Difference between revisions of "Online training materials"
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| − | + | {{online training material | |
| + | |description=Overview page on online training materials freely available | ||
| + | |fields=HPC training | ||
| + | }} | ||
| − | '' | + | 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 == | == 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. | ||
| + | |||
| + | * 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: | ||
| − | + | * HPC2N's [https://www.hpc2n.umu.se/batchsystem overview of batch system sub-pages] | |
| + | * 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] | ||
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* 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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=== Python programming === | === Python programming === | ||
* The teaching materials on [http://swcarpentry.github.io/python-novice-inflammation/ Python programming] of the [https://software-carpentry.org/ software carpentry] courses are available online. They are suitable for self study and provide a good introduction for novices. | * The teaching materials on [http://swcarpentry.github.io/python-novice-inflammation/ Python programming] of the [https://software-carpentry.org/ software carpentry] courses are available online. They are suitable for self study and provide a good introduction for novices. | ||
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* SeSE course on [http://sese.nu/python-for-matlab-users-ht15/ Python for Matlab users] | * SeSE course on [http://sese.nu/python-for-matlab-users-ht15/ Python for Matlab users] | ||
* BioExcel webinars on [http://bioexcel.eu/category/webinar/ computational biomolecular research]. Topics include best practices for using the Gromacs and CPMD codes. | * BioExcel webinars on [http://bioexcel.eu/category/webinar/ computational biomolecular research]. Topics include best practices for using the Gromacs and CPMD codes. | ||
| + | |||
| + | === Statistic package R === | ||
| + | |||
| + | * The [https://software-carpentry.org/ software carpentry] [https://swcarpentry.github.io/r-novice-inflammation/ course material] on the [https://www.r-project.org/ R package] provides a first introduction. | ||
=== Software development tools and helpers === | === Software development tools and helpers === | ||
* The teaching materials on [http://swcarpentry.github.io/git-novice/ Version Control with Git] of the [https://software-carpentry.org/ software carpentry] courses provide a good introduction to version control and the git package. | * The teaching materials on [http://swcarpentry.github.io/git-novice/ Version Control with Git] of the [https://software-carpentry.org/ software carpentry] courses provide a good introduction to version control and the git package. | ||
* NeIC's [https://coderefinery.org/ CodeRefinery] [http://coderefinery.org/lessons/ lessons on version control with Git, automated testing, CMake, etc.] | * NeIC's [https://coderefinery.org/ CodeRefinery] [http://coderefinery.org/lessons/ lessons on version control with Git, automated testing, CMake, etc.] | ||
| + | * ARM provides [https://developer.arm.com/products/software-development-tools/hpc/arm-forge/videos video demos and tutorial]s for the DDT debugger and MAP performance profiler components of the Forge suite, for which SNIC has licenses. | ||
=== Parallel programming === | === Parallel programming === | ||
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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 == | + | == Application Software == |
| + | === AMBER === | ||
| + | * [http://ambermd.org/tutorials/ AMBER tutorials] | ||
| + | === Bowtie2 === | ||
| + | * [https://github.com/alvaralmstedt/Tutorials/wiki/Bowtie2-mapping Bowtie2 tutorial] | ||
| + | === CASTEP === | ||
| + | * Link to [http://www.castep.org/CASTEP/OnlineTutorials Online tutorials] | ||
| + | === CESM (Community Earth System Model) === | ||
| + | * Link to material including practical sessions from the [http://www.cesm.ucar.edu/events/tutorials/2016/coursework.html 2016 CESM Tutorial] run by UCAR. See also [[Building CESM models on the NSC triolith system]] | ||
| + | === CHARMM (Chemistry at HARvard Macromolecular Mechanics) === | ||
| + | * [https://www.charmm.org/charmm/documentation/ Documentation] of CHARMM. | ||
| + | * [https://www.charmmtutorial.org/index.php/Full_example Full example] of a CHARMM simulation setup for a solvated protein. | ||
| + | |||
| + | === CP2K === | ||
| + | * Linkto [https://www.cp2k.org/howto HOWTOs] | ||
| + | === GATK === | ||
| + | * [https://software.broadinstitute.org/gatk/documentation/quickstart Quickstart] | ||
| + | * Link to [https://software.broadinstitute.org/gatk/documentation/topic?name=tutorials&v=3 Tutorials] | ||
| + | === GROMACS === | ||
| + | * [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 | ||
| + | === GULP === | ||
| + | * Link to [http://gulp.curtin.edu.au/gulp/help/manuals.cfm online manuals] | ||
| + | === HOMER === | ||
| + | * [http://homer.ucsd.edu/homer/ HOMER tutorials] | ||
