BoF group activity analysis

This document contains the analysed results from the group activities at the HPC Carpentry BoF at SC17.

• Actitivity 1: Groups were asked to brainstorm the characteristics of a potential learner on an HPC Carpentry course. (The precise level and content of the course was not specified but there was an implicit assumption running through the session that it was introductory level in some way.)

• Activity 2: Given a learner profile of a new graduate student in the biosciences who wants to potentially use HPC to help improve their research; the group was asked to specify what subjects should be covered in an HPC Carpentry course.

Learner Profile

Most important characteristics

Three groups produced sets of what they considered the most important characteristics of learners. Analysing these sets leads to 4 main characteristics of a potential learner:

• Vague idea of what HPC is but not sure how this translates to their research.
• Lack of experience with Linux, command line, text editors, batch systems etc. i.e. the working environment is foreign to me.
• Lack of knowledge about what HPC systems are: how are they put together, how do they enable faster/larger calculations and how are resources shared?
• Want to know how to support themselves when things don’t work and keen to learn more.

Grouped charateristics

Analysing the feedback from the groups, there were a number of common charateristic groupings. The individual statements from the groups that gave rise to these groups can be seen in Appendix A below.

• I do not have the basic technical skills to use HPC
• I am not sure how HPC can help my research?
• Just give me what I need to get on with my research on HPC
• What is an HPC system anyway? How does it differ from the comupter I am already using? What about “the Cloud”?
• HPC and programming are awesome, but I do not know much, tell me more!
• How do I get help and/or help my self when I get stuck?
• I feel unsure and out of my depth with HPC
• I do not understand the shared nature of HPC systems
• I am experienced technically, what do I need to know about HPC?
• Broad range of expertise and experience among researchers

Course and module design

The collected outputs from each of the groups for this exercise can be seen in Appendix A below.

Commonly-identified skills and topics

There were a number of key, generic skills that were commonly identified across multiple groups:

• Why HPC?
• Login, interactive access (ssh); transferring data (scp)
• HPC jargon
• Basic understanding of HPC architectures and practical implications for their use
  • HPC system components: processors, memory, I/O, interconnects
  • Parallelism
  • Performance: stong/weak scaling, speedup, best practice and basic metrics
  • Comparison: laptop, HPC, cloud
• File systems
  • Multiple file systems
  • Users and groups
  • File permissions
  • File organisation
• In-terminal text editors
  • Why do I need this skill?
• modules, environment, applications
  • Executing applications
  • Executing parallel applications (OpenMP, MPI)
  • The PATH
  • module load …
  • Compiling (parallel) applications
• The batch system and writing job submission scripts
  • Basic concepts
  • Batch system options
  • STDOUT/STDERR
  • Different job types: traditional MPI HPC, task farming, …
  • Best practice and troubleshooting
• Shared system etiquette
  • Being a good HPC citizen
• Troubleshooting strategies

Some skills were specific to the HPC system being used:

• How to get account and access the system
• System specific information, e.g.
  • Key information on using the system
  • File retention policies
  • How to get help

Prerequisite skills

Other skills were raised but some groups thought they were prerequisites to the course:

• Basic shell use and scripting
  • People could complete Codecademy track before attending: https://www.codecademy.com/catalog/language/bash

More advanced skills

Finally, some skills were seen to belong to more advanced or different courses

• Workflow optimisation

Other skills and topics

There were a number of ideas that were suggested by single groups rather than appearing across multiple groups:

• Version control (git) in HPC workflow
• Markdown for documentation

Appendix A: Collected responses for Learner Profile exercise

Analysing the feedback from the groups, there were a number of common charateristic groupings:

