Difference between revisions of "Main Page"

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[[Copying files with SCP/WinSCP/Filezilla/Cyberduck]]
 
[[Copying files with SCP/WinSCP/Filezilla/Cyberduck]]
 
[[Video conferencing and collaboration tools]]
 
  
 
[[Running graphical programs remotely]]
 
[[Running graphical programs remotely]]
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[[ABySS]]
 
[[ABySS]]
 
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== Tools to access the HPC (Windows) ==
 
== Tools to access the HPC (Windows) ==
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[[Filezilla]]
 
[[Filezilla]]
  
== Slides and Talks ==
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== Slides, Talks and Training Materials==
  
[[File:Sge queue changes.pdf]]
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Talk on using Containers - [[File:Containers.pdf]]
  
[[File:Containers.pdf]]
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[https://scw-aberystwyth.github.io/IBERS-HPC-tutorial/ Carpentries Style Lesson on using the HPC]
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[https://bioinformatics.ibers.aber.ac.uk/training/IBERS%20HPC%20Tutorial%20Recording.mp4 Recording of the lesson above]
  
 
== Bioinformatics Working Group related ==
 
== Bioinformatics Working Group related ==
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[[convert_fasta_to_1l_fasta.sh]]´
 
[[convert_fasta_to_1l_fasta.sh]]´
 
[[Your software/script uses threads and works locally, but crashes if run under the SGE's queue]]
 
 
[[Intermittent login failures on the HPC and some VMs]]
 
 
[[error importing function definition for `BASH_FUNC_module']]
 

Latest revision as of 12:15, 19 December 2022

IBERS-logo-Bi.jpg


Welcome to the HPC Wiki for the Bioinformatics research group at Aberystwyth University. The aim of this wiki is to allow researchers in the field of Bioinformatics in IBERS at Aberystwyth to document common tasks using the High Performance Computing cluster.

Editing this Wiki

Please email ibers-cs@aber.ac.uk to ask for access to edit this wiki.

Troubleshooting

Please read these sections if you are having trouble. There is a chance that you can resolve the problem on your own and ask for help more effectively otherwise. Some (most) of these ideas are shamelessly taken from the stackoverflow help pages.

Asking for Help

Remote Working Resources

VPN and SSH via central

Copying files with SCP/WinSCP/Filezilla/Cyberduck

Running graphical programs remotely

Super Computing Wales Guides

SCW Introduction

SCW Training Materials

SCW Access Procedures


IBERS HPC Guides

Overview

Bert and Ernie - An Overview

Nodes, Cores, Slots

Scheduling and queuing

Getting an account

Using the HPC

Quick start

Your disk space

Module Environment

Installing your own modules

Submitting your job using Slurm

Complex submissions

Monitoring your jobs

Available Software

UNIX Graphical interface

Array jobs

ABySS

Tools to access the HPC (Windows)

Putty

MobaXterm

Filezilla

Slides, Talks and Training Materials

Talk on using Containers - File:Containers.pdf

Carpentries Style Lesson on using the HPC

Recording of the lesson above

Bioinformatics Working Group related

Meeting minutes

Special HPC Workflows

Matlab

Blast

Active Perl

SPRINT

Progressive Cactus

OrthoMCL

Diamond Blast

Singularity Containers

Other Services

Blast2go

Best Practice

Running BLAST optimally

Use scratch space

Tutorials

RNA Seq on HPC

RNA Seq on HPC (using Trinity)

Genome Annotation

Tips

Splitting Multifastas

Workarounds

Java memory allocation issues

convert_fasta_to_1l_fasta.sh´