2021-10-21 <br> HPC1: Introduction to HPC at Leeds

--- tags: teaching, hpc1 --- # 2021-10-21 <br> HPC1: Introduction to HPC at Leeds Welcome to the hack pad for HPC1 course from Research Computing at the University of Leeds! You can edit this document using [Markdown syntax](https://guides.github.com/features/mastering-markdown/). ## Links to resources - **Contact Research Computing** - https://bit.ly/arc-help - **Request HPC account** - https://leeds.service-now.com/it?id=sc_cat_item&sys_id=4c002dd70f235f00a82247ece1050ebc - **Presentation for today** - https://bit.ly/hpc1intro - **Exercises for today** - https://docs.google.com/document/d/1SPaZ2kmzYpMFIkiMSi-Qnu-ZqLaW4reSpVal3aOrmmk/edit - **Github repository** - https://github.com/arctraining/hpc1-files - **How to transfer files** -https://arcdocs.leeds.ac.uk/getting_started/file_transfer.html ## Agenda Day 1 | Time | Agenda | | -------- | ------------------------------------------ | | 0900 | Intro, connecting to ARC, what and why HPC?| | 0950 | Break | | 1000 | Login, HOME directory and looking around <br> Exercise 1 | | 1050 | Break and Answers | | 1100 | Simple job submission, qstat, qdel | | 1150 | Questions | | 1200 | Close | ## Agenda Day 2 | Time | Agenda | | -------- | ------------------------------------------ | | 0900 | Intro, Data Transfer, Modules | | 0950 | Questions and break | | 1000 | Interactive sessions, ib v smp, node types | | 1050 | Questions and break | | 1100 | User guided section, talking through <br> your hopes/fears for HPC | | 1150 | Wrap up and questions | | 1200 | Close | ## Pre workshop prep If you haven’t already request an account for the HPC via this link - https://leeds.service-now.com/it?id=sc_cat_item&sys_id=4c002dd70f235f00a82247ece1050ebc ### For Windows Users For Windows users please consult our documentation page and video at https://arcdocs.leeds.ac.uk/getting_started/logon.html#connecting-from-windows You are required to download the software tool MobaXTerm for this workshop. ![](https://i.imgur.com/qM7ckB4.png) 1. Navigate using a web browser to https://mobaxterm.mobatek.net/ 2. Select Download ![](https://i.imgur.com/2OWkFeU.png) 3. Click Download Now for the Home Edition ![](https://i.imgur.com/z7snaxu.png) 4. Select MobaXTerm Home Edition v21.0 (Portable edition) ![](https://i.imgur.com/bmdYrg7.png) 5. This opens a download prompt for a .zip file. Select Save File and click OK ![](https://i.imgur.com/jqvN3SW.png) 6. Go to your Download folder and find the .zip file you have just downloaded ![](https://i.imgur.com/C9qIoQ5.png) 7. Click Extract in the Ribbon Bar and select Extract All ![](https://i.imgur.com/lAJtyXq.png) 8. Using the Wizard window extract the folder at the suggested location ![](https://i.imgur.com/rwAEDT2.png) 9. This should open the extracted folder immediately and allow you to double-click on the MobaXTerm_Personal_21.0 executeable to start the application ![](https://i.imgur.com/aYjt8bf.png) **And you're all set for HPC1!🎉** ### For Mac/Linux Users: **MacOS and Linux users do not need MobaXTerm** but can use your builtin Terminal application. - You should follow the steps outlined in the bitesize video titled “Connecting to ARC off-campus via Linux/MacOS” on this page (https://arc.leeds.ac.uk/help/videos/) - read carefully the documentation section here (https://arcdocs.leeds.ac.uk/getting_started/logon.html#connecting-from-linux-macos-systems) on connecting from Linux and MacOS, especially the section about configuring SSH for off-campus connections. In order to connect to ARC when you're off campus you'll need to do some extra configuration so that your SSH connection goes via our `remote-access` server. The following steps outline how to setup this configuration: 1. Open a Terminal on your Linux/macOS machine 2. Create a directory called `.ssh` in your home directory (if one doesn't already exist) ```bash $ mkdir ~/.ssh ``` 3. Then open a text editor of your choice and create a file called `config` in your `.ssh` directory ```bash # for instance use the simple nano text editor $ nano ~/.ssh/config ``` 4. Within this file include the following contents where `USERNAME` is replaced by your university username ```bash Host *.leeds.ac.uk !remote-access.leeds.ac.uk ProxyJump USERNAME@remote-access.leeds.ac.uk User USERNAME ``` 5. Save this file and attempt to connect using `ssh` to ARC4 ```bash # where USERNAME is your university username $ ssh USERNAME@arc4.leeds.ac.uk ``` 6. The first time you connect you will be prompted with several messages ```bash The authenticity of host 'remote-access.leeds.ac.uk (129.11.190.34)' can't be established. RSA key fingerprint is SHA256:SZN1IZ9rL0mhpnxhVG5uxbtVFMZAISg98X9ovHlh8Fg. Are you sure you want to continue connecting (yes/no)? ``` Type Yes and hit `Enter`. You will then be prompted to