[aspect-devel] ASPECT on Mac
Sylvia Rockel
sylvia.rockel at fu-berlin.de
Fri Oct 17 10:05:39 PDT 2014
Dear all,
I also tried it, but it does't work for me.
I still get the same error when running aspect
with mpi and trillions as before. With
In addition, I now get an segmentation fault when
running the step-32 example of deal.ii with mpi.
This is a new one. Terminal output is attached.
Luckily everything still seems to work with PETSc.
But thanks to Luca anyways.
Best,
Sylvia
> 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
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>
>> _______________________________________________
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>
> --
> 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
>
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