[Nek5000-users] Nek5000-users Digest, Vol 92, Issue 4
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Thu Oct 6 16:03:40 CDT 2016
Dear Yulia and Paul,
Thanks for your response regarding the Neknek issue. As Paul pointed
out, the simulations are working fine in HPC environments.
Best regards,
Sudhakar.
Quoting nek5000-users-request at lists.mcs.anl.gov:
> Send Nek5000-users mailing list submissions to
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> Today's Topics:
>
> 1. Re: Nek5000-users Digest, Vol 92, Issue 2
> (nek5000-users at lists.mcs.anl.gov)
> 2. Re: Open Boundary condition in NEK user Documentation
> (nek5000-users at lists.mcs.anl.gov)
> 3. Re: Open Boundary condition in NEK user Documentation
> (nek5000-users at lists.mcs.anl.gov)
> 4. Re: Open Boundary condition in NEK user Documentation
> (nek5000-users at lists.mcs.anl.gov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 6 Oct 2016 11:38:04 +0000
> From: nek5000-users at lists.mcs.anl.gov
> To: "nek5000-users at lists.mcs.anl.gov"
> <nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 92, Issue 2
> Message-ID:
> <mailman.4109.1475753886.3602.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Dear Sudhakar,
>
> Thank you for bringing this to our attention. We're looking into it.
>
> The issue is that mpi_irecv is not posted prior to the mpi_send.
> This situation yields platform-dependent behavior. (We normally would write
> mpi_irecv(X) followed by mpi_send(Y) to X.
>
> We're currently working with the neknek group on a rewrite that
> will fix the problem. In the meantime, if you are targeting an HPC system,
> you might find that there is no issue on that system and in fact be able to
> proceed with your development. (We've had many people using neknek in
> the past on fairly large systems without running into the problem---but
> it is technically not correct as written and we're going to resolve it.)
>
> 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: Thursday, October 06, 2016 4:41 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 92, Issue 2
>
> Hi all,
>
> Sorry for the confusion in the first post. Any 3D Neknek simulation is
> stuck endlessly in the following line
>
> call mpi_send(jsend,len,mpi_byte,id,100+nid, intercomm,ierr)
>
> within "intpts_locate" subroutine in multimesh.f.
>
> Could anyone please share if you have experienced similar issues, and
> how can this be resolved?
> Thank you very much,
>
> Best regards,
> Sudhakar
>
>
> Quoting nek5000-users-request at lists.mcs.anl.gov:
>
>> Send Nek5000-users mailing list submissions to
>> nek5000-users at lists.mcs.anl.gov
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>> or, via email, send a message with subject or body 'help' to
>> nek5000-users-request at lists.mcs.anl.gov
>>
>> You can reach the person managing the list at
>> nek5000-users-owner at lists.mcs.anl.gov
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Nek5000-users digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Issue in 3D NEKNEK simulations (nek5000-users at lists.mcs.anl.gov)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 5 Oct 2016 15:03:33 +0200
>> From: nek5000-users at lists.mcs.anl.gov
>> To: nek5000-users at lists.mcs.anl.gov
>> Subject: [Nek5000-users] Issue in 3D NEKNEK simulations
>> Message-ID:
>> <mailman.4026.1475672736.3602.nek5000-users at lists.mcs.anl.gov>
>> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>>
>> Hi,
>>
>> I am coupling the Navier-Stokes and Darcy equations using the NekNek
>> framework. Everything is working fine in 2D. However, any 3D example in
>> neknek is stuck endlessly in the following line
>>
>> callmpi_send
>> <http://www.mcs.anl.gov/research/projects/nek5/docs/html/mpi__dummy_8f.html#af98c20c7332635506f852083f7ee504a>(jsend,len,mpi_byte,id
>> <http://www.mcs.anl.gov/research/projects/nek5/docs/html/findpts__test_8c.html#a37e2ea357c25dfa93b154d03c233cd23>,100+nid,
>> intercomm,ierr)
>>
>> within the "intpts_locate" subroutine in multimesh.f. When I modify the
>> eddy_neknek test case given in the example folder, the behavior is the
>> same, so the issue is not specific to my examples. I already checked
>> that the problem is not the memory or the length of the data processed
>> in MPI_send. Did anyone experience the same before?
