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TLDR: Change your process pinning.
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This is an artifact of your process pinning. Due to the way in which modern CPUs are constructed certain CPU cores have faster access to certain hardware devices, and hence faster to connections to the CPUs of other nodes, than other cores. This manifests itself commonly in checkerboard patterns in the timing matrix. The checkerboard pattern can commonly be avoided by reorganizing the rows and columns. This reorganization can be achieved by changing the processor pinning when Linktest is executed. For more information on how this is done please see the documentation for the tools you use to execute Linktest in parallel, for example `mpiexec` or `srun`.
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# How can I generate an animated GIF of multiple indexed-images from the Python reports, e.g. for presentations?
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This can be done using [Image Magick](https://imagemagick.org/index.php), a command-line image-manipulation tool. The basic idea is to combine the various PDF reports that you want to include in the GIF into one PDF, for example using `pdfunite`, a commonly available tool on many Linux distributions. Then process the PDF using Image Magick as follows:
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```bash
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convert -density 150 -crop 1070x910+85+70 -delay 50 -dispose previous input.pdf -coalesce -layers OptimizePlus +repage output.gif
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```
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where `input.pdf` is the name and path of the combined PDF file containing the reports from which you wish to extract the indexed images and `output.gif` is the name and path of the output GIF file. The `-density` density option controls the image resolution. Increasing density increases file size. The `-crop` crop options crops loaded and rasterized PDF to the correct size. If you change the density you also need to change the crop, i.e. if you double the density you need to double the crop numbers as well. The `-delay` option controls the delay length between frames in the GIF, increase this number to increase the delay between frames. The `-dispose` option causes GIF frames to overwrite each other instead of stacking on top of each other. The `-coalesce` option causes the individual PDF pages to be coalesced into one GIF. The `-layers OptimizePlus` option optimizes the GIF to reduce file size. The `+repage` option causes the geometry information from the original PDF to be lost so that the GIF displays correctly. |
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