From 883ba618f83573893f1f0b895b0bf84dacccefe5 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 2 Jul 2019 23:20:04 +0100 Subject: [PATCH] =?utf8?q?JAL-3111=20JAL-3348=20removed=20pre=202.11=20instr?= =?utf8?q?uctions=20on=20setting=20Jalview=E2=80=99s=20memory=20settings.=20?= =?utf8?q?Needs=20information=20about=20configuring=20proportion=20of=20memo?= =?utf8?q?ry=20allocated.?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/help/html/memory.html | 127 ++++++-------------------------------------- 1 file changed, 16 insertions(+), 111 deletions(-) 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 @@

- 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.
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.
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).

Jalview Memory Usage Monitor: If you are concerned about @@ -52,105 +54,8 @@ window's background.

- Increasing the memory available to Jalview
The way - you increase the memory settings for the JVM depends on which - installation of Jalview you use: -

- -

- Please Note: 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. -

- Jalview doesn't start... What do the - memory settings mean ? - -

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).

-

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!

-

- 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 Jalview - 256MB JNLP. -

-

 

+ Increasing the memory available to Jalview
+ 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. +

 

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