• I do not have the basic technical skills to use HPC
  • G2: Don’t know LINUX, may know Windows
  • G2: Thinks a computer is a box under a desk or a laptop
  • G2: May be most comfortable with GUI
  • G2: No familiarity with command line
  • G3: I am unsure what the terminal is, how it works, etc
  • G3: I do not know what version control is
  • G3: I am a student and I do not know how to get access to the remote system I have been granted
  • G4: I don’t know Linux but HPC systems are typically running Linux
  • G4: I don’t know how to create and edit code
  • G4: Comfort with command line environment in a linux environment.
  • G4: Bash.
  • G4: I prefer graphical or web-based interfaces.
  • G5: I’ve never used a command line.
  • G5: I’ve never used a compiler.
• I am not sure how HPC can help my research?
  • G1: Why do I care?
  • G2: New graduate student in sciences/engineering
  • G2: Are only using HPC because their Advising professor told them to
  • G2: Biologists becoming bioinformaticians
  • G2: Usually stuck or bogged down due to limitation of current machine/resources
  • G4: Do I have a use for HPC?
• Just give me what I need to get on with my research on HPC
  • G1: I just want to do my science
  • G1: I want it to be interactive
  • G1: Just show me what I need to do to get my results
  • G3: I have a code with a new dataset that’s too big to fit in memory/needs multiple cores now
  • G4: My supervisor wants me to run his favourite modelling code. How do I do that?
  • G4: I know my science, I have code, how do I use this tool to accelerate my science?
  • G4: How can I run my analytics on the data from my instrument using the cluster?
  • G4: I have Malab code that is too slow now. Can I speed it up or use something else easy to get results faster
  • G4: I want to try using a GPU for my problem.
• What is an HPC system anyway? How does it differ from the comupter I am already using? What about “the Cloud”?
  • G1: Why aren’t things just faster automatically?
  • G1: Is this the fastest it can get ?
  • G1: Why is running more slowly?
  • G1: Why does my program not run on multiple nodes? And what do I have to do to have it run on multiple nodes?
  • G1: How much processing power is overkill ?
  • G1: Users have little idea of the resource they need (memory / CPU) so for safety go for exclusive sessions everywhere
  • G2: Does not know what parallel programming models are, parallel vs. SMP models, multicore vs multinode
  • G2: Thinks performance is how fast they can run Doom 4
  • G2: Bases notions of storage cost on $200 8TB drives at Frys or Microcenter
  • G2: Expect programs to run magically faster on a cluster
  • G3: I do not understand the difference between a cluster, supercomputer, cloud, etc
  • G4: Overview of HPC technologies - eg what’s a GPU and what is it good for?
  • G4: Concepts of why we use HPC systems and what they are
• HPC and programming are awesome, but I do not know much, tell me more!
  • G1: I just want to learn the “cool” stuff
  • G1: I’ve never programmed, how do I make cool things?
  • G3: Signed up for Software carpentry but I know there are things that it won’t cover
  • G5: Already have Software Carpentry and now want to apply that to HPC.
  • G5: I’ve just started working on a complex software problem with no computer science skills.
• How do I get help and/or help my self when I get stuck?
  • G1: Why does it take so long to get things done? (software installation assistance; head node compiling/bottleneck; single core desktop vs single core HPC)
• I feel unsure and out of my depth with HPC
  • G1: My novice HPC user is intimidated by HPC
  • G2: Researcher in soft/social sciences, scared by the thought of programming/scripting…
  • G2: …but, brave enough to show up to an HPC Carpentry session
  • G4: I don’t have mentor with HPC experience (pioneer in group)
• I do not understand the shared nature of HPC systems
  • G1: What is a scheduler and why do I need to use it?
  • G1: Why can’t I have root or administrator privileges
  • G1: Why do I have to wait
  • G1: Obviously I can run on the login node.
  • G1: Novice users don’t understand that resources are competed for with the other users\
  • G2: Multi-user system is foreign to them
  • G3: I don’t know how to use my system scheduler
  • G4: Understanding of job submission in batch environment.
• I am experienced technically, what do I need to know about HPC?
  • G1: How to debug my program on multi threads ?
  • G1: I’ve been programming for years, just run me through the basics.
  • G2: Somewhat comfortable, but need help with optimization
  • G3: I do not know how the linker works, I don’t understand why my dependencies are linking to different shared libraries, and what that means
  • G3: I am trying to use a profiler for the first time with MPI code and I don’t understand what normal MPI behavior is
  • G5: Informal education in programming (self taught)
  • G5: Lacks knowledge or experience of exploiting parallelism.
  • G5: I lack knowledge of optimisation or low level performance.
• Broad range of expertise and experience among researchers
  • G2: Broad spectrum – some quite good programmers, just not familiar with HPC
  • G2: All are good scientists in their own field with computing or data needs
  • G4: Generally have a science background, but not programming or comp.sci. Have taken 1 or 2 basic programming courses.
  • G4: Have run my apps on my laptop, but now want to go to the next level.

Appendix B: Collected responses for Course and Module Design exercise

Group1

Brainstorm the 5 – 10 skills you would like the provided user profile to have by the end of the workshop, and translate these skills into specific learning objectives, and group these learning objectives.

