RE: problems reading large dcd file

From: Joshua D. Moore (
Date: Fri Jan 13 2006 - 21:32:42 CST

Hey Jorge,

I have a 64bit version of NAMD compiled on AIX (DataStar at SDSC). I used
the flags that the SDSC people used for version 2.5 for their compilation.
 I was going to go back and try to compile using the suggestions given in
the AIX WIKI, but everything seems to be ok.

My initial tests show that I am getting slightly better performance
(time/step) compared to the binary I was using for 2.6b1. However, pretty
much it is the same. I tested up to 320 processors.

I haven't made any runs yet to make sure that the 2 GB problem is
overcome, but I am anticipating that it will since the default for AIX
from the source uses bmaxdata:0x80000000 which sets the limit on heap to 2
GB. I assume that the 32 bit binary was also compiled with this which I
think means that 2 GB was the limit.

If you want the binary I can post it somewhere or something.


On Wed, January 11, 2006 10:06 am, Jorge Pikunic wrote:
> Hi Michel,
> Gracias.
>> Regarding the first question, you shouldn't have any problem at loading
>> dcd files in either 32 or 64-bit machines. For example, I usually run my
> It seems to be a problem with the NAMD implementation on AIX (see Joshua's
> e-mail in this thread), which is used in the machine in which I ran the
> simulations.
>> Second, what do you mean with "recover" a part of the trajectory?
> The resulting dcd files are unreadable by most programs that can read dcd
> files. I was wondering if I can somehow recover the trajectories stored in
> these files. I think that the answer is no, after a couple of replies that
> I
> have received.
> Thank you,
> Jorge

Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470

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