>>
>> Thank you very much,
>>
>> Best regards,
>>
>> Sudhakar
>>
>> The Royal institute of Technology (KTH)
>>
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>>
>> _______________________________________________
>> Nek5000-users mailing list
>> Nek5000-users at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>
>>
>> End of Nek5000-users Digest, Vol 92, Issue 2
>> ********************************************
>
>
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 6 Oct 2016 11:58:39 +0000
> From: nek5000-users at lists.mcs.anl.gov
> To: "nek5000-users at lists.mcs.anl.gov"
> <nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
> Message-ID:
> <mailman.4110.1475755130.3602.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you for a good answer!
>
>
> Just to clarify, is it in LaTeX written as this:
>
>
> (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ?
>
>
> If the wall normal is in the z-direction, then the open boundary
> condition for the velocity is:
>
>
> d/dz u_z = 0?
>
>
> Best regards,
>
>
> Johan
>
>
>
>
> ________________________________
> 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: Thursday, October 6, 2016 12:40 PM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
>
>
> Dear Johan,
>
> The outflow boundary condition, 'O ', is indeed the same as 'I '
> for the thermal problem
> since they both enforce grad T . nhat = 0.
>
> However, both also admit thermal flux by advection for cases where U
> . nhat is > 0, and that is
> the intent of outflow --- to allow thermal flux to be carried out.
>
> For velocity, the situation is a bit more delicate. To leading
> order, however, 'O ' imposes
> d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the
> viscous fluxes and Dirichlet
> for pressure.
>
> hth,
>
> 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: Thursday, October 06, 2016 4:59 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation
>
>
> Dear Neks,
>
>
> I am trying to understand what is actually meant by an "open
> boundary" in Nek.
>
> Un the user documentation, eqn (4.5) sais that, for the temperature, it is
>
>
> grad(T) dot n = 0, where n is the normal to the boundary.
>
>
> Since the heat flux is q = - grad(T), I would rather interpret this
> as a zero flux boundary condition.
>
>
> And indeed, the insulated boundary described by equation (4.6) is
> identical to the open boundary condition.
>
>
> Is equation (4.5) a type-O or is the open boundary for the
> temperature actually the same as an insulated boundary?
>
>
> Also: Should not the open boundary condition for the "no-stress
> forumlation" also be given by the same expression as for the
> "stress-formulation" eqn (4.2)?
>
>
> Best Regards,
>
>
> Johan
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> <http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20161006/c8a704cc/attachment-0001.html>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 6 Oct 2016 12:22:03 +0000
> From: nek5000-users at lists.mcs.anl.gov
> To: "nek5000-users at lists.mcs.anl.gov"
> <nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
> Message-ID:
> <mailman.4111.1475756525.3602.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear Johan,
>
> Actually - I was mistaken.
>
> What we use is:
>
> d/dn (u_i) = 0
>
> for i=1,...,3
>
> We could however (and sometimes do) require Neumann only on the
> normal velocity component --
>
> grad (phi) . nhat = 0
>
> where phi = U . nhat
>
> The tangential components can be prescribed. That is the
> capability provided by the "on "
> BC.
>
> 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: Thursday, October 06, 2016 6:58 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
>
>
> Thank you for a good answer!
>
>
> Just to clarify, is it in LaTeX written as this:
>
>
> (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ?
>
>
> If the wall normal is in the z-direction, then the open boundary
> condition for the velocity is:
>
>
> d/dz u_z = 0?
>
>
> Best regards,
>
>
> Johan
>
>
>
>
> ________________________________
> 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: Thursday, October 6, 2016 12:40 PM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
>
>
> Dear Johan,
>
> The outflow boundary condition, 'O ', is indeed the same as 'I '
> for the thermal problem
> since they both enforce grad T . nhat = 0.
>
> However, both also admit thermal flux by advection for cases where U
> . nhat is > 0, and that is
> the intent of outflow --- to allow thermal flux to be carried out.
