[Trilinos-Users] Fwd: Krylov-Schur method with AztecOO
Alicia Klinvex
aklinvex at purdue.edu
Mon Nov 17 10:35:55 MST 2014
Hello,
I'm an external collaborator, so I really don't know much about AztecOO.
(The only things I wrote in Trilinos are TraceMin and some of the things
TraceMin depends on.) If you have questions about TraceMin, I would be
happy to answer them. Otherwise, you're more likely to get a useful
response by emailing the trilinos-users list. When you email the
trilinos-users list, your message will reach ALL of the developers
(including me).
Hopefully one of the AztecOO developers will be able to answer your
question :-)
Best wishes,
Alicia
---------- Forwarded message ----------
From: <maireni at cimne.upc.edu>
Date: Mon, Nov 17, 2014 at 11:11 AM
Subject: Re: Krylov-Schur method with AztecOO
To: Alicia Klinvex <aklinvex at purdue.edu>
Hi Alicia,
I understand how work Epetra matrix and i was able to
calculate eigen values with block Krylov-Schur method
using Amesos. However, changing to AztecOO i have a "nan"
as you see above. I dont know, but in this case
K and M are sparse stiffness and mass matrix respectively.
M is diagonal and have some zero terms in diagonal (rotational Dofs).
I don do understand what is the problem exactly.
Do you you have any idea about this mistake?.
Or just using AztecOO is limited to some special matrices,
due is a iterative solver.
Regards and best wishes
Nelson
iter: 0 residual = 1.000000e+00
iter: 1 residual = -nan
***************************************************************
Warning: a breakdown in this method
has occurred and solution has not converged.
Solver: bicgstab
number of iterations: 1
Recursive residual = -nan
Anasazi::BlockKrylovSchurSolMgr::solve() caught unexpected exception from
Anasazi::BlockKrylovSchur::iterate() at iteration 1
/usr/local/trilinos-11.12.1/include/AnasaziEpetraAdapter.hpp:1401:
Throw number = 1
Throw test that evaluated to true: ret != 0
Anasazi::OperatorTraits<double,Epetra_Multivector,Epetra_Operator>::Apply():
Error in Epetra_Operator::Apply(). Code -2
Anasazi::BlockKrylovSchurSolMgr::solve() returning Unconverged with no
solutions.
Anasazi::EigensolverMgr::solve() returned unconverged.
El 2014-11-13 02:49, Alicia Klinvex escribió:
> The convergence rate of each eigenpair is based on the quantity
> lambda_i / lambda_{s+1}, where s is the subspace dimension you
> selected. TraceMin by default selects 2*the number of desired
> eigenpairs. If the distribution of eigenvalues is bad, then it can
> take many iterations. There are still things we can do to fix it,
> like increasing the subspace dimension or using shifts.
>
> Looking at that quantity lambda_i / lambda_{s+1} will tell you a lot
> about why TraceMin is behaving this way.
>
> On Tue, Nov 11, 2014 at 10:50 AM, <maireni at cimne.upc.edu> wrote:
>
> Hi,
>> I am using TraceMin for solve the problem.
>> My problem is symmetric and sparse.
>> However when i use lapack(is time consuming because is for dense
>> matrix)
>> FEAST or for example , TraceMin takes time for converge.
>> When i look for 4 eigen-values TraceMin is fast but when i increase
>> the number of eigen-values
>> to 20 TraceMin make a lot iteration. I was thinking that maybe i
>> have a wrong parameter.
>> I dont know.
>>
>> Regards
>>
>> Thanks
>>
>> Nel
>>
>> El 2014-11-11 23:15, Alicia M Klinvex escribió:
>>
>> Hello,
>>
>> I'm a little confused by the fact that you're using LAPACK and
>> TraceMin on the same problem. Is this a dense or sparse problem?
>>
>> Yes, all of the Anasazi solvers should work with Tpetra as well as
>> Epetra.
