JAL-3477 Improved command line arguments description in memory.html

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

diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 4baebf2..0374dcb 100755 (executable)
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -61,8 +61,7 @@
     necessary to adjust them if you are working with particularly large
     datasets, or need to make room for other processes on the machine.<br />
     <br />Jalview 2.11 includes a launcher that automatically
-    configures the proportion of memory allocated to Jalview's JVM, and
-    its behaviour can be altered in a number of different ways:
+    configures the proportion of memory allocated to Jalview's JVM. By default it requests up to 90% of available memory whilst ensuring that at least 0.5G is available to the operating system and at least 0.5G is available to the Java runtime platform, or a specified 'maximum memory limit' - which ever is smaller. The amount of memory requested can be altered in a number of different ways:
   </p>
 
   <ul>
@@ -88,6 +87,21 @@
       open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa</pre><em>(put all the Jalview arguments <em>after</em> the --args
         parameter)
     </em><br/><br/></li>
+    <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 (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
       entirely possible, but is not recommended for regular interactive