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docs: remove Cori, update Perlmutter info
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@@ -17,7 +17,7 @@ proceed until you have been added to the metatlas group. | |
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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: | ||
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```bash | ||
ssh -L localhost:53682:localhost:53682 [email protected] \ | ||
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@@ -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: | ||
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@@ -162,10 +162,9 @@ like: | |
JGI-HILIC 20210804_JGI-AK_PA-CT_507784_Frtlzr_Set1_QE-139_HILICZ_USHXG01490 0 | ||
``` | ||
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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. | ||
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#### Evaluate Outputs | ||
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@@ -200,7 +199,7 @@ https://github.com/biorack/metatlas/blob/main/notebooks/reference/RT-Alignment.i | |
### Perform ISTDsEtc Analysis | ||
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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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