Skip to content

Update 02_bioinfx_example.Rmd #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
RFillinger wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update 02_bioinfx_example.Rmd #1

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 6 additions & 6 deletions 02_bioinfx_example.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 <username>
squeue --me
```

## **Create Directory**
Expand Down Expand Up @@ -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 <username>
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 <username>
squeue --me

# Go back to the project directory
cd /varidata/researchtemp/hpctmp/BBC_workshop_June2023/<username>
Expand Down Expand Up @@ -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 <username>
squeue --me

```

Expand Down