From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 2 Jul 2019 22:20:04 +0000 (+0100)
Subject: JAL-3111 JAL-3348 removed pre 2.11 instructions on setting Jalview’s memory settings... 
X-Git-Tag: Release_2_11_0~2^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=883ba618f83573893f1f0b895b0bf84dacccefe5;p=jalview.git

JAL-3111 JAL-3348 removed pre 2.11 instructions on setting Jalview’s memory settings. Needs information about configuring proportion of memory allocated.
---

diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 9437a60..e583398 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -29,17 +29,19 @@
     </center>
   </h2>
   <p>
-    Jalview sometimes runs out of memory. This is because of the way
-    that Java runs on a computer - what is actually run is a program
-    called a virtual machine (the JVM) which executes the java
-    instructions. The JVM has limits on the memory that can be allocated
-    to the java program - and you might need to increase them if you are
-    working with particularly large datasets.<br> If Jalview has
-    not explicitly told you that it has run out of memory, then a common
-    sign is that a function that normally works seems to have no effect
-    when working with a larger set of sequences (this might include open
-    dialog boxes for saving PNG files, or when interpreting the result
-    of a web service calculation).
+    When launched as an Application, Jalview automatically tries to
+    maximise the amount of memory allocated to it, but sometimes it may
+    run out of memory. This is because of the way that Java runs on a
+    computer - what is actually run is a program called a virtual
+    machine (the JVM) which executes the java instructions. The JVM has
+    limits on the memory that can be allocated to the java program - and
+    you might need to increase them if you are working with particularly
+    large datasets.<br> If Jalview has not explicitly told you that
+    it has run out of memory, then a common sign is that a function that
+    normally works seems to have no effect when working with a larger
+    set of sequences (this might include open dialog boxes for saving
+    PNG files, or when interpreting the result of a web service
+    calculation).
   </p>
   <p>
     <em>Jalview Memory Usage Monitor</em>: If you are concerned about
@@ -52,105 +54,8 @@
     window's background.
   </p>
   <p>
-    <em>Increasing the memory available to Jalview</em><br> The way
-    you increase the memory settings for the JVM depends on which
-    installation of Jalview you use:
-  </p>
-  <ul>
-    <li><em><font size="3">Web Start Version</font></em>
-      <p>
-        JavaWS sets the JVM parameters through special tags in the JNLP
-        file. You can obtain a JNLP file with modified memory settings
-        from our service with the following link (replace 2G with
-        desired memory in G or M):<br /> <a
-          href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
-      </p>
-      <p>
-        Alternatively, if you want to create your own JNLP file then
-        please download the latest JNLP file from <a
-          href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
-        and modify the max-heap-size parameter for the j2se tag in the
-        &lt;resources&gt; element. e.g.
-      <pre>
-&lt;j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/&gt;
-</pre> In both cases, you should save your new jnlp file somewhere and then
-      either point your web browser at the file's url, launch it from
-      your file browser, or from a terminal window run javaws (located
-      in your Java installation's bin directory) with the file location
-      as its argument. The file's url is something like :<br> <pre>
-file://&lt;full path to file&gt;
-</pre> If Jalview doesn't start up, see <a href="#memsetting">below</a>.
-      You'll have to edit the above settings in the JNLP file using a
-      text editor, save it, and try starting Jalview with it once more.
-      </p></li>
-    <li><em><font size="3">Install Anywhere version</font></em>
-      <p>You need to change the InstallAnywhere configuration
-        settings for the application. These are found in different
-        places depending upon which operating system you have :
-      <ul>
-        <li><em>Unix/Windows</em>
-          <p>Take a look inside the Jalview program installation
-            directory (this might be in C:\Program Files\Jalview on
-            windows). You should find a file called 'Jalview.lax' in it
-            - make a backup, and then add the following lines to the end
-            of the original file :
-          <pre>
-lax.nl.java.option.java.heap.size.max=1000m
-lax.nl.java.option.java.heap.size.initial=500m
-</pre> Case and (lack of) spaces are important here! Do not add any spaces
-          after the m in each line, and do not put any spaces before
-          'lax'.<br> Also there MUST be a carriage return after the
-          final line.
-          <p></p></li>
-        <li><em>Mac OSX</em>
-          <p>
-            The lines you need to change are in the <em>Info.plist</em>
-            file inside the <em>Jalview.app/Contents</em> directory
-            (which is where the installAnywhere installation was made) :
-
-          
-          <pre>
-&lt;key&ht;VMOptions&lt;/key&ht;
-&lt;array&gt;
-! &lt;string&gt;-Xms2M&lt;/string&gt;
-! &lt;string&gt;-Xmx64M&lt;/string&gt;
-&lt;/array&gt;
-</pre>Exchange the above two string tags for : <pre>
-&lt;string&gt;-Xms500M&lt;/string&gt;
-&lt;string&gt;-Xmx1000M&lt;/string&gt;
-</pre>
-          <p></p></li>
-      </ul>
-    <li><font size="3"><em>In all cases</em></font><br> Save
-      the file and try to start Jalview in the normal way. If it doesn't
-      start, see below...</li>
-  </ul>
-  <p>
-    <em>Please Note:</em> We do modify the default memory settings in
-    Jalview from time to time, so you may find different numbers to
-    those shown in the examples above.
-  </p>
-  <font size="3"><em>Jalview doesn't start... What do the
-      memory settings mean ?<a name="memsetting"></a>
-  </em></font>
-  <p>The 1000m value corresponds to the maximum number of megabytes
-    of space that java objects can occupy. The 500m is the initial heap
-    size that java will run in - increasing this can speed up memory
-    allocation if you know you will need 500 meg of memory to begin with
-    (ie it should speed up loading large alignments).</p>
-  <p>If, after setting the initial and maximum heap size to some
-    large value, you cannot actually start Jalview, then the max and
-    initial sizes are too big for your machine (there seems to be a
-    physical limit related to physical RAM - email the usual address to
-    enlighten us if you know better!). Our experiments found 1000m to be
-    the biggest setting that could be used on a 1GB machine. Just try
-    reducing the sizes until Jalview starts up properly!</p>
-  <p>
-    We increased the default memory in Jalview 2.10.5 to 1G. To launch
-    Jalview with the pre 2.10.5 default memory allocation, use the <a
-      href="http://www.jalview.org/webstart/jalview_256MB.jnlp">Jalview
-      256MB JNLP</a>.
-  </p>
-  <p>&nbsp;</p>
+    <em>Increasing the memory available to Jalview</em><br>
+    Since Jalview 2.11, the program automatically configures the JVM memory settings to set the maximum memory available to Jalview to be 90% of physical memory. 
+      <p>&nbsp;</p>
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