[aspect-devel] ASPECT on Mac
Timo Heister
heister at clemson.edu
Fri Oct 17 08:25:24 PDT 2014
Dear Menno,
Luca just released a new deal.II mac os package:
https://github.com/luca-heltai/dealii/releases/tag/v8.2pre_v3
Can you give it a try?
On Fri, Oct 17, 2014 at 10:32 AM, Menno Fraters
<menno.fraters at outlook.com> wrote:
> Dear all,
>
> The last few days I also have been working on getting ASPECT to work on a
> mac. Following the comments on the bug (which I also encountered in the free
> surface cookbook when running it on multiple mpi processors) by Timo, I
> installed first the newest version of deal.ii and when that didn't solve the
> problem also the newest version of trilinos separately from the package
> installed by the dmg. All other dependencies like p4est, openmpi and petsc
> are still linked to this package. This didn't solve the problem either.
> Furthermore I have also tried it with older version of trilinos (stable
> release 11.10.1 and 11.8.1). With PETSC it does work.
>
> I must note that to be able to successfully install the newest git clone of
> trilinos I had to disable the packeges Claps, RBGen, Aristos and FEApp in
> PackagesList.cmake, because they could not be found. This was not the case
> in the mentioned stabled releases I tried.
>
> To test if this is a problem with mac, or just the most recent version of
> trilinos, deal.ii and aspect, I installed it on a linux machine. It turned
> out this gave me the same problems.
>
> So my question is if the problem with trilinos and deal.ii is actually
> resolved or might I be doing something wrong with the installation (see
> settings below)?
>
> Hope anyone can help with this!
>
> Cheers,
>
> Menno
>
> parameters used for making trilinos:
> cmake -D TrilinosFramework_ENABLE_MPI:BOOL=ON -D
> CMAKE_INSTALL_PREFIX:PATH=/Users/Menno/Documents/Phd/aspect/trilinos/build/
> -D TPL_ENABLE_MPI:BOOL=ON -D BUILD_SHARED_LIBS:BOOL=ON -D
> CMAKE_BUILD_TYPE:STRING=RELEASE -D Trilinos_ENABLE_Fortran:BOOL=OFF -D
> Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" -D
> CMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -D Trilinos_ENABLE_TESTS:BOOL=OFF -D
> Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF -D
> Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON -D
> Trilinos_ENABLE_Epetra:BOOL=ON -D Trilinos_ENABLE_EpetraExt:BOOL=ON -D
> Trilinos_ENABLE_Tpetra:BOOL=ON -D Trilinos_ENABLE_Jpetra:BOOL=ON -D
> Trilinos_ENABLE_Kokkos:BOOL=ON -D Trilinos_ENABLE_Sacado:BOOL=ON -D
> Trilinos_ENABLE_Amesos:BOOL=ON -D Trilinos_ENABLE_AztecOO:BOOL=ON -D
> Trilinos_ENABLE_Ifpack:BOOL=ON -D Trilinos_ENABLE_Teuchos:BOOL=ON -D
> Trilinos_ENABLE_Rythmos:BOOL=ON -D Trilinos_ENABLE_Piro:BOOL=ON -D
> Trilinos_ENABLE_MOOCHO:BOOL=ON -D Trilinos_ENABLE_ML:BOOL=ON -D
> Trilinos_ENABLE_Thyra:BOOL=ON -D Trilinos_ENABLE_TrilinosCouplings:BOOL=ON
> $EXTRA_ARGS ../
>
> The resulting output for two mpi processes (the more mpi processes are used,
> the faster the problem is encountered):
> -----------------------------------------------------------------------------
> -- This is ASPECT, the Advanced Solver for Problems in Earth's ConvecTion.
> -- . version 1.2.pre
> -- . running in DEBUG mode
> -- . running with 2 MPI processes
> -- . using Trilinos
> -----------------------------------------------------------------------------
>
> Number of active cells: 10240 (on 6 levels)
> Number of degrees of freedom: 134692 (82818+10465+41409)
>
> Number of free surface degrees of freedom: 20930
> *** Timestep 0: t=0 years
> Solving mesh velocity system... 0 iterations.
