Configuring and building symPACK

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symPACK is a sparse symmetric matrix direct linear solver. It can be built using the following procedure.

First, download symPACK as follows:

git clone git@github.com:symPACK/symPACK.git  /path/to/sympack

External dependencies

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UPC++

SymPACK requires the UPC++ v1.0 library to be installed. The minimum supported release version is 2019.9.0. It can be downloaded at upcxx.lbl.gov. UPC++ contains a CMake config file which symPACK is using to link to the library. The install path needs to be provided to CMake as follows:

-DCMAKE_PREFIX_PATH=/path/to/upcxx-2019.9.0

Ordering libraries

Several environment variables can be optionally set before configuring the build:

• metis_PREFIX = Installation directory for MeTiS

• parmetis_PREFIX = Installation directory for ParMETIS

• scotch_PREFIX = Installation directory for SCOTCH

• ptscotch_PREFIX = Installation directory for PT-SCOTCH

Then, create a build directory, enter that directory and type:

cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/path/to/install/sympack -DCMAKE_PREFIX_PATH=/path/to/upcxx/install
 ...OPTIONS... /path/to/sympack

The ...OPTIONS... can be one of the following:

• -DENABLE_METIS=ON|OFF to make MeTiS ordering available in symPACK (metis_PREFIX must be set in the environment)

• -DENABLE_PARMETIS=ON|OFF to make ParMETIS ordering available in symPACK (parmetis_PREFIX must be set in the environment, metis_PREFIX is required as well)

• -DENABLE_SCOTCH=ON|OFF to make SCOTCH ordering available in symPACK (scotch_PREFIX must be set in the environment)

• -DENABLE_PTSCOTCH=ON|OFF to make PT-SCOTCH ordering available in symPACK (ptscotch_PREFIX must be set in the environment, scotch_PREFIX is required as well)

Notes for specific platforms

Some platforms have preconfigured toolchain files which can be used by adding the following option to the cmake command:

-DCMAKE_TOOLCHAIN_FILE=/path/to/sympack/toolchains/cori.cmake     
(To build on NERSC Cori for instance)

A sample toolchain file can be found in /path/to/sympack/toolchains/build_config.cmake and customized for the target platform.

Building symPACK

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The cmake command will configure the build process, which can now start by typing:

make
make install

Additionally, standalone drivers for symPACK can be built by typing make examples

Build options

SymPACK has several optional features. We have already mentioned the options related to sparse matrix ordering. The following list is the complete set of options available when building symPACK:

• -DENABLE_METIS to enable MeTiS ordering (ON|OFF)

• -DENABLE_PARMETIS to enable ParMETIS ordering (ON|OFF)

• -DENABLE_SCOTCH to enable SCOTCH ordering (ON|OFF)

• -DENABLE_PTSCOTCH to enable PT-SCOTCH ordering (ON|OFF)

• -DAMD_IDX_64 to use 64 bit integers for AMD ordering (ON|OFF)

• -DMMD_IDX_64 to use 64 bit integers for MMD ordering (ON|OFF)

• -DRCM_IDX_64 to use 64 bit integers for RCM ordering (ON|OFF)

• -DENABLE_MKL to enable Intel MKL through the -mkl flag (ON|OFF)

• -DENABLE_THREADS to enable multithreading (ON|OFF). UPCXX_THREADMODE=par is required during cmake configuration. SymPACK implements its own multithreading and as such should be linked with sequential BLAS/LAPACK libraries.

Running symPACK

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SymPACK uses both UPC++ and MPI, therefore, some preliminary environment variables may need to be defined on most platforms. More details can be found in the UPC++ documentation:

export UPCXX_NETWORK=udp #good option on most workstations, but NOT on high performance networks 
export GASNET_SPAWNFN='C'
export GASNET_CSPAWN_CMD='mpirun -np %N %C'

To run the standalone symPACK driver, for instance on a sample problem from the Suite Sparse matrix collection, the procedure below can be followed:

#first download the input matrix (we are using nasa2146 here)
wget https://sparse.tamu.edu/RB/Nasa/nasa2146.tar.gz
#extract the matrix
tar xzf nasa2146.tar.gz

#run sympack
upcxx-run -n 4 -- ./run_sympack -in nasa2146/nasa2146.rb -ordering MMD -nrhs 1

For larger problems, like audikw_1, it is strongly advised to use more efficient orderings (such as METIS). Note that to run symPACK, upcxx-run is used in the example above, but on some platforms, such as NERSC Cori, other launchers may be used to both spawn MPI and UPC++, such as srun if the system is using SLURM. Moreover, for larger problems, the -shared-heap XX argument to upcxx-run may be needed (Please refer to UPC++ documentation).

Publications

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Recent publications

• John Bachan, Scott B. Baden, Steven Hofmeyr, Mathias Jacquelin, Amir Kamil, Dan Bonachea, Paul H. Hargrove, Hadia Ahmed.
  "UPC++: A High-Performance Communication Framework for Asynchronous Computation" (see Section IV-D-4),
  In 33rd IEEE International Parallel & Distributed Processing Symposium (IPDPS'19), May 20-24, 2019, Rio de Janeiro, Brazil. IEEE. 11 pages.
  https://doi.org/10.25344/S4V88H
  Talk slides

Older publications (based on UPC++ v0.1 version of symPACK)

• Mathias Jacquelin, Yili Zheng, Esmond Ng, Katherine Yelick
  "An Asynchronous Task-based Fan-Both Sparse Cholesky Solver",
  arXiv:1608.00044 [cs.MS], Aug 2016.
  https://doi.org/10.48550/arXiv.1608.00044

• Mathias Jacquelin, Yili Zheng, Esmond Ng, Katherine Yelick
  "symPACK: a solver for sparse Symmetric Matrices",
  Research Poster at The International Conference for High Performance Computing, Networking, Storage and Analysis (SC16), Nov 2016.