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docs: remove Cori, update Perlmutter info
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wholtz committed Aug 25, 2023
1 parent 9582583 commit 5cac5ab
Showing 1 changed file with 6 additions and 7 deletions.
13 changes: 6 additions & 7 deletions docs/Targeted_Analysis.md
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ proceed until you have been added to the metatlas group.

1. On your local computer open a terminal.
1. Copy and paste the following command into the terminal,
where NERSC_USERID should be replaced with your NERSC username:
where `NERSC_USERID` should be replaced with your NERSC username:

```bash
ssh -L localhost:53682:localhost:53682 [email protected] \
Expand All @@ -37,7 +37,7 @@ proceed until you have been added to the metatlas group.
Please go back to rclone".
1. Go to [jupyter.nersc.gov](https://jupyter.nersc.gov/) and login using your
NERSC account.
1. Click the 'start' button for a Perlmutter 'Shared CPU Node' and wait for
1. Click the 'start' button for a Perlmutter 'Login Node' and wait for
the JupyterLab interface to load.
1. From the menu bar, select 'File' -> 'New' -> 'Terminal'.
1. Copy and paste the following command into the terminal:
Expand Down Expand Up @@ -162,10 +162,9 @@ like:
JGI-HILIC 20210804_JGI-AK_PA-CT_507784_Frtlzr_Set1_QE-139_HILICZ_USHXG01490 0
```

This will submit a slurm job. On Cori, you will receive an email when the job
starts executing and when it has completed. On Perlmutter, the SLRUM job
notifications emails are currently broken. Typical HILIC jobs take several hours
to complete.
This will submit a slurm job. You may receive an email when the job
starts executing and when it has completed. Typical HILIC jobs take several
hours to complete.

#### Evaluate Outputs

Expand Down Expand Up @@ -200,7 +199,7 @@ https://github.com/biorack/metatlas/blob/main/notebooks/reference/RT-Alignment.i
### Perform ISTDsEtc Analysis

1. Launch [jupyter.nersc.gov](https://jupyter.nersc.gov/) in your web browser
and start a 'Shared CPU Node' on Cori or Perlmutter.
and start a 'Login Node' session on Perlmutter.
1. Open
`~/metabolomics_data/<short_experiment_id>/<workflow_name>/<rt_alignment_number>/0/Targeted/<workflow_name>/<project_id>_<workflow_name>_ISTDsEtc-POS.ipynb`
within JupyterLab (you no longer need to use the Classic Notebook interface).
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