On Aug 21, 2014, at 6:54 AM, Reuti <re...@staff.uni-marburg.de> wrote:
> Am 21.08.2014 um 15:45 schrieb Ralph Castain:
>
>> On Aug 21, 2014, at 2:51 AM, Reuti <re...@staff.uni-marburg.de> wrote:
>>
>>> Am 20.08.2014 um 23:16 schrieb Ralph Castain:
>>>
>>>>
>>>> On Aug 20, 2014, at 11:16 AM, Reuti <re...@staff.uni-marburg.de> wrote:
>>>>
>>>>> Am 20.08.2014 um 19:05 schrieb Ralph Castain:
>>>>>
>>>>>>> <snip>
>>>>>>> Aha, this is quite interesting - how do you do this: scanning the
>>>>>>> /proc/<pid>/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 launch, we launch our own daemons using
>>>>>> the native launcher (e.g., qsub). So the external RM will bind our
>>>>>> daemons to the specified cores on each node. We use hwloc to determine
>>>>>> what cores our daemons are bound to, and then bind our own child
>>>>>> processes to cores within that range.
>>>>>
>>>>> Thx for reminding me of this. Indeed, I mixed up two different aspects in
>>>>> this discussion.
>>>>>
>>>>> a) What will happen in case no binding was done by the RM (hence Open MPI
>>>>> could use all cores) and two Open MPI jobs (or something completely
>>>>> different besides one Open MPI job) are running on the same node (due to
>>>>> the Tight Integration with two different Open MPI directories in /tmp and
>>>>> two `orted`, unique for each job)? Will the second Open MPI job know what
>>>>> the first Open MPI job used up already? Or will both use the same set of
>>>>> cores as "-bind-to none" can't be set in the given `mpiexec` command
>>>>> because of "-map-by slot:pe=$OMP_NUM_THREADS" was used - which triggers
>>>>> "-bind-to core" indispensable and can't be switched off? I see the same
>>>>> cores being used for both jobs.
>>>>
>>>> Yeah, each mpirun executes completely independently of the other, so they
>>>> have no idea what the other is doing. So the cores will be overloaded.
>>>> Multi-pe's requires bind-to-core otherwise there is no way to implement
>>>> the request
>>>
>>> Yep, and so it's no option in a mixed cluster. Why would it hurt to allow
>>> "-bind-to none" here?
>>
>> Guess I'm confused here - what does pe=N mean if we bind-to none?? If you
>> are running on a mixed cluster and don't want binding, then just say bind-to
>> none and leave the pe argument out entirely as it wouldn't mean anything
>> unless you are bound
>
> I would mean: divide the overall number of slots/cores in the machinefile by
> N (i.e. $OMP_NUM_THREADS).
>
> - Request made to the queuing system: I need 80 cores in total.
> - The machinefile will contain 80 cores
> - Open MPI will divide it by N, i.e. 8 here
> - Open MPI will start only 10 processes, one on each node
> - The application will use 8 threads per started MPI process
I see - so you were talking about the case where the user doesn't provide the
-np N option and we need to compute the number of procs to start. Okay, the
change you requested below will fix that one too. I can make that easily enough.
>
> -- Reuti
>
>
>>>
>>>
>>>>> Altering the machinefile instead: the processes are not bound to any
>>>>> core, and the OS takes care of a proper assignment.
>>>
>>> Here the ordinary user has to mangle the hostfile, this is not good (but
>>> allows several jobs per node as the OS shift the processes around).
>>> Could/should it be put into the "gridengine" module in OpenMPI, to divide
>>> the slot count per node automatically when $OMP_NUM_THREADS is found, or
>>> generate an error if it's not divisible?
>>
>> Sure, that could be done - but it will only have if OMP_NUM_THREADS is set
>> when someone spins off threads. So far as I know, that's only used for
>> OpenMP - so we'd get a little help, but it wouldn't be full coverage.
>>
>>
>>>
>>> ===
>>>
>>>>>> If the cores we are bound to are the same on each node, then we will do
>>>>>> this with no further instruction. However, if the cores are different on
>>>>>> the individual nodes, then you need to add --hetero-nodes to your
>>>>>> command line (as the nodes appear to be heterogeneous to us).
>>>>>
>>>>> b) Aha, it's not about different type CPU types, but also same CPU type
>>>>> but different allocations between the nodes? It's not in the `mpiexec`
>>>>> man-page of 1.8.1 though. I'll have a look at it.
>>>
>>> I tried:
>>>
>>> $ qsub -binding linear:2:0 -pe smp2 8 -masterq parallel@node01 -q
>>> parallel@node0[1-4] test_openmpi.sh
>>> Your job 247109 ("test_openmpi.sh") has been submitted
>>> $ qsub -binding linear:2:1 -pe smp2 8 -masterq parallel@node01 -q
>>> parallel@node0[1-4] test_openmpi.sh
>>> Your job 247110 ("test_openmpi.sh") has been submitted
>>>
>>>
>>> Getting on node03:
>>>
>>>
>>> 6733 ? Sl 0:00 \_ sge_shepherd-247109 -bg
>>> 6734 ? SNs 0:00 | \_ /usr/sge/utilbin/lx24-amd64/qrsh_starter
>>> /var/spool/sge/node03/active_jobs/247109.1/1.node03
>>> 6741 ? SN 0:00 | \_ orted -mca orte_hetero_nodes 1 -mca
>>> ess env -mca orte_ess_jobid 1493303296 -mca orte_ess_vpid
>>> 6742 ? RNl 0:31 | \_ ./mpihello
>>> 6745 ? Sl 0:00 \_ sge_shepherd-247110 -bg
>>> 6746 ? SNs 0:00 \_ /usr/sge/utilbin/lx24-amd64/qrsh_starter
>>> /var/spool/sge/node03/active_jobs/247110.1/1.node03
>>> 6753 ? SN 0:00 \_ orted -mca orte_hetero_nodes 1 -mca
>>> ess env -mca orte_ess_jobid 1506607104 -mca orte_ess_vpid
>>> 6754 ? RNl 0:25 \_ ./mpihello
>>>
>>>
>>> reuti@node03:~> cat /proc/6741/status | grep Cpus_
>>> Cpus_allowed:
>>> 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
>>> Cpus_allowed_list: 0-1
>>> reuti@node03:~> cat /proc/6753/status | grep Cpus_
>>> Cpus_allowed:
>>> 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000030
>>> Cpus_allowed_list: 4-5
>>>
>>> Hence, "orted" got two cores assigned for each of them. But:
>>>
>>>
>>> reuti@node03:~> cat /proc/6742/status | grep Cpus_
>>> Cpus_allowed:
>>> 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
>>> Cpus_allowed_list: 0-1
>>> reuti@node03:~> cat /proc/6754/status | grep Cpus_
>>> Cpus_allowed:
>>> 00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003
>>> Cpus_allowed_list: 0-1
>>>
>>> What I see here (and in `top` + pressing "1") that only two cores are used,
>>> and Open MPI assigns 0-1 to both jobs. The information in "status" is not
>>> the one OpenMPI gets from hwloc?
>>>
>>> -- Reuti
>>>
>>>
>>>> The man page is probably a little out-of-date in this area - but yes,
>>>> --hetero-nodes is required for *any* difference in the way the nodes
>>>> appear to us (cpus, slot assignments, etc.). The 1.9 series may remove
>>>> that requirement - still looking at it.
>>>>
>>>>>
>>>>>
>>>>>> So it is up to the RM to set the constraint - we just live within it.
>>>>>
>>>>> Fine.
>>>>>
>>>>> -- Reuti
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