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Extended Memory in 0.8.2

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Extended Memory in 0.8.2

Postby Big_Cat » 23 Apr 2013 21:05

"Computers throughout history have come in one size and one speed: too small and too slow." - Dan Reed, former head of NCSA-UIUC

We're generating some really cool visualizations, but (as expected) we are running out of memory frequently. We've tried the mod listed at https://gephi.org/users/install/#memory but it seems to be a bit intermittent in that it works on some machines and not others. Here's what we've tried so far:

    Make sure all the machines are on the same OS (In this case, Win 7x64).
    Make sure all the machines are on the same version of Gephi (v0.8.2).
    Make sure all the machines are on the same JRE (in this case, we downloaded jre-7u21-windows-x64.exe from Oracle).
    Explicitly set the path to the JRE using the jdkhome parameter.
    Make sure all the machines can start Gephi before we begin twiddling the parameters in the gephi.conf file.
    Make the same modifications to memory size on all machines (In this case, -J-Xms64m -J-Xmx10240m).

Some of the machines work great, others throw the dreaded "JRE creation failed" error on the last step. We have 24GB of RAM on the machines in question, so the 10240m allocation *should* go...and does, but not always.

Do we need to be running Gephi64.exe to take advantage of the larger heap allocation? We've tried switching between Gephi.exe and Gephi64.exe. When a machine works with the modified memory parameters, both executables work. When a machine doesn't work, it doesn't matter which executable we try to start.

Totally stumped on this one, and my head hurts from banging it on the desk!

Any ideas?
Big_Cat
 
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Re: Extended Memory in 0.8.2

Postby seinecle » 25 Apr 2013 14:37

I have no solution... (just to let you know your question has been read!).

The developers who would have suggestions for your problem are currently busy working on Gephi 0.9, which is precisely aimed at solving these memory issues:
https://gephi.org/2013/rebuilding-gephi ... 9-version/

Sorry for that. By the way, how large are you graphs? (how many nodes and edges?)

Best,

Clement
http://www.clementlevallois.net
Gephi tutorials and personalized trainings: http://www.clementlevallois.net/training.html
Join the Gephi Facebook group for help and support: https://www.facebook.com/groups/gephi/
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seinecle
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Re: Extended Memory in 0.8.2

Postby Big_Cat » 25 Apr 2013 18:19

Thanks for the ACK Clement ;)

The largest of our graphs are relatively small in nodes (1,000s) but high on edges that connect them (100,000+) because our edges represent different attributes overlayed on similar underlying structures. That let's us use the filtering to switch on and off different aspects of the visualization. For now we are splitting them into separate files and we can then load some of them into multiple workspaces...but this is clunky and doesn't really solve the underlying memory issue.

I can pry one of them open later (back at my desk) to get some more specific numbers if it would be useful.
Big_Cat
 
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Joined: 23 Apr 2013 20:47


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