Fantastic, Gus! Now I think I got framework pretty much done.
The rest is to work on 'problem solving' end with R.
Many thanks for your insight and kindness. I really appreciate it.
Regards,
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/13/11 2:40 PM, "Gus Correa" <g...@ldeo.columbia.edu> wrote:
> Tena Sakai wrote:
>> Hi,
>>
>> I have a script I call fib.r. It looks like:
>>
>> #!/usr/bin/env r
>>
>> fib <- function( n ) {
>> a <- 0
>> b <- 1
>> for ( i in 1:n ) {
>> t <- b
>> b <- a
>> a <- a + t
>> }
>> a
>> }
>>
>> print( fib(argv[1]) )
>>
>> When I run this script with a parameter, it generates a fibonocci number:
>>
>> $ fib.r 5
>> 5
>> $ fib.r 6
>> 8
>>
>> and if I stick this into <program> part of MIMD example I have used
>> previously:
>>
>> $ mpirun -H vixen -np 1 hostname : --hostfile myhosts -np 8 fib.r 7
>>
>> I get:
>>
>> vixen.egcrc.org
>> [1] 13
>> [1] 13
>> [1] 13
>> [1] 13
>> [1] 13
>> [1] 13
>> [1] 13
>> [1] 13
>>
>> This is good as proof of concept, but what I really want to do is to
>> have that 7
>> different for each (slave) process. Ie., I want to run ³rfib 5² on node
>> 0, ³rfib 6²
>> on node 1, ³rfib 7² on node 2, and so on. Is there any way to give a
>> different
>> parameter(s) to different process/slot?
>>
>> I thought maybe I can use rf option to do this, but I am leaning toward
>> app
>> option. Unfortunately, I see no example for the application context
>> file. Would
>> someone kindly explain how I can do what I describe?
>>
>> Thank you.
>>
>> Tena Sakai
>> tsa...@gallo.ucsf.edu
>>
>
> Hi Tena
>
> We ran MPMD/MIMD programs here using in the past.
> Coupled climate modes: atmosphere, ocean, sea ice, etc, each one one
> executable, communicating via MPI.
> Actually this was with MPICH1, somewhat different syntax than OpenMPI,
> the flag/file was called '-pgfile' not '-app',
> but I see no reason why it shouldn't work in your case with OpenMPI.
>
> I think if you create a 'appfile' with this content:
>
> -H node0 -np 1 rfib 5
> -H node0 -np 1 rfib 6
> ...
>
> and launch mpirun with
>
> mpirun -app appfile
>
> it is likely to work.
>
> Under Torque I cannot test this very easily,
> because I need to parse the Torque file that gives me the nodes,
> then write down the 'appfile' on the fly (which is what I used to
> do for the coupled climate models).
>
> However, I tried on a standalone machine (where the -H nodename didn't
> make sense, and was not used) and it worked.
> My appfile test was like this:
> -np 1 ls appfile
> -np 1 hostname
> -np 2 date
> -np 4 who
>
> You can add your -H nodename to each line.
>
> I hope this helps,
> Gus Correa
> ---------------------------------------------------------------------
> Gustavo Correa
> Lamont-Doherty Earth Observatory - Columbia University
> Palisades, NY, 10964-8000 - USA
> ---------------------------------------------------------------------
>
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