Difference between revisions of "Online training materials"

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We provide an overview on publicly available training materials that are available on the web.
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This page provides an overview on publicly available training materials available on the web.
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'''SNIC can not take responsibility for the contents provided by external sources or on external web sites'''
  
 
== Basic use of HPC systems ==
 
== Basic use of HPC systems ==
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* The teaching materials on [http://swcarpentry.github.io/shell-novice/ the UNIX shell] of the [https://software-carpentry.org/ software carpentry] courses are available online.  They are suitable for self study.
 
* The teaching materials on [http://swcarpentry.github.io/shell-novice/ the UNIX shell] of the [https://software-carpentry.org/ software carpentry] courses are available online.  They are suitable for self study.
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* The Aalto Scientific Computing center offers an extensive ~3 day workshop on Linux shell and shell scripting. Material is available on [http://scicomp.aalto.fi/training/linux-shell-tutorial.html this page]
  
 
=== Job schedulers ===
 
=== Job schedulers ===
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[https://www.schedmd.com/ SLURM] is currently the most widely used job scheduler by the [[centres|SNIC centres]].  Unless you are using software, whose GUI is well integrated into the scheduler, having some knowledge about it is required when working at a SNIC installation.  On the SLURM website you can access the [https://slurm.schedmd.com/documentation.html official SLURM documentation] an [https://slurm.schedmd.com/faq.html FAQ] and [https://slurm.schedmd.com/tutorials.html (video) tutorials].
 
[https://www.schedmd.com/ SLURM] is currently the most widely used job scheduler by the [[centres|SNIC centres]].  Unless you are using software, whose GUI is well integrated into the scheduler, having some knowledge about it is required when working at a SNIC installation.  On the SLURM website you can access the [https://slurm.schedmd.com/documentation.html official SLURM documentation] an [https://slurm.schedmd.com/faq.html FAQ] and [https://slurm.schedmd.com/tutorials.html (video) tutorials].
 
In addition the SNIC centres provide their own documentation, also describing local customisation:
 
In addition the SNIC centres provide their own documentation, also describing local customisation:
 
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* HPC2N's [https://www.hpc2n.umu.se/batchsystem overview of batch system sub-pages]
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* LUNARC's [https://lunarc-documentation.readthedocs.io/en/latest/batch_system/ batch system guide]
 
* NSC's [https://www.nsc.liu.se/support/batch-jobs/introduction/ Introduction to batch jobs]
 
* NSC's [https://www.nsc.liu.se/support/batch-jobs/introduction/ Introduction to batch jobs]
* LUNARC's [http://lunarc-documentation.readthedocs.io/en/latest/batch_system/ batch system guide]
 
 
* UPPMAX's [http://uppmax.uu.se/support/user-guides/slurm-user-guide/ Slurm user guide]
 
* UPPMAX's [http://uppmax.uu.se/support/user-guides/slurm-user-guide/ Slurm user guide]
  
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[https://www.olcf.ornl.gov/support/tutorials/ Online tutorials] from Oak Ridge National Laboratory
 
[https://www.olcf.ornl.gov/support/tutorials/ Online tutorials] from Oak Ridge National Laboratory
  
== Software ==
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== Application Software ==
 
=== AMBER ===
 
=== AMBER ===
 
* [http://ambermd.org/tutorials/ AMBER tutorials]
 
* [http://ambermd.org/tutorials/ AMBER tutorials]
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=== CP2K ===
 
=== CP2K ===
 
* Linkto [https://www.cp2k.org/howto HOWTOs]
 
* Linkto [https://www.cp2k.org/howto HOWTOs]
=== GULP ===
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=== GATK ===
* Link to [http://gulp.curtin.edu.au/gulp/help/manuals.cfm online manuals]
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* [https://software.broadinstitute.org/gatk/documentation/quickstart Quickstart]
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* Link to [https://software.broadinstitute.org/gatk/documentation/topic?name=tutorials&v=3 Tutorials]
 
=== GROMACS ===
 
=== GROMACS ===
 
* [http://www.gromacs.org/Documentation/Tutorials Tutorial section] of the GROMACS website
 
* [http://www.gromacs.org/Documentation/Tutorials Tutorial section] of the GROMACS website
 
* [http://www.mdtutorials.com/gmx/ GROMACS tutorials] by Justin A. Lemkul from Virginia Tech
 
* [http://www.mdtutorials.com/gmx/ GROMACS tutorials] by Justin A. Lemkul from Virginia Tech
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=== GULP ===
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* Link to [http://gulp.curtin.edu.au/gulp/help/manuals.cfm online manuals]
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=== HOMER ===
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* [http://homer.ucsd.edu/homer/ HOMER tutorials]
 
=== NAMD & VMD ===
 
=== NAMD & VMD ===
* [http://www.ks.uiuc.edu/Training/Tutorials/ collection of tutorials] of TCBG website. Both NAMD and VMD tutorials are presented on this link.
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* [http://www.ks.uiuc.edu/Training/Tutorials/ Collection of tutorials] of TCBG website. Both NAMD and VMD tutorials are presented on this link.
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=== OpenFOAM ===
 
=== OpenFOAM ===
 
* Link to material from [http://www.tfd.chalmers.se/~hani/kurser/OS_CFD/#YEAR_2016 CFD course given in Chalmers].
 
