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Documentation for Sigma2/NRIS services.

Home Page: https://documentation.sigma2.no

License: Creative Commons Attribution 4.0 International

Shell 10.01% Python 6.38% DIGITAL Command Language 0.49% C 49.89% Fortran 18.59% C++ 5.01% Cuda 9.02% CSS 0.26% HTML 0.34%

documentation's Introduction

Public Documentation for Sigma2 HPC Services

Served via https://documentation.sigma2.no

Unless explicitly noted, all text on this website is made available under the Creative Commons Attribution license (CC-BY-4.0) with attribution to the Sigma2/NRIS.

How the GitHub pages are built

Repository is mirrored from internal GitLab to GitHub using https://docs.gitlab.com/ee/user/project/repository/repository_mirroring.html#setting-up-a-push-mirror-from-gitlab-to-github.
gh-pages branch is generated using https://github.com/UNINETTSigma2/documentation/blob/main/.github/workflows/sphinx.yml

How the documentation works

Please see How to modify infohub or public documentation.

documentation's People

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danzelot blakegfitch maikenp sabryr eta000 korbinib nordugrid praveenmathan susmithp michaelschulzmetno trulspowers marco-foscato hanseide pavlokhmel

documentation's Issues

suggested updates adjusted to Fram

File: documentation/software/userinstallsw/python.md

Setup and installation with pip

it is suggested to use: `use 'module list Python' to see all`

using module list Python on Fram leads to

$ module list Python

Currently Loaded Modules Matching: Python
  None found.

Perhaps this needs to be updated in the documentation to only be available on Saga.

Load conda module

it is suggested:

$ ml purge
$ ml avail conda
$ ml Miniconda3/4.6.14

using ml avail conda on Fram leads to

$ ml avail conda

--------------------------------------------------------------------- /cluster/modulefiles/all ---------------------------------------------------------------------
   Anaconda2/2018.12    Anaconda2/2019.07    Anaconda3/2019.07

Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

Hence, Miniconda3 is not installed on Fram, but on Saga.

update python versions

File: documentation/software/installed_software/fram_modules.md

Python

Installed versions:
should be updated with Python/3.8.6-GCCcore-10.2.0 or the newest version available.

Request for information on serial and parallel R jobs

Dear All,

I am a user of Saga and would like to ask you if you could please point me to some information regarding how to run R jobs in Saga. I have found some information (source code) but no examples of how to run R jobs from R scripts, rather than from bash scripts.

In a previous HPC I used, I would have an R script (.R or .Rmd) along with a .com script. In the .com script, there was a call to the R module and a call to the R script. An example of a .com script for a serial job is below:

#$ -S /bin/bash

#$ -q serial
#$ -N name_of_my_job

source /etc/profile

module add R/4.0.2

R CMD BATCH --no-save name_of_my_job.R

Last, the .com script (for instance, named name_of_my_job.com) would be run in the HPC terminal with the following command:

qsub -m e -M [email protected] -l h_vmem=25G name_of_my_job.com

The system for parallel jobs was essentially the same, with subtle but important differences.

Thank you very much for your attention