enter your password for connecting to remote-access.leeds.ac.uk ```bash Warning: Permanently added 'remote-access.leeds.ac.uk,129.11.190.34' (RSA) to the list of known hosts. USERNAME@remote-access.leeds.ac.uk's password: ``` Please enter your password carefully, placeholder `*` characters will not appear but your keystrokes are being recorded. Once you have typed in your password press `Enter`. You have now connected to remote-access but will now be prompted with similar messages for connecting to ARC4 itself. ```bash The authenticity of host 'arc4.leeds.ac.uk (<no hostip for proxy command>)' can't be established. ECDSA key fingerprint is SHA256:lPkw/7SrBqqQkS7lUm+tBN9JIGX9B8Gw7FdkK3MrpLM. Are you sure you want to continue connecting (yes/no)? ``` Type Yes and hit `Enter`. You will then be prompted to enter your password for connecting to arc4.leeds.ac.uk ```bash Warning: Permanently added 'arc4.leeds.ac.uk' (ECDSA) to the list of known hosts. USERNAME@arc4.leeds.ac.uk's password: ``` Again enter your password carefully, placeholder `*` characters will not appear but your keystrokes are being recorded. Once you have typed in your password press `Enter`. 1. Once you have successfully entered your password you will be greeted by the following information on your Terminal ```bash Advanced Research Computing Node 4 (arc4) ________________________________________________________________________ Information on using this facility may be obtained at the following URL: http://www.arc.leeds.ac.uk Please remember to acknowledge the use of ARC facilities in your papers; details are on the website above. ________________________________________________________________________ [USERNAME@login1.arc4 ~]$ ``` And success! You are all connected and ready to go! 🎉 ## What's your name and where do you come from? And why do you want to use HPC? - Alex Coleman, Research Software Engineer, my research has previously been in natural language processing and clustering event descriptions data and simulating crime rates using historic data. - John Hodrien, Research Software Engineer. Long history of using parallel processing systems, starting back in 2000. - Lama Alqurashi, a PhD student in Natural Language Processing. - Luis Alfredo Avendaño Muñoz,I'm from Colombia, PhD student in Computer Science, Artificial Inteligence. I'll use the HPC for Neural Network optimization. - Francesca Appadoo. PhD student in virology and Cryo-EM, Using HPC to process Cryo-EM images with cryolo and relion. - Brett Hull, PhD student in Data Analytics. I need HPC for NLP on a large dataset of reviews - Qiuyu Zhu, PhD student in the School of Geography. - Eszter Kovacs, PhD student in SEE, working with satellite data - Jo Galloway, PDRA, Meldrum Group, Chemistry, cryo-EM data processing, MD simulation protein-mineral interactions - - Duncan Ewin - PhD Student in Microbiology - Carlo Arosio, PostDoc, visiting School of Earth and Environment. I'm going to run TOMCAT chemistry transport model to study ozone trends in the stratosphere. - Andrew Gillen, a postdoc working on paediatric leukaemia. I'm hoping to use HPC to reanalyse sequencing data. - Hsiao-Han (Grace) Chuang, postdoc in theoretical chemistry. - Charmaine Normington, Post-Doc, Medical Microbiology, using HPC for gut microbiome analysis - Shengyin Wang PhD student in computing - Tomás Zilhão Borges, 3rd year BSc MEng Computer Science, doing my individual project in code translation from NLP - Ollie Clark, Research Software Engineer with background in databases and web development. Recently working on Cloud computing. ## Glossary of Terms - Core: the basic computation unit of the CPU. This is unit that carries out the actual computations. - Node: the physical machine/server. In current systems, a node would typically include one or more processors, as well as memory and other hardware. - Parallel: run across multiple CPU cores, splitting the workload between them and solving the problem faster. - Processor: the central processing unit (CPU) inside the node, which contains one or more cores. - Serial: run on a single CPU core, solving one problem at a time - Batch processing: Jobs that are run as and when the system is able to, rather than jobs run interactively - Thread: A lightweight logical computation process. If a program is a sequence of instructions, this is the finger that works its way through the list of instructions. There can be many fingers, and you can have many more threads than you have hardware to run them. - GPU: Graphical Processing Unit. Not necessarily graphical, but this type of hardware is good at some high parallelism problems. We have a small number of these in ARC3/4. Massive speed ups are possible - one GPU can be as powerful as 40 machines. ## Code along `git clone https://github.com/arctraining/hpc1-files`