> Solving temperature system... 0 iterations.
> Rebuilding Stokes preconditioner...
> Solving Stokes system... 30+3 iterations.
>
> Postprocessing:
> Writing graphical output: output/solution-00000
> Topography min/max: 0 m, 0 m,
> RMS, max velocity: 0.0109 m/year, 0.0297 m/year
>
> *** Timestep 1: t=5255.3 years
> Solving mesh velocity system... 9 iterations.
> Solving temperature system... 11 iterations.
> Rebuilding Stokes preconditioner...
> Solving Stokes system... 30+5 iterations.
>
> Postprocessing:
> Topography min/max: -53.33 m, 93.26 m,
> RMS, max velocity: 0.00578 m/year, 0.0176 m/year
>
> *** Timestep 2: t=14136.7 years
> Solving mesh velocity system... 12 iterations.
> Solving temperature system... 11 iterations.
> Rebuilding Stokes preconditioner...
> Solving Stokes system... 30+5 iterations.
>
> Postprocessing:
> Topography min/max: -15.43 m, 36.03 m,
> RMS, max velocity: 0.00694 m/year, 0.023 m/year
>
> *** Timestep 3: t=20932.2 years
> Solving mesh velocity system... 25 iterations.
> Solving temperature system... 11 iterations.
> Rebuilding Stokes preconditioner...
> Solving Stokes system... 30+4 iterations.
>
> Postprocessing:
> Topography min/max: -20.8 m, 59.68 m,
> RMS, max velocity: 0.00612 m/year, 0.0212 m/year
>
> *** Timestep 4: t=28303.4 years
> Solving mesh velocity system... 90 iterations.
> Solving temperature system... 10 iterations.
> Rebuilding Stokes preconditioner...
> Solving Stokes system... 30+3 iterations.
>
> Postprocessing:
> Topography min/max: -21.81 m, 61.13 m,
> RMS, max velocity: 0.00608 m/year, 0.0211 m/year
>
> *** Timestep 5: t=35711.1 years
> Solving mesh velocity system... 27 iterations.
> Solving temperature system... 10 iterations.
> Rebuilding Stokes preconditioner...
> Solving Stokes system... 30+1 iterations.
>
> Postprocessing:
> Topography min/max: -21.59 m, 61.11 m,
> RMS, max velocity: 0.00609 m/year, 0.0211 m/year
>
> *** Timestep 6: t=43113.6 years
>
>
> ----------------------------------------------------
> Exception on processing:
>
> --------------------------------------------------------
> An error occurred in line <486> of file
> </Users/Menno/Documents/Phd/aspect/dealii/build/include/deal.II/lac/solver_cg.h>
> in
>
> ----- function
> void
> ---------dealii::SolverCG<de----------------------alii::Tr------------ilinosWrapper----
> Exceptis::MPI::Vector>:on on processing:
> :solve(const MATRIX &, VECTOR &, const VECTOR &, const PRECONDI
> ----TIONER &) [VE------CTOR =
> de------------alii::TrilinosWrap------pers::MP----------I::Vector, MATRIX =
> -------------dealii::Tri-----
> An error olinosWrappers::Sccurred iparseMatrn line <486> of filix,
> PRECONDITIONER = dealii::TrilinosWrappers::PreconditionAMG]
> The violae </Users/Menno/Docted condition was:
> false
> The name uments/Phd/aspeand call sect/dealii/build/includequence of the
> exception was:/deal.II/lac/s
> SolverContrololver_cg::NoConvergen.h> in functionce (this->control()
> voi.last_step(),d dealii::Solve this->control().lasrCG<dealit_value())
> Addi::TrilinosWraitional Information:
> ppers::MPIterative method reported convergeI::Vector>::solve(const Mnce
> failure in step 10ATRIX &, VECTOR &4650. The residual in the las, const Vt
> step was 4.25519e-19.