| + | === 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. | ||
| + | |||
| + | === OpenFOAM === | ||
| + | * Link to material from [http://www.tfd.chalmers.se/~hani/kurser/OS_CFD/#YEAR_2016 CFD course given in Chalmers]. | ||
| + | * Link to material at [https://sourceforge.net/projects/openfoamplus/files/v1812/ OpenFOAM v1812 at Sourceforge]. | ||
| + | |||
=== Quantum Espresso === | === Quantum Espresso === | ||
| − | * Link to the [ | + | * Link to the [https://www.quantum-espresso.org/resources/tutorials Quantum Espresso web page for tutorials and lectures] from workshops. |
| + | === Snakemake=== | ||
| + | * [https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html#tutorial Snakemake tutorial]. | ||
=== VASP === | === VASP === | ||
| − | * | + | * 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. |
| + | |||
=== 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. | ||
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=== WRF ARW (Weather Research and Forecasting Model) === | === WRF ARW (Weather Research and Forecasting Model) === | ||
* Link to [http://www2.mmm.ucar.edu/wrf/OnLineTutorial/ WRF ARW online tutorial] made available by UCAR. See also [[Building and testing WRF on Triolith]]. | * Link to [http://www2.mmm.ucar.edu/wrf/OnLineTutorial/ WRF ARW online tutorial] made available by UCAR. See also [[Building and testing WRF on Triolith]]. | ||
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== Other topics == | == Other topics == | ||
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
Contents
- 1 Basic use of HPC systems
- 2 Programming and code development
- 3 Application Software
- 3.1 AMBER
- 3.2 Bowtie2
- 3.3 CASTEP
- 3.4 CESM (Community Earth System Model)
- 3.5 CHARMM (Chemistry at HARvard Macromolecular Mechanics)
- 3.6 CP2K
- 3.7 GATK
- 3.8 GROMACS
- 3.9 GULP
- 3.10 HOMER
- 3.11 NAMD & VMD
- 3.12 OpenFOAM
- 3.13 Quantum Espresso
- 3.14 Snakemake
- 3.15 VASP
- 3.16 WIEN2k
- 3.17 WRF ARW (Weather Research and Forecasting Model)
- 4 Other topics
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:
- Texas Advanced Computing Center (TACC) has produced a clear and general set of slides about HPC Linux.
- 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 teaching materials on the UNIX shell of the software carpentry courses are available online. They are suitable for self study.
- 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:
- HPC2N's overview of batch system sub-pages
- LUNARC's batch system guide
- NSC's Introduction to batch jobs
- UPPMAX's Slurm user guide
Programming and code development
Python programming
- The teaching materials on Python programming of the software carpentry courses are available online. They are suitable for self study and provide a good introduction for novices.
- SeSE course on Python for Matlab users
- BioExcel webinars on computational biomolecular research. Topics include best practices for using the Gromacs and CPMD codes.
Statistic package R
- The software carpentry course material on the R package provides a first introduction.
Software development tools and helpers
- The teaching materials on Version Control with Git of the software carpentry courses provide a good introduction to version control and the git package.
- NeIC's CodeRefinery lessons on version control with Git, automated testing, CMake, etc.
- ARM provides video demos and tutorials for the DDT debugger and MAP performance profiler components of the Forge suite, for which SNIC has licenses.
Parallel programming
- General HPC training material from PRACE
- General HPC training material from XSEDE
Distributed memory programming with MPI
For MPI related training and documents see the resource section of our MPI page
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
- Link to Online tutorials
CESM (Community Earth System Model)
- Link to material including practical sessions from the 2016 CESM Tutorial run by UCAR. See also Building CESM models on the NSC triolith system
CHARMM (Chemistry at HARvard Macromolecular Mechanics)
- Documentation of CHARMM.
- Full example of a CHARMM simulation setup for a solvated protein.
CP2K
- Linkto HOWTOs
GATK
- Quickstart
- Link to Tutorials
GROMACS
- Tutorial section of the GROMACS website
- GROMACS tutorials by Justin A. Lemkul from Virginia Tech
GULP
- Link to online manuals
HOMER
NAMD & VMD
- Collection of tutorials of TCBG website. Both NAMD and VMD tutorials are presented on this link.
OpenFOAM
- Link to material from CFD course given in Chalmers.
- Link to material at OpenFOAM v1812 at Sourceforge.
Quantum Espresso
- Link to the Quantum Espresso web page for tutorials and lectures from workshops.
Snakemake
VASP
- Refer to the VASP wiki, in particular check out Workshops and Lectures, which include videos of presentations and slides.
WIEN2k
- Link to material from WIEN2k workshop 2016 at McMasters University, with videos and presentation slides.
WRF ARW (Weather Research and Forecasting Model)
- Link to WRF ARW online tutorial made available by UCAR. See also Building and testing WRF on Triolith.
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).
