From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Dec 01 2003 - 12:19:28 CST
Hello
Has anyone had experience with VMD-IMD-NAMD on a massively parallel
system?
In my case I have NAMD working in an MPI environment on a couple of
thousand processors. Each job is started with a native 'srun' command
which is similar to the prun command noted in the docs.
Which host would I tell the IMD interface to connect with?
Thank you for your comments.
Brian
On Mon, 1 Dec 2003, Fangqiang Zhu wrote:
> Hi,
>
> Please find comments from Justin Gullingsrud below. Hope it helps.
>
> Zhu
>
>
>
> From: "David E. Konerding" <dekonerding_at_lbl.gov>
> Date: November 26, 2003 12:09:10 PM PST
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: updating coordinates using IMD
>
>
> Hi,
>
> I am interested in using IMD, I've gone through the code and managed
> to write a simple Python extension (yes, I know about the python IMD
> wrappers, but
> I wanted a pure python version). It works OK in most cases, although
> I find that the NAMD side is a bit flaky; sometimes it disconnects telling
> me my
> VMD version number is too old. When it does work I can collect forces
> and energies.
>
>
> What is probably happening is that you are not sending the GO message soon
> enough after receiving the handshake message from NAMD. If NAMD doesn't
> receive a
> response within one second it drops the connection with an error message
> about incompatible IMD versions. That message could admittedly be a bit
> more helpful.
>
>
> I have a few questions:
>
> 1) Is the IMD socket protocol truly asynchronous: the read and write
> messages are totally distinct from each other (I'm more accustomed to
> call/response style
> protocols).
>
>
> Yes, neither VMD nor NAMD wait for a response from each other. The idea is
> that there is no point in resending coordinates or forces if something was
> lost in transmission.
> VMD is continually redrawing the screen based on the most recent
> coordinates, and, when steering atoms with something like a haptic device,
> forces are continually changing.
> Making either system wait would decrease the responsiveness.
>
> 2) IMD doesn't seem to have any support for changing the coordinates
> directly and getting an energy evaluation. IE, I want to NAMD to remain
> paused, I
> update all atomic coords to new ones, get back the energy given those
> coords,
> and NAMD goes back to a paused state.
>
>
> Yes, there is currently support only for sending forces to a dynamics
> simulation.
>
> My thinking was to add a new message, IMD_COORDS, which the client
> could send to NAMD and update the coordinates. Then, another message,
> IMD_GO_ONCE, would cause NAMD to evaluate forces/energies, send one
> IMD_ENERGIES and one IMD_FCOORDS, and return to paused.
>
>
> IMD_GO_ONCE shouldn't be any problem. For technical reasons I think it
> would be difficult to make NAMD accept a new set of coordinate while the
> simulation was running.
> Jim Phillips could comment more precisely, but I think one would need to
> suspend the simulation momentarily, apply the new coordinates, then resume,
> and I'm not sure if the
> current interface is capable of that.
>
> Cheers,
> Justin
>
>
-- ***************************************************************** **Brian Bennion, Ph.D. ** **Computational and Systems Biology Division ** **Biology and Biotechnology Research Program ** **Lawrence Livermore National Laboratory ** **P.O. Box 808, L-448 bennion1_at_llnl.gov ** **7000 East Avenue phone: (925) 422-5722 ** **Livermore, CA 94550 fax: (925) 424-6605 ** *****************************************************************
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