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Welcome to the HPC Wiki for the [http://bioinformatics.ibers.aber.ac.uk Bioinformatics] research group at [http://www.aber.ac.uk 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.
 
Welcome to the HPC Wiki for the [http://bioinformatics.ibers.aber.ac.uk Bioinformatics] research group at [http://www.aber.ac.uk 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.
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== Editing this Wiki ==
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Please email ibers-cs@aber.ac.uk to ask for access to edit this wiki.
  
 
== Troubleshooting ==
 
== Troubleshooting ==
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[[Asking for Help]]
 
[[Asking for Help]]
  
[[Minimal, Verifiable, Complete example]]
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== Remote Working Resources ==
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[[VPN and SSH via central]]
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[[Copying files with SCP/WinSCP/Filezilla/Cyberduck]]
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[[Video conferencing and collaboration tools]]
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[[Running graphical programs remotely]]
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== Super Computing Wales Guides ==
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[[SCW Introduction]]
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[[SCW Training Materials]]
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[[SCW Access Procedures]]
  
  
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[[Module Environment]]
 
[[Module Environment]]
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[[Installing your own modules]]
  
 
[[Submitting your job using SGE]]
 
[[Submitting your job using SGE]]
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[[WinSCP from external]]
 
[[WinSCP from external]]
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== Tools to access the HPC (Windows) ==
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[[Putty]]
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[[MobaXterm]]
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[[Filezilla]]
  
 
== Slides and Talks ==
 
== Slides and Talks ==
  
 
[[File:Sge queue changes.pdf]]
 
[[File:Sge queue changes.pdf]]
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[[File:Containers.pdf]]
  
 
== Bioinformatics Working Group related ==
 
== Bioinformatics Working Group related ==
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[[OrthoMCL]]
 
[[OrthoMCL]]
  
[[How to run BLAST with DIAMOND]]
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[[Diamond Blast]]
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[[Singularity Containers]]
  
 
== Other Services ==
 
== Other Services ==
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[[Genome Annotation]]
 
[[Genome Annotation]]
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== Tips ==
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[[Splitting Multifastas]]
  
 
== Workarounds ==
 
== Workarounds ==
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[[Java memory allocation issues]]
 
[[Java memory allocation issues]]
  
[[convert_fasta_to_1l_fasta.sh]]
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[[convert_fasta_to_1l_fasta.sh]]´
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[[Your software/script uses threads and works locally, but crashes if run under the SGE's queue]]
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[[Intermittent login failures on the HPC and some VMs]]
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[[error importing function definition for `BASH_FUNC_module']]

Revision as of 09:50, 4 May 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

Video conferencing and collaboration tools

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 SGE

Complex submissions

Monitoring your jobs

Available Software

UNIX Graphical interface

Array jobs

ABySS

Updated Scheduler

WinSCP from external

Tools to access the HPC (Windows)

Putty

MobaXterm

Filezilla

Slides and Talks

File:Sge queue changes.pdf

File:Containers.pdf

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´

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'