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
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