Re: Make and Clusters

[David Delahaye]

Hello,

Thanks a lot to everyone for the numerous clues.

Best regards,

David.

Le 10/10/2017 à 18:55, Shaun Jackman a écrit :
> Hi, David. Two options:
>
> 1. Use Biomake, which is mostly compatible with GNU Make, and supports 
> submitting jobs to Slurm.
> https://github.com/evoldoers/biomake
>
> It can be installed with Linuxbrew on Linux or Homebrew on macOS.
> brew install homebrew/science/biomake
>
> 2. Precede each command that you want to run on the cluster with 
> $qsub. Set that variable qsub to submit a job and wait for it to 
> finish. For example:
>
> # Slurm
> qsub=sbatch --wait
>
> # SGE
> qsub=qsub -sync y
>
> # PBS
> qsub=qsub -Wblock=true
>
> I haven't tried but it seems possible that you could set the variables 
> SHELL and .SHELLFLAGS to run qsub for every command. See 
> https://www.gnu.org/software/make/manual/html_node/Choosing-the-Shell.html
>
> Cheers,
> Shaun

--

David Delahaye

Professor
Université de Montpellier
LIRMM (UMR 5506)
address@hidden
Phone: (+33) (0)4 67 41 86 01
http://www.lirmm.fr/~delahaye/ <http://www.lirmm.fr/%7Edelahaye/>         


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