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Make and Clusters
From: |
Shaun Jackman |
Subject: |
Make and Clusters |
Date: |
Tue, 10 Oct 2017 09:55:37 -0700 |
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
andĀ .SHELLFLAGS to run qsub for every command. SeeĀ
https://www.gnu.org/software/make/manual/html_node/Choosing-the-Shell.html
Cheers,
Shaun