From af2e52a8a12ccafb733ca34eb0bbc313c3771900 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 11 Jan 2008 13:54:27 +0000 Subject: [PATCH] jalview memory monitor instructions added --- help/html/memory.html | 195 +++++++++++++++++++++++++------------------------ 1 file changed, 101 insertions(+), 94 deletions(-) diff --git a/help/html/memory.html b/help/html/memory.html index ba1a72c..10ef708 100755 --- a/help/html/memory.html +++ b/help/html/memory.html @@ -1,94 +1,101 @@ - -Memory Settings - -

-
- Memory Usage Settings for Jalview -
-

-

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).

-

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

- -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!

-

 

- - + +Memory Settings + +

+
+ Memory Usage Settings for Jalview +
+

+

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).

+

Jalview Memory Usage Monitor: If you are concerned about memory, or think that things might be behaving + strangely because of a shortage of memory, then you can check this by enabling the + memory usage monitor. This is done by selecting the Tools→Show Memory Usage + option. Once enabled, the memory usage monitor displays the currently + available memory, the total memory, and the percentage free at the + bottom left hand side of the Jalview Desktop 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:

+ +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!

+

 

+ + -- 1.7.10.2