The main page of the Doxygen documentation is organized as follows:
Amesos supports the following classes:
Amesos_Lapack- Interface to LAPACK's serial dense solver DGETRF.
Amesos_Scalapack- Interface to ScaLAPACK's parallel dense solver PDGETRF.
Amesos_Klu- Interface to Tim Davis serial solver KLU (distributed within Amesos).
Amesos_Umfpack- Interface to Tim Davis's UMFPACK (version 4.3 or later)
Amesos_Pardiso- Interface to PARDISO (prototype)
Amesos_Taucs- Interface to TAUCS
Amesos_Superlu- Interface to Xiaoye Li's SuperLU serial memory code with serial input interface (version 3.0 or later).
Amesos_Superludist- Interface to Xiaoye Li's SuperLU Distributed memory code with serial input interface (version 2.0 or later).
Amesos_Dscpack- Interface to Padma Raghavan's DSCPACK
Amesos_Mumps- Interface to CERFACS' MUMPS (version 4.3.1 or later)
We refer to the Sandia report SAND-2004-2188 for a detailed overview of Amesos. A PDF version of this report can be found the
Most of the Amesos classes are based on a third party code (that is, not distributed within Trilinos). Each third party code comes with its own copyright and/or licensing requirements. It is responsibility of the user to fulfill the requirements of each supported package' copyright.
Most of these third party codes are intended to be made available at no cost to users. Much of the copyright and licensing restrictions concern rights to modify, redistribute the code and generally include a request that credit be given in any papers which make use of their code. Please refer to the web page for the package that you are interested in for details.
The following tables reports an overview of the Amesos classes.
|Package is written in||FORTRAN77||C||C||C||FORTRAN77|
|Processes used for Factorization/Solve||Process 0||Process 0||Process 0||Process 0||Any|
|Distributed input matrix||Yes||Yes||Yes||Yes||Yes|
|Package is written in||--||C||C||FORTRAN90||C|
|Processes used for Factorization/Solve||Any||Any||Any||Any (*)||Any (**)|
|Distributed input matrix||Yes||Yes||Yes||Yes||Yes|
(*) MUMPS required FORTRAN communicators. Some architectures (e.g., SGI) does not allow portable conversions from C/C++ communicator and FORTRAN. On these architectures, therefore,
MPI_COMM_WORLD will be used by MUMPS. Instead, if C/C++ communicators can be converted to FORTRAN ones, then any number of prosesses can be used by Amesos_Mumps.
(**) DSCPACK requires a number of processes that is a power of 2.
The following table details the supported matrix formats for each class.
Each of the Amesos classes provides an interface to a third party direct sparse solver code. (Exception is KLU, whose sources are distributed within Amesos.) In order to install a particular class, you must first install the underlying direct sparse solver code.
As all other Trilinos packages, Amesos is configured and built using the GNU autoconf and automake tools. To configure Amesos from the Trilinos top directory, a possible procedure is as follows. Let
TRILINOS_HOME be a shell variable representing the location of the Trilinos source directory, and % the shell prompt sign. Let us suppose that we want to configure Amesos on a LINUX machine with MPI, with support for KLU and UMFPACK. Header files for UMFPACK are located in directory
/usr/local/umfpack/include, while the library, called
libumfpack.a is located in
/usr/local/umfpack/lib. The configure like will look like:
% cd $TRILINOS_HOME % mkdir LINUX_MPI % cd LINUX_MPI % ../configure \ --with-mpi-compilers \ --prefix=$TRILINOS_HOME/LINUX_MPI \ --enable-amesos \ --enable-amesos-klu \ --enable-amesos-umfpack \ --with-incdirs="-I/usr/local/umfpack/include" \ --with-ldflags="-L/usr/local/umfpack/lib" \ --with-libs="-lumfpack" % make % make install
Other flags may be required depending on the location of MPI, BLAS and LAPACK. The table below reports the architectures and compilers tested with each of the Amesos classes. "nightly" means that these tests are included in out routine (though not always nightly) testing. "yes" means that theses tests were run at least once.
