From: Ben Soares <b.soares@dundee.ac.uk>
Date: Mon, 3 Aug 2020 10:20:05 +0000 (+0100)
Subject: JAL-3477 added help documentation for executable jar command line arguments -jvmmempc... 
X-Git-Tag: Release_2_11_1_1~13^2~29
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2f160359d38a4d475b0f96eb7da61f823d9ef7bd;p=jalview.git

JAL-3477 added help documentation for executable jar command line arguments -jvmmempc and -jvmmemmax
---

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 5c9e314..89560e9 100644
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -234,6 +234,25 @@
           </div>
       </td>
     </tr>
+    <tr>
+      <td><div align="center">-jvmmempc=PERCENT</div></td>
+      <td><div align="left"><em>Standalone executable jar only.</em>
+          Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
+	  This defaults to 90 if total physical memory can be detected.
+	  See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+          </div>
+      </td>
+    </tr>
+    <tr>
+      <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
+      <td><div align="left"><em>Standalone executable jar only.</em>
+          Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
+	  gigabytes(g) or if you're lucky enough, terabytes(t).
+	  This defaults to 32g if total physcial memory can be detected, or to 8g if total physical memory cannot be detected.
+	  See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
+          </div>
+      </td>
+    </tr>
   </table>
 </body>
 </html>
diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 81190a9..80bffa3 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -90,7 +90,16 @@
     <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)</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),
+      then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=N</em>
+      and <em>-jvmmemmax=M</em> respectively, 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/><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