* Link to material from [http://www.tfd.chalmers.se/~hani/kurser/OS_CFD/#YEAR_2016 CFD course given in Chalmers].
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* Link to material at [https://sourceforge.net/projects/openfoamplus/files/v1812/ OpenFOAM v1812 at Sourceforge].
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=== Quantum Espresso ===
 
=== Quantum Espresso ===
 
* Link to the [https://www.quantum-espresso.org/resources/tutorials Quantum Espresso web page for tutorials and lectures] from workshops.
 
* Link to the [https://www.quantum-espresso.org/resources/tutorials Quantum Espresso web page for tutorials and lectures] from workshops.
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=== Snakemake===
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* [https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html#tutorial Snakemake tutorial].
 
=== VASP ===
 
=== VASP ===
* Link to 3-day [http://www.nersc.gov/users/training/events/3-day-vasp-workshop/ VASP workshop at NERSC 2016], including videos of presentations and slides.
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* Refer to the [https://www.vasp.at/wiki/index.php/The_VASP_Manual VASP wiki], in particular check out [https://www.vasp.at/wiki/index.php/VASP_workshop Workshops] and [https://www.vasp.at/wiki/index.php/Lectures_and_presentations Lectures], which include videos of presentations and slides.
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=== WIEN2k ===
 
=== WIEN2k ===
 
* Link to material from [http://susi.theochem.tuwien.ac.at/onlineworkshop/ WIEN2k workshop 2016 at McMasters University], with videos and presentation slides.
 
* Link to material from [http://susi.theochem.tuwien.ac.at/onlineworkshop/ WIEN2k workshop 2016 at McMasters University], with videos and presentation slides.

Latest revision as of 12:24, 6 April 2020

Name Online training materials
Description Overview page on online training materials freely available

This page provides an overview on publicly available training materials available on the web.

SNIC can not take responsibility for the contents provided by external sources or on external web sites

Basic use of HPC systems

Overview material about HPC systems

The HPC-Carpentry initiative has online training material for a 1-day introduction to HPC. It covers both Linux command line and SLURM.

UNIX and LINUX

Almost all current HPC system use UNIX or LINUX as their operating system. Basic UNIX/LINUX skills are essential for using such a system:

  • This video about Unix from 1982 is surprisingly relevant today, and can impart an understanding of the underlying philosophy behind the *NIX operating system.
  • The Aalto Scientific Computing center offers an extensive ~3 day workshop on Linux shell and shell scripting. Material is available on this page

Job schedulers

SLURM

SLURM is currently the most widely used job scheduler by the SNIC centres. Unless you are using software, whose GUI is well integrated into the scheduler, having some knowledge about it is required when working at a SNIC installation. On the SLURM website you can access the official SLURM documentation an FAQ and (video) tutorials. In addition the SNIC centres provide their own documentation, also describing local customisation:

Programming and code development

Python programming

Statistic package R

Software development tools and helpers

Parallel programming

Distributed memory programming with MPI

For MPI related training and documents see the resource section of our MPI page

Shared memory programming with OpenMP

For OpenMP related training materials refer to the resource section of the OpenMP page.

GPU programming

Online tutorials from Oak Ridge National Laboratory

Application Software

AMBER

Bowtie2

CASTEP

CESM (Community Earth System Model)

CHARMM (Chemistry at HARvard Macromolecular Mechanics)

CP2K

GATK

GROMACS

GULP

HOMER

NAMD & VMD

OpenFOAM

Quantum Espresso

Snakemake

VASP

WIEN2k

WRF ARW (Weather Research and Forecasting Model)

Other topics

Data Management

The Data Management Seminar Online is a 3-hour seminar aimed at any UPPMAX or SNIC user who deals with large data volumes — many files, or large files, or both. The seminar focuses both on practical aspects and general best practices, e.g. how to use rsync to move files, where to place data, etc.

SNIC Science Cloud

The SNIC Science Cloud Workshop Material on Github takes 3-5 hours to complete, and teaches how to work with OpenStack-based Infrastructure-as-a-Service (IaaS).