Statistics:Posted by martin.pernollet — 07 Jul 2011 16:02
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Clement, to make sure you run Gephi under a 64 bit virtual machine you have to install a 64 bit jre/jdk.
Then you can edit {gephi installation}/etc/gephi.conf file and set larger maximum memory.
If you have problems because other jre/jdk versions are installed then uncomment the jdkhome and put, for example:
CODE:
jdkhome="C:\Program Files\Java\jdk1.6.0_25"Eduardo
Statistics:Posted by eduramiba — 04 Jul 2011 23:45
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Thx,
Clement
Statistics:Posted by seinecle — 04 Jul 2011 23:07
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Statistics:Posted by admin — 02 Jul 2011 09:44
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Since the repulsion in O(n2) is where most of the time is spent, I wrote a small function in Fortran that performs the repulsion on all nodes at once. This Fortran function is wrapped in a C++ function which is compiled as a DLL and the DLL is called from Java using JNI.
I have tested it with graphs up to 75000 nodes and it performs very well (around 50x faster than the Java implementation on an 8 cores workstation). However, it obviously doesn’t outperform the O(nlogn) Barnes-Hut repulsion of the new Force Atlas 2 layout. I have therefore started working on a parallel version of the Force Atlas 2 and I’ll release a plug-in containing the two parallel implementations when it is finished.
I think that the performance of the parallel Force Atlas 2 will increase by the number of cores you have (4 times faster with 4 cores) which would be great. It doesn’t solve the issue with the amount of RAM required to handle very large graphs but running Force Atlas 2 on a 100,000 nodes graph will hopefully be quite smooth.
My main concern for the plug-in is portability since the DLL has to be compiled separately for each architecture. The first version of the plug-in may only be available on Windows 64bits.
Then, I may have a look at the OpenOrd layout to make it even faster or I may try to use CUDA to speedup Force Atlas using GPGPU. I have very little experience with CUDA but the O(n2) repulsion of Force Atlas looks like a perfect candidate.
Any suggestion?
Statistics:Posted by pbittner — 01 Jul 2011 20:48
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Statistics:Posted by PMR3349 — 01 Jul 2011 20:41
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Statistics:Posted by mbastian — 01 Jul 2011 18:01
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I got the memory allocation up by increasing it for Java, which helped. It seems that Gephi isn't made to use multiple cores on the CPU though since I can't get it above 25% CPU usage on my quad-core
Statistics:Posted by PMR3349 — 01 Jul 2011 17:42
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And also, I think that Gephi in 64bits allows more RAM and can handle bigger graphs (if you have a 64bits CPU and at least 4Go RAM).
Statistics:Posted by jacomyma — 01 Jul 2011 16:55
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Clearly such a monstrosity is going to take some time, but after letting a force-atlas attempt run overnight I check it out this morning to find the program crashed. Is there a better algorithm to use for a gigantic network like this one?
I still haven't ruled out the possibility that the hardware could be the limiting factor, but in case it's not, I'm wondering if one of the algorithms is best. Thanks
Statistics:Posted by PMR3349 — 01 Jul 2011 14:19
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