How to run 2 programme one after another using single SLURM?

Question

[kabir.deb]

Hello experts,

I want to run 2 programme simultaneously using SLURM (serially) script by which output of 1st programme used as input of second programme. I have multiple fasta file as input, how can I do that!

Thanks

[Ram]

What have you tried? You can pipe the output from program 1 to program 2 or save the output from program 1 to a file and use it as input to program 2. You cannot run them simultaneously as program 2 depends on the successful completion of program 1.

Answer 1

[Mensur Dlakic]

If the output of first program is used for second, that is not running them simultaneously but sequentially.

Simply have two lines in your SLURM script, each of which is running the required programs in correct order.

Answer 2

[h.mon]

I think you want one job start to be dependent on the previous job being finished, correct? You can do this with SLURM by using --dependency=afterok:jobid, where jobid is the ID number of the job you want to finish in order to run the second job.