This table may soon be replaced by a table which reports only the results of the routine, "nightly", tests. MANUAL TESTING will continue to list of architectures and compilers on which Amesos solvers have been tested manually.
|LINUX (GNU), SERIAL||yes||yes||yes||yes||yes||no|
|LINUX (Intel), MPI||yes||yes||yes||no||no||no|
|LINUX (GNU), MPI||nightly||nightly||yes||yes||yes||nightly|
|SGI 64, MPI||nightly||nightly||nightly||no||no||nightly|
|MAC OSX, SERIAL||no||yes||yes||no||yes||no|
|MAC OSX, MPI||nightly||nightly||no||no||no||no|
|Sun OS, MPI||nightly||yes||yes||no||no||no|
|Sandia Cplant, MPI||no||yes||yes||no||no||no|
|LINUX (GNU), SERIAL||yes||yes||no||yes|
|LINUX (Intel), MPI||no||no||yes||no|
|LINUX (GNU), MPI||nightly||nightly||no||nightly|
|SGI 64, MPI||yes||no||nightly||nightly|
|MAC OSX, SERIAL||yes||no||no||no|
|MAC OSX, MPI||no||no||no||no|
|Sun OS, MPI||nightly||no||no||nightly|
|Sandia Cplant, MPI||yes||yes||no||no|
Once Amesos has been compiled, it can be tested using the example
compare_solvers.exe, as follows:
% cd amesos/example % make % ./compare_solvers.exe
or, using MPI,
% mpirun -np 4 ./compare_solvers.exe
This will test all the supported solvers on an example matrix.
#include "Amesos.h" #include "Amesos_BaseSolver.h"
Note that these header files will not include the header files for the supported libraries (which are of course needed to compile the Amesos library itself). Now, let define the linear system matrix, the vector that will contain the solution, and the right-hand side as:
Epetra_LinearProblem Problem; Epetra_RowMatrix* A; // linear system matrix Epetra_MultiVector* LHS; // vector that will contain the solution Epetra_MultiVector* RHS; // right-hand side
Amesos_BaseSolver * Solver; Amesos Factory; char* SolverType = "Amesos_Klu"; Solver = Factory.Create(SolverType, *Problem);
Factory object will create an Amesos_Klu object (if Amesos has been configure to support this solver).
Factory.Create() returns 0 if the requested solver is not available. Parameter names are case-sensitive; misspelled parameters will not be recognized. Method
Factory.Query() can be used to query the factory about the availability of a given solver:
char* SolverType = "Amesos_Klu"; bool IsAvailable = Factory.Query(SolverType);
Here, we simply recall that the parameters list can be created as
and parameters can be set as
ParameterName is a string containing the parameter name, and
ParameterValue is any valid C++ object that specifies the parameter value (for instance, an integer, a pointer to an array or to an object). Please consult the Amesos Reference Guide for more details. The Doxygen documentation of each class can also be of help.
Problem is still empty. After setting the pointer to the linear system matrix, we can perform the symbolic factorization of the linear system matrix:
AMESOS_CHK_ERR is a macro, that checks the return error and, if not null, prints out a message and returns.) This phase does not require the numerical values of
A, that can therefore be changed after the call to
SymbolicFactorization(). However, the nonzero pattern of
A cannot be changed.
The numeric factorization is performed by
The values of
RHS must be set before solving the linear system, which simply reads
Should the user need to re-factorize the matrix, he or she must call
NumericFactorization(). If the structure of the matrix is changed, he or she must call
SymbolicFactorization(). However, it is supposed that the linear system matrix and the solution and right-hand side vectors are still defined with the same
Please consult the examples reported in the amesos/example subdirectory:
You can browse all of Amesos as a single doxygen collection. Warning, this is not the recommended way to learn about Amesos software. However, this is a good way to browse the directory structure of amesos, to locate files, etc.
Amesos has an interface to PyTrilinos, and therefore all the enabled third-party libraries can be used within Python to solve problems defined using Python/Epetra objects. Please refer to the PyTrilinos documentation http://trilinos.sandia.gov/packages/pytrilinos/overview.html for more details.
The Amesos to Thyra Linear Solver Adapters in Stratimikos take
Thyra::LinearOpBase objects that wrap
Epetra_Operator objects and turn them into
Thyra::LinearOpWithSolveBase objects which can then be used to solve linear systems using
Amesos_BaseSolver implementations. Please refer to the Stratimikos documentation http://trilinos.sandia.gov/packages/stratimikos/documentation.html for more details.
Versions of Superlu and Superludist prior to August 2005 exhibit some mutual incompatibility as well as incompatbility with KLU and UMFPACK.
Depending on the version of SuperLU and SuperLU_DIST, you may or may not configure Amesos with support for both. This is due to conflicts in the header files of SuperLU/SuperLU_DIST.
Superludist fails on some matrices
Error handling on singular and near singular matrices is inconsistent
This page is maintained by Marzio Sala, SNL 9214 and Ken Stanley.
This page last updated 26-Aug-05.