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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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Can it run on a Slurm? #24

Open vasilislenis opened 5 years ago

vasilislenis commented 5 years ago

Hello,

I am trying to apply SQuiRE on my data but I have access on a Slurm scheduler and not on an SGE. So, I have changed the scheduler commands but I am getting the following error:

sbatch: error: Invalid numeric value "wd" for cpus-per-task.

Which apparently is the SGE command for cpus.

Here are my sbatch commands:

`##!/bin/bash --login

$ -cwd

SBATCH --job-name=fetch

SBATCH -p compute

SBATCH -n 1 --core-spec=40

SBATCH --tasks-per-node=40`

BTW, I am trying to run Fetch.

Thank you very much in advance, Vasilis.

cpacyna commented 5 years ago

Hi Vasilis,

We just switched over to Slurm and have been able to run SQuIRE jobs. Here's the format we've been using:

`

SBATCH

SBATCH --job-name=fetch

SBATCH --time=24:0:0

SBATCH --partition=parallel

number of tasks (processes) per node

SBATCH --ntasks=8

SBATCH --ntasks-per-node=8

SBATCH --mail-type=end

SBATCH --mail-user=email@email.com

`

Hope this helps!

Regards, Chloe

vasilislenis commented 5 years ago

Thank you very much, Chloe! My job is submitted but it is on PD condition, yet. It seems ok, so far... Fingers crossed! :)