Increase RAM in the Mac application & unloading read data

[Nick Brouwers]

Hi,

Is there a way to increase the RAM higher than 8GB (to for instace 32GB)?

Besides that, since my limitation is now stuck at 8GB, the program often crashes when I use multiple BAM files where I view regions of 48 kb and also scroll through chromosomes.

The read data quickly adds up to 7-8GB of RAM data but does not seem to unload reads that are out of the viewing range. Any tips/tricks would be very helpful.

Thx!

[James Robinson]

Hi, what version of IGV are you using?

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[Nick Brouwers]

Version 2.3.90

Op maandag 13 februari 2017 18:20:36 UTC+1 schreef Jim Robinson:

Hi, what version of IGV are you using?

On Mon, Feb 13, 2017 at 2:51 AM, Nick Brouwers <nickbro...@gmail.com> wrote:

Hi,

Is there a way to increase the RAM higher than 8GB (to for instace 32GB)?

Besides that, since my limitation is now stuck at 8GB, the program often crashes when I use multiple BAM files where I view regions of 48 kb and also scroll through chromosomes.

The read data quickly adds up to 7-8GB of RAM data but does not seem to unload reads that are out of the viewing range. Any tips/tricks would be very helpful.

Thx!

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[Stan M]

The original plist contained in the app package contents has a couple errors in it.  The maximum heap option (-Xmx4g) and the -Xdock:name=IGV were contained within the JVMArguments section of the plist file.  This caused an error when the application was launched as they are not arguments, but options for the JVM.  Moving these options under the JVMOptions section corrected the memory allocation issue.  With the original error, the maximum heap size was not extended to 4G. Moving the -Xmx4g option under the JVMOptions section did extend the max heap size to 4G.  On machines with larger memories, you don't see the issue since the default max heap is 1/4 of the physical memory which is usually enough to run the program successfully.

[Stan Manoski]

Once these changes are made to the plist file, you can adjust the max heap size to a larger value to meet your needs (e.g. -Xmx16G).

[Stan Manoski]

Also, note that once the heap exceeds physical memory, paging out to disk comes into play which is something you really want to avoid. Thrashing could occur during the garbage collection process within the JVM and your app will slow down significantly. Not a good thing.

[James Robinson]

Stan,  thanks,  could you post the corrected plist file?

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[James Robinson]

Yes, thanks.  The plist file is generated with some Oracle utility,  possibly out of date,  I will see if I can update it or perhaps script the packaging manually.

On Fri, Feb 17, 2017 at 10:16 PM, Stan Manoski <sjma...@gmail.com> wrote:

Sure. Hope this helps.

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[Stan Manoski]

Sure. After you download this file, rename it to Info.plist  

On Friday, February 17, 2017 at 11:38:16 PM UTC-5, Jim Robinson wrote: