Mondriaan for sparse matrix partitioning


Mondriaan partitioner

Mondriaan is a sequential program written in C that can be used to partition a rectangular sparse matrix, an input vector, and an output vector for parallel sparse matrix-vector multiplication. The program is based on a recursive bipartitioning algorithm that cuts the matrix horizontally and vertically, in a manner resembling some of the famous Mondriaan paintings. The algorithm is multilevel, hypergraph-based, and two-dimensional. It reduces the amount of communication and it spreads both computation and communication evenly over the processors. The program can partition hypergraphs with integer vertex weights and uniform hyperedge costs, but it is primarily intended as a matrix partitioner.

Download

Download the latest version of the Mondriaan software, version 4.2 (tar gzipped), released September 14, 2017. The user's guide and MATLAB documentation can be found here. The latest development version of the Mondriaan software can be found in the git repository.

Optimal partitoning

Database of optimally partitioned matrices using the MondriaanOpt program. Under development. Slides of related lecture, Sparse Days at St. Girons, June 30, 2015. The user's guide for MondriaanOpt can be found here.

New features of version 4.2 (September 14, 2017)

Version 4.2 contains several improvements compared to version 4.1. These are:

New features of version 4.1 (November 7, 2016)

Version 4.1 contains several improvements compared to version 4.0. These are:

New features of version 4.0 (August 29, 2013)

Version 4.0 contains several improvements compared to version 3.11. These are:

New features of version 3.11 (December 15, 2010)

Version 3.11 contains several improvements compared to version 3.0. These are:

Minor update version 3.01 (August 3, 2010)

This update repairs a small bug with ordering to Bordered Block Diagonal (BBD) form.

New features of version 3.0 (July 27, 2010)

Version 3 contains many improvements compared to version 2. These are:

minor bug-fix version 2.01 (June 9, 2009)

Alexander Gusak from the Belarusian State University, Faculty of Applied Mathematics and Computer Science, found and fixed a few errors: a memory leak, an opened file which was not closed, and an an uninitialised string terminator. He also suggested a few improvements to prevent overflow for huge sparse matrices. These allowed him to partition matrices of 6 million rows and columns and 400 million nonzeros.

New features of version 2.0 (July 14, 2008)

Version 2 contains many improvements compared to version 1 (released May 10, 2002). These are: One bug fix compared to version 1.02: versions 1.X contained a small memory leak, discovered by Albert-Jan Yzelman using Valgrind. It was fixed by adding statements: free (C[nc]1.Start); free (C[nc]1.Match) inside the uncoarsening loop of function RunMLGraphPart in file HKLFM.c. You may have run out of memory earlier than needed when using version 1.02. Now you can solve larger problems!

Minor update version 1.02 (March 7, 2005)

Changes the data structure used in the inner product matching of the coarsening. This makes the software about 10 times faster. Thanks to Umit Catalyurek who pointed out an inefficiency in my previous version. This concerns function FindMatchIM in file HKLFM.c. Another change is that the (non-default) option of weighted edges is removed. This option was inferior to the default option and hence should not be used anyway. Note that to use V1.02 you must discard the old file mondriaan.defaults. Mondriaan will then automatically create a new default file.

Minor update version 1.01 (December 17, 2003)

Makes comments ANSI-C compliant, delimiting them by /* ... */. Fixes the following two bugs.

  1. May 31, 2002. Wouter Meesen: For compiling on a Windows system with the visual c++ compiler, you have to remove all the words 'inline' from the source code. This word occurs in the files: DistributeVec.h, GainBucket.c, GainBucket.h, HKLFM.c, HKLFM.h. Same remark holds for Cray T3E compiler CC (Joris Koster, May 2002).
  2. Sept. 2, 2003. A remark by a sharp-eyed anonymous referee of our paper led us to reexamine the conversion from a sparse symmetric matrix to the full version in the function SparseMatrixSymmetric2Full from the file SparseMatrix.c. This function contains an error affecting the first nonzero. The error only occurs for symmetric matrices stored in symmetric input format. Thanks to the referee!

Initial release Mondriaan version 1.0 (May 10, 2002)

Related papers

The original Mondriaan algorithm and implementation has been published in "A Two-Dimensional Data Distribution Method for Parallel Sparse Matrix-Vector Multiplication", by Brendan Vastenhouw and Rob H. Bisseling, SIAM Review, 47, No. 1 (2005) pp. 67-95.

The new vector partitioning algorithms and implementations have been published in "Communication balancing in parallel sparse matrix-vector multiplication", by Rob H. Bisseling and Wouter Meesen, Electronic Transactions on Numerical Analysis, 21 (2005) pp. 47-65, special issue on Combinatorial Scientific Computing.

The new matrix ordering algorithms and implementations have been published in Cache-oblivious sparse matrix-vector multiplication by using sparse matrix partitioning methods by Albert-Jan N. Yzelman and Rob H. Bisseling, SIAM Journal on Scientific Computing, 31, No. 4 (2009) pp. 3128-3154.

An extension to 2D is given in Two-dimensional cache-oblivious sparse matrix-vector multiplication by A. N. Yzelman and Rob H. Bisseling, Parallel Computing, 37, No. 12 (2011) pp. 806-819.

The hybrid between the original Mondriaan method and the finegrain method has been published as a book chapter Two-Dimensional Approaches to Sparse Matrix Partitioning by Rob H. Bisseling, Bas O. Fagginger Auer, A. N. Yzelman, Tristan van Leeuwen and Ümit V. Çatalyürek, Chapter 12 of Combinatorial Scientific Computing, Chapman and Hall/CRC, pp. 321-349 (2012).

The lambda*(lambda - 1)-metric is introduced in A new metric enabling an exact hypergraph model for the communication volume in distributed-memory parallel applications by O. Fortmeier, H. M. Bücker, B. O. Fagginger Auer, R. H. Bisseling, Parallel Computing, 39, No. 8 (2013) pp. 319-335.

The medium-grain method is described in A medium-grain method for fast 2D bipartitioning of sparse matrices by D. M. Pelt and R. H. Bisseling, Proceedings IEEE International Parallel & Distributed Processing Symposium 2014, IEEE Press, pp. 529-539.

An exact algorithm for obtaining an optimal partitioning of small matrices for 2 processors is given in An exact algorithm for sparse matrix bipartitioning, by Daniel M. Pelt and Rob H. Bisseling, Journal of Parallel and Distributed Computing, 85 (2015) pp. 79-90. Postprint version. The corresponding program MondriaanOpt has been included in Mondriaan version 4.1.

The zero-volume search and the load balance improvement by moving free nonzeros (and some other improvements) introduced in version 4.2 are described in the MSc thesis of Marco van Oort, Accelerating the Mondriaan sparse matrix partitioning package, Utrecht University, May 2017.

Extensive background reading on the parallel sparse matrix-vector multiplication problem, including a detailed discussion of the Mondriaan algorithm, can be found in Chapter 4 (pp. 163-250) of Parallel Scientific Computation: A Structured Approach using BSP and MPI, by Rob H. Bisseling, Oxford University Press, March 2004. 324 pages. ISBN 978-0-19-852939-2. OUP home page of the book.

Trailer

Trailer announcing Mondriaan version 2 by Sarai Bisseling (Quicktime movie, 11.6 MB).

Selected related lectures by Rob Bisseling

Copyright

This software is copyrighted (2002, 2008, 2010, 2013, 2016, 2017) by Rob Bisseling, Bas Fagginger Auer, Tristan van Leeuwen, Wouter Meesen, Marco van Oort, Daan Pelt, Brendan Vastenhouw, Albert-Jan Yzelman. You can use and modify it under the GNU Lesser General Public License, see GNU Licenses. Also see the files, README, COPYING, COPYING.LESSER. Anything free, as usual, comes with no guarantee!

Contributions

Besides the authors mentioned in the copyright notice, others have contributed as well: Other contributions are welcome!

Test matrices

Most matrices we use in our tests can be obtained from Tim Davis' University of Florida Sparse Matrix Collection. The term-by-document matrices used in the SIAM Review paper are: tbdmatlab.mtx (430171 nonzeros, 3.2 Mbyte) and tbdlinux.mtx (2157675 nonzeros, 18.9 Mbyte), both in gzip-compressed Matrix Market format. The RSA matrices used in the paper "Mondriaan sparse matrix partitioning for attacking cryptosystems by a parallel block Lanczos algorithm - a case study" by Rob H. Bisseling and Ildiko Flesch, Parallel Computing 32 Nr. 7/8 (2006) pp. 551-567, Final preprint (Sept 2006), are: rsa_c82.mtx (16338 rows, 16307 columns, 507716 nonzeros) and rsa_c98.mtx 56274 rows, 56243 columns, 2075889 nonzeros). Note that the paper uses the transposed of the matrices given here. The matrices are courtesy of Richard Brent.


Last updated September 14, 2017.
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