Just on Christmas the snow came to southern Finland and we had some ‘white powdered Christmas’. However, now, a few day after that we got quite a nice amount of snow and looking at the temperatures it seems it came to stay. Lets see, maybe I’ll manage even this winter to learn better skiing or skating.
Today I noticed for the first time the concept of submodules in git. While cloning a repository from GitHub I noticed that one folder in it remained empty. After having a closer look, I noticed a reference to another repository tree like this:
Here, the folder htslib is actually from a tree in a different repository. After I cloned the repository like this (I forked it before):
git clone https://github.com/fischuu/SE-MEI.gitthe folder htslib remained empty. That is because files from submodules are not fetched by default. This needs to be done separately by first initializing the submodules (first, cd into the cloned repository)
git submodule initand then update the files from it
git submodule updateAfter these steps, the repository should be complete. However, instead of initializing the submodule separately, there is also a shortcut to fetch them all in one step by adding an additional parameter to the cloning like this:
git clone --recurse-submodules https://github.com/fischuu/SE-MEI.gitMore details to git submodules can be found here.
In order to permanently add an external HDD, the best way is to first identfy the UUID and the corresponding file system by typing
sudo blkidwith that information one can edit the fstab
sudo vim /etc/fstaband enter then there a line with the format
UUID=<UUID> \tab <mountPoint> \tab <filesystem> \tab <options> \tab 0 \tab 1
Here, the values for <UUID> and <filesytem> we get from the blkid command, the mount point is ‘free choice’ and as option, I choose e.g. errors=remount-ro
Once the fstab is populated like this, just try to mount the disc by typing
sudo mount -aSometimes 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.
This morning something strange happened on my way to the office – I noticed a bright, shiny, yellowish thing on the sky! It was the first time this winter, that the sun was up before I arrived at the office. Finally it seems that the winter is going to be over ‘soon’.