VMD-L Mailing List

From: Salvatore Mario Cosseddu (S.M.Cosseddu_at_warwick.ac.uk)
Date: Thu Feb 16 2012 - 12:04:17 CST

Don't worry then,

I can safely wait :) . I'll use your suggestion on use exec command to
run new vmd process meanwhile. I just need to slightly modify my scripts
in order to load the trajectory files from $argv.

I'm look forward to see the new tutorial.

Many thanks indeed for your (and all VMD developers) very useful work.

Regards
Salvatore

On 16/02/12 17:52, John Stone wrote:
> Salvatore,
> I'm working on a new VMD parallel analysis tutorial, and it will
> give examples of how to use these commands to do trajectory analysis
> efficiently on MPI-based clusters. In the mean time I can help you out
> with some example scripts etc if you like.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Feb 16, 2012 at 05:49:55PM +0000, Salvatore Mario Cosseddu wrote:
>> Many thanks for the prompt reply,
>>
>> I'll try to look for the best way. Just the last thing. I've not been able
>> to find the documentation of the command "parallel".
>> parallel allgather and allreduce look intuitive enough, but, if it is
>> available, I always prefer to refer to a manual.
>>
>> Regards
>> Salvatore
>>
>> On 16/02/12 17:40, John Stone wrote:
>>
>> Hi,
>> It isn't currently possible to create parallel sub-interpreters due to
>> the need to incorporate the Tcl threads package, and the subsequent need
>> to make the VMD Tcl interfaces thread-safe for simultaneous access by
>> multiple interpreters.
>>
>> That said, it IS possible to compile VMD with MPI, and have VMD scripts
>> run in parallel among multiple VMD instances using the VMD "parallel"
>> commands. If using the MPI-related VMD features isn't convenient, then
>> another option would be to launch independent VMD instances using "exec",
>> and have them run in the background, collecting your results upon
>> completion.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, Feb 16, 2012 at 05:23:15PM +0000, Salvatore Mario Cosseddu wrote:
>>
>> Dear all,
>>
>> using the command source I run the command in the script within the actual
>> tcl instance (Is it the right terminology?), freezing everything until the
>> calculation is finished.
>>
>> I'd like to create children instances, similar to what happens when
>> running a bash script or a tcl script from bash.
>> The problem would be easily solved in tcl (calling a new tclsh session)
>> but I don't know how to do it in VMD.
>> This would be very useful to use all my cores with my scripts.
>>
>> May you suggest any solution?
>>
>> Regards
>> Salvatore
>>
>> --
>> Salvatore Cosseddu
>> PhD student
>>
>> Centre for Scientific Computing and School of Engineering
>> University of Warwick
>> Coventry CV4 7AL
>> United Kingdom
>>
>> email: S.M.Cosseddu_at_warwick.ac.uk
>>
>> --
>> Salvatore Cosseddu
>> PhD student
>>
>> Centre for Scientific Computing and School of Engineering
>> University of Warwick
>> Coventry CV4 7AL
>> United Kingdom
>>
>> email: S.M.Cosseddu_at_warwick.ac.uk 

-- 
Salvatore Cosseddu
PhD student
Centre for Scientific Computing and School of Engineering
University of Warwick
Coventry CV4 7AL
United Kingdom
email: S.M.Cosseddu_at_warwick.ac.uk