>>
>> Best wishes,
>> Alicia
>>
>> ----- Original Message -----
>> From: maireni at cimne.upc.edu
>> To: "Alicia M Klinvex" <aklinvex at purdue.edu>
>> Sent: Tuesday, November 11, 2014 10:09:07 AM
>> Subject: Re: TraceMin-Davidson failurem
>>
>> Hi Alice,
>>
>> It is works now. I tested and give the similar values
>> of lapack eigen solver. However, why if increase the number
>> of eigen-values to looking for (at instance from 4 to 20
>> eigen-values),
>> it is take more time.
>> My toler is 1E-6.
>>
>> I will try other eigen-solver too. I suppose Tpetra
>> can be use in the others eigen-solver.
>>
>> Regards and thanks again
>>
>> Nel
>>
>> El 2014-11-11 01:51, Alicia M Klinvex escribió:
>> Hello,
>>
>> Thank you so much for giving our newest solver a try!
>>
>> Anasazi calls a function called isFillComplete, which tells us
>> whether
>> you finished putting things in a matrix. If you did NOT finish
>> putting things in the matrix, it breaks and outputs the error
>> message
>> you saw.
>>
>> You may be thinking, "but I WAS finished modifying the entries of
>> the
>> matrix!" You need to let Anasazi know that by calling the Tpetra
>> function fillComplete
>>
>> (http://trilinos.org/docs/dev/packages/tpetra/doc/html/
> classTpetra_1_1CrsMatrix.html#a27c06cd71c7542742a731a6cc91180d2
>
>> [1]).
>> In your code, this will look like K->fillComplete() and
>> M->fillComplete().
>>
>> Does that answer your question?
>>
>> Best wishes,
>> Alicia
>>
>> ----- Original Message -----
>> From: maireni at cimne.upc.edu
>> To: "Alicia M Klinvex" <aklinvex at purdue.edu>
>> Sent: Monday, November 10, 2014 2:54:46 AM
>> Subject: Re: [Trilinos-Users] Returned mail: see transcript for
>> details
>>
>> Hi Alicia,
>> At first so sorry for reply you a lot time for questions.
>> I am using the example you defined in the list that use
>> TraceMin-Davidson to solve a generalized eigenvalue problem
>> using Tpetra (and reading file).
>>
>> The thing is i can not yet run my eigen problem.
>> In fact i have this mistakes and no reported in google
>> exist. Here it is.
>>
>> Teuchos::ArrayRCP<unsigned
>>
>> long>{ptr=0x46f9130,lowerOffset=0,upperOffset=
> 8238,size=8239,node=0x4d6c7c0,strong_count=2,weak_count=0}
>
>> >> Allocating X_
>> >> Allocating KX_
>> >> Allocating MX_
>> >> Allocating R_
>> >> Allocating V_
>> >> Allocating KV_
>> >> Allocating MV_
>> >> done allocating.
>> Computing MV
>> terminate called after throwing an instance of 'std::runtime_error'
>> what():
>> /usr/local/trilinos-11.12.1/include/Tpetra_CrsMatrix_def.hpp:3517:
>>
>> Throw number = 1
>>
>> Throw test that evaluated to true: ! isFillComplete ()
>>
>> What do you think i am doing wrong. I attached the code function
>> if you have time to check it for a while. I really interesting
>> about
>> you tell me before, because i want to use any eigen-solver you
>> defined
>> in anasazi.
>>
>> Thanks a lot
>>
>> Nelson
>>
>> El 2014-11-06 22:20, Alicia M Klinvex escribió:
>> Hello,
>>
>> a) The matrix should be the total matrix. If your matrix comes
>> from a
>> matrix-market or harwell-boeing file, we do have a function that
>> will
>> read the symmetric matrix from a file and store it as general. (I
>> believe this is to optimize matrix-vector multiplications.)
>> Alternatively, you can define your own matrix-vector multiplication
>> operator, in which case Anasazi never needs to see your matrix.
>> There's an example of this for TraceMin-Davidson.
>>
>> b) Are you using BKS? If you're not using block Krylov-Schur, you
>> shouldn't need to create your own solver. RTR and
>> TraceMin/TraceMin-Davidson have solvers built-in.
