[R] Problem with memory consuming algorithm

Simon Zehnder szehnder at uni-bonn.de
Fri Sep 16 22:45:43 CEST 2011

Hi guyz,

I have serious problems with an algorithm I let run on a supercomputer:

You find the functions under the following URLs:

simuFunctionCaller: http://pastebin.com/6gw2fJFb

calls Function simuFunctionNBM (http://pastebin.com/QeJDUnqx) 

after reading a csv-file ordered like the following:


Reading and running without an exception is no problem. But the algorithm needs hours to run and seems to use more memory than available:

I have given a time limit of 48 h and a memory limit of 128 GB RAM on the supercomputer (it is a cluster, a BATCH System)…..nevertheless the computer shuts down the algorithm after a certain time because of memory problems. 

Does anyone of u guys see a problem in the algorithm? Especially with so much RAM and time available?

I am very thankful for your suggestions!


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