Hi,
Here is a very simple patch, but Ralph might have a different idea.
So I'd like him to decide how to treat it. As far as I checked, I
believe it has no side effect.
(See attached file: patch.bind-to-none)
Tetsuya
> Hi,
>
> Am 27.08.2014 um 09:57 schrieb Tetsuya Mishima:
>
> > Hi Reuti and R
Hi,
Am 27.08.2014 um 09:57 schrieb Tetsuya Mishima:
> Hi Reuti and Ralph,
>
> How do you think if we accept bind-to none option even when the pe=N option
> is provided?
>
> just like:
> mpirun -map-by slot:pe=N -bind-to none ./inverse
Yes, this would be ok to cover all cases.
-- Reuti
> If
Hi Reuti and Ralph,
How do you think if we accept bind-to none option even when the pe=N option is
provided?
just like:
mpirun -map-by slot:pe=N -bind-to none ./inverse
If yes, it's easy for me to make a patch.
Tetsuya
Tetsuya Mishima tmish...@jcity.maeda.co.jp
Am 21.08.2014 um 16:50 schrieb Reuti:
> Am 21.08.2014 um 16:00 schrieb Ralph Castain:
>
>>
>> On Aug 21, 2014, at 6:54 AM, Reuti wrote:
>>
>>> Am 21.08.2014 um 15:45 schrieb Ralph Castain:
>>>
On Aug 21, 2014, at 2:51 AM, Reuti wrote:
> Am 20.08.2014 um 23:16 schrieb Ralph Cas
Am 21.08.2014 um 16:50 schrieb Reuti:
> Am 21.08.2014 um 16:00 schrieb Ralph Castain:
>
>>
>> On Aug 21, 2014, at 6:54 AM, Reuti wrote:
>>
>>> Am 21.08.2014 um 15:45 schrieb Ralph Castain:
>>>
On Aug 21, 2014, at 2:51 AM, Reuti wrote:
> Am 20.08.2014 um 23:16 schrieb Ralph Cas
Am 21.08.2014 um 16:50 schrieb Reuti:
> Am 21.08.2014 um 16:00 schrieb Ralph Castain:
>
>>
>> On Aug 21, 2014, at 6:54 AM, Reuti wrote:
>>
>>> Am 21.08.2014 um 15:45 schrieb Ralph Castain:
>>>
On Aug 21, 2014, at 2:51 AM, Reuti wrote:
> Am 20.08.2014 um 23:16 schrieb Ralph Cas
Am 21.08.2014 um 16:00 schrieb Ralph Castain:
>
> On Aug 21, 2014, at 6:54 AM, Reuti wrote:
>
>> Am 21.08.2014 um 15:45 schrieb Ralph Castain:
>>
>>> On Aug 21, 2014, at 2:51 AM, Reuti wrote:
>>>
Am 20.08.2014 um 23:16 schrieb Ralph Castain:
>
> On Aug 20, 2014, at 11:16
On Aug 21, 2014, at 6:54 AM, Reuti wrote:
> Am 21.08.2014 um 15:45 schrieb Ralph Castain:
>
>> On Aug 21, 2014, at 2:51 AM, Reuti wrote:
>>
>>> Am 20.08.2014 um 23:16 schrieb Ralph Castain:
>>>
On Aug 20, 2014, at 11:16 AM, Reuti wrote:
> Am 20.08.2014 um 19:05 schrieb
Am 21.08.2014 um 15:45 schrieb Ralph Castain:
> On Aug 21, 2014, at 2:51 AM, Reuti wrote:
>
>> Am 20.08.2014 um 23:16 schrieb Ralph Castain:
>>
>>>
>>> On Aug 20, 2014, at 11:16 AM, Reuti wrote:
>>>
Am 20.08.2014 um 19:05 schrieb Ralph Castain:
>>
>> Aha, this is quite in
On Aug 21, 2014, at 2:51 AM, Reuti wrote:
> Am 20.08.2014 um 23:16 schrieb Ralph Castain:
>
>>
>> On Aug 20, 2014, at 11:16 AM, Reuti wrote:
>>
>>> Am 20.08.2014 um 19:05 schrieb Ralph Castain:
>>>
>
> Aha, this is quite interesting - how do you do this: scanning the
> /proc//
sheds some light on it.
