This is a Linux issue.  You're reaching the limit 2 ** 10, minus the 3 files STDIN, STDOUT and STDERR.

First off, do you really need to be opening that many files at once?  Maybe it's just a matter of rethinking your algorithm.

Secondly, if you do need to increase the number, do something like the the following (as described by this site):

# echo 5000 > /proc/sys/fs/file-max

Then edit /etc/sysctl.conf, and append the line:
fs.file-max = 5000

Then make the new value take effect with:
# sysctl -p
or, alternatively, logout and back in again.
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