Installation

Dependencies

PEXSI requires an external parallel \(LU\) factorization or \(LDL^T\) factorization routine, and an external parallel matrix reordering routine to reduce the fill-in of the factorization routine.

Starting from v1.0, PEXSI requires both symPACK and SuperLU_DIST. symPACK is the default option for the \(LDL^T\) factorization of symmetric matrices, and use SuperLU_DIST as the default option for the \(LU\) factorization of unsymmetric matrices. SuperLU_DIST can also be used for symmetric matrices, by means of treating the matrix as a general matrix but use symmetric reordering.

Starting from v1.0, PEXSI uses the PT-Scotch as the default package for matrix reordering. The ParMETIS package can also be used.

The installation procedure and dependencies of every version of the PEXSI package may be slightly different. Please follow the documentation of the version of the PEXSI package you are working with. (provided in the Download Page )

Build PT-Scotch

PT-Scotch can be downloaded from (latest version 6.0.0) https://gforge.inria.fr/frs/download.php/31831/scotch_6.0.0.tar.gz

Follow the installation step to install PT-Scotch. In INSTALL.TXT, pay special attention to the following sections in order to compile PT-Scotch correctly.

2.3) Integer size issues

2.5) Threads issues

PT-Scotch is also METIS-Compatible. See the following section in INSTALL.TXT for more information.

2.9) MeTiS compatibility library

In src/ directory, you need

make ptscotch

to compile PT-Scotch.

NOTE: Just typing make will generate the Scotch library but not PT-Scotch. Then all libraries will be given in lib/ directory.**

Build symPACK

symPACK is a sparse symmetric matrix direct linear solver. More information can be found at http://www.sympack.org/.

To use symPACK, first, download the package as follows

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

Several environment variables can be set before configuring the build:

`SCOTCH_DIR` = Installation directory for **SCOTCH** and **PT-SCOTCH**

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

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

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

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

* `-DENABLE_PARMETIS=ON|OFF`   to make **ParMETIS** ordering available in **symPACK** (`PARMETIS_DIR` must be set in the environment, `METIS_DIR` is required as well)

* `-DENABLE_SCOTCH=ON|OFF`   to make **SCOTCH** / **PT-SCOTCH** orderings available in **symPACK** (`SCOTCH_DIR` must be set in the environment)

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/edison.cmake
(To build on NERSC Edison machine for instance)

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

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

make
make install

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

Note Since cmake also compiles UPCxx and GASNET, the compilation time may be long especially on certain clusters.

Build SuperLU_DIST

Download SuperLU_DIST (latest version 5.2.1) from

http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_5.2.1.tar.gz

Follow the installation step to install SuperLU_DIST.

Our experience shows that on some machines it may be better to build SuperLU_DIST with -O2 option than the more aggresive optimization options provided by vendors.

  • In SuperLU_DIST v5.1.3, some functions conflict when both real and complex arithmetic factorization is needed. This can be temporarily solved by adding -Wl,–allow-multiple-definition in the linking option.
  • In SuperLU_DIST v5.1.3, there could be some excessive outputs. This can be removed by going to the SRC/ directory of superlu, and comment out the line starting with printf(”.. dQuery_Space in dmemory_dist.c. Do the same thing for the line starting with printf(”.. zQuery_Space..) in zmemory_dist.c.
  • Please note that the number of processors for symbolic factorization cannot be too large when PARMETIS is used together with SuperLU. The exact number of processors for symbolic factorization is unfortunately a magic parameter. See FAQ page.

(Optional) Build ParMETIS

Download ParMETIS (latest version 4.0.3) from

http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz

Follow the installation step to install ParMETIS.

After untar the ParMETIS package, in Install.txt

Edit the file metis/include/metis.h and specify the width (32 or 64 bits) of the elementary data type used in ParMetis (and METIS). This is controled by the IDXTYPEWIDTH constant.

For now, on a 32 bit architecture you can only specify a width of 32, whereas for a 64 bit architecture you can specify a width of either 32 or 64 bits.

In our experience for most cases, the following setup work fine.:

#define IDXTYPEWIDTH 32

Build PEXSI

Edit make.inc

Configuration of PEXSI is controlled by a single make.inc file. Examples of the make.inc file are given under the config/ directory.

Find make.inc with the most similar architecture, and copy to the main PEXSI directory (using Edison for example, the latest Intel computer at NERSC, a CRAY X30 machine). ${PEXSI_DIR} stands for the main directory of PEXSI.

cd ${PEXSI_DIR}
cp config/make.inc.CRAY_XC30.intel make.inc

Edit the variables in make.inc.

PEXSI_DIR     = Main directory for PEXSI
DSUPERLU_DIR  = Main directory for SuperLU_DIST
PARMETIS_DIR  = Main directory for ParMETIS
PTSCOTCH_DIR  = Main directory for PT-Scotch

Edit the compiler options, for instance

CC           = cc
CXX          = CC
FC           = ftn
LOADER       = CC

The USE_SYMPACK option can be set to use the symPACK solver in PEXSI. It is set to 0 by default. When set to 1, the SYMPACK_DIR variable must be pointing to symPACK’s installation directory.

Note

  • Starting from PEXSI v0.8.0, -std=c++11 is required in CXXFLAGS.
  • Starting from PEXSI v0.9.2, -std=c99 is required in CFLAGS to be compatible with SuperLU_DIST starting from v4.3.
  • For FORTRAN users, CPP_LIB=-lstdc++ -lmpi -lmpi_cxx is often needed. Check this if there is link error.
  • PEXSI can be compiled using debug or release mode in by the variable COMPILE_MODE in make.inc. This variable mainly controls the compiling flag -DRELEASE. The debug mode introduces tracing of call stacks at all levels of functions, and may significantly slow down the code. For production runs, use release mode.
  • The USE_PROFILE option is for internal test purpose. Usually set this to 0.

Build the PEXSI library

The installation procedure and dependencies of every version of the PEXSI package may be different. Please follow the documentation of the version of the PEXSI package you are working with (provided in the Download Page )

If make.inc is configured correctly,:

make
make install

Should build the PEXSI library under the build directory ready to be used in an external package. If the FORTRAN interface is needed, type:

make finstall

If examples are needed (not necessary if you use PEXSI in an external package), type

make examples

which will generate C examples in examples/ directory and FORTRAN examples in fortran/ directory, respectively.:

make all

will make the library and the examples.

For more information on the examples, see Tutorial Page.

Tests

After example files are compiled, go to the examples/ directory, and:

examples$ mpirun -n 1 ./driver_pselinv_complex_(suffix)

should return the diagonal of the matrix \((A + i I)^{-1}\) saved on the 0-th processor, where \(A\) is the five-point discretization of a Laplacian operator on a 2D domain. The result can be compared with examples/driver_pselinv_complex.out to check the correctness of the result. For more examples see Tutorial Page.