Re: Spreading parallel across nodes on HPC system

[Christian Meesters]

Hi,

Take a look here for a template: https://mogonwiki.zdv.uni-mainz.de/dokuwiki/start:working_on_mogon:workflow_organization:node_local_scheduling#running_on_several_hosts

Of course, you need to adjust the partition names and the like, and the example is unmaintained, but it worked for me for quite a while.

Best regards,

Christian

On 11/10/22 20:49, Ken Mankoff wrote:

> Hello,
>
> I'm trying to run parallel on multiple nodes. Each node may have a different number of CPUs. It appears the best syntax for this is from the man page --slf section:
>
> 8/my-8-cpu-server.example.com
> 2/my_other_username@my-dualcore.example.net
>
> My problem is that I'm running in the SLURM environment. I can get the hostnames with
>
> scontrol show hostnames $SLURM_JOB_NODELIST > nodelist.0
>
> But I cannot easily get the CPUS-per-node. From the SLURM docs,
>
> SLURM_JOB_CPUS_PER_NODE: Count of CPUs available to the job on the nodes in the allocation, using the format CPU_count[(xnumber_of_nodes)][,CPU_count [(xnumber_of_nodes)] ...]. For example: SLURM_JOB_CPUS_PER_NODE='72(x2),36' indicates that on the first and second nodes (as listed by SLURM_JOB_NODELIST) the allocation has 72 CPUs, while the third node has 36 CPUs.
>
> So, parsing '72(x2),36' seems complicated.
>
> If I requested a total of 1000 tasks, but have no control over how many nodes, can I just call parallel with -j1000 and pass it a hostfile without the "CPUs/" prepended to the hostname? Would parallel then start however many jobs it can per node, and if for some reason I was allocated 1000 CPUS on 1 node, that would work fine, as would 1 CPU on 1000 different nodes?
>
> Thanks,
>
>   -k.
>
>