Helix/Software: Difference between revisions
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S Richling (talk | contribs) (Created page with "== Environment Modules == Most software is provided as Modules. Required reading to use: Environment Modules == Available Software == Visit [https://www.bwhpc.de/softwar...") |
H Schumacher (talk | contribs) (Added mention of Alphafold and Link to BioStructureHub Tutorials) |
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== Environment Modules == |
== Environment Modules == |
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Most software is provided as Modules. |
Most software is provided as [[Environment Modules]]. |
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Required reading to use: [[Environment Modules]] |
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== Available Software == |
== Available Software == |
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Visit [https://www.bwhpc.de/software.php https://www.bwhpc.de/software.php], select <code>Cluster → bwForCluster Helix</code> |
Visit [https://www.bwhpc.de/software.php https://www.bwhpc.de/software.php], select <code>Cluster → bwForCluster Helix</code> |
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On cluster: <code>module avail</code> |
On the cluster: <code>module avail</code> |
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== Documentation == |
== Documentation on the Cluster == |
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Documentation |
Documentation for each environment module is available on the cluster: |
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* with command <code>module help</code> |
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{| style="width:100%;" |
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* examples are in <code>$<SOFTNAME>_EXA_DIR</code> (batch script + other needed input files). This environment variable is available as soon as the module is loaded. |
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|- style="background:#eeeeee;" | |
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** Some modules, e.g. the Alphafold module, include an especially extensive example. |
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| <code>module help</code> || See section: [[Environment_Modules#module_help]] |
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|- style="background:#dddddd; " | |
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| examples in <code>$SOFTNAME_EXA_DIR</code> || See section: [[Environment_Modules#Software_job_examples]] |
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|- style="background:#eeeeee; " | |
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| this wiki || See below |
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|} |
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== Documentation in the Wiki == |
== Documentation in the Wiki == |
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For some environment modules additional documentation is provided here. |
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* [[Helix/Software/Singularity | Singularity]] (containers) |
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* [[Development/Conda | Conda]] |
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* [[Python | Python]] |
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* [[Helix/Software/R | R]] |
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** [[Helix/Software/R/Rstan | Rstan]] |
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* [[Helix/Software/Matlab | Matlab]] |
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* [[Helix/Software/SAS | SAS ]] |
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* [[Helix/Software/Stata | Stata]] |
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== External Documentation == |
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* '''BioStructureHub Heidelberg:''' Tutorials are provided for using Helix software modules like Alphafold, RFDiffusion etc. and related software on the Helix cluster and on [[Helix/bwVisu | bwVisu]]. |
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*: → [https://github.com/ssciwr/BioStructureHub/tree/main/docs/tutorials Tutorials] |
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Latest revision as of 17:22, 10 September 2026
Environment Modules
Most software is provided as Environment Modules.
Available Software
Visit https://www.bwhpc.de/software.php, select Cluster → bwForCluster Helix
On the cluster: module avail
Documentation on the Cluster
Documentation for each environment module is available on the cluster:
- with command
module help - examples are in
$<SOFTNAME>_EXA_DIR(batch script + other needed input files). This environment variable is available as soon as the module is loaded.- Some modules, e.g. the Alphafold module, include an especially extensive example.
Documentation in the Wiki
For some environment modules additional documentation is provided here.