Hi Stefan,

I tried cl<-makeCluster(type="MPI", workers). The following error popped
up.
Error in mpi.comm.spawn(slave = mpitask, slavearg = args, nslaves = count,
:
  'Calloc' could not allocate memory (18446744071562067968 of 4 bytes)
Calls: makeCluster -> makeMPIcluster -> mpi.comm.spawn -> .Call
In addition: Warning messages:
1: In if (nslaves <= 0) stop("Choose a positive number of slaves.") :
  the condition has length > 1 and only the first element will be used
2: In mpi.comm.spawn(slave = mpitask, slavearg = args, nslaves = count,  :
  NAs introduced by coercion
Execution halted


When I try cl<-makeCluster(type="MPI", 4). It creates nodes in the same
machine.

Also when I try cl<-makeCluster(type="SOCK", workers) , gives the following
error
Fatal error: cannot open file
'/home/pghadoop01/R/x86_64-pc-linux-gnu-library/3.1/snow/RSOCKnode.R': No
such file or directory

I read in some blogs that snow and doSNOW have some issues.

Thanks in advance,

Best Regards,
Rajendra Kumar M
Graduate Student.

School of Medical Science & Technology,
IIT Kharagpur,
West Bengal-721302.
India



On 8 August 2014 11:48, Stefan Thomas <9sthomas@informatik.uni-hamburg.de>
wrote:

> Hi Rajendra Kumar,
>
> I think you are trying to start a SOCKS cluster (same machine) in a MPI
> environment (distributed machines).
> Have you tried
>
> cl<-makeCluster(type="MPI",4)
>
> after creating and setting the orte-hostfile?
>
> best
> stef
>
> Am 08.08.2014 um 07:13 schrieb Rajendra Kumar:
>
>> Dear R HPC Users,
>>
>> I'm trying to parallelize a code on 4 nodes(type = "SOCK"). Here is my
>> code.
>>
>>
>>      library(itertools)
>>      library(foreach)
>>      library(doParallel)
>>      library(parallel)
>>
>>      workers <- ip address of 4 nodes
>>      cl = makePSOCKcluster(workers, master="ip address of master")
>>      registerDoParallel(cl)
>>
>>      z <- read.csv("ProcessedData.csv", header=TRUE, as.is=TRUE)
>>      z <- as.matrix(z)
>>
>>
>>      system.time({
>>        chunks <- getDoParWorkers()
>>        b <- foreach (these = isplitIndices(nrow(z),
>>                                            chunks=chunks),
>>                      .combine = c) %dopar% {
>>                        a <- rep(0, length(these))
>>                        for (i in 1:length(these)) {
>>                          a[i] <- mean(z[these[i],])
>>                        }
>>                        a
>>                      }
>>      })
>>
>>
>>
>>
>>
>> I get this error..4 nodes produced errors; first error: object
>> '.doSnowGlobals' not found. This code runs fine if I'm using doMC i.e
>> using
>> the same machine's cores. But when I try to use other computers for
>> parallel computing I get the above error. When I change it to
>> registerDoSNOW the error persists.
>>
>> Does snow and DoSNOW work in a cluster? I could create nodes on the
>> localhost using snow but not on the cluster. Anyone out there using snow?
>>
>> Thanks in advance.
>>
>> With Warm Regards,
>> Rajendra Kumar M
>> Graduate Student.
>>
>> School of Medical Science & Technology,
>> IIT Kharagpur,
>> West Bengal-721302.
>>
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>>
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>>
>
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