From: Robert Elder (rmelder_at_gmail.com)
Date: Fri Jul 06 2012 - 13:40:23 CDT
Hi all,
I am having the same issue with replica exchange simulations as the user
below, where using the +replicas flag throws the error:
FATAL ERROR: Unknown command-line option +replicas
I'm using the latest NAMD2.9 binary and simply attempting to run on my
local workstation, not a cluster as with the user below. However, I would
like to run REMD simulations on a Cray XT5 (Kraken), so I would prefer to
use the MPI version rather than the TCL socket version of REMD.
I can provide any details that seem relevant. Your help is appreciated!
Thanks,
Robert Elder
CU Boulder Chemical Engineering Graduate Student
On Mon, Jun 4, 2012 at 3:57 PM, Cade Markegard <cmarkega_at_uci.edu> wrote:
> Hi All,
>
> I am currently trying to run the NAMD 2.9 replica exchange example. I am
> on a Rocks Cluster (v. 5.4.3) with all the rolls installed, and the NAMD
> binary I am using is from NAMD_2.9_Linux-x86_64. When I run the example
> command located in fold_alanin.conf but without the hostfile option (since
> I am trying to run this on a single node):
>
> mpirun -np 8 $bindir/namd2 +replicas 8 job0.conf +stdout
> output/%d/job0.%d.log
>
> where $bindir is my NAMD 2.9 path, I am currently receiving the error:
>
> *FATAL ERROR: Unknown command-line option +replicas*
>
> Is this the wrong pre-compiled NAMD binary or is there something else that
> I am missing here? Could someone please point me to the correct binary? I
> rather not have to compile NAMD from the source... Also I really like the
> idea of the new MPI based method implemented in 2.9 rather than the TCL
> method in 2.8, so when it comes time it will be easier to run a simulation
> across multiple nodes.
>
> Any help regarding this subject would be greatly appreciated!
>
> Many thanks,
> Cade Markegard
> UC Irvine Chemical Engineering Graduate Student
> http://compnano.eng.uci.edu
>
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