-- Reuti
> can I set a maximum number of threads in the queue one.q (e.g. 15 ) and
> change the number in the 'export' for my convenience
>
> I feel like a child hearing the adults speaking
> Thanks I'm learning a lot
>
>
>
t;>> -nostdin -V compute-1-12.local PATH=/opt/openmpi/bin:$PATH ; exp
>>>>>>>>> 17802 ? Sl 0:00 \_ /opt/gridengine/bin/linux-x64/qrsh -inherit
>>> -nostdin -V compute-1-13.local PATH=/opt/openmpi/bin:$PATH ; exp
>>>>>>>>> 17803 ? Sl 0
Am 20.08.2014 um 23:16 schrieb Ralph Castain:
>
> On Aug 20, 2014, at 11:16 AM, Reuti wrote:
>
>> Am 20.08.2014 um 19:05 schrieb Ralph Castain:
>>
Aha, this is quite interesting - how do you do this: scanning the
/proc//status or alike? What happens if you don't find enough fr
in the 'export' for my convenience
>
> I feel like a child hearing the adults speaking
> Thanks I'm learning a lot
>
>
> Oscar Fabian Mojica Ladino
> Geologist M.S. in Geophysics
>
>
> > From: re...@staff.uni-marburg.de
> > Date: Tue, 19 Aug 2014
threads,
i.e.
> > OMP_NUM_THREADS must be defined by "qsub -v ..." outside of the
jobscript
> > (tricky scanning
> >>> of the submitted jobscript for OMP_NUM_THREADS would be too nasty)
> >>>> - limits to use inside the jobscript calls to libraries behaving i
On Aug 20, 2014, at 11:16 AM, Reuti wrote:
> Am 20.08.2014 um 19:05 schrieb Ralph Castain:
>
>>>
>>> Aha, this is quite interesting - how do you do this: scanning the
>>> /proc//status or alike? What happens if you don't find enough free
>>> cores as they are used up by other applications al
Am 20.08.2014 um 19:05 schrieb Ralph Castain:
>>
>> Aha, this is quite interesting - how do you do this: scanning the
>> /proc//status or alike? What happens if you don't find enough free
>> cores as they are used up by other applications already?
>>
>
> Remember, when you use mpirun to launc
27;m learning a lot
Oscar Fabian Mojica Ladino
Geologist M.S. in Geophysics
> From: re...@staff.uni-marburg.de
> Date: Tue, 19 Aug 2014 19:51:46 +0200
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] Running a hybrid MPI+openMP program
>
> Hi,
>
> Am 19.08.2014
gt;>>>> queuingsystem should get a proper request for the overall amount of
>>>> slots the user needs. For now this will be forwarded to Open MPI and it
>>>> will use this
>>>>>> information to start the appropriate number of processes (which was an
>>
should the generated list of machines be
>>> adjusted; there are several options:
>>>>>>
>>>>>> a) The PE of the queuingsystem should do it:
>>>>>>
>>>>>> + a one time setup for the admin
>>>>>> + in SGE the
ricky scanning
>>>> of the submitted jobscript for OMP_NUM_THREADS would be too nasty)
>>>>> - limits to use inside the jobscript calls to libraries behaving in
>> the same way as Open MPI only
>>>>>
>>>>>
>>>>> b) The
aving a mixture of
> users and jobs a different
>>> handling would be necessary to handle this in a proper way IMO:
>>>>>>
>>>>>> a) having a PE with a fixed allocation rule of 8
>>>>>>
>>>>>> b) requesting this PE
>>>> c) The user should do it
>>>>
>>>> + no change in the SGE installation
>>>> - each and every user must include it in all the jobscripts to adjust
> the list and export the pointer to the $PE_HOSTFILE, but he could change it
> forth and b
t;> d) Open MPI should do it
> >>
> >> + no change in the SGE installation
> >> + no change to the jobscript
> >> + OMP_NUM_THREADS can be altered for different steps of the jobscript
while staying inside the granted allocation automatically
> >> o sh
obscript
>> + OMP_NUM_THREADS can be altered for different steps of the jobscript while
>> staying inside the granted allocation automatically
>> o should MKL_NUM_THREADS be covered too (does it use OMP_NUM_THREADS
>> already)?
