From: Florian Janetzko (f.janetzko_at_fz-juelich.de)
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,
Florian
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