Add Gromacs Info #37
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Waiting for GROMACS group to produce documentation. |
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Will add a stub of a page during #67 pointing to the hecbiosim module, with room for further information to be added via the gromacs bede taskforce at a later date. |
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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.
ptheywood
added a commit
that referenced
this issue
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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For the time being, we use the hecbiosim module for gromacs, which is made available by the command "module load hecbiosim gromacs" .
This info should be added under "Software". Very important: credits and thanks to HECBioSim for allowing us to use it!
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