[Nek5000-users] Fwd: Re: proj_ortho error in pipe flow
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Sep 8 02:29:05 CDT 2017
Hi Neks,
sorry to revive this old thread again but I am still facing problems
with the projection for temperature and passive scalars.
I restart the simulation from a fully developed turbulent pipe flow
(Re_b=5300) with temperature and one passive scalar where I have set:
20.0000 P093: Number of previous pressure solns saved
0.00000 P094: start projecting velocity after p94 step
9.00000 P095: start projecting pressure after p95 step
to achieve fully turbulent flow (velocity, temperature and passive
scalar look chaotic in instantaneous flow fields).
Now, when I set P094 to e.g. 9, I get the following error in the logfile
(complete logfile: https://paste.fedoraproject.org/paste/msifJj~amNLIqb6kVVQdOQ#):
Step 11, t= 6.2706400E+02, DT= 1.0000000E-03, C= 0.495 4.1211E+01
6.5177E+00
Solving for Hmholtz scalars
11 Project TEMP 7.8093E+11 7.8149E+11
9.9929E-01 1 0
11 Error Hmholtz TEMP 100 2.0068E+25 9.5028E+14
1.0000E-06
11proj_ortho: 1 2 TEMP Detect rank deficiency:
-8.7444E+09 1.0000E+00
11 Project PS 1 4.2282E+11 1.0213E+21
4.1398E-10 1 0
11 Error Hmholtz PS 1 100 3.2943E+10 1.3653E+24
1.0000E-06
11proj_ortho: 1 2 PS 1 Detect rank deficiency:
-8.7444E+09 1.0000E+00
11 Scalars done 6.2706E+02 4.3821E+00
Solving for fluid
11 Project velx 8.1238E-03 3.3574E-05
2.4196E+02 2 0
11 Hmholtz velx 7 8.9632E-10 2.9060E-02 1.0000E-08
11proj_ortho: 2 3 velx project ok. 6.1900E-02 1.0000E+00
11proj_ortho: 1 3 velx project ok. 8.2185E-02 1.0000E+00
11 Project vely 8.5570E-03 3.4362E-05
2.4902E+02 2 0
11 Hmholtz vely 7 1.0419E-09 3.1223E-02 1.0000E-08
11proj_ortho: 2 3 vely project ok. 6.2766E-02 1.0000E+00
11proj_ortho: 1 3 vely project ok. 8.1871E-02 1.0000E+00
11 Project velz 7.2548E-03 2.6975E-05
2.6895E+02 2 0
11 Hmholtz velz 6 2.1993E-09 2.1138E-02 1.0000E-08
11proj_ortho: 2 3 velz project ok. 5.7485E-02 1.0000E+00
11proj_ortho: 1 3 velz project ok. 7.1883E-02 1.0000E+00
11 U-PRES gmres 29 7.3794E-09 2.5720E-03
1.0000E-08 3.2994E-01 1.4955E+00
11 DNORM, DIVEX 5.311956927469261E-007 7.379406391030144E-009
11 0.6270640E+03 1.11112E-03 4.75093E-07 7.85398E-01
7.85398E-01 volflow Z
11 Fluid done 6.2706E+02 2.7400E+00
11 3 qfilt: 4.2972E-04 5.0005E-04 4.3352E-04
Can this be caused by a faulty mesh? I have generated the mesh myself.
Best Regards,
Steffen Straub
On 04/10/2017 07:00 PM, nek5000-users-request at lists.mcs.anl.gov wrote:
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 10 Apr 2017 14:32:33 +0200
> From: nek5000-users at lists.mcs.anl.gov
> To: <nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] proj_ortho error in pipe flow
> Message-ID:
> <mailman.4827.1491827560.2967.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> Hi Paul & Philipp,
>
> thanks for your quick replies and suggestions. I started the simulation
> again with a slightly perturbed laminar flow field as initial conditions
> and there are no proj_ortho errors anymore.
