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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. | ||
+ | |||
+ | == 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 [https://stackoverflow.com/help/ 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 == | == IBERS HPC Guides == | ||
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[[Module Environment]] | [[Module Environment]] | ||
+ | |||
+ | [[Installing your own modules]] | ||
[[Submitting your job using SGE]] | [[Submitting your job using SGE]] | ||
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[[Updated Scheduler]] | [[Updated Scheduler]] | ||
+ | |||
+ | [[WinSCP from external]] | ||
+ | |||
+ | == Tools to access the HPC (Windows) == | ||
+ | |||
+ | [[Putty]] | ||
+ | |||
+ | [[MobaXterm]] | ||
+ | |||
+ | [[Filezilla]] | ||
== Slides and Talks == | == Slides and Talks == | ||
[[File:Sge queue changes.pdf]] | [[File:Sge queue changes.pdf]] | ||
+ | |||
+ | [[File:Containers.pdf]] | ||
== Bioinformatics Working Group related == | == Bioinformatics Working Group related == | ||
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[[OrthoMCL]] | [[OrthoMCL]] | ||
+ | |||
+ | [[Diamond Blast]] | ||
+ | |||
+ | [[Singularity Containers]] | ||
== Other Services == | == Other Services == | ||
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[[RNA Seq on HPC]] | [[RNA Seq on HPC]] | ||
+ | |||
+ | [[RNA Seq on HPC (using Trinity)]] | ||
[[Genome Annotation]] | [[Genome Annotation]] | ||
+ | |||
+ | == Tips == | ||
+ | |||
+ | [[Splitting Multifastas]] | ||
== Workarounds == | == Workarounds == | ||
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[[Java memory allocation issues]] | [[Java memory allocation issues]] | ||
− | [[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']] |
Revision as of 09:50, 4 May 2022
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.
Contents
- 1 Editing this Wiki
- 2 Troubleshooting
- 3 Remote Working Resources
- 4 Super Computing Wales Guides
- 5 IBERS HPC Guides
- 6 Tools to access the HPC (Windows)
- 7 Slides and Talks
- 8 Bioinformatics Working Group related
- 9 Special HPC Workflows
- 10 Other Services
- 11 Best Practice
- 12 Tutorials
- 13 Tips
- 14 Workarounds
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.
Remote Working Resources
Copying files with SCP/WinSCP/Filezilla/Cyberduck
Video conferencing and collaboration tools
Running graphical programs remotely
Super Computing Wales Guides
IBERS HPC Guides
Overview
Using the HPC
Tools to access the HPC (Windows)
Slides and Talks
Special HPC Workflows
Other Services
Best Practice
Tutorials
RNA Seq on HPC (using Trinity)
Tips
Workarounds
Your software/script uses threads and works locally, but crashes if run under the SGE's queue