On Wed, Apr 22, 2009 at 12:42 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> On Wed, Apr 22, 2009 at 7:11 AM, Dirk Eddelbuettel <edd@debian.org> wrote:
>
>>
>> On 21 April 2009 at 16:40, Sean Davis wrote:
>> | I am running sge6.2, openmpi 1.3.1, and Rmpi 0.5.7 on openSUSE linux.  I
>> can
>> | start up an arbitrarily-sized cluster using sge, see the appropriate
>> | universe.size using Rmpi, and start a cluster using mpi.spawn.Rslaves().
>> | However, it appears that all the slaves then run at 100% cpu on all
>> nodes.
>> | Even using Rmpi under openmpi with a simple hostfile produces the same
>> | result.  Any suggestions to figure out what is going on on the slaves?
>>
>> There is a known issue with Open MPI and blocking which you may be hitting
>> here.  Upstream Open MPI considers it a feature. But as this has come up a
>> few times on their mailing list as well, I believe the last word was that
>> it
>> will go away in a future release.
>>
>
> Just a follow up:
>
> http://www.open-mpi.org/community/lists/users/2009/04/9016.php
>
> If one searches the OMPI mailing list for "100% CPU", there are many hits.
>
>
> I'll let folks know if I implement a solution....
>

Just a bit more follow up:

http://www.open-mpi.org/community/lists/users/2008/04/5457.php

So, as Dirk suggested, the 100% CPU usage is thought to be a feature and not
a bug.

Sean



>
>
>
>>
>> Hth, Dirk
>>
>> | Thanks,
>> | Sean
>> |
>> |
>> | > library(Rmpi)
>> | library(Rmpi)
>> | > mpi.universe.size()
>> | mpi.universe.size()
>> | [1] 24
>> | > mpi.spawn.Rslaves()
>> | mpi.spawn.Rslaves()
>> |         24 slaves are spawned successfully. 0 failed.
>> | master  (rank 0 , comm 1) of size 25 is running on: Mahfouz
>> | slave1  (rank 1 , comm 1) of size 25 is running on: Mahfouz
>> | slave2  (rank 2 , comm 1) of size 25 is running on: Mahfouz
>> | slave3  (rank 3 , comm 1) of size 25 is running on: Mahfouz
>> | slave4  (rank 4 , comm 1) of size 25 is running on: Mahfouz
>> | slave5  (rank 5 , comm 1) of size 25 is running on: Mahfouz
>> | slave6  (rank 6 , comm 1) of size 25 is running on: Mahfouz
>> | slave7  (rank 7 , comm 1) of size 25 is running on: Mahfouz
>> | slave8  (rank 8 , comm 1) of size 25 is running on: Grass
>> | slave9  (rank 9 , comm 1) of size 25 is running on: Grass
>> | slave10 (rank 10, comm 1) of size 25 is running on: Grass
>> | slave11 (rank 11, comm 1) of size 25 is running on: Grass
>> | slave12 (rank 12, comm 1) of size 25 is running on: Grass
>> | slave13 (rank 13, comm 1) of size 25 is running on: Grass
>> | slave14 (rank 14, comm 1) of size 25 is running on: Grass
>> | slave15 (rank 15, comm 1) of size 25 is running on: Grass
>> | slave16 (rank 16, comm 1) of size 25 is running on: shakespeare
>> | slave17 (rank 17, comm 1) of size 25 is running on: shakespeare
>> | slave18 (rank 18, comm 1) of size 25 is running on: shakespeare
>> | slave19 (rank 19, comm 1) of size 25 is running on: shakespeare
>> | slave20 (rank 20, comm 1) of size 25 is running on: shakespeare
>> | slave21 (rank 21, comm 1) of size 25 is running on: shakespeare
>> | slave22 (rank 22, comm 1) of size 25 is running on: shakespeare
>> | slave23 (rank 23, comm 1) of size 25 is running on: shakespeare
>> | slave24 (rank 24, comm 1) of size 25 is running on: Mahfouz
>> | > mpi.close.Rslaves()
>> | mpi.close.Rslaves()
>> | [1] 1
>> |
>> | > sessionInfo()    # on the master
>> | R version 2.9.0 Under development (unstable) (2009-02-21 r47969)
>> | x86_64-unknown-linux-gnu
>> |
>> | locale:
>> |
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>> |
>> | attached base packages:
>> | [1] stats     graphics  grDevices utils     datasets  methods   base
>> |
>> | other attached packages:
>> | [1] Rmpi_0.5-7
>> |
>> |       [[alternative HTML version deleted]]
>> |
>> | _______________________________________________
>> | R-sig-hpc mailing list
>> | R-sig-hpc@r-project.org
>> | https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>
>> --
>> Three out of two people have difficulties with fractions.
>>
>
>

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