[Rd] FW: R Process Killed out of logical swap space: Case id #259-4945 (PR#7732)

From: <DMoore_at_exchange.hsc.mb.ca>
Date: Thu 17 Mar 2005 - 17:08:24 GMT

Dear Professor Ripley,

I am attempting a large scale mixed-model analysis of longitudinal gene array data using R. I use a 64-bit SGI with 7GB available RAM and 40G logical swap space together with unlimited virual swap space. The OS is IRIX 6.5.24. I use R version 1.9.0 since I have had problems upgrading to R 2.0.1 at 64-bit using native SGI compiler build.

I write a serial for (i in 1:length(y)) { } containing the call to lme as follows

f1<-lme( expr ~ time + age + sex,random = ~ time | id, correlation=cs3,data=gg.data.frame,method="ML",weights=varIdent(form= ~id))

After ~ 200 - 300 loops the process is killed by the OS with the following errors

Mar 17 08:55:56 1A:helmholtz unix: ALERT: R.bin [1157] - out of logical swap space during stack growth - see swap(1M) [filter /usr/sbin/klogpp failed: killed by signal 9]
Mar 17 08:55:56 1A:helmholtz unix: ALERT: R.bin [1157] - out of logical swap space during stack growth - see swap(1M) Mar 17 08:55:56 1A:helmholtz unix: ALERT: R.bin [1157] - out of logical swap space during stack growth - see swap(1M) Mar 17 08:55:56 1A:helmholtz unix: ALERT: R.bin [1157] - out of logical swap space during stack growth - see swap(1M) Mar 17 08:55:56 1A:helmholtz unix: |$(0x6dc)ALERT: Process [R.bin] pid 1157 killed: not enough memory to grow stack
Mar 17 08:55:56 1A:helmholtz unix: |$(0x6dc)ALERT: Process [R.bin] pid 1157 killed: not enough memory to grow stack
Mar 17 08:55:56 1A:helmholtz unix: ALERT: syslogd[1642] was killed; Dynamic Loader cannot get enough memory to map exe Mar 17 08:55:56 1A:helmholtz unix: ALERT: syslogd[1642] was killed; Dynamic Loader cannot get enough memory to map exe Mar 17 08:55:56 1A:helmholtz unix: ALERT: syslogd [1642] - out of logical swap space during exec - see swap(1M)
Mar 17 08:55:56 1A:helmholtz unix: ALERT: syslogd [1642] - out of logical swap space during exec - see swap(1M)

I have observed the crash while examining the system memory and stack allocations - these do not appear to be growing during execution of the process loops. I have checked with SGI and the view is that this is likely related to R. While there are several work-arounds it would be ideal to 'batch' this job and further it is unclear to me what is happening. I am grateful for your attention and potential insights.

Sincerely

David F. Moore
Associate Professor of Vascular Neurology University of Manitoba

This e-mail and/or any documents in this transmission is intended for the address(s) only and may contain legally privileged or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this transmission in error, please notify the sender immediately and return the original.



R-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri Mar 18 04:12:12 2005

This archive was generated by hypermail 2.1.8 : Mon 20 Feb 2006 - 03:21:02 GMT