ENDE

Category: Know-how

  • Cancel all slurm jobs larger job ID X

    Sometimes it happens that we have running a whole bunch of slurm jobs from different projects, some of them are running already for days, while others are just fired – and then we noticed, damn, the 100 jobs that I just fired are wrong and they need to be canceled. Unfortunately, there is no slurm command that can do that, it requires some kind of scripting to do that.

    The following script takes as an input a slurm job ID and cancels all jobs larger than that (that belong to the logged in user…).

    #!/bin/bash

declare -a jobs=()

if [ -z "$1" ] ; then
    echo "Minimum Job Number argument is required.  Run as '$0 jobnum'"
    exit 1
fi

minjobnum="$1"

myself="$(id -u -n)"

for j in $(squeue --user="$myself" --noheader --format='%i') ; do
  if [ "$j" -gt "$minjobnum" ] ; then
    jobs+=($j)
  fi
done

scancel "${jobs[@]}"

    If you store this e.g as killLarger.sh in your PATH somewhere, you can just use it from anywhere and cancel slurm jobs that are larger than this ID.

  • Another update of bitools

    During the last two weeks, I updated the bitools container twice. Two new tools were added to it:

    1. velvet

    An easy to apply de-novo assembler that I use for metagenome studies

    2. Bandage

    A tool to visualize the graphs that are provided from velvet

  • New version of the bitools docker container

    I updated the docker container that I maintain (bitools) to keep all the bioinformatics tools together that I recently use. Yesterday I added the tool FEELnc to it, a tool to detect lncRNAs from RNA-seq data.

    UPDATE: Apparently there was an issue with the Forkmanages perl module in the docker container, I fixed that on 7.12.2017 and udated the docker image v0.1.6 on Docker Hub.