|
|
|
|
This directory contains the PSBLAS library, version 3.5.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
New features: additional Krylov methods FCG and GCR.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Existing codes will work untouched with version 3.5, but they will
|
|
|
|
|
have to be recompiled; new methods have been added for the sake of GPU
|
|
|
|
|
computations, plus the usual bunch of bug fixes.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
This version requires a working Fortran 2003 compiler; we do not use
|
|
|
|
|
all of the language features (specifically, so far we did not employ
|
|
|
|
|
FINAL subroutines), but the features we use were sufficient in
|
|
|
|
|
identifying bugs in ALL compilers we tried (all the bugs have been
|
|
|
|
|
reported and mostly fixed by the respective vendors).
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
The new internals have been completely overhauled, and in many cases
|
|
|
|
|
rewritten; they now enable a much better interfacing with user-defined
|
|
|
|
|
storage formats. If the user is only interested in the predefined
|
|
|
|
|
formats, then the user's guide should be sufficient; what is somewhat
|
|
|
|
|
lacking is documentation on how to add to the library, i.e. a
|
|
|
|
|
developers' guide; stay tuned.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
The architecture of the Fortran 2003 sparse BLAS is described in
|
|
|
|
|
S. Filippone, A. Buttari:
|
|
|
|
|
Object-Oriented Techniques for Sparse Matrix Computations in Fortran
|
|
|
|
|
2003,
|
|
|
|
|
ACM Trans. on Math. Software, vol. 38, No. 4, 2012.
|
|
|
|
|
|
|
|
|
|
The ideas are explored further with the paper:
|
|
|
|
|
|
|
|
|
|
V. Cardellini, S. Filippone and D. Rouson
|
|
|
|
|
Design Patterns for sparse-matrix computations on
|
|
|
|
|
hybrid CPU/GPU platforms,
|
|
|
|
|
Scientific Programming, 22(2014), pp.1-19.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Version 1.0 of the library was described in:
|
|
|
|
|
S. Filippone, M. Colajanni
|
|
|
|
|
PSBLAS: A library for parallel linear algebra computation on sparse matrices
|
|
|
|
|
ACM Trans. on Math. Software, 26(4), Dec. 2000, pp. 527-550.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
UTILITIES
|
|
|
|
|
The test/util directory contains some utilities to convert to/from
|
|
|
|
|
Harwell-Boeing and MatrixMarket file formats.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
DOCUMENTATION
|
|
|
|
|
|
|
|
|
|
See docs/psblas-3.4.pdf; an HTML version of the same document is
|
|
|
|
|
available in docs/html.
|
|
|
|
|
Please consult the sample programs, especially
|
|
|
|
|
test/pargen/ppde[23]d.f90
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
OTHER SOFTWARE CREDITS
|
|
|
|
|
|
|
|
|
|
We originally included a modified implementation of some of the
|
|
|
|
|
Sparker (serial sparse BLAS) material; this has been completely
|
|
|
|
|
rewritten, way beyond the intention(s) and responsibilities of the
|
|
|
|
|
original developers.
|
|
|
|
|
The main reference for the serial sparse BLAS is:
|
|
|
|
|
Duff, I., Marrone, M., Radicati, G., and Vittoli, C.
|
|
|
|
|
Level 3 basic linear algebra subprograms for sparse matrices: a user
|
|
|
|
|
level interface
|
|
|
|
|
ACM Trans. Math. Softw., 23(3), 379-401, 1997.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
INSTALLING
|
|
|
|
|
|
|
|
|
|
To compile and run our software you will need the following
|
|
|
|
|
prerequisites (see also SERIAL below):
|
|
|
|
|
|
|
|
|
|
1. A working version of MPI
|
|
|
|
|
|
|
|
|
|
2. A version of the BLAS; if you don't have a specific version for
|
|
|
|
|
your platform you may try ATLAS available from
|
|
|
|
|
http://math-atlas.sourceforge.net/
|
|
|
|
|
|
|
|
|
|
3. We have had good results with the METIS library, from
|
|
|
|
|
http://www-users.cs.umn.edu/~karypis/metis/metis/main.html
|
|
|
|
|
This is optional; it is used in the util and test/fileread
|
|
|
|
|
directories but only if you specify --with-metis.
|
|
|
|
|
|
|
|
|
|
4. If you have the AMD package of Davis, Duff and Amestoy, you can
|
|
|
|
|
specify --with-amd (see ./configure --help for more details).
|
|
|
|
|
|
|
|
|
|
The configure script will generate a Make.inc file suitable for
|
|
|
|
|
building the library.
|
|
|
|
|
The script is capable of recognizing the needed libraries with their
|
|
|
|
|
default names; if they are in unusual places consider adding the paths
|
|
|
|
|
with --with-libs, or explicitly specifying the names in --with-blas, etc.
|
|
|
|
|
Please note that a common way for the configure script to fail is to
|
|
|
|
|
specify inconsistent MPI vs. plain compilers, either directly or
|
|
|
|
|
indirectly via environment variables; e.g. specifying the Intel
|
|
|
|
|
compiler with FC=ifort while at the same time having an MPIFC=mpif90
|
|
|
|
|
which points to GNU Fortran.
