48 -ntmax48

There is 24 CUPs in each node, but iq-tree was interrupted with error message: 

ERROR: You have specified more threads than CPU cores available

---

srun -N2 -n 48 iqtree -s seq.fa -bb 2000 -nt AUTO -ntmax48

This command can run without error, but iq-tree only use 24 CUPs.

---

Could you please shoe me how to utilize CUP for iq-tree in a slurm system.

[Dominik Schrempf]

Hello Ye,

You need to use mpirun. E.g.,

srun -N2 -n48 mpirun -np 2 iqtree -nt 24 ...

This will run two iqtree processes with 24 threads each. You just need to make sure that those two processes run on the two different nodes that you reserve!

Regards,
Dominik

[Dominik Schrempf]

I just checked, and it seems that slurm can now directly run MPI programs (--mpi).

See https://slurm.schedmd.com/mpi_guide.html

On September 20, 2018 5:56:22 AM GMT+02:00, Chang Ye <yech...@gmail.com> wrote:

[Chang Ye]

Seems that there is multiple mpi type available on the cluster. Which one is the right choice for iq-tree? 

srun --mpi=list
srun: MPI types are...
srun: mpi/mpichgm
srun: mpi/mpichmx
srun: mpi/mpich1_p4
srun: mpi/pmi2
srun: mpi/mpich1_shmem
srun: mpi/openmpi
srun: mpi/none
srun: mpi/lam
srun: mpi/mvapich

BTW, will the command become:

srun -N2 -n48 --mpi=openmpi iqtree -nt 48 ...

[Chang Ye]

or just

srun -N2 -n48 --mpi=openmpi iqtree -nt 24 ...

will `-nt AUTO` work in mpi process

srun -N2 -n48 --mpi=openmpi iqtree -nt AUTO ...

[Chang Ye]

It taking a very long time to initiate mpi process when run iqtree with this command.

The the job failed with such error message:

```

 error: cn7032: tasks 120-121,123-125,127,129-136,138-139,141-143: Floating point exception

 error: cn7032: tasks 122,126,128,140: Floating point exception (core dumped)

```