>>
>> c) I'm not sure I understand what you mean by the matrix being
>> dense
>> and sparse. Also, are you looking for the smallest or largest
>> eigenvalues? Are you looking for interior or extreme eigenvalues?
>>
>> By the way, one of the cool things about Anasazi is that all of the
>> eigensolvers use the same interface. If you want to try a couple
>> of
>> them, it only involves changing maybe 5 lines of code in your
>> driver.
>>
>> Best wishes,
>> Alicia
>>
>> PS: We should copy the user list in our correspondence, since some
>> people are better equipped than I am to answer certain types of
>> questions. For instance, I am not an Amesos developer. The
>> Amesos
>> developers can probably do a better job answering your questions
>> about
>> Amesos.
>>
>> ----- Original Message -----
>> From: maireni at cimne.upc.edu
>> To: "Alicia M Klinvex" <aklinvex at purdue.edu>
>> Sent: Thursday, November 6, 2014 7:05:34 AM
>> Subject: Re: [Trilinos-Users] Returned mail: see transcript for
>> details
>>
>> Hello Alicia,
>>
>> Just simple questions
>>
>> a) When i use Anasazi with Tpetra in CSR format.
>> Should be the total matrix even if it is symmetric or it is ok if i
>> take
>> for Anasazi the upper or lower one?. How to do that?
>>
>> b) I see Amesos accept now Pardiso solver. I use normally this
>> Solver.
>> My matrices is sparse and lapack is call when i use anasazi. How
>> can
>> i
>> set amesos for use Pardiso or SuperLU(shared Memory). I see some
>> macros
>> but, i think should be another way no?
>>
>> c) The problem i have is symmetric dense and sparse. According
>> to your experience with is the fastest method in Anasazi?
>>
>> Sorry again for ask you a lot, but i really excited with Trilinos.
>>
>> Regards
>>
>> Nelson
>>
>> El 2014-11-06 10:38, Alicia M Klinvex escribió:
>> Hello,
>>
>> Have you tried contacting the SLEPC team about your problems?
>> They're
>> a helpful group as well. (I'm obviously not trying to tell you
>> not
>> to
>> use Trilinos; I just want you to be aware of the packages that can
>> solve your specific problem. We don't currently support finding
>> all
>> eigenvalues in an interval. I should have that complete by the
>> end
>> of
>> the month though.)
>>
>> FEAST is slow because of its reliance on direct solvers such as
>> PARDISO and all of the factorizations it requires. You may want
>> to
>> contact the FEAST developers to see whether it would be appropriate
>> to
>> reduce the number of contour integration points, which can speed up
>> the code.
>>
>> Anasazi does have very powerful tools, and I'm glad you've decided
>> to
>> give them a try. :-)
>>
>> I'm not familiar with AMLS. Are these small matrices dense or
>> sparse?
>> Regarding the linear systems, if they are sparse, Amesos and
>> Belos
>> are both really nice packages to use, depending on what your matrix
>> is
>> like. Amesos contains direct solvers, and Belos is for iterative
>> solvers such as CG.
>>
>> Best wishes, and please keep us updated!
>> Alicia
>>
>> ----- Original Message -----
>> From: maireni at cimne.upc.edu
>> To: "Alicia M Klinvex" <aklinvex at purdue.edu>
>> Sent: Wednesday, November 5, 2014 8:57:55 PM
>> Subject: Re: [Trilinos-Users] Returned mail: see transcript for
>> details
>>
>> Hi Alicia M Klinvex,
>> Thanks for replying.
>> I was trying to use SLEPC's Krylov Schur but not successful yet.
>> I know the FEAST eigen-solver and is integrated in my code and
>> works.
>> I call directly from MKL libraries, but is slow than other
>> eigen-solvers,
>> at least block Lanzcos method like BLZPACK. Another problem is
>> ARPACK++,
>> that when i call the AReig functions not works correctly. It use a
>> format
>> of CSC. My matrices is symmetric and could be lower or upper
>> matrix.
>> In
>> any case,
>> the eigen-values is not ok. I saw Anasazi is inspired and have
>> better
>> tools than ARPACK. This is why i
>> try to use Anasazi.
