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18 May

  • Content
  • line-up
  • Letter info
  • Workshop page

How?

  • one full day
  • workshop
  • Fri 2 YES
  • Tue 6 sep? NO
  • (7 Sep maintenance)

Learning outcomes

  • load and run python
  • find installed packages
  • install package with pip
  • install package with conda
  • create a venv
  • use a venv
  • jupyter on calculation node (more or less about)
    • HPC2N perhaps working but different approach? Pedro looks up
  • run batch jobs with python code
  • run parallel
    • calc pi with mpi
  • run workflows
    • how much??
  • load and use ML packages
    • tensor flow example (UPPMAX)
  • gpu

Learning experience

  • webinar
  • pair-teaching
  • code along
  • problem-based approach
    • find out an example or two?
  • group or pair work? TBD
    • exercise
  • more?

Prerequisites

  • basic Bash commandline + scirpting

    • explicit

  • basic Python

  • basic Slurm

Content

Morning

  • Python modules (LMOD)
  • python packages
  • installations
  • Kebnekaise/Bianca separated session
    • user specific session as well
  • workflow

Afternoon

  • interactive
  • jupyter on calculation nodes
  • batch
  • parallel computing
  • tensorflow??
  • Problem-based approach
    • how to approach a problem at the site to solve it
    • a number of example problems
      • OOM-related (out of memory?)
    • numerical- as well as data/ I/O-based
  • check how the resources are used
    • graphana
    • jobstats

Plan

Time Topic Activity Description Goal
Morning 2 hours 45 + 40m
10 Intro Lecture Outline Get overview and LOs
10 Load and run Lecture+code along Show modules Learn how to load a python version
25 packages Lecture + code along + (exercise) Check current, Pip, Conda List packages, do pip installation,do conda installation
10 Isolated environ Lecture + code along Venv Understand virtual environ
25 Kebnekaise/Bianca separated session Lecture Cluster specific practice and installed packages, User interaction Understand cluster limitations
5 Summary Lecture Describe when to do what Keypoints
Afternoon 2 hours 45+45m
30 batch with python and conda Lecture+code along + exercise python with batch write batch script with right envs
15 interactive jupyter Lecture + code along +exercise run jupyter on calculation nodes run jupyter on calculation nodes
30 workflows?
15 Summary

Letter info

  • Sep 2
  • Sep 6
  • Sep 9

Online workshop: "Python at UPPMAX & HPC2N", Sep 9, 2022

UPPMAX and HPC2n is organising a joint workshop on how to run Python and install additional Python packages on the computer resources provided by UPPMAX and HPC2N and how to use the HPC capabilities. Participants will be able to bring their particular software request for discussion as well.

The following will be covered:

  • Loading the appropriate Python module
  • Packages
    • checking installed packages
    • pip install
    • Conda install
  • Virtual environments
  • Kebnekaise / Bianca session
  • HPC
    • interactive jupyter
    • batch jobs with Python
    • Machine Learning environment
    • workflows

Prerequisities:

  • basic Linux
  • basic Python
  • basic Slurm

When: Friday, Sep 9, 2022. Time: 9:15 - 12:00, 13.15-16.00 Where: online.

Registration opens in June

SNIC training letter

  • 25 May (Wed)

Web page later

21 April

To be decided today

  • Content
  • Just UPPMAX/HPC2N?
  • Length
  • Style (one-way, workshop, course)
  • One or two instances
  • Month (at least)
  • Who wants to contribute

Intro

  • Pedro asked: "I thought we could join efforts and collaborate in a Python course where we could talk about the workflows at UPPMAX and HPC2N? If you think this is doable, maybe we could run it in the summer/autumn? "

Content

  • core from “Python at Uppmax” and made general - [Broken link] https://python-at-uppmax.readthedocs.io/en/main/

    HPC

:::warning same at HPC2N? (except Bianca)

  • not Conda

:::

  • More workflows

    • snakemake?
      • can submit slurm jobs
    • Own workshop?

  • Hpc possibilities

    • Focus on site-specific systems
      • modules
      • sbatch
      • interactive
    • parallel computing
    • GPU?
    • TensorFlow

  • More…?

    • jupyter on calculation nodes??

  • Problem-based approach

    • how to approach a problem at the site to solve it
    • a number of example problems
      • OOM-related
    • numerical- as well as data/ I/O-based
    • check how the resources are used

What other courses/workshops/training are there? Not to collide (in content) with

Prerequisites

  • basic Slurm
  • basic Bash scripting
  • basic Python

How?

  • Divided into
    • packages and
    • HPC python computing
  • One instance
  • Seminar(s)
  • Workshop
  • Hackaton? Another time?
  • Course?
  • Also updated documentation
  • new topics/examples gradually

Length?

  • 3 hours
  • Full day
  • Several days?

When?

  • Python-at-UPPMAX+HPC2 May 18 10-12
  • Aug, probably not
  • Sep 2, Sep 6-8 somewhere
  • Oct

Who?

  • Any other SNIC centre?
    • not this time
    • they can learn from

Other

Next steps

  • Further planning
    • Content
    • line-up
    • Letter info
    • Workshop page
  • Who wants to be part?
    • Björn
    • (Lars)
    • Pedro
  • SNIC training letter
    • 28 April
    • 12 May
    • 25 May (Wed)

Next meeting

  • 19 or 20 May, Doodle
import numpy
from mpi4py import MPI
comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()