[aspect-devel] ASPECT on Mac
Timo Heister
heister at clemson.edu
Thu Oct 30 07:02:18 PDT 2014
Just a small update:
This is not a MAC problem, but another bug in the interplay of deal.II
and Trilinos newer than 11.08, see the discussion at
https://groups.google.com/d/msg/dealii/iowW9okgkSc/Nal05792xlkJ
I think we have a fix in deal.II now, but until the binary package is
updated, you need to use Trilinos 11.08.
Sorry about that.
On Fri, Oct 17, 2014 at 1:05 PM, Sylvia Rockel
<sylvia.rockel at fu-berlin.de> wrote:
> 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
>>>> >
>>>>
>>>> _______________________________________________
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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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--
Timo Heister
http://www.math.clemson.edu/~heister/
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