Memory issue

[Yujin Kim]

Hello,

I was wondering what network size i could display in Cytoscape with the following configuration:

MacBook Pro (2010) i5 2,53 GHz Intel Core
8 Go 1067 MHz DDR3 RAM
NVIDIA GeForce GT 330M 512 Mo

I'm posting this because i'm trying to display 3 networks with about 250 nodes and same number of edges approximately in total and Cytoscape eats up 6 Go of RAM which is problematic considering i'll probably work with larger networks.
I already displayed bigger networks which ran fine but these littles networks are making me worried.

Yujin

[Scooter Morris]

Hi Yunjin,
    When you say that Cytoscape is using 6Gb of RAM, is that based on your Mac or on the Memory button?  Basically, Java allocates the memory it will use at start up and won't allocate any more (Cytoscape tries to figure out how much memory you have and saves that information when you first run it).  It wouldn't surprise me that Java would be set to allocate 6Gb on your system, but Cytoscape should only use a small portion of it.  On my machine, when I click the Memory button with a sample network loaded, I see: "5.5% used of 13.33 Gb".  Which means Cytoscape is using a very small amount of memory and has room for a lot of growth.

-- scooter

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[Yujin Kim]

I'm talking about the Mac (i'm using iStat). I also noticed that the memory allocation on the computer is maxed :
-Xms2048M
-Xmx7168M
And the Memory button indicates that 65% of the 7.06 Go allocated are used.

Le mercredi 10 mai 2017 15:06:48 UTC+2, Scooter Morris a écrit :

Hi Yunjin,
    When you say that Cytoscape is using 6Gb of RAM, is that based on your Mac or on the Memory button?  Basically, Java allocates the memory it will use at start up and won't allocate any more (Cytoscape tries to figure out how much memory you have and saves that information when you first run it).  It wouldn't surprise me that Java would be set to allocate 6Gb on your system, but Cytoscape should only use a small portion of it.  On my machine, when I click the Memory button with a sample network loaded, I see: "5.5% used of 13.33 Gb".  Which means Cytoscape is using a very small amount of memory and has room for a lot of growth.

-- scooter

On 5/10/17 7:01 AM, Yujin Kim wrote:

Hello,

I was wondering what network size i could display in Cytoscape with the following configuration:

MacBook Pro (2010) i5 2,53 GHz Intel Core
8 Go 1067 MHz DDR3 RAM
NVIDIA GeForce GT 330M 512 Mo

I'm posting this because i'm trying to display 3 networks with about 250 nodes and same number of edges approximately in total and Cytoscape eats up 6 Go of RAM which is problematic considering i'll probably work with larger networks.
I already displayed bigger networks which ran fine but these littles networks are making me worried.

Yujin

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