Am 21.08.2014 um 16:00 schrieb Ralph Castain:
>
> 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
Yes. Even if -np is specified: AFAICS Open MPI fills up the given slots in the
machinefile from the beginning (first nodes get all the processes, remaining
nodes are free). Making it in a round-robin way would work better for this case.
> 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.
Therefore I wanted to start a discussion about it (at that time I wasn't aware
of the "-map-by slot:pe=N" option), as I have no final syntax which would cover
all cases. Someone may want the binding by the "-map-by slot:pe=N". How can
this be specified, while keeping an easy tight-integration for users who don't
want any binding at all.
The boundary conditions are:
- the job is running inside a queuingsystem
- the user requests the overall amount of slots to the queuingsystem
- hence the machinefile has entries for all slots
- the user sets OMP_NUM_THREADS
case 1) no interest in any binding, other jobs may exist on the nodes
case 2) user wants binding: i.e. $OMP_NUM_THREADS cores assigned to each MPI
process, maybe with "-map-by slot:pe=N"
In both cases only (overall amount of slots) / ($OMP_NUM_THREADS) MPI processes
should be started, not (overall amount of slots) processes AFAICS.
-- Reuti
>> -- 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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