1. ISG We build general capability Introduction to Olympus Shawn T. Brown, PhD ISG MISSION 2.0 Lead Director of Public Health Applications Pittsburgh Supercomputing Center MISSION 2.0 Training, Dec 11 th, 2014 1

2. ISG We build general capability This presentation will answer the following questions… What is Olympus? Why do I need Olympus? How do I and my group get access to Olympus? How do I use Olympus? What will I learn in the hands-on training? 2

3. ISG We build general capability What is Olympus? 3 Olympus is a compute cluster hosted by ISG to provide CPU time for MIDAS network research.

4. ISG We build general capability RAM Disk What is Olympus? Core – a single processing unit capable of performing computations. Multicore Processor – a unit that contains two or more independent cores Socket – place where a multicore processor is plugged in and connects to other resources in the computer Node – collection of sockets and share a common memory space Cluster – a collection of nodes connected through an external network 4 What is a cluster?

5. ISG We build general capability What is Olympus? It is a cluster (1536 cores, 7.5 TB of RAM) 24 nodes (64 cores each) 4 sockets AMD multicore processor 16 cores (1.4 GHz) 512 GB of RAM (8 Nodes) 256 GB of RAM (16 Nodes) Local 3TB hard disk Nodes connected to each other by Gigabit Ethernet Shared file System (2TB) Upgraded Q1 2015 with ~50 TB file system Software available: Python, R, gcc, openmpi Simulators available: FRED and FluTE Additional software installed on request Email: remarks@psc.eduremarks@psc.edu 5

6. ISG We build general capability Why do I need Olympus? I can do more work, more quickly. More capacity allows for more simulations 1 million FRED county level influenza simulations per day 100,000 FRED state level influenza simulations per day I can do larger work. Large memory nodes allow bigger simulations 28 FRED national level influenza simulations per day I can work more efficiently and effectively. Queuing system allows setting up large batches of runs through scripting rather than manual input creation Support from PSC/ISG staff to help you work more efficiently. 6

7. ISG We build general capability How do I get access to Olympus? Can I get an account? Anyone doing MIDAS related research can get an account on Olympus. How? Request an account through the MIDAS Portal http://www.epimodels.org/drupal/?q=node/480 I have an account, now what do I do? You can access the machine through ssh at the address olympus.psc.edu. What does an account get me? Home directory for storing files Ability to submit jobs to the machine Support if you run into trouble and/or need software installed Consultation for working more efficiently and effectively 7

8. ISG We build general capability How do I use Olympus? When you log onto the machine, you will be on the head node. A limited machine that allows you to interact with the full cluster. What should I do on the head node? Manage your files Setup work that you plan to submit to the machine How I do I actually run a job on Olympus? Jobs will need to be submitted to a queuing system which will put the job in line for execution when resources are available. 8

9. ISG We build general capability ssh How do I use Olympus? What is a queuing system? Software allowing users to submit jobs on a multiuser machine by scheduling jobs on the machine and running when the resources are available. Olympus runs the PBS / TORQUE queuing system ( as standard in the world of supercomputing) How do I use the queuing system? Prepare your job on the head node Create a job submission script Defines the job to be accomplished Defines the resources needed to accomplish the job (e.g. how many cores do I need) Submit the job to the queue Check status of the job (queued, running, done) The job will run when the resources are available When finished, collect results on the head node I want to run simulations. I am going to create a whole lot of inputs to run. I need 32 cores, 128 GB of RAM and 2 hours of time. Head Node olympus.psc.edu Olympus Cluster PBS / TORQUE Queuing System WORK Inputs Queued Running Output Wow, I got a lot of work done! I am going to go get coffee. Done 9

10. ISG We build general capability What will I learn in the hands- on training at noon? How do I log on to Olympus? How do I create a submission script? How do I submit and monitor work through the queuing system? What more do I need to know? How do I run interactively on Olympus? How do I effectively use the file systems on Olympus? 10