> For now, this perturbation is more or less random and probably not ideal
> for tripping the laminar flow to turbulence. Therefore, I might try to
> implement a more effective numerical tripping method in the future. I
> can let you know when (and if) I succeed.
>
> The parameters p94 and p95 are set to "9" just because I have found that
> in another simulation somewhere. Do you suggest trying different values
> here?
> The Nek5000 version was downloaded as a zip file on 21/03/2017 so I
> suppose it is the commit 95b42f08c960d522679e0f0881d284ec841ae09
>
>
> \Steffen
>
>
> On 09/04/17 19:00, nek5000-users-request at lists.mcs.anl.gov wrote:
>> Message: 1
>> Date: Sat, 8 Apr 2017 19:55:36 +0200
>> From: nek5000-users at lists.mcs.anl.gov
>> To: nek5000-users at lists.mcs.anl.gov
>> Subject: Re: [Nek5000-users] proj_ortho error in pipe flow
>> Message-ID:
>> <mailman.4792.1491674149.2967.nek5000-users at lists.mcs.anl.gov>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>> Hi Steffen,
>> which revision of the code are you using? Is the initial field you are
>> using already turbulent, or are you going through transition? Any
>> special reason why you have 9 for p94/95?
>>
>> Philipp
>>
>> On 2017-04-07 19:54, nek5000-users at lists.mcs.anl.gov wrote:
>>> Hi Steffen,
>>>
>>> It looks like your solution is hitting a steady-state condition and that the
>>> projection onto prior solutions is thus projecting in to a set of linearly-dependent
>>> vectors.
>>>
>>> In principle, the code is supposed to correct for this condition but apparently
>>> it is not doing so correctly.
>>>
>>> I see you're running at Re > 5000, so presumably you are interested in turbulence,
>>> rather than laminar steady state. I would recommend adding a random perturbation
>>> to the initial condition or, better still, adding something with bound vorticity near the
>>> walls that will get stretched and bring about a more rapid transition.
>>>
>>> I find that something like the attached works well with channel flow (snap through within
>>> about 10 convective time units). I was disappointed that it didn't work as well with pipe
>>> flow, where I had to go up to Re=40k to get the thing started and then bring it down.
>>> I assume this has something to do with the lack of linear transition in Hagen-Poiseuille flow.
>>> If you find a better mechanism to speed transition, I'd be interested to find out about it.
>>>
>>> Best,
>>>
>>> Paul
>>>
>>> ________________________________________
>>> From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
>>> Sent: Friday, April 07, 2017 10:18 AM
>>> To: nek5000-users at lists.mcs.anl.gov
>>> Subject: [Nek5000-users] proj_ortho error in pipe flow
>>>
>>> Dear Nek users,
>>>
>>> I am running a simple pipe flow on a Cray XC40 (Hazel Hen). After 32
>>> steps, I get this problem (see attachment for complete logfile):
>>>
>>> Step 32, t= 3.2000000E-02, DT= 1.0000000E-03, C= 0.025 3.2660E-01
>>> 1.0526E-02
>>> Solving for fluid
>>> 32 Project velx 6.6444E-09 2.4759E-09
>>> 2.6836E+00 8 0
>>> 32 Hmholtz velx 1 3.9238E-09 6.7918E-07 1.0000E-08
>>> 32 Project vely 6.8730E-09 2.1046E-09
>>> 3.2656E+00 8 0
>>> 32 Hmholtz vely 1 3.6166E-09 5.9974E-07 1.0000E-08
>>> 32 Project velz 5.2396E-03 2.5121E-06
>>> 2.0858E+03 8 0
>>> 32 Hmholtz velz 3 7.6028E-10 9.3795E-04 1.0000E-08
>>> 32proj_ortho: 2 8 velz Detect rank deficiency: NaN
>>> 1.0000E+00
>>> 32proj_ortho: 1 8 velz Detect rank deficiency: NaN
>>> 1.0000E+00
>>> 32 U-PRES gmres 29 9.9376E-09 5.2213E-04
>>> 1.0000E-08 8.7926E-03 1.7780E-02
>>> 32 DNORM, DIVEX 2.704668739973178E-005 9.937641774554489E-009
>>> 32 0.3200000E-01 1.61568E-01 6.88948E-05 7.85330E-01
>>> 7.85399E-01 volflow Z
>>> 32 Fluid done 3.2000E-02 2.4042E-02
>>>
>>> In the next step I get CFL, CTarg! and the simulation exits.
