Not sure exactly how but back up and running, with all cores. Thanks to
all. Hopefully the new binary for Ubuntu with open-mpi 3.0.0 won't be too
far away.
Very Best,
J
On 3 October 2017 at 21:06, r...@open-mpi.org <r...@open-mpi.org> wrote:
> You can add it to the default MCA param file, if you want -
> <prefix>/etc/openmpi-mca-params.conf
>
> On Oct 3, 2017, at 12:44 PM, Jim Maas <jimmaa...@gmail.com> wrote:
>
> 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
>> d...@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
>>> d...@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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>>>
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