[Nek5000-users] [*] Re: Performance problem
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Aug 6 11:24:17 CDT 2010
2D is generally always fast but more attention is required in 3D.
Regardless of the parameter settings I would concur w/ Stefan's
analysis that there is something happening on the machine.
Are others occupying the resource during the run ? (Sometimes
there are rogue processes on a cluster from a prior run, etc.)
Paul
On Fri, 6 Aug 2010, nek5000-users at lists.mcs.anl.gov wrote:
> This is weird. I have a 2D equivalent of this system, with the same
> parameters, mesh structure and it is quite fast.
> On 08/06/2010 06:49 PM, nek5000-users at lists.mcs.anl.gov wrote:
>> I guess your system has a problem. The TEMP solve takes ~0.14 sec for step
>> 6 and 22.2 sec for step 7. Overall step 6 takes 8.4 sec and step 7 51.1 sec
>> although the iteration counts are very similar!
>>
>> Stefan
>>
>>
>>
>> Check this:
>>
>> 0: Step 6, t= 2.0307248E-01, DT= 3.0347043E-05, C= 2.043 4.8383E+01
>> 3.0220E+00
>> 0: Solving for heat
>> 0: Solving for fluid
>> 0: 0.000000000000000E+000 p22 6 2
>> 0: 6 Hmholtz TEMP: 64 7.0899E-08 7.6377E+01
>> 7.7888E-08
>> 0: 6 2.0307E-01 1.3816E-01 Heat done
>> 0: 0.000000000000000E+000 p22 6 1
>> 0: 6 Hmholtz VELX: 57 1.0070E-05 5.8954E+04
>> 1.2278E-05
>> 0: 0.000000000000000E+000 p22 6 1
>> 0: 6 Hmholtz VELY: 56 1.1755E-05 5.8020E+04
>> 1.2278E-05
>> 0: 0.000000000000000E+000 p22 6 1
>> 0: 6 Hmholtz VELZ: 57 1.0011E-05 7.7873E+04
>> 1.2278E-05
>> 0: 6 U-Pres gmres: 48 1.6044E-09 2.3009E-09
>> 2.3009E+00 4.5887E+00 6.8322E+00
>> 0: 6 DNORM, DIVEX 1.604430720383758E-009
>> 1.604426975107925E-009
>> 0: 6 2.0307E-01 7.4035E+00 Fluid done
>> 0: Step 7, t= 2.0310283E-01, DT= 3.0347043E-05, C= 2.052 5.6850E+01
>> 8.4673E+00
>> 0: Solving for heat
>> 0: Solving for fluid
>> 0: 0.000000000000000E+000 p22 7 2
>> 0: 7 Hmholtz TEMP: 64 6.9851E-08 7.6526E+01
>> 7.8021E-08
>> 0: 7 2.0310E-01 2.2240E+01 Heat done
>> 0: 0.000000000000000E+000 p22 7 1
>> 0: 7 Hmholtz VELX: 57 1.0101E-05 5.8874E+04
>> 1.2295E-05
>> 0: 0.000000000000000E+000 p22 7 1
>> 0: 7 Hmholtz VELY: 56 1.1723E-05 5.7947E+04
>> 1.2295E-05
>> 0: 0.000000000000000E+000 p22 7 1
>> 0: 7 Hmholtz VELZ: 57 9.9682E-06 7.7881E+04
>> 1.2295E-05
>> 0: 7 U-Pres gmres: 48 1.6001E-09 2.2892E-09
>> 2.2892E+00 1.9881E+00 3.3138E+00
>> 0: 7 DNORM, DIVEX 1.600110264916237E-009
>> 1.600109913837109E-009
>> 0: 7 2.0310E-01 1.9966E+01 Fluid done
>> 0: Step 8, t= 2.0313318E-01, DT= 3.0347043E-05, C= 2.060 1.0837E+02
>> 5.1516E+01
>>
>> On Aug 6, 2010, at 3:08 PM,<nek5000-users at lists.mcs.anl.gov> wrote:
>>
>>> Mani,
>>>
>>> I think there must be something else wrong ... I'm seeing about
>>> 5 sec/step on a 64 proc. linux cluster.
