Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa
On 10/04/2012 12:00, r-sig-hpc-request at r-project.org wrote:
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> 1. Re: Rmpi spawning across nodes. (Stephen Weston)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 Apr 2012 16:55:55 -0400
> From: Stephen Weston<stephen.b.weston at gmail.com>
> To: Ben Weinstein<bweinste at life.bio.sunysb.edu>
> Cc: r-sig-hpc at r-project.org, Jan Kasiak<j.kasiak at gmail.com>
> Subject: Re: [R-sig-hpc] Rmpi spawning across nodes.
> Message-ID:
> <CALh21iJsUG-QiFxZU1QbP-_dmqOeFrCJS5L=2U9LvfQ7T_Q9Aw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Ben,
>
> What machines are listed when you execute:
>
> cat $PBS_NODEFILE
>
> in your batch script? Is it definitely four different nodes?
>
> - Steve
>
>
> On Mon, Apr 9, 2012 at 3:28 PM, Ben Weinstein
> <bweinste at life.bio.sunysb.edu> wrote:
>> Hi Stephen,
>>
>> I've tried to follow your answer, but i'm still getting the same results.
>> the heart of my qsub looks like:
>>
>> mpirun -hostfile $PBS_NODEFILE -np 1 R --slave -f
>> /nfs/user08/bw4sz/Files/Seawulf.R
>>
>>
>> Before i run the foreach statement, i ask what node am i on?
>> [1] "Original Node wulfie121"
>>
>> I make sure the open MPI library is there.
>> [1] "/usr/local/pkg/openmpi-1.4.4/lib/"
>>
>> I make the cluster and ask how many slaves were spawn
>> 4 slaves are spawned successfully. 0 failed.
>>
>> Then i ask what are the nodenames of each of my slaves. I believe that if
>> this is working correctly, each of the nodenames should be different, since
>> i specified?#PBS -l nodes=4:ppn=1
>>
>> However, all the slaves still spawn on that one node.
>> [[1]]
>> ? ?nodename ? ? machine
>> "wulfie121" ? ?"x86_64"
>>
>> [[2]]
>> ? ?nodename ? ? machine
>> "wulfie121" ? ?"x86_64"
>>
>> [[3]]
>> ? ?nodename ? ? machine
>> "wulfie121" ? ?"x86_64"
>>
>> [[4]]
>> ? ?nodename ? ? machine
>> "wulfie121" ? ?"x86_64"
>>
>> Finally, i'm testing how long the process takes to see if i'm actually
>> getting parrelization.
>> [1] 4
>> ? ?user ?system elapsed
>> ?17.650 ?39.990 159.632
>>
>> Again, the heart of the code looks like
>>
>> cl<- makeCluster(4, type = "MPI")
>> print(clusterCall(cl,function() Sys.info()[c("nodename","machine")]))
>> registerDoSNOW(cl)
>> print(getDoParWorkers())
>> system.time(five.ten<- rbind.fill(foreach(j=1:times ) %dopar%
>> drop.shuffle(j,iterations)))
>> stopCluster(cl)
>>
>> I am about to change over to a different parralel backend as suggested, but
>> i doubt that is the root of the problem in this case.
>>
>>
>> I appreciate the continued help,
>>
>> Ben Weinstein
>>
>> On Thu, Mar 29, 2012 at 2:56 PM, Stephen Weston<stephen.b.weston at gmail.com>
>> wrote:
>>> Hi Ben,
>>>
>>> You have to run R via mpirun, otherwise all of the workers start
>>> on the one node.
>>>
>>>> I have tried using mpirun -np 4 in front of the R - call, but this just
>>>> fails without message.
>>> You have to use '-np 1', otherwise your script will be executed
>>> by mpirun four times, each trying to spawn four workers.
>>> I'm not sure if that explains failing without a message, however.
>>>
>>> Try something like this:
>>>
>>> #!/bin/bash
>>> #PBS -o 'qsub.out'
>>> #PBS -e 'qsub.err'
>>> #PBS -l nodes=4:ppn=1
>>> #PBS -m bea
>>> cat $PBS_NODEFILE
>>> hostname
>>>
>>> cd $PBS_O_WORKDIR
>>>
>>> # Run an R script
>>> mpirun -hostfile $PBS_NODEFILE -np 1 R --slave -f
>>> /nfs/user08/bw4sz/Files/Seawulf.R
>>>
>>> You may not need to use '-hostfile $PBS_NODEFILE', depending on
>>> how your Open MPI was built, but I don't think if ever hurts, and
>>> it may be required for your installation.
>>>
>>> - Steve
>>
>>
>>
>> --
>> Ben Weinstein
>> Graduate Student
>> Ecology and Evolution
>> Stony Brook University
>>
>> http://life.bio.sunysb.edu/~bweinste/index.html
>>
>
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