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I don't understand the problem. If you open a lot of files, the open() 
loop will stop an exception (IOError: too many open files), and so 
subprocess is not used.
If I open <limit>-1 files, subprocess._get_handles() will fail on 
os.pipe().
If I open <limit>-4 files, the script doesn't fail.
I'm using Linux. Here is my script:
---
# open <limit>-4 files
import subprocess
files = []
while 1:
 try:
 newfile = open("/etc/passwd")
 except IOError, err:
 print "ERR: %s" % err
 break
 files.append(newfile)
# use -3 to get an error
for file in files[-4:]:
 print "close"
 file.close()
# success
subprocess.Popen(["date"], stdout=subprocess.PIPE).communicate()
---