[GAT] Fix slurm and tpv trainings

[pauldg]

There are some legacy configuration options for slurm and TPV in the trainings.

For the connecting to a cluster training:

training-material/topics/admin/tutorials/connect-to-compute-cluster/tutorial.md

Line 165 in e822f5f

> + SelectType: select/cons_res

cons_res is legacy and is replaced by cons_tres
For the TPV training:

training-material/topics/admin/tutorials/job-destinations/tutorial.md

Line 732 in e822f5f

> + native_specification: --nodes=1 --ntasks=1 --cpus-per-task={cores} --time={params['walltime']}:00:00

params['walltime'] should be entity.params.get('walltime')

[mvdbeek]

This seems odd, if you anticipate walltime isn't set you would need to set a default, otherwise indexing via [] is what I'd use ... there's an obvious error if the value isn't set.

... also if {cores} works, i would keep it consistent and use {params['walltime']} ?

[pauldg]

Good point, I was testing the training on one of the EU training vms and was getting an error saying params was undefined. I'll post the logs in a couple of hours.

[mvdbeek]

I'm rerunning the tutorials and will make sure it works (or not 😆 )

[mvdbeek]

OK, I think I get it now, it does need to be entity, because params is evaled as an f-string and is not a top level attribute of the EntityModel. I've used [ though since I don't think we'd ever want None:00:00 as walltime.

[lldelisle]

While you are working on this. I was surprised that the native spec do not use the mem (for example --mem={round(mem*1024)} while mem is defined in the tpv example).
Also, maybe this is helpful for you, here is how they deal with runtime in the shared tpv:
https://github.com/galaxyproject/tpv-shared-database/blob/9e497f53c2e72bf0467952f0d11bde80ae5e3fc3/tools.yml#L2941

[mvdbeek]

While you are working on this. I was surprised that the native spec do not use the mem (for example --mem={round(mem*1024)} while mem is defined in the tpv example).

I know now why:

:04:32,995 [pN:handler_0,p:684732,tN:SlurmRunner.work_thread-3] (14) native specification is: --nodes=1 --ntasks=1 --cpus-per-task=2 --mem=8192
Nov 23 12:04:33 gat-1.eu.training.galaxyproject.eu galaxyctl[684732]: python: error: Memory specification can not be satisfied

I'll check how slurm is configured, maybe we'll just have to tune this down a little

[lldelisle]

😍