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Command issued in R:(no commands were issued before this, so R env has no prior objects)

library("e1071");
train <- read.csv("training_data.csv");
train$node_sub_structure_validity = NULL;
train$obj.modified_invalid_loop_nodes_with_incoming_path = NULL;
fit = svm(self_containment_index~.,train,cachesize = 400);

error received:

Error: cannot allocate vector of size 316.0 Mb

System specification:

 Linux masterx-Studio-1535 3.5.0-45-generic #68-Ubuntu SMP Mon Dec 2 22:02:00 UTC 2013 i686 i686 i686 GNU/Linux

memory details using vmstat:

 procs -----------memory---------- ---swap-- -----io---- -system-- ----cpu----
 r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa
 1  0  14600 459512 145428 513316    2    7   358   214  319 1142 16  3 74  6

SessionInfo() details:

 R version 3.0.2 (2013-09-25)
 Platform: i686-pc-linux-gnu (32-bit)

 locale:
 [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN       
 [4] LC_COLLATE=en_IN     LC_MONETARY=en_IN    LC_MESSAGES=en_IN   
 [7] LC_PAPER=en_IN       LC_NAME=C            LC_ADDRESS=C        
 [10] LC_TELEPHONE=C       LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C 

 attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] e1071_1.6-2 class_7.3-4

ulimit -a output

core file size          (blocks, -c) 0   
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 32184
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 32184
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

I tried running on 64bit architecture, still it doesn't run. the file size 7751925.

Please help me debug this issue.

priyanka
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  • Have you read through [this](http://stackoverflow.com/questions/10917532/r-memory-allocation-error-cannot-allocate-vector-of-size-75-1-mb) and [this](http://stackoverflow.com/questions/5171593/r-memory-management-cannot-allocate-vector-of-size-n-mb)? – jbaums Feb 16 '14 at 08:08
  • yes i read through them. But except using 64 bit architecture, no solution that fits my problem. – priyanka Feb 16 '14 at 08:22
  • You may have ~460 Mb of RAM available, but it needs to be contiguous. Have you tried closing other unnecessary processes, restarting R, and seeing if that helps? – jbaums Feb 16 '14 at 08:28
  • i tried that, i closed all applications and then ran R. It still doesnt work... – priyanka Feb 16 '14 at 08:28
  • Why don't you just reduce the cache size "cachesize = 400)"? – lejlot Feb 16 '14 at 11:14
  • i tried that also(cachesize of 40(Default), 400,700 and 1000 and 2000), it still doesn't work. – priyanka Feb 16 '14 at 13:43
  • i also tried cachesize 200 and 300MB,they too dont work. – priyanka Feb 16 '14 at 13:50
  • Hi Priyanka. Same issue here - Did you work this out? Best, J – JDG Feb 28 '19 at 13:33

0 Answers0