Re: [AMBER] limit of joining residues

From: Jio M <jiomm.yahoo.com>
Date: Wed, 10 Feb 2010 08:12:58 -0800 (PST)

Dear Bill  Ross;



Sorry for delay, I couldn't reply  you



I am using red hat linux. Honestly saying I never tried this command before and not  fully understood what you suggested.



 limit command is not found.



ulimit -a is giving this information:

ulimit -a

core file size          (blocks, -c) 0

data seg size           (kbytes, -d) unlimited

file size               (blocks, -f) unlimited

pending signals                 (-i) 1024

max locked memory       (kbytes, -l) 32

max memory size         (kbytes, -m) unlimited

open
files                     
(-n) 1024

pipe size            (512 bytes, -p) 8

POSIX message queues     (bytes, -q) 819200

stack size              (kbytes, -s) 10240

cpu time               (seconds, -t) unlimited

max user processes              (-u) 16239

virtual memory          (kbytes, -v) unlimited

file
locks                     
(-x) unlimited




What should I increase here. Should I modify some file in etc/....





sorry, thanks and regards;

JIomm




--- On Mon, 2/8/10, Bill Ross <ross.cgl.ucsf.edu> wrote:

From: Bill Ross <ross.cgl.ucsf.edu>
Subject: Re: [AMBER] limit of joining residues
To: amber.ambermd.org
Date: Monday, February 8, 2010, 5:32 PM

> =A0/opt/amber10/exe/tleap: line 8: 17065 Killed

I wonder if you reached some limit on memory. Try 'limit' or 'limits'
in your unix shell, e.g.

% limit
cputime      unlimited
filesize     unlimited
datasize     524288 kbytes
stacksize    32768 kbytes
coredumpsize unlimited
memoryuse    65011176 kbytes
vmemoryuse   16777216 kbytes
descriptors  4096

For this setup in your shoes I would try

% ulimit datasize

Bill

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Received on Wed Feb 10 2010 - 08:30:04 PST
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