[R] OpenBSD and large R vectors

jon butchar butchar.2 at osu.edu
Tue Jul 26 13:37:38 CEST 2005

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?


jon butchar

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