>>
>> Respect to size of problem, the idea is to use AMLS method. AMLS
>> method
>> is a condensation method
>> that can convert a huge matrix, millions of dofs, to just a little
>> thousands. In need to solve
>> a lot of eigen-values problems, but this eigen problems is so small
>> that
>> the corresponding one.
>> Also i need to solve a lot equations with a lot rigth hand side. I
>> was
>> thinking in use
>> Pardiso, but trilnos have good tools and i want to explot too.
>>
>> Allow me try what you talk me and then i let you know.
>> Thanks for your help. Thanks a lot.
>>
>> Nel
>>
>> El 2014-11-06 01:27, Alicia M Klinvex escribió:
>> Hello Nelson,
>>
>> What you want is this constructor:
>>
>> http://trilinos.org/docs/r11.12/packages/tpetra/doc/html/
> classTpetra_1_1Map.html#aeb556362352e2ae62804601e36672a6c
>
>> [2]
>>
>> Map( global_size_t numGlobalElements, GlobalOrdinal indexBase,
>> const
>> Teuchos::RCP< const Teuchos::Comm< int > > & comm, LocalGlobal lg =
>> GloballyDistributed, const Teuchos::RCP< Node > & node =
>> defaultArgNode< Node >() )
>>
>> Here's what this constructor expects:
>> * The number of rows of your matrix
>> * The index base (which is generally 0)
>> * The communicator (which we will come back to)
>> * Whether the matrix is locally replicated or globally distributed
>> (which we will come back to)
>> * The node type, which defines the type of architecture you are
>> using
>>
>> You may be thinking at this point, "I have to provide a
>> communicator?
>> But I don't want to use MPI!" You can define a serial Teuchos
>> communicator which never communicates, as in this example:
>>
>> http://trilinos.org/docs/r11.12/packages/tpetra/doc/html/
> lesson01_no_mpi_8cpp-example.html
>
>> [3]
>>
>> For a sequential example, it doesn't matter whether you specify
>> that
>> the matrix is locally replicated or globally distributed. We can
>> come
>> back to this when you're ready to use MPI.
>>
>> Regarding finding all eigenvalues in an interval, you have several
>> options:
>> * You can compute the number of eigenvalues in an interval using
>> inertia computations (meaning sparse factorizations will be
>> involved),
>> then call any eigensolver you want.
>> * You can try Eric Polizzi's FEAST eigensolver (which requires an
>> estimate of the number of eigenvalues in an interval). You can
>> download it here: http://www.feast-solver.org/ [4] It can also be
>> found
>> in certain versions of the Intel Math Kernel Library.
>> * You can try SLEPC's Krylov Schur, which is supposed to support
>> this
>> feature. Just as a warning, I've personally never gotten it to
>> work
>> successfully.
>>
>> We are currently working on adding that functionality (computing
>> all
>> eigenvalues in an interval) to Anasazi. Just out of curiosity,
>> roughly how many eigenvalues are there in your interval of
>> interest?
>> Also, how big is your matrix?
>>
>> Best wishes,
>> Alicia
>>
>> ----- Original Message -----
>> From: maireni at cimne.upc.edu
>> To: "Alicia M Klinvex" <aklinvex at purdue.edu>
>> Sent: Wednesday, November 5, 2014 1:08:00 AM
>> Subject: Re: [Trilinos-Users] Returned mail: see transcript for
>> details
>>
>> Hi Alicia M Klinvex,
>>
>> Thanks for reply.
>> In my case, as in research area, i compile Trilinos for
>> not running in MPI process, just in serial way. I know i can not
>> exploits
>> all tools of Trilinos, but is just for research. It have really
>> interesting tools.
>> When the code and the idea is working, migration to MPI is really
>> well.
>>
>> For the case of column map and row map i need your help.
>> At the moment, just a class matrix works fine in Ananazi is ok for
>> me.
