========== Onboarding ========== .. tip:: **Contact** `Secretariat System Administrators`_ **with HPC Questions!** +------------------+----------------+--------------------+ | `Vijay Shankar`_ | `John Poole`_ | `Maria E. Adonay`_ | +------------------+----------------+--------------------+ .. code-block:: text vshanka@clemson.edu,jopoole@clemson.edu,madonay@clemson.edu .. raw:: html

**Contact** `IHG Research Cores`_ **with Research Questions!** .. code-block:: text ihgcores@clemson.edu ---- Welcome to the Secretariat Community! We look forward to you joining us. ---- HPC Basics Workshop #################### We recommend that all Secretariat users attend the HPC Basics Workshop, even if they already have cluster experience. `Please see this page for more information`_. ---- Account + Access ################ Once an account has been created for you on Secretariat, you can connect via command line terminal using the following command: ``ssh -X [username]@130.127.173.136`` *Insert your own username in the place of [username] – you do not need the brackets.* You may also `access Secretariat through the Open OnDemand web interface`_ (e.g. `https://secretariat-master`_), similar to `Palmetto's setup`_. When you are not connected to the Clemson network (e.g. when you are away from campus), make sure you connect to the `Clemson Virtual Private Network (CUVPN)`_ before trying to log into Secretariat! ---- Groups ###### All Secretariat users are members of specific groups. The purpose of these group memberships is to help set specific directory and file permissions. If you have questions about how this works, please reach out! (We cover this on Day 1 of the `HPC Basics Workshop`_!) ---- Directories ########### Each Secretariat user receives a directory in **/home** and **/scratch2** as well as a directory for data storage and analyses in **/data** or **/data2**. Scratch storage is extremely fast (compared with /data, /data2, and /data3), so it can significantly shorten the runtime for jobs which read and / or write large files (including intermediate files) as well as jobs which perform a lot of random disk access. Storage quotas are not enforced on /scratch2, but please consult with us if you plan to use more than 10 Tb. Scratch storage is for temporary use to speed computations and therefore should NOT be considered long-term storage for a number of reasons: - Scratch storage intentionally trades redundancy for significant increases in speed (all other storage on Secretariat has built-in redundancy to provide the maximum possible data integrity in case of drive failures and, even then, you should still have independent off-site backups). - Scratch is a limited shared resource (100 Tb total) so leaving large amounts of data for months after jobs have completed reduces the amount available to other users with active jobs. - Scratch is much more expensive per Tb than other storage. Once you sign in, you should have permission to access these directories using the `cd`_ command-line shell command. If you have trouble with this, please let us know! ---- Communications on Slack ####################### The `#secretariat`_ channel in the IHG `Slack`_ Workspace will be used to communicate things including, but not limited to, scheduled or emergency maintenance of Secretariat and new software installations. All Secretariat users are welcome to join this channel to follow updates or post questions. ---- HPC Etiquette ############## *Resources*: We ask that all resource requests (e.g. cpus, memory, time) be reasonable and aligned with the needs of your workload. Generally, being on the conservative side helps manage everyone’s needs and uses. If you are unclear about how you should request resources, please reach out to us once you are ready to run analyses on Secretariat! *Home directory* (**/home**): Make sure to keep your home directory small (<5 Gb) and clean. If you are unclear about what this means or how to monitor this once you start using Secretariat, please let us know and we can help get you started! *If you fill up the quota for your home directory, you will likely begin to encounter issues with things such as logging in and accessing the* `Open OnDemand interface`_. *Data directory* (**/data**, **/data2**): Your software libraries / packages / environments (e.g. R, Python, conda), data files, and related resources for analyses should be kept within your data directory. Please keep in mind that this data directory will not be backed up unless a Palmetto backup has been set up with us or you generate another copy through other means (e.g. upload to cloud storage). *Login node*: Do not run analyses or resource intensive tasks on the login / head node (secretariat-master). Instead, we recommend that you submit a script to one of the computational nodes. If you would like any assistance, please let us know and we can advise you on how to do this properly! ---- .. _Please see this page for more information: https://secretariat.readthedocs.io/en/latest/additional-resources/workshops.html#hpcc-basics-workshop .. _access Secretariat through the Open OnDemand web interface: https://secretariat.readthedocs.io/en/latest/compute/ood.html .. _Open OnDemand interface: https://secretariat.readthedocs.io/en/latest/compute/ood.html .. _https://secretariat-master: https://secretariat-master .. _Palmetto's setup: https://docs.rcd.clemson.edu/openod .. _Clemson Virtual Private Network (CUVPN): https://secretariat.readthedocs.io/en/latest/additional-resources/vpn.html .. _HPC Basics Workshop: https://secretariat.readthedocs.io/en/latest/additional-resources/workshops.html#hpc-basics-workshop .. _cd: https://www.geeksforgeeks.org/cd-command-in-linux-with-examples .. _#secretariat: https://cu-chg.slack.com/archives/C0472VDJ8PL .. _Slack: https://slack.com .. _Palmetto: https://docs.rcd.clemson.edu/palmetto .. _Vijay Shankar: https://scienceweb.clemson.edu/chg/dr-vijay-shankar-2/ .. _John Poole: https://scienceweb.clemson.edu/chg/dr-john-poole/ .. _Maria E. Adonay: https://scienceweb.clemson.edu/chg/maria-adonay/ .. _Secretariat System Administrators: https://scienceweb.clemson.edu/ihg/research-cores/bsc-core/ .. _IHG Research Cores: https://scienceweb.clemson.edu/ihg/research-cores/