Frequently-Asked-Questions.md

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 # My SION files are HUGE! What can I do?
-See [SION File Defragmentation](Usage#sion-file-defragmentation). Note that you can still load the defragmented SION file into python, see [Linktest Python Reader](Linktest-Python-Reader), and it can still be used to generate reports, see [Linktest Report](Linktest-Report). After defragmentation the file can be further compressed using any non-lossy compression tools. The resultant compressed file can no longer be loaded into python and hence reports based on it cannot be generated unless the file is decompressed first.
+If you write out your SION files in parallel, which causes fragmented SION files to be written out, see [SION File Defragmentation](Usage#sion-file-defragmentation), otherwise only non-lossy compression can help you further.
+
+Note that you can still load defragmented SION files into python, see [Linktest Python Reader](Linktest-Python-Reader), and they can still be used to generate reports, see [Linktest Report](Linktest-Report). After defragmentation compressed SION files can be further compressed using any non-lossy compression tools. The resultant compressed file can no longer be loaded into python and hence reports based on it cannot be generated unless the file is decompressed first.
 
 # In Linktest Report (the python tool) I cannot read the indexed-image tick labels. Can I increase the font size?
 You may be able to indirectly increase the font size. The font size is limited by two factors, the number of ticks, which limits the vertical height of the text of each tick, and the maximum length of each tick label. See the `--downsampling_factor_matrix_ticks` option in [the Linktest Report options](Linktest-Report#options) to learn how to reduce the number of ticks plotted, which increases the vertical space allocated to each tick label. See the `--domain` option in [the Linktest Report options](Linktest-Report#options) to earn how domains, or any string, can be removed from the tick labels. Shortening tick labels allows for larger font sizes for a given maximum tick-label width.
@@ -15,11 +17,11 @@ Probably, here are a few things that will speed up report generation:
 
 3. If you are prone to cancelling seemingly hanging processes early because of no command-line output use the `verbose` option to see timing information for segments of the report generation.
 
-4. Use a newer version of Python or MatPlotLib. Although the report tool was originally developed for Python 3.8.5 and MatPlotLib version 3.3.1 upgrading MatPlotLib version 3.3.4 improved a 2 minute run using a defragmented SION file by approximately 15%. Upgrading to Python 3.9.0 cut the time to just above 1 minute. The problem is mostly the slow MatPlotLib back end for generating plots. The backends are optimized for quality, not performance. Profiling indicates that for larger SION files, 500 MiB and above after defragmentation, the MatPlotLib back end takes up about 80% of the compute time of the report.
+4. Use a newer version of Python or MatPlotLib. Although the report tool was originally developed for Python 3.8.5 and MatPlotLib version 3.3.1 upgrading MatPlotLib version 3.3.4 improved a 2 minute run using a defragmented SION file by approximately 15%. Upgrading to Python 3.9.0 cut the time to just above 1 minute. The problem is mostly the slow MatPlotLib back end for generating plots. The back ends are optimized for quality, not performance. Profiling indicates that for larger SION files, 500 MiB and above after defragmentation, the MatPlotLib back end takes up about 80% of the compute time of the report.
 
 5. Use the supplied pingponganalysis tools. These create postscript files that can be converted to pdf. Generating a comparable PDF report to the above mentioned 2 minute report only takes about 5 to 10 seconds. Please note that the pingponganalysis tools are only kept up-to-date with the current version of Linktest.
 
-6. Read the SION files directly into Python and inspect the data there using the [Linktest Python Reader](Linktest-Python-Reader). This does not substitute a nice and easy to read report but gives you the flexibility of looking at the data more in depth or to produce figures that better fit your needs.
+6. Read the SION files directly into Python and inspect the data there using the [Linktest Python Reader](Linktest-Python-Reader). This does not substitute a nice and easy to read report, but gives you the flexibility of looking at the data more in depth or to produce figures that better fit your needs.
 
 # What do the weird unit prefixes, like ki, Mi and Gi, mean?
 TLDR: They are binary prefixes.
@@ -36,7 +38,7 @@ Here is a comparison table between the two standards:
 |G|$`10^9`$|Ti|$`2^{30}`$|1.073|
 |T|$`10^{12}`$|Gi|$`2^{40}`$|1.100|
 
-A common problem with these unit prefixes is that they are equated to metric prefixes, however, for larger units the difference between prefixes grows substantially as indicated in the fifth column of the table, which shows the ratio of binary prefix value to the corresponding metric prefix value. Lesson to learn, do not equate these prefixes! A 7.3% difference may not  seem like a lot but when benchmarking connections it can be the difference between the value you expect and the one Linktest returns.
+A common problem with these unit prefixes is that they are equated to metric prefixes, however, for larger units the difference between prefixes grows substantially as indicated in the fifth column of the table, which shows the ratio of binary prefix value to the corresponding metric prefix value. Lesson to learn, do not equate these prefixes! A 7.3% difference may not seem like a lot but when benchmarking connections it can be the difference between the value you expect and the one Linktest returns.
 
 # I am running a latency test and the first row in my timings matrix is much slower than the others. What can I do?
 TLDR: You likely forgot to use warm-up messages.