>
> This errECTOR &, const PRECONDor messageITIONER &) [V can indicate that you
> have simpECTOR = dealii::Trilinoly not allowed a suffisWrappersciently large
> number ::MPI::Vector, MATRIX of iteratio= dealii:ns for
> your:TrilinosWrappers::SparseMa iterative solver to trix, PRECONDconverge.
> This often ITIONER = deahappens when you increalii::Trilise the size of
> ynosWraouppers:r prob:Precondilem. In tionAMG]such cas
> The ves, the last reiolated conditionsidual was:
> will likely s false
> till be veThe name ry small, aand cnd you call sean make thequence of the
> exception was:
> error go away by i SolverConncreasing trol::NoConvergence
> (this->control().last_step(), this->controlthe allowed number of iterations
> when setting up the SolverCont().last_varol object that determlue())
> Additional Infoines the maximal number of irmation:
> Iterative methoterations yd reported conou allow.
>
> Thvergencee other si failure in stetuation where this errp 104650. The
> residuaor may occur l in the last is when your mstep was 4.25519e-19.
>
> atrix is not invertibleThis error (e.g., y message can inour matrix has
> dicate tha null-sat you have sipace), or if ymply not allowou try to appled
> a sufficiently large ny the wrong solver to a matrix (eumber of iterations
> for your ite.g., using CG for a matrrative solver to conix that is not
> symmetverric or not positive definite)ge. This often happ. In these caens
> whenses, the resi you incrdual in the laease the size of st iteration is
> likelyyour problem. In suc going to be large.
> h cases, the last-------------------------- residual will
> l----------------------ikely --------still be v
>
> Abortiery smallng!
> ------------, an----------------d you can make the---------------------
> error go aw---
> ay by increasing the allowed number of iterations when setting up the
> SolverControl object that determines the maximal number of iterations you
> allow.
>
> The other situation where this error may occur is when your matrix is not
> invertible (e.g., your matrix has a null-space), or if you try to apply the
> wrong solver to a matrix (e.g., using CG for a matrix that is not symmetric
> or not positive definite). In these cases, the residual in the last
> iteration is likely going to be large.
> --------------------------------------------------------
>
> Aborting!
> ----------------------------------------------------
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> --------------------------------------------------------------------------
>
>
>
>
>> Date: Sat, 11 Oct 2014 19:18:45 +0200
>> From: sylvia.rockel at fu-berlin.de
>> To: aspect-devel at geodynamics.org
>> Subject: Re: [aspect-devel] ASPECT on Mac
>
>>
>> Dear all,
>>
>> with PETSc instead of Trilinos the mpirun seems to work (step 480 now and
>> still running). Thanks for the hint.
>>
>> Concerning the Trilinos bug, I was totally aware of the fact that I'll
>> have to wait until it's fixed in the mac package, since unfortunately it
>> is Trilinos which I just can't manage to get it compiled without errors
>> after I reset my whole computer. Wolfgang's reply was just to an older
>> mail. So everything is fine. Until the Trilinos bug is fixed I can now use
>> the Aspect_with_PETCs-version in the meantime.
>>
>> But thanks anyways for your time and help.
>>
>> Best,
>> Sylvia
>>
>> > Hey all,
>> >
>> > maybe I wasn't clear enough about this:
>> >
>> > The mac package deal.ii-8.2pre-v2 is broken because it bundles a
>> > Trilinos version that is not compatible. As a result the code will
>> > produce strange errors after a couple of timesteps in parallel
>> > (basically the matrix is assembled wrong). You _have_ to wait until
>> > Luca releases a new version or setup and compile deal.II by yourself.
>> >
>> >
>> >> Since you have the deal.II package installed, you should also have
>> >> PETSc.
>> >> Can you try to compile ASPECT with PETSc support instead of using
>> >> Trilinos?
>> >> Maybe that gets you any further.
>> >
>> > Yes, that might work.
>> >
>> >
>> > --
>> > Timo Heister
>> > http://www.math.clemson.edu/~heister/
>> > _______________________________________________
>> > Aspect-devel mailing list
>> > Aspect-devel at geodynamics.org
>> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>> >
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
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>
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--
Timo Heister
http://www.math.clemson.edu/~heister/
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