RE: IMD on MPI versions of NAMD

From: Cesar Delgado (beettlle_at_hotmail.com)
Date: Mon Dec 01 2003 - 16:44:05 CST

Are you starting up NAMD in some sort of queue? We use PBS as our queue
and node 0 (zero) is determined by the queue and I have to extract that
information.

When MPI processes are started most MPI implementations (I use MPICH)
use a machine file that names the machines that are to be used to run
the jobs. Process 0 (zero) is, @ least in MPICH, the first computer in
the machine file. I would ask your sys-admin which version of MPI you
are using and how this machine file is created.

-Cesar Delgado
---------------------------------------------
Research Computing Facility @ UNL
http://rcf.unl.edu
cdelgad2_at_bigred.unl.edu, beettlle_at_hotmail.com

> -----Original Message-----
> From: Brian Bennion [mailto:brian_at_youkai.llnl.gov]
> Sent: Monday, December 01, 2003 2:00 PM
> To: Cesar Delgado
> Subject: Re: namd-l: IMD on MPI versions of NAMD
>
>
> hmmm...my knowledge here is not very substantial, how would I find out
> which node started the first mpi process?
>
> could I assume that it is the first node assigned by the batch
handler?
>
> Brian
>
> On Mon, 1 Dec 2003, Cesar Delgado wrote:
>
> > The master process is the one you have to connect to in order to do
IMD
> with
> > the MPI version of NAMD. Basicaly MPI's process 0 (zero).
> >
> >
> > -Cesar Delgado
> > ---------------------------------------------
> > Research Computing Facility @ UNL
> > http://rcf.unl.edu
> > cdelgad2_at_bigred.unl.edu, beettlle_at_hotmail.com
> >
> >
> >
> >
> >
> > >From: Brian Bennion <brian_at_youkai.llnl.gov>
> > >To: Fangqiang Zhu <fzhu_at_ks.uiuc.edu>
> > >CC: "David E. Konerding" <dekonerding_at_lbl.gov>,
<namd-l_at_ks.uiuc.edu>
> > >Subject: namd-l: IMD on MPI versions of NAMD
> > >Date: Mon, 1 Dec 2003 10:19:28 -0800 (PST)
> > >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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> >
>
> --
> *****************************************************************
> **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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