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
>
>
>>> 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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>>
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>
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