From ab1dce80c1a6f45b2071016f1ce07a3466d81a2e Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 4 Jul 2019 00:59:39 +0100 Subject: [PATCH] JAL-3348 memory.html documentation finished for 2.11.0 --- help/help/html/memory.html | 85 +++++++++++++++++++++++++++++--------------- 1 file changed, 56 insertions(+), 29 deletions(-) diff --git a/help/help/html/memory.html b/help/help/html/memory.html index b784451..396507b 100755 --- a/help/help/html/memory.html +++ b/help/help/html/memory.html @@ -67,7 +67,7 @@
  • JVL file

    The easiest way to launch Jalview with a different percentage of physical memory available is to - create a text file with extension .jvl and with content that looks like + create a text file with extension .jvl and with content that contains the line 

           jalview.jvmmempc=50
    @@ -84,51 +84,78 @@

    - If you want to use a memory setting like this and open a file you can use both files as arguments in the command line, but you must put the jvl file first, e.g. + 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 jvl file first, e.g. 

           /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa
    - - + alternatively, you can use the standard Jalview command line arguments with or without the jvl file (first), e.g. + 
    +       /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
+

    -
    • - - -
  • +

    + You can use command line arguments to control memory settings in Windows and macOS too: +
    + In Windows you must use, e.g. + 

    +      \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa
+
    + and in macOS you can use the macOS open command like this: + 
    +      open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa
+
    + (put all the Jalview arguments after the --args parameter). +

    • - - -
  • +
  • Directly opening Jalview with a JVM

    + Launching Jalview directly with a JVM is entirely possible, but is not recommended as automatic updates and some other default settings will not operate.

    -
    • - - - - -

  • + However by launching Jalview in this way you have full access to the Java command line arguments. + In particular you can set the maximum allowed memory with the -Xmx... JVM argument. +
    + -Xmx should be immediately followed (no space or equals) by the maximum amount of memory that you might want to launch Jalview with. This can be specified in bytes as just a number, + or in kilobytes, megabytes or gigabytes by following the number with a "k", "m" or "g" respectively. e.g. + 

    +      -Xmx8g
+

    -
    • - - - - -

  • + Jalview binaries for Windows and macOS are distributed with their own JVM which you will find in +

    + For linux and other unixes you will have to install a Java 1.8 JRE (we recommend the ones found at https://adoptopenjdk.net/)

    -
    • - - - - -

  • + You will also need to reference the "appdir" release folder with all of the Jalview jar files. +
    + On Windows this will be + 

    \PATH_TO_JALVIEW\release
    + whereas on macOS it will be + 
    /Applications/Jalview.app/Contents/Resources/app/release
    + and on linux or unix + 
    /PATH_TO_JALVIEW/release

    +

    + Assuming the java (or java.exe on Windows) commands are available to you, you can run, e.g. + 

    +      java -Xmx1500m -cp "/PATH_TO_RELEASE_DIR/*" jalview.bin.Jalview
+
    + or on Windows + 
    +      java.exe -Xmx1500m -cp "\PATH_TO_RELEASE_DIR\*" jalview.bin.Jalview
+
    + Note that the classpath argument wildcard must be simply a '*' and not '*.jar'. This is a limitation of Java. +

    +

    + You can also add other Jalview command line arguments as above after the jalview.bin.Jalview class name (you cannot use jvl files if launching Jalview in this way).

    • -- 1.7.10.2