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
-- 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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