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Summary

I can transfer files to/from Bianca using rsync

ssh sven@transit.uppmax.uu.se
mount_wharf sens2023598
rsync my_local_file.txt sven@transit.uppmax.uu.se:sens2023598
rsync --recursive my_folder sven@transit.uppmax.uu.se:sens2023598

I can see the CPU and memory usage of jobs

jobstats --plot 1234567

I understand how to set up jobs efficiently

  • Enough cores for memory
  • CPU limited? Consider adding more until CPU usage is around 80% on average
  • Consider addigng 1 core for safety

I can schedule a simple workflow of jobs that depend on each other using Slurm

sbatch --A sens2023598 --dependency=afterok:5000000,5000001 do_c.sh

I can schedule a simple workflow of jobs that depend on each other using Nextflow

[not discussed much]

I can run replicate jobs using Slurm job arrays

#SBATCH --array=0-10

I understand how to install software myself

[many steps]

I understand how to use packages and libraries for scripts

[many steps]

I understand what containers are

[many steps]

I understand how to build from source

[many steps]

I can can run the voted-for IDE on Bianca

nteractive -A sens2023598 -n 2 -t 8:00:00
module load R/4.3.1 R_packages/4.3.1 RStudio/2023.06.2-561
rstudio