Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / help / help / html / memory.html

diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 81190a9..7d6fb85 100755 (executable)
--- a/help/help/html/memory.html
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@@ -80,7 +80,7 @@
       arguments, but you must put the <em>jvl</em> file first, e.g. <pre>
       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
       arguments with or without the jvl file (first), e.g. <pre>
-       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
+       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre> You can use command line arguments to control memory
       settings in Windows and macOS too: <br /> In Windows you must
       use, e.g. <pre>
       \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre> In macOS you can use the macOS <em>open</em> command like this: <pre>
@@ -90,7 +90,17 @@
     <li><em><font size="3">Maximum memory limit</em><br/>
       Since 2.11.1.0, Jalview's configuration includes a 'maximum memory limit':
       <pre>jalview.jvmmemmax = 32G</pre>
-      Adjusting this default (via a JVL file, above) will allow larger amounts of memory to be allocated to Jalview in connjunction with the jalview.jvmmempc setting. 
+      Adjusting this default (via a JVL file, above) will allow larger amounts (or can limit the amount) of memory to be allocated to Jalview in conjunction with the jalview.jvmmempc setting. 
+      <br/><br/>
+    </li>
+    <li><em><font size="3"><a name="jar">Command line arguments when using the executable jar (jalview-all.jar) or jalview.bin.Launcher</a></em><br/>
+      If you are using the Jalview standalone executable jar (usually named <em>jalview-all-....jar</em> with a Jalview and Java version designation) or using <em>jalview.bin.Launcher</em> to start Jalview,
+      then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=PERCENT</em>
+      and <em>-jvmmemmax=MAXMEMORY</em> respectively.  <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
+      <pre>java -jar jalview-all-2.11.1.0-j1.8.jar -jvmmempc=50 -jvmmemmax=20g</pre>
+      (this example will launch Jalview with a maximum heap size of the smaller of 20GB or 50% of physical memory detected).
+      <br/>The default value for jvmmempc is 90, whilst the default value for jvmmemmax is 32g if Jalview can determine a total physical memory size of the host system, and a more cautious 8g if Jalview is unable to determine a total physical memory size.
+      <br/><br/>
     </li>
     <li><em><font size="3"><a name="jvm"/>Directly opening Jalview
           with a JVM</font></em> <br /> Launching Jalview directly with a JVM is