Plain: Problem with Rmpi

Dear List,

I have the following problem with R (2.10.0) Rmpi using OpenMPI 1.3.3.:

I use Dirk Eddelbuettels test script for testing if Rmpi works.
(http://dirk.eddelbuettel.com/papers/ismNov2009introHPCwithR.pdf, the
example is on Slide 96)

The script looks as follows:

require(Rmpi)
rk <- mpi.comm.rank(0)
sz <- mpi.comm.size(0)

name <- mpi.get.processor.name()
cat("Hello, rank", rk, "size", sz, "on", name, "\n")

mpi.close.Rslaves()
mpi.quit()

According to Dirk's slides, the output should look something like:
Hello, rank 4 size 8 on ron
Hello, rank 0 size 8 on ron
Hello, rank 3 size 8 on mccoy
Hello, rank 7 size 8 on mccoy
Hello, rank Hello, rank 21 size 8 on joe
size 8 on tony
Hello, rank 6 size 8 on tony
Hello, rank 5 size 8 on joe

I call the script:

/programs/openmpi-1.3.3/bin/orterun -host node02,node03 -n 4
/programs/R/R-2.10.0/bin/Rscript mpiTest_03.R

The output looks like:

master (rank 0, comm 1) of size 4 is running on: node02
slave1 (rank 1, comm 1) of size 4 is running on: node03
slave2 (rank 2, comm 1) of size 4 is running on: node02
slave3 (rank 3, comm 1) of size 4 is running on: node03
Hello, rank 0 size 4 on node02

So, in my understanding there is a master and 3 slaves are spawned. But
the call for the processor name is executed only on the master. Right?
Any suggestions on what could be the problem?

Thanks a lot!

Sebastian




? ? ? ?[[alternative HTML version deleted]]

Why are you calling mpi.close.Rslaves?  I believe that you should
only do that if you've started the slaves via mpi.spawn.Rslaves.

I'm not sure if that has any bearing on your problem, however.
But I wouldn't draw too many conclusions based on not seeing
messages to stdout from the slaves right before quitting,
especially messages that are produced on different machines.
To improve the chances of it working, I suggest that you
add a call to flush(stdout()) after the cat.  But you might want
to do something else to prove whether the slaves are really
running.

- Steve


On Mon, Jan 18, 2010 at 8:42 AM,  <sebastian.rohrer at basf.com> wrote:

Dear List,

I have the following problem with R (2.10.0) Rmpi using OpenMPI 1.3.3.:

I use Dirk Eddelbuettels test script for testing if Rmpi works.
(http://dirk.eddelbuettel.com/papers/ismNov2009introHPCwithR.pdf, the
example is on Slide 96)

The script looks as follows:

require(Rmpi)
rk <- mpi.comm.rank(0)
sz <- mpi.comm.size(0)

name <- mpi.get.processor.name()
cat("Hello, rank", rk, "size", sz, "on", name, "\n")

mpi.close.Rslaves()
mpi.quit()

According to Dirk's slides, the output should look something like:
Hello, rank 4 size 8 on ron
Hello, rank 0 size 8 on ron
Hello, rank 3 size 8 on mccoy
Hello, rank 7 size 8 on mccoy
Hello, rank Hello, rank 21 size 8 on joe
size 8 on tony
Hello, rank 6 size 8 on tony
Hello, rank 5 size 8 on joe

I call the script:

/programs/openmpi-1.3.3/bin/orterun -host node02,node03 -n 4
/programs/R/R-2.10.0/bin/Rscript mpiTest_03.R

The output looks like:

master (rank 0, comm 1) of size 4 is running on: node02
slave1 (rank 1, comm 1) of size 4 is running on: node03
slave2 (rank 2, comm 1) of size 4 is running on: node02
slave3 (rank 3, comm 1) of size 4 is running on: node03
Hello, rank 0 size 4 on node02

So, in my understanding there is a master and 3 slaves are spawned. But
the call for the processor name is executed only on the master. Right?
Any suggestions on what could be the problem?

Thanks a lot!

Sebastian




? ? ? ?[[alternative HTML version deleted]]

From looking over the Rmpi Rprofile, it appears that it is used to put the

Hao and Stephen,
thanks a lot. Your comments took me a good step further. But I must
confess, I am a bit confused about the significance of the .Rprofile
provided with Rmpi. I'm quite sure this is because I am a total noob
concerning HPC but maybe you can help me understand the issue.
After Stephen's response I changed my script to:

require(Rmpi)

print(mpi.remote.exec(rnorm(5)))

mpi.close.Rslaves()
mpi.quit()

and called it with

/programs/openmpi-1.3.3/bin/orterun -host node02,node03 -n 4 Rscript
mpiTest_03.R

,which ran without error and procduced the following output:

master (rank 0, comm 1) of size 4 is running on: node02
slave1 (rank 1, comm 1) of size 4 is running on: node03
slave2 (rank 2, comm 1) of size 4 is running on: node02
slave3 (rank 3, comm 1) of size 4 is running on: node03
? ? ? ? ?X1 ? ? ? ? X2 ? ? ? ? ? X3
1 ?0.6422312 -1.4176550 -0.864957823
2 -0.9049865 ?1.3221402 ?0.322550244
3 ?1.1318463 -0.3170188 -0.001224240
4 ?0.8153995 ?1.4860591 -1.507712241
5 -0.1545055 ?0.3834336 -0.104543321
[1] 1

So everything seems OK, three slaves are running and therefore
mpi.remote.exec(rnorm(5)) is executed on three slaves.
BTW: if I leave out "mpi.close.Rslaves()" the program will produce the
same output, but then hang indefinitely.

