Document how to use Amber #78
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ptheywood
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…ich are much more manageable, with their own easier to find rendered pages. Closes #61 Whilst splitting this file into many smaller files, a number of additions and changes were made to the documentation, including: + Adds (basic) documentation for: + IBM XL compilers (Closes #61) + Amber (Part of #78) + EMAN2 + GRACE + Gromacs (Closes #37, part of #79) + NAMD + OpenMM + PLUMED + Singularity (Apptainer) (Closes #49) + Generic python information, with more detailed conda usage (Closes #47) + nvidia-smi (Closes #75) + HECBioSim project + IBM Collaboration project + Boost Module + FFTW module + NVTX library + PLUMED library + VTK + CMake + Make + Creates new `guides` section + Migrates the `profiling` documentation into the guides section + Migrates the `wanderings` about CUDA into the guides section + Adds some notes/warnings about potential WMLCE + RHEL 8 incompatibility. Larger changes still required (#63) + CSS/JS/_templates changes for a useful sidebar with the bootstrap theme with split source files + New issue #87 opened to consider replacing the theme to an actively maintained theme. + Removes relations.html from the sidebar, as styling issues were difficult to resolve nicely (Closes #77) + Adds sphinxext-rediraffe plugin for redirects for moved .html files (see conf.py) + Assorted RST improvements (links, crossrefs, quoteblocks, code-block, note, etc.) + Clarify module loads for RHEL 7 vs RHEL 8 where appropriate (Part of #73). + Assorted other improvements throughout the documentation History was a little messy, so has been squashed to avoid `.git` bloat.
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ptheywood
added a commit
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Jan 31, 2022
…ich are much more manageable, with their own easier to find rendered pages. Closes #61 Whilst splitting this file into many smaller files, a number of additions and changes were made to the documentation, including: + Adds (basic) documentation for: + IBM XL compilers (Closes #61) + Amber (Part of #78) + EMAN2 + GRACE + Gromacs (Closes #37, part of #79) + NAMD + OpenMM + PLUMED + Singularity (Apptainer) (Closes #49) + Generic python information, with more detailed conda usage (Closes #47) + nvidia-smi (Closes #75) + HECBioSim project + IBM Collaboration project + Boost Module + FFTW module + NVTX library + PLUMED library + VTK + CMake + Make + Creates new `guides` section + Migrates the `profiling` documentation into the guides section + Migrates the `wanderings` about CUDA into the guides section + Adds some notes/warnings about potential WMLCE + RHEL 8 incompatibility. Larger changes still required (#63) + CSS/JS/_templates changes for a useful sidebar with the bootstrap theme with split source files + New issue #87 opened to consider replacing the theme to an actively maintained theme. + Removes relations.html from the sidebar, as styling issues were difficult to resolve nicely (Closes #77) + Adds sphinxext-rediraffe plugin for redirects for moved .html files (see conf.py) + Assorted RST improvements (links, crossrefs, quoteblocks, code-block, note, etc.) + Clarify module loads for RHEL 7 vs RHEL 8 where appropriate (Part of #73). + Assorted other improvements throughout the documentation + Adds the sphinx-copybutton plugin, for easy to copy code-block contents. History was a little messy, so has been squashed to avoid `.git` bloat.
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#67 adds very basic amber docs, at Additional, more detailed docs can be added to this file once it has been approved and merged on actual amber use (ideally by someone who has used amber) |
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Now #67 is merged, the very basic Amber documentation can be exapended by editing software/applications/amber.rst |
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Closing this as the docs taskforce is being closed, and minimal amber docs are present. The docs page can still be expanded if required with bede-speicifc additions if required. |
Repository owner
moved this from On Hold/Low Prio
to Done
in Documentation
Jun 7, 2022
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Talk to James Gebbie about access to Amber and add the info to the docs
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