>
> For velocity, the situation is a bit more delicate. To leading
> order, however, 'O ' imposes
> d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the
> viscous fluxes and Dirichlet
> for pressure.
>
> hth,
>
> 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: Thursday, October 06, 2016 4:59 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation
>
>
> Dear Neks,
>
>
> I am trying to understand what is actually meant by an "open
> boundary" in Nek.
>
> Un the user documentation, eqn (4.5) sais that, for the temperature, it is
>
>
> grad(T) dot n = 0, where n is the normal to the boundary.
>
>
> Since the heat flux is q = - grad(T), I would rather interpret this
> as a zero flux boundary condition.
>
>
> And indeed, the insulated boundary described by equation (4.6) is
> identical to the open boundary condition.
>
>
> Is equation (4.5) a type-O or is the open boundary for the
> temperature actually the same as an insulated boundary?
>
>
> Also: Should not the open boundary condition for the "no-stress
> forumlation" also be given by the same expression as for the
> "stress-formulation" eqn (4.2)?
>
>
> Best Regards,
>
>
> Johan
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> <http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20161006/900a276b/attachment-0001.html>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 6 Oct 2016 13:12:15 +0000
> From: nek5000-users at lists.mcs.anl.gov
> To: "nek5000-users at lists.mcs.anl.gov"
> <nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
> Message-ID:
> <mailman.4114.1475759540.3602.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you,
>
>
> this makes sense to me.
>
>
> /Johan
>
>
> ________________________________
> 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: Thursday, October 6, 2016 2:22 PM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
>
>
> Dear Johan,
>
> Actually - I was mistaken.
>
> What we use is:
>
> d/dn (u_i) = 0
>
> for i=1,...,3
>
> We could however (and sometimes do) require Neumann only on the
> normal velocity component --
>
> grad (phi) . nhat = 0
>
> where phi = U . nhat
>
> The tangential components can be prescribed. That is the
> capability provided by the "on "
> BC.
>
> 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: Thursday, October 06, 2016 6:58 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
>
>
> Thank you for a good answer!
>
>
> Just to clarify, is it in LaTeX written as this:
>
>
> (\hat{n} \cdot \nabla)(u \cdot \hat{n}) = 0 ?
>
>
> If the wall normal is in the z-direction, then the open boundary
> condition for the velocity is:
>
>
> d/dz u_z = 0?
>
>
> Best regards,
>
>
> Johan
>
>
>
>
> ________________________________
> 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: Thursday, October 6, 2016 12:40 PM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Open Boundary condition in NEK user
> Documentation
>
>
> Dear Johan,
>
> The outflow boundary condition, 'O ', is indeed the same as 'I '
> for the thermal problem
> since they both enforce grad T . nhat = 0.
>
> However, both also admit thermal flux by advection for cases where U
> . nhat is > 0, and that is
> the intent of outflow --- to allow thermal flux to be carried out.
>
> For velocity, the situation is a bit more delicate. To leading
> order, however, 'O ' imposes
> d/dn (U.nhat) = 0 and p=0. That is, Neumann conditions for the
> viscous fluxes and Dirichlet
> for pressure.
>
> hth,
>
> 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: Thursday, October 06, 2016 4:59 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: [Nek5000-users] Open Boundary condition in NEK user Documentation
>
>
> Dear Neks,
>
>
> I am trying to understand what is actually meant by an "open
> boundary" in Nek.
>
> Un the user documentation, eqn (4.5) sais that, for the temperature, it is
>
>
> grad(T) dot n = 0, where n is the normal to the boundary.
>
>
> Since the heat flux is q = - grad(T), I would rather interpret this
> as a zero flux boundary condition.
>
>
> And indeed, the insulated boundary described by equation (4.6) is
> identical to the open boundary condition.
>
>
> Is equation (4.5) a type-O or is the open boundary for the
> temperature actually the same as an insulated boundary?
>
>
> Also: Should not the open boundary condition for the "no-stress
> forumlation" also be given by the same expression as for the
> "stress-formulation" eqn (4.2)?
>
>
> Best Regards,
>
>
> Johan
> -------------- next part --------------
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>
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>
> _______________________________________________
> 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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