Re: any experiences with executing parallel NAMD in a NAMD simulation

From: Yinglong Miao (
Date: Mon Feb 09 2009 - 19:56:44 CST

Dear Peter,

Thanks for your reply!

Peter Freddolino wrote:
> Hi Yinglong,
> how long is your embedded run, relative to your overall simulation? Is
> it on the same system? Do you end up running on the same nodes? Have you
> verified that you're running on as many processors as you think you are?
I have been running cycles for my overall simulation. In each cycle, the
embedded run is basically energy-minimization of the system of the
overall simulation excluding water and ions. It accounts for about 1/5
of the computation time with the speed expected. I have double checked
the output: the same nodes are used for the embedded run and the overall
> What you're doing is quite unusual, and depending on the exact
> relationship between your two systems there is probably a better way to
> handle it. Especially if the embedded runs are small relative to the
> full run, please keep in mind that namd has a high startup cost. If your
> embedded run is on a system whose topology doesn't change (and only
> needs coordinates once in awhile) you will probably be better off
> starting two separate namd jobs on disjoint sets of nodes and having
> them communicate with sockets (as is done in the replica exchange
> scripts distributed with namd). This gets around both the startup costs
> and other potential problems with having two copies of namd running (if
> your system is large, for example, you're putting a lot of stress on the
> head node in terms of memory).
As mentioned above, the system input to the embedded run is basically
that for the overall simulation excluding host medium, and they are
different. The systems are pretty large, about half a million atoms for
the core structure and much more for the entire system. I have been
thinking of writing batch scripts to invoke NAMD sequentially, but that
will take a lot of efforts to rewrite my NAMD configuration scripts to
set up the running cycles. It would be great if the technical issues can
be solved to have embedded run executed at a reasonable speed.

> Best,
> Peter
> Yinglong Miao wrote:
>> Dear NAMD developers/users,
>> I have been trying to embed a parallel NAMD run in a bigger NAMD
>> simulation; that is by calling "exec mpirun -np $nprocessors
>> -machinefile $machinelist namd2 ${str}.conf" in a NAMD configuration
>> script to run a different structure and generate proper output for the
>> big simulation. The program runs fine except that the embedded part is
>> executed much more slowly than expected (~1/5 of the speed) and
>> sometimes such error messages pop up: "Max retransmit retries reached
>> (829) for message". I thought it's because the message passing is
>> slowed down and the MPI environment is messed up upon NAMD exit for
>> the embedded run. Is there anybody have experiences with this? How to
>> run the embedded part with normal speed? Any suggestions will be
>> greatly appreciated.
>> Thanks!
>> --
>> Yinglong Miao
>> Ph.D. Candidate
>> Center for Cell and Virus Theory
>> Chemistry Department, Indiana University
>> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
>> Tel: 1-812-856-0981

Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Department of Chemistry, Indiana University
Address: 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Phone: 1-812-856-0981 (office) 1-812-272-8196 (cell)

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