After Hao's response, I removed the .Rprofile from Rmpi from the working
directory. The sample script above wouldn't run anymore, but this is
expected if I understood Hao's comment in the right way.
What really strikes me, is that a test script I prepared for testing
Stephen's doMPI package (this is my ultimate goal: foreach, iterators and
doMPI) now ran smoothly:

library(doMPI)
cl <- startMPIcluster()
registerDoMPI(cl)

foreach(i = 1:3) %dopar% sqrt(i)

closeCluster(cl)
mpi.quit()

/programs/openmpi-1.3.3/bin/orterun -host node02,node03 -n 4 Rscript
mpiTest_04.R

Output:

[[1]]
[1] 1

[[2]]
[1] 1.414214

[[3]]
[1] 1.732051

So this seems to work allright. The same is true for the bootMPI.R example
provided with doMPI. Both, however, don't work if I restore the Rmpi
.Rprofile.

I'm sorry to bother you with these newbie questions, but I really would
like to understand what is going on here.

Thanks a lot for your support and thanks to both of you Hao and Stephen
for providing these great packages!

Cheers, Sebastian






"Hao Yu" <hyu at stats.uwo.ca>
18.01.2010 19:43
Bitte antworten an
hyu at stats.uwo.ca


An
"Stephen Weston" <stephen.b.weston at gmail.com>
Kopie
sebastian.rohrer at basf.com, "R-sig-hpc at r-project.org"
<r-sig-hpc at r-project.org>
Thema
Re: [R-sig-hpc] Plain: Problem with Rmpi






mpi.spawn.Rslaves is not needed since orterun is used to create 1 master
and 3 slaves.

I assume Rprofile in Rmpi is used. Then all slaves are in infinite loop
waiting for master instructions. They will not take any R scripts through
BATCH mode (only master will process them).

You may use mpi.remote.exec to get what you want or modify slave.hostinfo.

Hao


Stephen Weston wrote:

Why are you calling mpi.close.Rslaves? ?I believe that you should
only do that if you've started the slaves via mpi.spawn.Rslaves.

I'm not sure if that has any bearing on your problem, however.
But I wouldn't draw too many conclusions based on not seeing
messages to stdout from the slaves right before quitting,
especially messages that are produced on different machines.
To improve the chances of it working, I suggest that you
add a call to flush(stdout()) after the cat. ?But you might want
to do something else to prove whether the slaves are really
running.

- Steve


On Mon, Jan 18, 2010 at 8:42 AM, ?<sebastian.rohrer at basf.com> wrote:

Dear List,

I have the following problem with R (2.10.0) Rmpi using OpenMPI 1.3.3.:

I use Dirk Eddelbuettels test script for testing if Rmpi works.
(http://dirk.eddelbuettel.com/papers/ismNov2009introHPCwithR.pdf, the
example is on Slide 96)

The script looks as follows:

require(Rmpi)
rk <- mpi.comm.rank(0)
sz <- mpi.comm.size(0)

name <- mpi.get.processor.name()
cat("Hello, rank", rk, "size", sz, "on", name, "\n")

mpi.close.Rslaves()
mpi.quit()

According to Dirk's slides, the output should look something like:
Hello, rank 4 size 8 on ron
Hello, rank 0 size 8 on ron
Hello, rank 3 size 8 on mccoy
Hello, rank 7 size 8 on mccoy
Hello, rank Hello, rank 21 size 8 on joe
size 8 on tony
Hello, rank 6 size 8 on tony
Hello, rank 5 size 8 on joe

I call the script:

/programs/openmpi-1.3.3/bin/orterun -host node02,node03 -n 4
/programs/R/R-2.10.0/bin/Rscript mpiTest_03.R

The output looks like:

master (rank 0, comm 1) of size 4 is running on: node02
slave1 (rank 1, comm 1) of size 4 is running on: node03
slave2 (rank 2, comm 1) of size 4 is running on: node02
slave3 (rank 3, comm 1) of size 4 is running on: node03
Hello, rank 0 size 4 on node02

So, in my understanding there is a master and 3 slaves are spawned. But
the call for the processor name is executed only on the master. Right?
Any suggestions on what could be the problem?

Thanks a lot!

Sebastian




? ? ? ?[[alternative HTML version deleted]]

--
Department of Statistics & Actuarial Sciences
Fax Phone#:(519)-661-3813
The University of Western Ontario
Office Phone#:(519)-661-3622
London, Ontario N6A 5B7
http://www.stats.uwo.ca/faculty/yu


? ? ? ?[[alternative HTML version deleted]]

But I must 
confess, I am a bit confused about the significance of the .Rprofile 
provided with Rmpi. I'm quite sure this is because I am a total noob 
concerning HPC but maybe you can help me understand the issue.
After Stephen's response I changed my script to: 

require(Rmpi)

print(mpi.remote.exec(rnorm(5)))

mpi.close.Rslaves()
mpi.quit()

and called it with

/programs/openmpi-1.3.3/bin/orterun -host node02,node03 -n 4 Rscript 
mpiTest_03.R