X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Fmemory.html;h=ec57530a42f937fdf5387179d64e7ca4573710ef;hb=2319ef1a410ce35bf2ef1800fd0be4e779ee44eb;hp=81190a90dd764b318f3ab2736e7497f05b50d7b0;hpb=a58be5fb3401c0b0f74d6089d2eaaf7691e6418f;p=jalview.git

diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 81190a9..ec57530 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -30,9 +30,13 @@
   </h2>
   <p>When launched as an Application, Jalview will automatically
     configure the amount of memory allocated to the program to be 90% of
-    physical memory. You may wish to change this behaviour -
-    particularly if you are working on a machine that runs other memory
-    intensive processes.
+    physical memory, or 32GB - which ever is smaller.</p>
+  <p>
+    This behaviour might not be ideal if you are working on a machine
+    that runs other memory intensive processes, and (<em>since
+      Jalview 2.11.2</em>) can be changed via the <a
+      ref="preferences.html#startup">Startup Preferences</a> panel.
+  </p>
   <p>
     <em>Signs that Jalview is Running out of Memory</em><br /> If
     Jalview has not explicitly told you that it has run out of memory,
@@ -65,32 +69,50 @@
   </p>
 
   <ul>
-    <li><em><font size="3">JVL file</font></em> <br /> The easiest
-      way to launch Jalview with a different percentage of physical
-      memory available is to create a text file with extension <em>.jvl</em>
+    <li><em><font size="3">Jalview's Startup
+          Preferences panel</font></em> <br /> The easiest way to launch Jalview
+      with a different percentage of physical memory available is to
+      adjust your user preferences via the <a
+      ref="preferences.html#startup">Startup Preferences</a> panel.</li>
+    <li><em><font size="3">JVL file</font></em> <br />Another way
+      to adjust launch settings is with a text file with extension <em>.jvl</em>
       and a single line to specify the percentage of memory you wish
       Jalview to request: <pre>
-      jalview.jvmmempc=50</pre> In Windows and in macOS you can then launch Jalview by
-      double clicking on this file, and your memory setting will be used
-      instead of the default value. <br /> <br /> In Linux or other
-      unix variants you can launch Jalview on the command line and
-      provide your JVL file as an argument with <pre>
-      /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl</pre> If you want to use a memory setting like this and open a
-      file you can use both the jvl and alignment files as command line
-      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
+      jalview.jvmmempc=50</pre> In Windows and in macOS you can then launch
+      Jalview by double clicking on this file, and your memory setting
+      will be used instead of the default value. <br /> <br /> In
+      Linux or other unix variants you can launch Jalview on the command
+      line and provide your JVL file as an argument with <pre>
+      /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl</pre> If you
+      want to use a memory setting like this and open a file you can use
+      both the jvl and alignment files as command line 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
-      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>
-      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>
+       /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>
+      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 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