>>>
>>> This problem does neither show up on my local machine nor on another
>>> smaller cluster. Moreover, when I set either parameter 94 or 95 to 0, I
>>> do not see this error. It only appears when p94 and p95 are both unequal
>>> 0. In my case I set them to 9.
>>>
>>> Do you know what might be causing this issue and how to solve it for the
>>> Cray XC40 system?
>>>
>>>
>>> Best Regards
>>> Steffen
>>>
>>>
>>>
>>> _______________________________________________
>>> Nek5000-users mailing list
>>> Nek5000-users at lists.mcs.anl.gov
>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>>
>>>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 10 Apr 2017 14:42:42 +0200
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] proj_ortho error in pipe flow
> Message-ID:
> <mailman.4836.1491828206.2967.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> ok, great!
>
> As Paul says, ideally one wants an initial condition that quickly leads
> to turbulence, and that is done with some streamwise vorticity near the
> walls. The way we typically do that is not with an initial condition,
> but rather with our trip force, because this leads to an efficient
> vertical mixing (across the shear), and thus to quick transition. We
> then turn the force off after a short time. This way, you do not need to
> care much about continuity, and you can just have a force in the
> wall-normal direction at some selected positions in the flow. This works
> well for higher Reynolds numbers, at least from our experience.
>
> Another thought that one could experiment a bit is to use the synthetic
> eddy method as a way to generate not just boundary conditions, but also
> initial conditions.
>
> Philipp
>
> On 2017-04-10 14:32, nek5000-users at lists.mcs.anl.gov wrote:
>> Hi Paul & Philipp,
>>
>> thanks for your quick replies and suggestions. I started the simulation
>> again with a slightly perturbed laminar flow field as initial conditions
>> and there are no proj_ortho errors anymore.
>> For now, this perturbation is more or less random and probably not ideal
>> for tripping the laminar flow to turbulence. Therefore, I might try to
>> implement a more effective numerical tripping method in the future. I
>> can let you know when (and if) I succeed.
>>
>> The parameters p94 and p95 are set to "9" just because I have found that
>> in another simulation somewhere. Do you suggest trying different values
>> here?
>> The Nek5000 version was downloaded as a zip file on 21/03/2017 so I
>> suppose it is the commit 95b42f08c960d522679e0f0881d284ec841ae09
>>
>>
>> \Steffen
>>
>>
>> On 09/04/17 19:00, nek5000-users-request at lists.mcs.anl.gov wrote:
>>> Message: 1
>>> Date: Sat, 8 Apr 2017 19:55:36 +0200
>>> From: nek5000-users at lists.mcs.anl.gov
>>> To: nek5000-users at lists.mcs.anl.gov
>>> Subject: Re: [Nek5000-users] proj_ortho error in pipe flow
>>> Message-ID:
>>> <mailman.4792.1491674149.2967.nek5000-users at lists.mcs.anl.gov>
>>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>>
>>> Hi Steffen,
>>> which revision of the code are you using? Is the initial field you are
>>> using already turbulent, or are you going through transition? Any
>>> special reason why you have 9 for p94/95?
>>>
>>> Philipp
>>>
>>> On 2017-04-07 19:54, nek5000-users at lists.mcs.anl.gov wrote:
>>>> Hi Steffen,
>>>>
>>>> It looks like your solution is hitting a steady-state condition and
>>>> that the
>>>> projection onto prior solutions is thus projecting in to a set of
>>>> linearly-dependent
>>>> vectors.
