Re: Replica Exhange error: POSIX EINTR {interrupted system call}

From: Peter Freddolino (
Date: Fri Aug 24 2007 - 20:08:14 CDT

Hi Arturas,
my apologies for being slow to follow up on this; I realize that you
asked me a couple extra questions a few days ago. Did you manage to
figure those out?

As for what you're seeing now, I've had this block up my replica
exchange attempts from time to time. It seems to be dependent on the
exact environment you're running in, and how many replicas you have. So,
can I ask:
-how many replicas are you running?
-what do your nodes look like?

Also, could you please send me everything in about a 10 line radius of
line 52 from namd_replica_server.tcl? I found that there's a catch
statement that had to be modified in some of my cases.

Depending on your architecture, you may also need to use something other
than the standard tcl release as an interpreter for the repex scripts,
as the socket code appears to have trouble coping with large numbers of
replicas on some platforms.


Arturas Ziemys wrote:
> Hi,
> I test REMD (Replica Exchange) with alanine example , which comes with
> replica scripts and NAMD. I managed to run NAMD spawned jobs with 'rsh'.
> I get an error after the first run of NAMD after NAMD exhange
> temperatures and starting next run NAMD starts to output error in
> non-stopping fashion from "write_config" routine in
> "namd_replica_server.tcl" script:
> POSIX EINTR {interrupted system call}
> I check that it could be related to wrong interruption of 'gets' in
> line 52: "while [catch {gets $server_channel cmd} rval] {". It can
> not reach channel ?
> How to solve this ?
> Best
> Arturas

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