>>
>> -- Reuti
>>
>&
atically
>o should MKL_NUM_THREADS be covered too (does it use OMP_NUM_THREADS already)?
>
>-- Reuti
>
>
>> echo "PE_HOSTFILE:"
>> echo $PE_HOSTFILE
>> echo
>> echo "cat PE_HOSTFILE:"
>> cat $PE_HOSTFILE
>>
>> Thanks fo
rit -nostdin
> > > -V compute-1-13.local PATH=/opt/openmpi/bin:$PATH ; exp
> > > 17803 ? Sl 0:00 \_ /opt/gridengine/bin/linux-x64/qrsh -inherit -nostdin
> > > -V compute-1-14.local PATH=/opt/openmpi/bin:$PATH ; exp
> > > 17804 ? Sl 0:00 \_ /opt/gridengi
mails, your advices had been very useful
PS: The version of SGE is OGS/GE 2011.11p1
Oscar Fabian Mojica Ladino
Geologist M.S. in Geophysics
> From: re...@staff.uni-marburg.de
> Date: Fri, 15 Aug 2014 20:38:12 +0200
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] Running a hybrid M
-inherit -nostdin -V compute-1-4.local
> PATH=/opt/openmpi/bin:$PATH ; expo
> 17826 ?R 31:36 \_ ./inverse.exe
> 3429 ?Ssl0:00 automount --pid-file /var/run/autofs.pid
>
> So the job is using the 10 machines, Until here is all right OK.
> Date: Thu, 14 Aug 2014 23:54:22 +0200
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] Running a hybrid MPI+openMP program
>
> Hi,
>
> I think this is a broader issue in case an MPI library is used in conjunction
> with threads while running inside a queuing system.
chines trying to gain more time. the
> results were the same in both cases. In the last case i could prove that the
> processes were distributed to all machines correctly.
>
> What I must to do?
> Thanks
>
> Oscar Fabian Mojica Ladino
> Geologist M.S. in Geophysics
>
ug 2014 10:10:17 -0400
> From: maxime.boissonnea...@calculquebec.ca
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] Running a hybrid MPI+openMP program
>
> Hi,
> You DEFINITELY need to disable OpenMPI's new default binding. Otherwise,
> your N threads will run on a s
Hi,
You DEFINITELY need to disable OpenMPI's new default binding. Otherwise,
your N threads will run on a single core. --bind-to socket would be my
recommendation for hybrid jobs.
Maxime
Le 2014-08-14 10:04, Jeff Squyres (jsquyres) a écrit :
I don't know much about OpenMP, but do you need t
Hi,
Am 14.08.2014 um 15:50 schrieb Oscar Mojica:
> I am trying to run a hybrid mpi + openmp program in a cluster. I created a
> queue with 14 machines, each one with 16 cores. The program divides the work
> among the 14 processors with MPI and within each processor a loop is also
> divided in
I don't know much about OpenMP, but do you need to disable Open MPI's default
bind-to-core functionality (I'm assuming you're using Open MPI 1.8.x)?
You can try "mpirun --bind-to none ...", which will have Open MPI not bind MPI
processes to cores, which might allow OpenMP to think that it can us
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