>>>>
>>>> In principle, the code is supposed to correct for this condition but
>>>> apparently
>>>> it is not doing so correctly.
>>>>
>>>> I see you're running at Re > 5000, so presumably you are interested
>>>> in turbulence,
>>>> rather than laminar steady state. I would recommend adding a random
>>>> perturbation
>>>> to the initial condition or, better still, adding something with
>>>> bound vorticity near the
>>>> walls that will get stretched and bring about a more rapid transition.
>>>>
>>>> I find that something like the attached works well with channel flow
>>>> (snap through within
>>>> about 10 convective time units). I was disappointed that it didn't
>>>> work as well with pipe
>>>> flow, where I had to go up to Re=40k to get the thing started and
>>>> then bring it down.
>>>> I assume this has something to do with the lack of linear transition
>>>> in Hagen-Poiseuille flow.
>>>> If you find a better mechanism to speed transition, I'd be interested
>>>> to find out about it.
>>>>
>>>> Best,
>>>>
>>>> Paul
>>>>
>>>> ________________________________________
>>>> From: nek5000-users-bounces at lists.mcs.anl.gov
>>>> [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
>>>> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
>>>> Sent: Friday, April 07, 2017 10:18 AM
>>>> To: nek5000-users at lists.mcs.anl.gov
>>>> Subject: [Nek5000-users] proj_ortho error in pipe flow
>>>>
>>>> Dear Nek users,
>>>>
>>>> I am running a simple pipe flow on a Cray XC40 (Hazel Hen). After 32
>>>> steps, I get this problem (see attachment for complete logfile):
>>>>
>>>> Step 32, t= 3.2000000E-02, DT= 1.0000000E-03, C= 0.025 3.2660E-01
>>>> 1.0526E-02
>>>> Solving for fluid
>>>> 32 Project velx 6.6444E-09 2.4759E-09
>>>> 2.6836E+00 8 0
>>>> 32 Hmholtz velx 1 3.9238E-09 6.7918E-07 1.0000E-08
>>>> 32 Project vely 6.8730E-09 2.1046E-09
>>>> 3.2656E+00 8 0
>>>> 32 Hmholtz vely 1 3.6166E-09 5.9974E-07 1.0000E-08
>>>> 32 Project velz 5.2396E-03 2.5121E-06
>>>> 2.0858E+03 8 0
>>>> 32 Hmholtz velz 3 7.6028E-10 9.3795E-04 1.0000E-08
>>>> 32proj_ortho: 2 8 velz Detect rank deficiency: NaN
>>>> 1.0000E+00
>>>> 32proj_ortho: 1 8 velz Detect rank deficiency: NaN
>>>> 1.0000E+00
>>>> 32 U-PRES gmres 29 9.9376E-09 5.2213E-04
>>>> 1.0000E-08 8.7926E-03 1.7780E-02
>>>> 32 DNORM, DIVEX 2.704668739973178E-005
>>>> 9.937641774554489E-009
>>>> 32 0.3200000E-01 1.61568E-01 6.88948E-05 7.85330E-01
>>>> 7.85399E-01 volflow Z
>>>> 32 Fluid done 3.2000E-02 2.4042E-02
>>>>
>>>> In the next step I get CFL, CTarg! and the simulation exits.
>>>>
>>>> This problem does neither show up on my local machine nor on another
>>>> smaller cluster. Moreover, when I set either parameter 94 or 95 to 0, I
>>>> do not see this error. It only appears when p94 and p95 are both unequal
>>>> 0. In my case I set them to 9.
>>>>
>>>> Do you know what might be causing this issue and how to solve it for the
>>>> Cray XC40 system?
>>>>
>>>>
>>>> Best Regards
>>>> Steffen
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Nek5000-users mailing list
>>>> Nek5000-users at lists.mcs.anl.gov
>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>>>
>>>>
>> _______________________________________________
>> Nek5000-users mailing list
>> Nek5000-users at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
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>
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> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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