Re: [AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files"

From: Daniel Roe <>
Date: Thu, 3 May 2018 10:28:19 -0400


On Tue, May 1, 2018 at 7:55 PM, Jason Ku Wang <> wrote:
> *Error: Could not open ensemble remd.mdcrd.0001.*
> *Too many open files*

What you are running into here is not a cpptraj limitation, but limits
baked into your Linux system. Typically the number of allowed open
files for a user is set somewhere between 1024 and 4096. To check the
current limit for number of open files, type:

ulimit -n

To check what the current max is type:

ulimit -Hn

If this number is larger than 5120, great - set the new limit like so:

ulimit -n <max>

However, if it's less than 5120 you'll have to modify the max allowed
by editing your /etc/security/limits.conf file. You'll have to add an
entry in there that's something like:

<user name> hard nofile <max>

Then you'll have to log out and log back in to ensure the changes take
effect. If you don't have root on your system you'll have to ask your
sysadmin to do this for you.

Hope this helps,


PS - I'd be really interested to see what system you've got that
requires 5120 replicas! With that many you may want to try parallel
ensemble processing with cpptraj.MPI.

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Thu May 03 2018 - 07:30:05 PDT
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