[R] OpenBSD and large R vectors

From: jon butchar <butchar.2_at_osu.edu>
Date: Tue 26 Jul 2005 - 21:37:38 EST


Is anyone running R on OpenBSD? I've got R-2.1.1 installed on OpenBSD -current and have some microarray datasets that took ~1.4 GB RAM on FreeBSD (computer has 4 GB total, Pentium 4 system). With FreeBSD, setting maxdsiz in /boot/loader.conf worked very well.

With OpenBSD, even after setting maxdsiz to ~1.8 GB for a new kernel and changing /etc/login.conf, R runs into memory problems and gives the "could not allocate vector of..." error. Then R locks up and starts taking progressively more CPU time until it gets killed. This is a stock R installation and a generic OpenBSD except for the altered MAXDSIZ in vmparam.h. I'm guessing that these problems stem at least in part from OpenBSD's memory allocation safety mechanisms. Still, are there any R or OpenBSD compile options / tweaks I can do to make things work?

Thanks,

jon butchar



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