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# Using Python in an HPC environment

**Welcome!**

Link to this document: <https://hackmd.io/@bclaremar/HPC-python>

Link to first part of Q/A: https://hackmd.io/IoseeprATrWH0ZI7z6wJ-w?view

**Lecture Zoom link**: https://umu.zoom.us/j/68897489502?pwd=TXlraXI5UkFvNWxIV0xGcWZ4M1lQdz09

**Separate UPPMAX session Zoom**: https://uu-se.zoom.us/j/68160935750

Password: 298853

**Separate HPC2N session Zoom**: https://umu.zoom.us/j/64721465122?pwd=NGtZM2h0bmJBTU4xNThjT0t5eFZndz09

**Course material**: <https://uppmax.github.io/HPC-python/index.html>

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## MPI session

- Q: Do you have an example for C/C++ interface also?
- A: pybind11 is great for this: https://github.com/pybind/pybind11. This cookiecutter https://github.com/scikit-hep/cookie is a really good place to get started writing C/C++ bindings.
- Participant comment: `ctypes` is a low-level good start to interface already existing C code without automatic "intent" guessing, also `#include <Python.h>` is a slightly harder way to write a python module in C. I have written some examples for my students [here](https://danielk.developer.irf.se/software_contribution_guide/mixed_coding_arts.html)
- :+1:

:::info
- we have a reservation on UPPMAX:
- add ``--reservation=snic2022-22-641_1`` as slurm flag in bash script or in command line for ``sbatch`` or ``interactive``
- this is only for today until 4PM

:::

- Q: Why keeps this hackmd deleting what I write? Should I setup something?
- A: Appologies for the annoyance. It happens sometime if several people edit at the same time. Please re-type if it happens.

- Q: Cores vs. processes vs. threads, what is the difference?
- A: **Core**: part of a multicore CPU, processor. Hardware. Think of it like a small CPU, I guess, inside the CPU. Usually cores share memory with other cores in the same socket on the CPU. **Process**: it's a task or instance of a program that is active. **Thread**: software. A process can do stuff concurrently by having several threads. Shares memory
- A: so with MPI
- a copy of the program (**process**)
is copied to several instances (**tasks**)
they work independently from each-other but has to communicate to exchange data and to wait for some calculations to be finished before continuing.
- A: https://davescomputertips.com/cpu-cores-versus-threads-explained/
- A: https://www.geeksforgeeks.org/difference-between-process-and-thread/
- A: https://smileipic.github.io/Smilei/parallelization.html
- A: something that really improved my low-level optimization skills was understanding of CPU/GPU memory cache levels and how to chunk memory between communication and calculations (this seems to explain levels pretty OK: https://www.makeuseof.com/tag/what-is-cpu-cache/ )
- A: A node is the physical box containing a computer. An hpc cluster usually has several nodes.

- Each motherboard in each node might have several sockets and can have a cpu chip in each socket.
- Each cpu has multiple cores.
- Depending on your configuration each core can run multiple threads to have several processes running at once (our cluster has multi threading turned off so 1core=1thread).

- A: At UPPMAX our clusters has multi threading turned off so 1core=1thread. The same at HPC2N.

- Q: In the GPU example you login to snowy with `interactive` but in the snowy user guide they write that you must use `salloc`. So can I use `interactive` for snowy?
- A: well it worked for me, put please follow instructions on UPPMAX web!
- A: `interactive` is a wrapper around `salloc`, it works for Snowy too.

## Machine Learning session

- Q: In order to run the "example-tf.sh" on Uppmax I had to change to **#SBATCH --gres=gpu:0** Does this mean that no gpus are available? Followup question: is everyone allowed to use Snowy? It seems not to work with -A SNIC2022-22-641
- A: There are GPUs on Snowy but not on Rackham

## UPPMAX session - Conda and Bianca

- Q: Once I got an error "the environment is inconsistent, please check the package plan carefully" when I used conda before. How to solve it?
- A: Was it in a clean enviroment or just when adding more packages?
- A2: In general environment inconsistencies can show up due to a multitude of reasons e.g. using both `conda install` and `pip install` for the same environment. Many answers seem to suggest that `conda update --all` could solve the issue.

- Q:
- A:

- Q:
- A:

## HPC2N session: Machine learning (continued)

- Q: Why are we now using **python -m pip install package** instead of the **pip install --no-cache-dir --no-build-isolation package**? Is python needed? Will this still avoid other environments/be isolated?
- A: the second option is the recommended one, I will update this information

## Q/A on demand

- Storage basics UPPMAX and similar to HPC2N

- All nodes can access:

Your home directory
Your project directories
Its own local scratch disk (2-3 TB)

- If you’re reading/writing a file once, use a directory on Crex or Castor

- If you’re reading/writing a file many times:
- Copy the file to ”scratch”, the node local disk:

- cp myFile ``$SNIC_TMP``

## Exercise help

Please write the number of the breakout room here if you need help:

:::warning
Archive Q&A from the earlier sessions: https://hackmd.io/@dianai/HPC-Python-2022
:::