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update the PSC and Delta usage info #188

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update the PSC and Delta usage info #188

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152 changes: 79 additions & 73 deletions _posts/2022-01-01-psc-usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,33 +6,58 @@ description: PSC cluster usage.
comments: false
---

# Misc. resources
<table class="table">
<thead>
<tr>
<th> </th>
<th>PSC(Bridges-2)</th>
</tr>
</thead>
<tbody>
<tr>
<td>User Guide</td>
<td>https://www.psc.edu/resources/bridges-2/user-guide-2/</td>
</tr>
<tr>
<td>Connect from browser</td>
<td>https://ondemand.bridges2.psc.edu/</td>
</tr>
<tr>
<td>ESPnet installation guide</td>
<td colspan="2">https://espnet.github.io/espnet/installation.html</td>
</tr>
<tr>
<td>Step-by-step guide with pictures</td>
<td colspan="2">https://granite-echidna-ff2.notion.site/Access-for-PSC-07c3d4c05b54426895e3ddc87276e4b5</td>
</tr>
</tbody>
</table>
## Step by step starting towards successful ssh login
- Look for guide with some screenshots above

1. Create an account for [ACCESS](https://identity.access-ci.org/new-user)
- This account is used for both PSC and Delta
- When you create, [Register with an existing identity](https://identity.access-ci.org/new-user-federated). Don't do Register without an existing identity.

2. Send the username to allocation managers (e.g. Xuankai) to add the user in our group.
- After this step is done, you should be able to see `list of resources` at https://allocations.access-ci.org/allocations/summary

3. Initialise your PSC password (used for ssh login)
- Go to https://www.psc.edu/resources/bridges-2/user-guide-2-2/ and click `PSC Password Change Utility`
- **It may take few hours** for your `username` and `email` to be recognised, even if they're correct.

4. Access via ssh
- ssh [username]@[resource_dir]
- E.g., `[email protected]`
- Use the password you initialised in step 3.

# Important
1. `Home` directory is of limited space. Please do most of your work in ocean storage (`$ cd ${PROJECT}`)
2. When you publish a paper, please **acknowledge the PSC and ACCESS**. We will get benefit when we apply for PSC credits next time.
* [Acknowledgement webpage](https://access-ci.org/about/acknowledging-access/)
* Example: Experiments of this work used the Bridges2 system at PSC through allocations CIS210014 and IRI120008P from the Advanced Cyberinfrastructure Coordination Ecosystem: Services \& Support (ACCESS) program, supported by National Science Foundation grants \#2138259,\#tel:2138286, \#tel:2138307, \#tel:2137603, and \#tel:2138296.
<details>
<summary> Add the following references </summary>

```
@ARTICLE{xsede,
author = {J. Towns and T. Cockerill and M. Dahan and I. Foster and K. Gaither and A. Grimshaw and V. Hazlewood and S. Lathrop and D. Lifka and G. D. Peterson and R. Roskies and J. R. Scott and N. Wilkins-Diehr},
journal = {Computing in Science \& Engineering},
title = {XSEDE: Accelerating Scientific Discovery},
year = {2014},
volume = {16},
number = {5},
pages = {62-74},
keywords={Knowledge discovery;Scientific computing;Digital systems;Materials engineering;Supercomputers},
doi = {10.1109/MCSE.2014.80},
url = {doi.ieeecomputersociety.org/10.1109/MCSE.2014.80},
ISSN = {1521-9615},
month={Sept.-Oct.}
}
@inproceedings{nystrom2015bridges,
title={Bridges: a uniquely flexible HPC resource for new communities and data analytics},
author={Nystrom, Nicholas A and Levine, Michael J and Roskies, Ralph Z and Scott, J Ray},
booktitle={Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure},
pages={1--8},
year={2015}
}
```
</details>


# Summary of PSC usage and the partitions
* Both PSC have limited service units (SUs) for resource availability.
Expand Down Expand Up @@ -64,24 +89,35 @@ comments: false
</tbody>
</table>

## Step by step starting towards successful ssh login
- Look for guide with some screenshots above

1. Create an account for [ACCESS](https://identity.access-ci.org/new-user)
- This account is used for both PSC and Delta
- When you create, [Register with an existing identity](https://identity.access-ci.org/new-user-federated). Don't do Register without an existing identity.

2. Send the username to allocation managers (e.g. Xuankai) to add the user in our group.
- After this step is done, you should be able to see `list of resources` at https://allocations.access-ci.org/allocations/summary

3. Initialise your PSC password (used for ssh login)
- Go to https://www.psc.edu/resources/bridges-2/user-guide-2-2/ and click `PSC Password Change Utility`
- **It may take few hours** for your `username` and `email` to be recognised, even if they're correct.
## Misc. resources
<table class="table">
<thead>
<tr>
<th> </th>
<th>PSC(Bridges-2)</th>
</tr>
</thead>
<tbody>
<tr>
<td>User Guide</td>
<td>https://www.psc.edu/resources/bridges-2/user-guide-2/</td>
</tr>
<tr>
<td>Connect from browser</td>
<td>https://ondemand.bridges2.psc.edu/</td>
</tr>
<tr>
<td>ESPnet installation guide</td>
<td colspan="2">https://espnet.github.io/espnet/installation.html</td>
</tr>
<tr>
<td>Step-by-step guide with pictures</td>
<td colspan="2">https://granite-echidna-ff2.notion.site/Access-for-PSC-07c3d4c05b54426895e3ddc87276e4b5</td>
</tr>
</tbody>
</table>

4. Access via ssh
- ssh [username]@[resource_dir]
- E.g., `[email protected]`
- Use the password you initialised in step 3.