>>>
>>> If you'd like to send me a gzip'd file w/ the essentials, contact
>>> me off-list (fischer at mcs.anl.gov) and I can take a closer look.
>>>
>>> Paul
>>>
>>>
>>> On Fri, 6 Aug 2010, nek5000-users at lists.mcs.anl.gov wrote:
>>>
>>>> If you set p94& p95 to 5 (say), I recommend strongly to set p12 (dt) to
>>>>
>>>> -3e-5
>>>>
>>>> in your case. The reason for this is that the projection scheme is much
>>>> more stable for fixed dt.
>>>>
>>>> On the whole, however, Stefan's earlier comments about using, say, lx1=8
>>>> and fewer elements is a better strategy. It's also possible that we
>>>> should switch your coarse-grid solve at this scale to AMG.
>>>>
>>>> Paul
>>>>
>>>>
>>>> On Fri, 6 Aug 2010, nek5000-users at lists.mcs.anl.gov wrote:
>>>>
>>>>>> - set param(102) and param(103) to 5 (this will turn on the residual
>>>>>> projection)
>>>>> Should this be param 94& 95 ?
>>>>>
>>>>> - Paul
>>>>> On Fri, 6 Aug 2010, nek5000-users at lists.mcs.anl.gov wrote:
>>>>>> Ok here are some suggestions to improve the performance:
>>>>>> - set timestep, param(12), to -3e-5
>>>>>> - set param(102) and param(103) to 5 (this will turn on the residual
>>>>>> projection)
>>>>>> - increase lgmres (in SIZE) to 40
>>>>>> - you have want to tune the Helmholtz (velocity) and pressure tolerance
>>>>>> (e.g. 1e-8 and 1e-5)
>>>>>> btw: what's the Reynolds number of this flow?
>>>>>> Stefan
>>>>>> On Aug 6, 2010, at 11:13 AM,<nek5000-users at lists.mcs.anl.gov>
>>>>>> <nek5000-users at lists.mcs.anl.gov> wrote:
>>>>>>> Dear Mani,
>>>>>>> I haven't checked your logfile yet but there are my first thoughts:
>>>>>>> N=4 is low
>>>>>>> Your polynomial order (N=4) is low and the tensor-product formulation
>>>>>>> won't buy you much. The performance of all matrix-matrix multiplies
>>>>>>> (MxM) will limited by the memory access times. This is in particular a
>>>>>>> problem on multi-core and multi-socket machines. We have seen that the
>>>>>>> performance drop can be significant.
>>>>>>> On top of that you carry around a large number of duplicate DOF and
>>>>>>> your surface to volume ratio is high (more communication). I
>>>>>>> Parallel Performance
>>>>>>> Your gridpoints per core (~4700) is quite small!
>>>>>>> On Blue Gene (BG) systems we can scale well (e.g. 70-80% parallel
>>>>>>> efficiency) with around 10k gridpoints per core. On other system (e.g.
>>>>>>> Cray XT5) you need much more gridpoints per core (say 80k) because the
>>>>>>> network has a higher latency (NEK is sensitive to latency not
>>>>>>> bandwidth) and the processors are much faster.
>>>>>>> Cheers,
>>>>>>> Stefan
>>>>>>> On Aug 6, 2010, at 10:51 AM,<nek5000-users at lists.mcs.anl.gov> wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I'm solving for Rayleigh-Benard convection in a 3D box of 37632,
>>>>>>>> 4rth order elements. I fired the job on 512 processors on a machine
>>>>>>>> with quad-core, quad socket configuration (32 nodes with 16 cores
>>>>>>>> each ) with a 20 Gbps infiniband interconnect. In 12 hours it has run
>>>>>>>> 163 time steps. Is this normal or is there maybe some way to improve
>>>>>>>> performance? Attached is the SIZE file.
>>>>>>>> Regards,
>>>>>>>> Mani chandra
>>>>>>>> <SIZE.txt>_______________________________________________
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>>>>>>>> Nek5000-users at lists.mcs.anl.gov
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