These are chat archives for nextflow-io/nextflow
Hi all. I'm looking to run
nextflow run . -with-mpi on a slurm cluster. My submission scripts look like this:
#!/bin/bash --login #SBATCH --job-name=nf-chickpea #SBATCH --time=2:00:00 #SBATCH --ntasks=2 #SBATCH --ntasks-per-node=1 #SBATCH --cpus-per-task=16 module load java export NXF_CLUSTER_SEED=$(shuf -i 0-16777216 -n 1) srun nextflow run -resume . -with-mpi
But the slurm output suggests that nextflow is expecting the OMPI_COMM_WORLD_RANK environment variable:
Missing `$OMPI_COMM_WORLD_RANK` variable -- it looks you are not running in a MPI environment Missing `$OMPI_COMM_WORLD_RANK` variable -- it looks you are not running in a MPI environment srun: error: z012: task 0: Exited with exit code 1 srun: error: z013: task 1: Exited with exit code 1
Missing $OMPI_COMM_WORLD_RANK variable errors from nextflow?
--cpus-per-taskis there to ensure that each 'task' gets enough CPUs on the same machine. The
sbatchmanual page gives an example where you have a job with 4 tasks, each requiring 3 cpus - 12cpus in total. Without stipulating
--cpus-per-task 3, the schedule would think - "this person requires 12 cpus, so I'll give them 3 quad-core nodes".
--cpus-per-task 3, the slurm scheduler will allocate you four quad-core cpus. One of the cpus on each node will be wasted, but at least each of your tasks gets 3 cpus on the same node.
--cpus-per-task, the controller will just allocate one cpu per task.
ERROR ~ Unable to parse config file: '/work/projects/nn9305k/software/Bifrost/nextflow.config'
Cannot get property 'l' on null object