## GPU Partitions
* In `GPU / GPU-shared` partitions, each node consists of 8 v100 GPU devices
Expand Down Expand Up @@ -203,36 +239,6 @@ comments: false
print(f"sbatch -p {machine_name}-shared {gpus} {cpus} -t {hours}:00:00")
```

# Important
* `Home` directory is of limited space. Please do most of your work in ocean storage (`$ cd ${PROJECT}`)
* When you publish a paper, please acknowledge the PSC. We will get benefit when we apply for PSC credits next time.
* [Acknowledgement webpage](https://www.psc.edu/resources/bridges/acknowledgement-in-publications/)
* Example: This work used the Extreme Science and Engineering Discovery Environment (XSEDE) ~\cite{ecss}, which is supported by National Science Foundation grant number ACI-1548562. Specifically, it used the Bridges system ~\cite{nystrom2015bridges}, which is supported by NSF award number ACI-1445606, at the Pittsburgh Supercomputing Center (PSC).

```
@ARTICLE{xsede,
author = {J. Towns and T. Cockerill and M. Dahan and I. Foster and K. Gaither and A. Grimshaw and V. Hazlewood and S. Lathrop and D. Lifka and G. D. Peterson and R. Roskies and J. R. Scott and N. Wilkins-Diehr},
journal = {Computing in Science \& Engineering},
title = {XSEDE: Accelerating Scientific Discovery},
year = {2014},
volume = {16},
number = {5},
pages = {62-74},
keywords={Knowledge discovery;Scientific computing;Digital systems;Materials engineering;Supercomputers},
doi = {10.1109/MCSE.2014.80},
url = {doi.ieeecomputersociety.org/10.1109/MCSE.2014.80},
ISSN = {1521-9615},
month={Sept.-Oct.}
}
@inproceedings{nystrom2015bridges,
title={Bridges: a uniquely flexible HPC resource for new communities and data analytics},
author={Nystrom, Nicholas A and Levine, Michael J and Roskies, Ralph Z and Scott, J Ray},
booktitle={Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure},
pages={1--8},
year={2015}
}
```

# ESPnet installation steps
1. Miniconda installation
```bash
Expand Down
28 changes: 12 additions & 16 deletions _posts/2023-04-02-delta-usage.md
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Expand Up @@ -6,12 +6,22 @@ description: Delta cluster usage.
comments: false
---

# Misc. resources
# Account creation
- Create an account for NCSA on [ACCESS](https://allocations.access-ci.org/)
- Send the username to allocation managers (e.g. Xuankai) to add the user in our group.

## login
* Delta: check https://wiki.ncsa.illinois.edu/display/DSC/Delta+User+Guide#DeltaUserGuide-DirectAccesslogin_nodes

[General user guide for Delta](https://wiki.ncsa.illinois.edu/display/DSC/Delta+User+Guide)
# Important
1. `Home` directory is of limited space. Please do most of your work in ocean storage (`$ cd ${PROJECT}`)
2. When you publish a paper, please **acknowledge the Delta and ACCESS**. We will get benefit when we apply for Delta credits next time.
* [Acknowledgement webpage](https://access-ci.org/about/acknowledging-access/)
* Example: Experiments of this work used the Bridges2 system at PSC and Delta system at NCSA through allocations CIS210014 and IRI120008P from the Advanced Cyberinfrastructure Coordination Ecosystem: Services \& Support (ACCESS) program, supported by National Science Foundation grants \#2138259,\#tel:2138286, \#tel:2138307, \#tel:2137603, and \#tel:2138296.

# Summary of NCSA usage and the partitions
* NCSA has limited service units (SUs) for resource availability.
* [General user guide for Delta](https://wiki.ncsa.illinois.edu/display/DSC/Delta+User+Guide)
* `sinfo` lists all the available partitions in NCSA and their status.
<table class="table">
<thead>
Expand Down Expand Up @@ -40,13 +50,6 @@ comments: false
</tbody>
</table>

## Account creation
- Create an account for NCSA on [ACCESS](https://allocations.access-ci.org/)
- Send the username to allocation managers (e.g. Xuankai) to add the user in our group.

## login
* Delta: check https://wiki.ncsa.illinois.edu/display/DSC/Delta+User+Guide#DeltaUserGuide-DirectAccesslogin_nodes

## Other usage
* Submitting jobs with dependency
* This can be used to submit a job which is expected to start run after some specific jobs finish. In many cases, training a model can take a few days. However, Delta has the restriction that each job can run for 2 days at most. In this case, we can start a job with dependency for long jobs. For example, you already start a job ID is 000001 and you want a following job right after it. You can submit jobs like:
Expand Down Expand Up @@ -117,13 +120,6 @@ comments: false
slurm-tool v|version Print versions of slurm-tool tool and slurm itself
```

# Important
* `Home` directory is of limited space. Please do most of your work in ocean storage (`$ cd ${PROJECT}`)
* When you publish a paper, please acknowledge the Delta. We will get benefit when we apply for Delta credits next time.
* [Acknowledgement webpage](https://wiki.ncsa.illinois.edu/display/DSC/Delta+User+Guide#DeltaUserGuide-Acknowledge/)
* Example: This research is part of the Delta research computing project, which is supported by the National Science Foundation (award OCI 2005572), and the State of Illinois. Delta is a joint effort of the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications.


# ESPnet installation steps

## ESPnet installation
Expand Down
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