>> Epectra or Tpectra is ok. I am using now Tpectra and i see i can
>> define
>> a typedef
>> like this
>>
>> typedef double scalar_type;
>> typedef Tpetra::CrsMatrix<scalar_type> TpetraCrsMatrix;
>>
>> the other parameters is a default values, so i assumed with they
>> Anasazi works. My dude is in how to contruct the maps for serial
>> code.
>>
>> Another thing i would like to ask you is about the eigen-solver.
>> Anasazi can provide me the number of desired eigenvalues,
>> but is possible it give to me an interval of eigen-values
>> i.e [0, fecuency cuttof]?
>>
>> I really appreciate your help.
>>
>> Best wishes,
>>
>> Nelson
>>
>> El 2014-11-04 21:57, Alicia M Klinvex escribió:
>> Hello Nelson,
>>
>> My name is Alicia, and I am an Anasazi developer. I'm glad you've
>> decided to try Anasazi :-)
>>
>> I assume what you're asking is how to take your three CSR arrays
>> and
>> turn them into a CrsMatrix that you can pass to an Anasazi
>> eigensolver. If you're using Tpetra, the constructor you're
>> looking
>> for is this:
>>
>> http://trilinos.org/docs/r11.10/packages/tpetra/doc/html/
> classTpetra_1_1CrsMatrix.html#a139a91ad9430f012bfb3bcb8fe413ae1
>
>> [5]
>> (If you're using Epetra instead, or want to know the difference
>> between Epetra and Tpetra, let me know.)
>>
>> Note that this constructor will expect the row map and column map,
>> which define how the data is distributed over the MPI processes.
>> If
>> you don't understand how to create those maps, please let me know
>> and
>> I'll help you out.
>>
>> Does that answer your question?
>>
>> Best wishes,
>> Alicia Klinvex
>>
>> ----- Original Message -----
>> From: maireni at cimne.upc.edu
>> To: trilinos-users at software.sandia.gov
>> Sent: Tuesday, November 4, 2014 3:41:49 AM
>> Subject: Re: [Trilinos-Users] Returned mail: see transcript for
>> details
>>
>> Dear Heidi Thornquist,
>>
>> Allow me introduce myself first. My name is Nelson Lafontaine,
>> i am a PhD student from UPC, Barcelona, Spain. Now i am Beijing
>> China
>> working with the Psor Chen Pu in the Automatic Multilevel
>> Substructure
>> Methods (AMLS).
>> I see you are a Anasazi developer and i write to you because i
>> am
>> interested in use
>> this library. My installation of Trilinos (trilinos-11.12.1) was
>> successfully,
>> even i can run some test examples that you are define in
>> Anasazi
>> files.
>>
>> However, like you create your own class of matrices and vector,
>> my data i can provided to solve my eigen problem is in the form
>> of
>> a Compressed Sparse Row (CSR). My question is if exist a way
>> to
>> call
>> the eigen-solver defined in Anasazi just providing the data of
>> compressed
>> Sparse row format, or if is possible to create the matrices
>> types
>> defined
>> in Anasazi just using the CRS format.
>>
>> Thanks in advance for your time.
>>
>> Nelson
>> _______________________________________________
>> Trilinos-Users mailing list
>> Trilinos-Users at software.sandia.gov
>> https://software.sandia.gov/mailman/listinfo/trilinos-users [6]
>>
>
>
>
> Links:
> ------
> [1]
> http://trilinos.org/docs/dev/packages/tpetra/doc/html/
> classTpetra_1_1CrsMatrix.html#a27c06cd71c7542742a731a6cc91180d2
> [2]
> http://trilinos.org/docs/r11.12/packages/tpetra/doc/html/
> classTpetra_1_1Map.html#aeb556362352e2ae62804601e36672a6c
> [3]
> http://trilinos.org/docs/r11.12/packages/tpetra/doc/html/
> lesson01_no_mpi_8cpp-example.html
> [4] http://www.feast-solver.org/
> [5]
> http://trilinos.org/docs/r11.10/packages/tpetra/doc/html/
> classTpetra_1_1CrsMatrix.html#a139a91ad9430f012bfb3bcb8fe413ae1
> [6] https://software.sandia.gov/mailman/listinfo/trilinos-users
>
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