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my server crashes whenever one of my users is running a 'R' script (this script requires a large amount of memory). Below is the last top I saw:

top - 11:32:39 up 20 min,  4 users,  load average: 1.08, 0.85, 0.46
Tasks: 336 total,   2 running, 334 sleeping,   0 stopped,   0 zombie
Cpu(s):  6.1%us,  0.2%sy,  0.0%ni, 93.7%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st
Mem:  65939968k total,  5131440k used, 60808528k free,    88256k buffers
Swap: 68124664k total,        0k used, 68124664k free,  1077612k cached

10392 cdina     25   0 3702m 3.5g 2428 R 100.0  5.6   7:51.82 R
10430 root      15   0 12872 1272  804 R  0.7  0.0   0:02.42 top
    1 root      15   0 10348  704  592 S  0.0  0.0   0:02.95 init
    2 root      RT  -5     0    0    0 S  0.0  0.0   0:00.00 migration/0

is there a way to prevent my server from crashing ("don't run that script" is not an option :-) ) ? something like fixing a 'quota' for the memory allowed ?


uname -a
Linux myserver 2.6.18-194.3.1.el5 #1 SMP Sun May 2 04:17:42 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
#R was compiled on the server. just a simple configure/make/install
R --version
R version 2.11.0 (2010-04-22)
file /usr/local/lib64/R/bin/exec/R
R: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped
share|improve this question
You have 64GB of ram and 64GB of swap and it still not enough? How is swap usage before the crash? – mkudlacek Jun 16 '10 at 10:08
What are the architectures of the kernel and the R interpreter? – Ignacio Vazquez-Abrams Jun 16 '10 at 10:10
I'm more curious what the script is doing if it's eating 64 gig of RAM plus the swapfile. The weird part is that your swap isn't being used, and if it were running out of RAM I'd expect the swap file to be full and system thrashing like crazy unless you're locking it in active memory somehow. Can the file contents be posted? Sounds like something the script is doing that is causing the crash. Can you elaborate on what kind of crash it is? – Bart Silverstrim Jun 16 '10 at 10:17
@Ignacio I've updated my question. @mkudlacek How/where can I get this information about the swap ? – Pierre Jun 16 '10 at 10:18
Unfortunately that isn't enough for R. Run file against the executable. It should show eiher "ELF 32-bit LSB executable, Intel 80386" or "ELF 64-bit LSB executable, x86-64". – Ignacio Vazquez-Abrams Jun 16 '10 at 10:20
up vote 2 down vote accepted

what about using /etc/security/limits.conf to limit the amount of cpu for the user.

Or with:

ulimit -m <size in megabytes>

in the shell, and then executing the process.

share|improve this answer
Thanks, that's the kind of suggestion I was looking for. Of course, it doesn't solve the problem of WHY does my server stop... – Pierre Jun 16 '10 at 13:17

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