From 63375f5f6d3da31e7b687aa78a131cadd8746bf5 Mon Sep 17 00:00:00 2001 From: Robert Fillinger <10966085+RFillinger@users.noreply.github.com> Date: Thu, 17 Oct 2024 13:41:06 -0400 Subject: [PATCH] Update 02_bioinfx_example.Rmd --- 02_bioinfx_example.Rmd | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/02_bioinfx_example.Rmd b/02_bioinfx_example.Rmd index 29b7e05..acebe9e 100755 --- a/02_bioinfx_example.Rmd +++ b/02_bioinfx_example.Rmd @@ -16,16 +16,16 @@ Here, we will combine some of the commands we have learned today to perform a to While simple file manipulations can be done on the submit node, computationally intensive operations should be performed using preallocated computational resources. An **interactive job** allows us to preallocate resources while still being able to run commands line by line. -We will start an interactive job, requesting one CPU core and 6 hours of walltime. +We will start an interactive job, requesting one CPU core and 1 hour, 30 minutes of walltime. ```{bash, eval= FALSE, engine= "sh"} -srun --nodes=1 --ntasks-per-node=1 --time=06:00:00 --pty bash +srun --nodes=1 --ntasks-per-node=1 --time=01:30:00 --pty bash ``` After a job has been submitted, users can check on the status (e.g. how long it has been running) of it using the following. ```{bash, eval= FALSE, engine= "sh"} -squeue -u +squeue --me ``` ## **Create Directory** @@ -152,13 +152,13 @@ First, we `exit` from our interactive job because we want to get back on to the ```{bash, eval=FALSE, engine="sh"} # You should see one job when you run this command, corresponding to your interactive job. -squeue -u +squeue --me # Exit the interactive job exit # Now you should see no jobs when you run this command because the interactive job has ended. -squeue -u +squeue --me # Go back to the project directory cd /varidata/researchtemp/hpctmp/BBC_workshop_June2023/ @@ -221,7 +221,7 @@ sbatch -p big run_salmon.sh Users can check if the job is running with the following command. The job should take about two minutes to complete. ```{bash, eval=FALSE, engine="sh"} -squeue -u +squeue --me ```