Thanks RHC .... where do I put that so it will be in the environment?
J
On 3 October 2017 at 16:01, r...@open-mpi.org <r...@open-mpi.org> wrote:
> As Gilles said, we default to slots = cores, not HTs. If you want to treat
> HTs as independent cpus, then you need to add
> OMPI_MCA_hwloc_base_use_hwthreads_as_cpus=1
> in your environment.
>
> On Oct 3, 2017, at 7:27 AM, Jim Maas <jimmaa...@gmail.com> wrote:
>
> Tried this and got this error, and slots are available, nothing else is
> running.
>
> > cl <- startMPIcluster(count=7)
> --------------------------------------------------------------------------
> There are not enough slots available in the system to satisfy the 7 slots
> that were requested by the application:
> /usr/local/lib/R/bin/Rscript
>
> Either request fewer slots for your application, or make more slots
> available
> for use.
> --------------------------------------------------------------------------
> Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves =
> count, :
> MPI_ERR_SPAWN: could not spawn processes
> >
>
> On 3 October 2017 at 15:07, Gilles Gouaillardet <gilles.
> gouaillar...@gmail.com> wrote:
>
>> Thanks, i will have a look at it.
>>
>> By default, a slot is a core, so there are 6 slots on your system.
>> Could your app spawn 6 procs on top of the initial proc ? That would be 7
>> slots and there are only 6.
>> What if you ask 5 slots only ?
>>
>> With some parameters i do not know off hand, you could either
>> oversubscribe or use hyperthreads as slots. In both cases, 7 slots would be
>> available.
>>
>> Cheers,
>>
>> Gilles
>>
>> Jim Maas <jimmaa...@gmail.com> wrote:
>> Thanks Gilles, relative noob here at this level, apologies if nonsensical!
>>
>> I removed previous versions of open mpi which were compiled from source
>> using sudo make uninstall ...
>> downloaded new open-mpi 3.0.0 in tar.gz
>> configure --disable-dlopen
>> sudo make install
>>
>>
>> then ran sudo ldconfig
>>
>> updated R, downloaded R-3.4.2.tar.gz
>> ./configure
>> sudo make install
>>
>>
>> Then run R from sudo
>>
>> sudo R
>> once running
>> install.packages("Rmpi")
>> install.packages("doMPI")
>>
>> both of these load and test fine during install
>>
>> Then from R run
>>
>> rm(list=ls(all=TRUE))
>> library(doMPI)
>>
>> ## load MPI cluster
>> cl <- startMPIcluster(count=6)
>>
>>
>> At this point it throws the error, doesn't find any of the slots.
>>
>> There is a precompiled version of Rmpi that installs an older version of
>> open-mpi directly from Ubuntu, but I think the mpi version is an older one
>> so I wanted to try using the new version.
>>
>>
>> I use this 6 core (12) as test bed before uploading to a cluster. It is
>> Ubuntu 16.04 Linux, lstopo pdf is attached.
>>
>> Thanks,
>>
>> J
>>
>>
>> On 3 October 2017 at 14:06, Gilles Gouaillardet <gilles.
>> gouaillar...@gmail.com> wrote:
>>
>>> Hi Jim,
>>>
>>> can you please provide minimal instructions on how to reproduce the
>>> issue ?
>>> we know Open MPI, but i am afraid few or none of us know about Rmpi nor
>>> doMPI.
>>> once you explain how to download and build these, and how to run the
>>> failing test,
>>> we ll be able to investigate that.
>>>
>>> also, can you describe your environment ?
>>> i assume one ubuntu machine, can you please run
>>> lstopo
>>> on and post the output ?
>>>
>>> did you use to have some specific settings in the system-wide conf
>>> file (e.g. /.../etc/openmpi-mca-params.conf) ?
>>> if yes, can you post these, the syntax might have changed in 3.0.0
>>>
>>> Cheers,
>>>
>>> Gilles
>>>
>>> On Tue, Oct 3, 2017 at 7:34 PM, Jim Maas <jimmaa...@gmail.com> wrote:
>>> > I've used this for years, just updated open-mpi to 3.0.0 and reloaded
>>> R,
>>> > have reinstalled doMPI and thus Rmpi but when I try to use
>>> startMPICluster,
>>> > asking for 6 slots (there are 12 on this machine) I get this error.
>>> Where
>>> > can I start to debug it?
>>> >
>>> > Thanks
>>> > J
>>> > ------------------------------------------------------------
>>> --------------
>>> > There are not enough slots available in the system to satisfy the 6
>>> slots
>>> > that were requested by the application:
>>> > /usr/lib/R/bin/Rscript
>>> >
>>> > Either request fewer slots for your application, or make more slots
>>> > available
>>> > for use.
>>> > ------------------------------------------------------------
>>> --------------
>>> > Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves =
>>> count,
>>> > :
>>> > MPI_ERR_SPAWN: could not spawn processes
>>> > --
>>> > Jim Maas
>>> >
>>> > jimmaasuk at gmail.com
>>> >
>>> >
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>>
>>
>>
>> --
>>
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