On 09/03/2014 10:24 PM, Leek, Jim wrote:
Thanks for the tips. I'll take a look around for for loops in the morning.
I think the example you provided worked for OpenMPI. (The default on our
machine is MPICH2, but it gave the same error about calling spawn.) Anyway,
with OpenMPI I got this:
# salloc -n 12 orterun -n 1 R -f spawn.R
library(Rmpi)
## Recent Rmpi bug -- should be mpi.universe.size() nWorkers <-
mpi.universe.size()
(the '## Recent Rmpi bug' comment should have been removed, it's a holdover from
when the script was written several years ago)
nslaves = 4
mpi.spawn.Rslaves(nslaves)
The argument needs to be named
mpi.spawn.Rslaves(nslaves=4)
otherwise R matches unnamed arguments by position, and '4' is associated with
the 'Rscript' argument.
Martin
Reported: 2 (out of 2) daemons - 4 (out of 4) procs
Then it hung there. So things spawned anyway, which is progress. I'm just not
sure is that expected behavior for parSupply or not.
Jim
-----Original Message-----
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: Wednesday, September 03, 2014 5:08 PM
To: Leek, Jim; r-help@r-project.org
Subject: Re: [R] snow/Rmpi without MPI.spawn?
On 09/03/2014 03:25 PM, Jim Leek wrote:
I'm a programmer at a high-performance computing center. I'm not very
familiar with R, but I have used MPI from C, C++, and Python. I have
to run an R code provided by a guy who knows R, but not MPI. So, this
fellow used the R snow library to parallelize his R code
(theoretically, I'm not actually sure what he did.) I need to get
this code running on our machines.
However, Rmpi and snow seem to require mpi spawn, which our computing
center doesn't support. I even tried building Rmpi with MPICH1
instead of 2, because Rmpi has that option, but it still tries to use spawn.
I can launch plenty of processes, but I have to launch them all at
once at the beginning. Is there any way to convince Rmpi to just use
those processes rather than trying to spawn its own? I haven't found
any documentation on this issue, although I would've thought it would be quite
common.
This script
spawn.R
=======
# salloc -n 12 orterun -n 1 R -f spawn.R
library(Rmpi)
## Recent Rmpi bug -- should be mpi.universe.size() nWorkers <-
mpi.universe.size()
mpi.spawn.Rslaves(nslaves=nWorkers)
mpiRank <- function(i)
c(i=i, rank=mpi.comm.rank())
mpi.parSapply(seq_len(2*nWorkers), mpiRank)
mpi.close.Rslaves()
mpi.quit()
can be run like the comment suggests
salloc -n 12 orterun -n 1 R -f spawn.R
uses slurm (or whatever job manager) to allocate resources for 12 tasks and
spawn within that allocation. Maybe that's 'good enough' -- spawning within the
assigned allocation? Likely this requires minimal modification of the current
code.
More extensive is to revise the manager/worker-style code to something more
like single instruction, multiple data
simd.R
======
## salloc -n 4 orterun R --slave -f simd.R
sink("/dev/null") # don't capture output -- more care needed here
library(Rmpi)
TAGS = list(FROM_WORKER=1L)
.comm = 0L
## shared `work', here just determine rank and host
work = c(rank=mpi.comm.rank(.comm),
host=system("hostname", intern=TRUE))
if (mpi.comm.rank(.comm) == 0) {
## manager
mpi.barrier(.comm)
nWorkers = mpi.comm.size(.comm)
res = list(nWorkers)
for (i in seq_len(nWorkers - 1L)) {
res[[i]] <- mpi.recv.Robj(mpi.any.source(), TAGS$FROM_WORKER,
comm=.comm)
}
res[[nWorkers]] = work
sink() # start capturing output
print(do.call(rbind, res))
} else {
## worker
mpi.barrier(.comm)
mpi.send.Robj(work, 0L, TAGS$FROM_WORKER, comm=.comm)
}
mpi.quit()
but this likely requires some serious code revision; if going this route then
http://r-pbd.org/ might be helpful (and from a similar HPC environment).
It's always worth asking whether the code is written to be efficient in R -- a
typical 'mistake' is to write R-level explicit 'for' loops that
"copy-and-append" results, along the lines of
len <- 100000
result <- NULL
for (i in seq_len(len))
## some complicated calculation, then...
result <- c(result, sqrt(i))
whereas it's much better to "pre-allocate and fill"
result <- integer(len)
for (i in seq_len(len))
result[[i]] = sqrt(i)
or
lapply(seq_len(len), sqrt)
and very much better still to 'vectorize'
result <- sqrt(seq_len(len))
(timing for me are about 1 minute for "copy-and-append", .2 s for "pre-allocate
and fill", and .002s for "vectorize").
Pushing back on the guy providing the code (grep for "for" loops, and look for
that copy-and-append pattern) might save you from having to use parallel
evaluation at all.
Martin
Thanks,
Jim
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