REMD on AIX5.3

From: Florian Janetzko (
Date: Tue May 19 2009 - 06:44:34 CDT

Dear all,

I am trying to run a Replica Exange MD (REMD) using NAMD 2.6 on an IBM
Power6 with AIX 5.3. I have modified the "spawn_namd" command in the
following way:

proc spawn_namd_pwr6 {namd nodes conffiles logfiles} {
  set i_file 1
  set ncpus [llength $nodes]
  set nrep [llength $conffiles]
  set nprocperrep [expr $ncpus/$nrep]

  split_pwr6_nodes $nrep $nodes $nprocperrep
  foreach conf $conffiles log $logfiles {
    puts "Spawning job with config file $conf"
    lappend channels [open \
      "| bash \"poe -hostfile [pwd]/$i_file.hosts -procs $nprocperrep\
         $namd [pwd]/$conf > [pwd]/$log\" << {} |& cat" "r"]
    incr i_file 1
  return $channels

I am running the alanin example within a loadleveler jobscript:

tclsh8.5 ../replica_exchange.tcl fold_alanin.conf

However, in "start_replicas" (tcl file "namd_replica_server.tcl") the
fileevent command returns the following error and the calculation hangs
(all files specified after bash: exist in the pwd, the error message
still occurs if I am including all absolute paths):

errpipe 0: bash: poe -hostfile 1.hosts -procs 1 namd2 \
                      replica.0.log.nrc > replica.1.log:
A file or directory in the path name does not exist.
disconnect errpipe 1

I have searched the web and the NAMD-L archive but I could not find an
answer. I'd appreciate very much if someone could help.

Thanks and best regards,


Forschungszentrum Jülich GmbH
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Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt

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