Re: NAMD on ranger.tacc

From: Jesper Sørensen (
Date: Tue Jan 24 2012 - 11:46:11 CST

Yes it was a good start. But I want to make use of the "runbatch_2.8" script tailored for Ranger, and when I use my own compiled version it does not work. It looks like there are several switches/flags set that are intended for a performance speedup on ranger, that I would normally otherwise not set myself, so I want to make use of these.
The updated versions of NAMD, charm++, tcl and fftw also does not make it possible to follow the script on the site completely, although I have made a functioning version.

Here is the error I get when I try to use my own compiled version of NAMD 2.8 with a modified runbatch_2.8.

Running on 32 processors:  ++mpiexec ++remote-shell /share/home/00288/tg455591/NAMD_scripts/mpiexec ++runscript tacc_affinity /share/home/01859/jsx/Apps/NAMD_2.8_M
D6/namd2 heat.conf
charmrun>  /usr/bin/setarch x86_64 -R  mpirun -np 32  ++mpiexec ++remote-shell /share/home/00288/tg455591/NAMD_scripts/mpiexec ++runscript tacc_affinity /share/hom
e/01859/jsx/Apps/NAMD_2.8_MD6/namd2 heat.conf
Warning: Command line arguments for program should be given
after the program name.  Assuming that ++remote-shell is a
command line argument for the program.
Unrecognized argument ++mpiexec ignored.
Need to provide machinefile or a list of machines
Without hostfile option, hostnames must be specified on command line.
usage: mpirun_rsh [-v] [-rsh|-ssh] [-paramfile=pfile] [-debug] -[tv] [-xterm] [-show] [-legacy] [-use_xlauncher][xlauncher-width W] -np N (-hostfile hfile | h1 h2 
.. hN) a.out args
	v          => Show version and exit
	rsh        => to use rsh for connecting
	ssh        => to use ssh for connecting
	paramfile  => file containing run-time MVICH parameters
	debug      => run each process under the control of gdb
	tv         => run each process under the control of totalview
	xterm      => run remote processes under xterm
	show       => show command for remote execution but dont run it
	legacy     => use old startup method (1 ssh/process)
	np         => specify the number of processes
	h1 h2...   => names of hosts where processes should run
or	hostfile   => name of file contining hosts, one per line
	a.out      => name of MPI binary
	args       => arguments for MPI binary
On Jan 23, 2012, at 9:26 AM, George M Giambasu wrote:
> This link might be a good start:
> 2012/1/23 Jesper Sørensen <>:
>> Dear NAMD list,
>> I was wondering who compiled NAMD on Ranger (TACC)
>> The version in:
>> /share/home/00288/tg455591/NAMD_scripts/runbatch_2.8
>> There is not a problem with it, but I was wondering if I could get a copy of the install instructions. I need to compile a version with  modified source code and I would like one that performs equally fast.
>> Best regards,
>> Jesper

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