From: Teerapong Pirojsirikul (tpirojsi_at_ucsd.edu)
Date: Thu Sep 05 2013 - 18:48:42 CDT
Hi Axel and Norman,
Thank you very much for your advice. As for writing a C plugin, it
sounds worth trying to me. However, I don't quite have a clear picture
how this works actually because I have no experiences writing any
plugins before. For example, how can I make use of the tcl built-in
commands such as getbond, vecsub, and other stuff in writing c plugin?
Anyway, I have searched through namd mailing list and found the
following thread but I'm not sure whether it might be applied my
problem.
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/15455.html
Also, may I put the part of the 'for loop' I would like to speedup
calculating here.
//This piece of code is in the calcforces proc
for {set i 1} {$i <= $oxnum} {incr i } {
set indx [lindex $ox [expr $i-1]]
set coor $coords($indx)
set blength [getbond $coor $r1c]
// if Mg_O distance less than the cutoff skip to next o atom
if {$blength <= $cutoff} {
// do sth
}
Here the $oxnum ~ 10000 atoms and I have to search through this set of
atoms just to get a few particles (oxygens) within the $cutoff of the
target atom (Mg) in every step. This is the most time-consuming part
that I want to improve.
Any further advice would be appreciated.
Tee
2013/9/5 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> On Thu, Sep 5, 2013 at 8:45 AM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
>> I would expect NAMD to have the full TCL included, so therefore if it is
>> possible in general with TCL, why not. If you google around a little "tcl
>> parallel" "tcl threading" or what might be even more interesting "tcl mpi"
>> you will find a lot. You will also find a nice looking tcl/mpi interface on
>> Axels Homepage. In addition with a NAMD build against MPI, you might be able
>> to use the same startup environment to run your tcl script on the same nodes
>> out of namd directly.
>
> i don't think the latter will work for two reasons:
>
> 1) you are only allowed call MPI_Init() once in an application, so you
> would have to implement a way to pass the MPI communicator from
> charm++ through NAMD to TclMPI
> 2) TclForces scripts are only called on the head node (unlike TclBC),
> if i remember correctly
>
> threading may be tricky as well, since threading in Tcl has been
> supported for a while as a compile time option, it has not been
> compiled in by default until the very latest release.
>
> in any case, over many years i have observed that when people ask
> about needing to parallelize script code, that the best solution is
> usually a different one. thus what i would recommend to do is to first
> benchmark how much time is spent on the TclForces script relative to
> the total time of the time step. it only makes sense to optimize or
> parallelize something that takes a lot of time. second, i would try to
> optimize the script. many times, there is significant optimization
> potential and then the need to parallelize may vanish. third, it may
> be possible to write a C plugin to do the same task (same as many VMD
> plugins have little "helper modules" written in C) to do the same task
> and gain a significant speedup. at that level it would also be trivial
> to include OpenMP based multi-threading for additional parallelization
> at least on the head node.
>
> axel.
>
>
>>
>> Norman Geist.
>>
>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>>> Auftrag von Teerapong Pirojsirikul
>>> Gesendet: Donnerstag, 5. September 2013 05:03
>>> An: NAMD list
>>> Betreff: namd-l: parallel code in tclforce script
>>>
>>> Hi NAMD users,
>>>
>>> Anyone has any idea whether or not we can write a parallel code in
>>> tclforce script. I have a 'for loop' that goes through a large no. of
>>> atoms and would like to parallelize it.
>>>
>>> Best,
>>> Tee
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
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