Page Comparison

...

The newest update to SLURM has better handling of backfill, which means if you specify a expected time for your program to run it can be placed earlier as nodes open up. Using sbatch you can specify a limit on the total run-time with -t or --time d-h:m:s. Times can be specified as min, min:sec, hr:min:sec, day-hr, day-hr:min, and day-hr:min:sec. So -t 5 means five minutes -t 5:00:00 is five hours.

Here are some approximate run times (min sec) for BWA-mem, bowtie2, and samtools with 7, 15, 30, and 60 million fastq sequences. Samtools was used to convert SAM files and then sort the resulting BAM files.  These runs were done with 8 cores and 16 GB memory. The timings were obtained using the time command  ( e.g. time bwa mem -t 8  <hg38 ref> <sequences (human)> ) though some  programs report the runtimes in the output. To effectively use the back fill, take note of how long your programs run and add a bit more time to give your programs some extra run time using the -t parameter.or --time parameter.  Make sure to add run times for workflows, e.g. a bwa mem  run followed by  samtools reformatting as well as accounting for multiple runs, e.g. processing 6 fastq files. 

...