Setting the Stack Size

09-May-2008

Introduction

Stacks are regions of memory where a data for a process is stored, such as process arguments and variables. When a function executes, it adds state data to the stack and removes it when the function terminates. Recursive function calls will continue to add data to the stack in a Last-In First-Out manner until the recursion ends and the functions terminate. If the stack allocated to your process is too small, your process will crash. Therefore it may be necessary to increase the size of the stack.

Increasing the Stack Size

For bash shell users, use the ulimit command to view or set the stack size as follows:

username@hostname:~> 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) 128
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) 16305
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

username@hostname:~> ulimit -s 20480

For tcsh shell users, use the limit command as follows:

username@hostname:~> limit
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    10240 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors 1024
memorylocked 128 kbytes
maxproc      16305

username@hostname:~> limit stacksize 20480

These examples show the stack size as 10MB (10240 kbytes) and show it being set to a new size of 20MB (20480 kbytes). Some systems support setting the value to "unlimited" but this practice is not encouraged.

Setting the Stack Size in a PBS Job

In order to set the stack size such that all of the compute nodes used in your job will see the new setting, follow the example below.

Create a shell script such as myjob.sh:

#!/bin/bash
ulimit -s 20480
cd some_dir
./my_exec

In the PBS script, use mpiexec to launch myjob.sh. This will work even with MPI executables.

#!/bin/bash
#PBS -N Test
#PBS -l nodes=1:ppn=2
#PBS -M emailaddress@rice.edu
#PBS -V
#PBS -m abe
#PBS -o /home/username/directory
#PBS -e /home/username/directory
#
echo "I ran on:"
cat $PBS_NODEFILE
#

cd /home/username/directory
mpiexec ./myjob.sh