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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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. | ||
|
|
@@ -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 | ||
|
|
@@ -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 | ||
|
|
||
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