• How do I get an account? How to get access? What is the status of my account?
• How to sign on to the system - portal? Ssh? Off campus?
• Cluster Architecture (building a mental model of an HPC system starting from their desktop/laptop, highlight the system components and translate them to HPC system architecture)
  • What is a compute node
  • What is a storage node
  • Login vs compute node
  • Network and it’s importance
  • File system (shared)
• Basic linux -
  • what is a shell?
  • Basic commands, navigation, creating and saving files
• Basic scripting
• Editor
• How to be a user
  • File management
  • being in a group
  • Center policies - how long can I keep my files, backup policies, scheduled downtime
  • Being a good citizen
  • How to get help
  • How to write up your request for help…what to include (error message), system name…
• Batch scheduler:
  • What is it?
  • why do we need it?
  • how do I use it?
  • How do I run a job?
  • What is a network?
  • Understanding exit codes - why jobs fail, stop, etc.

Group 2

Brainstorm the 5 – 10 skills you would like the provided user profile to have by the end of the workshop, and translate these skills into specific learning objectives, and group these learning objectives.

• Ability to submit jobs to the cluster
• Ability to schedule Jobs
• Understand resource limits in scheduler
• File system and transfer basics (Globus?)
• Understand environment variables/execution environment
• Understand Remote access to systems
• Appreciation for the meaning of Speed-Up
• Process automation
• Understand process control
• Understand pipes, background/foreground, redirection, stdio/sterr
• Understand impact of data placement, understand parallel file system and data locality, understand the differences between traditional HPC programming model on PFS and Big Data models (MapReduce)

An example workshop outline with lesson modules is provided. Assuming a 1 day workshop:, What lessons are missing? What should be dropped or combined? If a longer workshop were given, what could be in Day 2?

• Drop workflow optimization? (too advanced)
• Drop/condense login/shell/basic Linux and assume prerequisite
• Good Citizenship may vary too much from site to site
• Maybe add Basic Performance Metrics

Group 3

Brainstorm the 5 – 10 skills you would like the provided user profile to have by the end of the workshop, and translate these skills into specific learning objectives, and group these learning objectives.

• Log in to remote cluster
• Remote file transfer, access
• Software module environments
• Run ”Pleasantly”/“Delightfully”/”Embarrassingly” Parallel interactively
• Submit a batch job for ^
• Use git/version control for workflow management (batch files, directory structure)
• Make a change to ^ batch script and commit change
• How to compile (and run) a code

An example workshop outline with lesson modules is provided. Assuming a 1 day workshop:, What lessons are missing? What should be dropped or combined? If a longer workshop were given, what could be in Day 2?

• Missing
  • Version controlled workflow(s)
  • Markdown (for docs)

Other resources/quality references for further learning:

• Oakridge national lab trainings etc. (TACC, XSEDE, git scm)
• Communities to join: SIGHPC, SIGHPC-ED,

Vocabulary/jargon for/in HPC:

• What is QoS?

Interacting with your support community:

• How (and who) to ask for help
• How to find/read bug reports for software you are using
• How to file a (helpful) bug ticket

Group 4

Brainstorm the 5 – 10 skills you would like the provided user profile to have by the end of the workshop, and translate these skills into specific learning objectives, and group these learning objectives.

Practical (technical)

• ssh and scp: data transfer
• Command line basics
• File system: creating, organising, navigating, file permissions
• Executing applications (either your own or centrally installed)
• Being able to run batch jobs (and find your output), checking status of jobs

Practical (non-technical)

• Where to get help when you get stuck (e.g. documentation)
• Etiquette on a multi-user system and implications for you
• Troubleshootling strategies

Conceptual:

• Basic HPC architecture and implications
• Differences from your laptop/workstation
• Why should I use HPC? What can it give me? When should should I use HPC?
• Parallelism and parallel processing
• Understand terminology and jargon

An example workshop outline with lesson modules is provided. Assuming a 1 day workshop:, What lessons are missing? What should be dropped or combined? If a longer workshop were given, what could be in Day 2?

Missing:

• Conceptual content missing: why HPC? Basic HPC architectures

What should be on day 2:

• Intermediate shell topics
• Testing jobs while running interactively
• Using software modules
• Running parallel tasks
• Running parallel code
• Optimizing workflows

Group 5

Brainstorm the 5 – 10 skills you would like the provided user profile to have by the end of the workshop, and translate these skills into specific learning objectives, and group these learning objectives.

• Understand how to access the system.
  • What is SSH? (or alternative)
• Understand the basic software environment.
  • Basic system environment.
  • Editing files.
  • Compilers
• Understand the scheduler
  • What is a scheduler?
  • What is a job?
  • How to submit a job
  • How to check the status of a job
  • How to kill a job
  • What is the wall clock
  • Why hasn’t my job started yet? Why is my job queued?
  • Where’s my output?
• Understand that simply running on a supercomputer will not speed up my code
  • Users should understand they will have to modify/parallelize their code to get an improvement.