problems running Replica Exchange simulations using SSH to spawn the processes

From: Ana Celia Araujo Vila Verde (
Date: Thu Feb 01 2007 - 13:28:06 CST

Dear NAMD developers,
I want to run replica exchange jobs in a cluster using PBS queueing system. I tried using command:
set spawn_namd_command \
  [list spawn_namd_ssh "cd [pwd]; [file join $namd_bin_dir namd2] +netpoll" \
   [read [open $env(PBS_NODEFILE) "r"]] ]
However, this doesn't work because it's trying to use SSH to spawn the processes and the cluster doesn't have passwordless SSH setup. Given that setting up passwordless SSH is not a viable option here, we tried using passwordless RSH, which is available in our system. Since an RSH command does not exist in the Replica Exchange scripts, we're unsure about its reliability. If you have any experience with this command, could you let us know if it is expected to cause problems, and offer guidelines about how to make it work (or certainty that it won't work...)?
The text we used for these commands is given below my signature in case you need to look at it.
Ana CÚlia Ara˙jo Vila Verde
Penn State University
Department of Chemical Engineering
Fenske Laboratory
University Park, PA 16802
Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846 <> <>

We used the command (in the *conf file)
set spawn_namd_command \
   [list spawn_namd_rsh "cd [pwd]; [file join $namd_bin_dir namd2] +netpoll" \
   [read [open $env(PBS_NODEFILE) "r"]] ]
In the spawn_namd.tcl script, we used.
proc spawn_namd_rsh {namd hosts conffiles logfiles} {
  set i 0
  set nhosts [llength $hosts]
  foreach conf $conffiles log $logfiles {
    set host [lindex $hosts $i]
    incr i
    if {$i >= $nhosts} {set i 0}
    puts "SPAWNING $conf on $host"
    lappend channels [open \
      "| rsh $host \"$namd $conf > $log\" << {} |& cat" "r"]
  return $channels


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