SLURM + hello

[Félix C. Morency]

Hi,

I'm new to Nextflow and SLURM. I built a small SLURM cluster using [1] and I can launch jobs on it with `srun` and `sbatch`. However, I'm unable to launch the Nextflow `hello` pipeline using the SLURM executor. The output is

ddhpc@slurmctld:~$ ./nextflow run hello
N E X T F L O W  ~  version 0.22.2
Launching `nextflow-io/hello` [clever_wescoff] - revision: 6b9515aba6 [master]
[warm up] executor > slurm
[83/8fdf78] Submitted process > sayHello (4)
[d1/6659b6] Submitted process > sayHello (3)
[4c/f5fd30] Submitted process > sayHello (2)
[e4/8eb3c4] Submitted process > sayHello (1)

and it just hangs there. I can see that the `slurmd` node receives the job, but no `slurm-JID.out` is ever created.

  [1]: https://github.com/datadrivenhpc/docker-slurmbase

Any ideas? Thanks,
-F

[Paolo Di Tommaso]

Hi there, 

Does this cluster shared a common directory? nextflow needs to be launched in a directory that is accessible by all cluster nodes or you can specify this path by using the command line option `-w` 

Hope it helps.

Cheers,

Paolo

--
You received this message because you are subscribed to the Google Groups "Nextflow" group.
To unsubscribe from this group and stop receiving emails from it, send an email to nextflow+unsubscribe@googlegroups.com.
Visit this group at https://groups.google.com/group/nextflow.
For more options, visit https://groups.google.com/d/optout.

[Félix C. Morency]

Hi Paolo,

That was it! Added a volume via convoy-nfs and everything works as expected.

Thanks,
-F

On Tuesday, October 11, 2016 at 1:24:52 PM UTC-4, Paolo Di Tommaso wrote:

Hi there, 

Does this cluster shared a common directory? nextflow needs to be launched in a directory that is accessible by all cluster nodes or you can specify this path by using the command line option `-w` 

Hope it helps.

Cheers,

Paolo

On Tue, Oct 11, 2016 at 7:20 PM, Félix C. Morency <felix....@gmail.com> wrote:

Hi,

I'm new to Nextflow and SLURM. I built a small SLURM cluster using [1] and I can launch jobs on it with `srun` and `sbatch`. However, I'm unable to launch the Nextflow `hello` pipeline using the SLURM executor. The output is

ddhpc@slurmctld:~$ ./nextflow run hello
N E X T F L O W  ~  version 0.22.2
Launching `nextflow-io/hello` [clever_wescoff] - revision: 6b9515aba6 [master]
[warm up] executor > slurm
[83/8fdf78] Submitted process > sayHello (4)
[d1/6659b6] Submitted process > sayHello (3)
[4c/f5fd30] Submitted process > sayHello (2)
[e4/8eb3c4] Submitted process > sayHello (1)

and it just hangs there. I can see that the `slurmd` node receives the job, but no `slurm-JID.out` is ever created.

  [1]: https://github.com/datadrivenhpc/docker-slurmbase

Any ideas? Thanks,
-F

--
You received this message because you are subscribed to the Google Groups "Nextflow" group.

To unsubscribe from this group and stop receiving emails from it, send an email to nextflow+u...@googlegroups.com.

[Paolo Di Tommaso]

Cool! 

p