|
|
|
|
|
The best way to avoid this situation is (in our opinion) to use the
|
|
|
|
|
environment modules package (see http://modules.sourceforge.net/), and
|
|
|
|
|
load the relevant variables with (e.g.)
|
|
|
|
|
module load gnu46 openmpi
|
|
|
|
|
This will delegate to the modules setup to make sure that the version
|
|
|
|
|
of openmpi in use is the one compiled with the gnu46 compilers.
|
|
|
|
|
After the configure script has completed you can always tweak the
|
|
|
|
|
Make.inc file yourself.
|
|
|
|
|
|
|
|
|
|
After you have Make.inc fixed, run
|
|
|
|
|
make
|
|
|
|
|
to compile the library; go to the test directory and its
|
|
|
|
|
subdirectories to get test programs done.
|
|
|
|
|
If you specify --prefix=/path you can do make install and the
|
|
|
|
|
libraries will be installed under /path/lib, while the module files
|
|
|
|
|
will be installed under /path/include.
|
|
|
|
|
|
|
|
|
|
SERIAL
|
|
|
|
|
|
|
|
|
|
Configuring with --enable-serial will provide a fake MPI stub library
|
|
|
|
|
that enables running in pure serial mode; no MPI installation is
|
|
|
|
|
needed in this case (but note that the fake MPI stubs are only
|
|
|
|
|
guaranteed to cover what we use internally, it's not a complete
|
|
|
|
|
replacement).
|
|
|
|
|
|
|
|
|
|
EXPERIMENTAL
|
|
|
|
|
|
|
|
|
|
We have an experimental flag --enable-long-integers that will enable having
|
|
|
|
|
8-byte integer data, allowing an index space larger than 2G; some
|
|
|
|
|
small cases have been tested but we do not offer full guarantee (yet).
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
COMPILER NOTES.
|
|
|
|
|
|
|
|
|
|
This code is confirmed to work with the following compilers (or
|
|
|
|
|
later versions thereof):
|
|
|
|
|
NAGware 5.2;
|
|
|
|
|
GNU 4.7.3;
|
|
|
|
|
Cray CCE 8.0.1;
|
|
|
|
|
|
|
|
|
|
They are all recognized by the configure script.
|
|
|
|
|
|
|
|
|
|
To make the script work with the Cray CCE environment, it is
|
|
|
|
|
recommended to use the following:
|
|
|
|
|
./configure FC=ftn F77=ftn CC=cc MPF90=ftn MPF77=ftn MPCC=cc
|
|
|
|
|
with both CCE and GNU lower-level compilers.
|
|
|
|
|
|
|
|
|
|
XLF 13.1 configures correctly, but then fails with ICEs (Internal
|
|
|
|
|
Compiler Error) at build time. We do not yet know whether XLF 14
|
|
|
|
|
compiles correctly.
|
|
|
|
|
|
|
|
|
|
For the GNU compilers 4.6.x we are aware of a number of memory management
|
|
|
|
|
issues that might surface in your applications; most of them (that
|
|
|
|
|
we're aware of) are solved in version 4.7.2 or later.
|
|
|
|
|
|
|
|
|
|
The Intel compiler up to version 12.1 fails to compile, as of the last
|
|
|
|
|
version we got access to.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
KNOWN ISSUES.
|
|
|
|
|
|
|
|
|
|
An annoying problem exists with some versions of MPI: if the configure
|
|
|
|
|
script sets -DMPI_MOD the MPI call interfaces will be resolved by
|
|
|
|
|
using the MPI Fortran module.
|
|
|
|
|
However usage of the module may cause compilation to fail when
|
|
|
|
|
coupled with the debugging option -g, because the compiler complains
|
|
|
|
|
that it cannot find a matching interface for some of the
|
|
|
|
|
communication routines.
|
|
|
|
|
The solution: either take out the -g option, or, if you really need to
|
|
|
|
|
debug, edit Make.inc to force -DMPI_H in place of -DMPI_MOD.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
TODO:
|
|
|
|
|
Fix all reamining bugs. Bugs? We dont' have any ! ;-)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
The PSBLAS team.
|
|
|
|
|
|
|
|
|
|
RELATED SOFTWARE
|
|
|
|
|
|
|
|
|
|
If you are looking for more sophisticated preconditioners, you may be
|
|
|
|
|
interested in the package MLD2P4 from http://www.mld2p4.it
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Contact: Salvatore Filippone salvatore.filippone@cranfield.ac.uk
|
|
|
|
|
|
|
|
|
|
Credits for version 3:
|
|
|
|
|
Salvatore Filippone
|
|
|
|
|
Alfredo Buttari
|
|
|
|
|
Ambra Abdullahi Hassan
|
|
|
|
|
Pasqua D'Ambra
|
|
|
|
|
Daniela di Serafino
|
|
|
|
|
|
|
|
|
|
Credits for version 2.2:
|
|
|
|
|
Michele Martone contributed the initial version of the configure
|
|
|
|
|
machinery.
|
|
|
|
|
|
|
|
|
|
Credits for version 2.0:
|
|
|
|
|
Salvatore Filippone
|
|
|
|
|
Alfredo Buttari
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Credits for version 1.0:
|
|
|
|
|
|
|
|
|
|
Salvatore Filippone
|
|
|
|
|
Michele Colajanni
|
|
|
|
|
Fabio Cerioni
|
|
|
|
|
Stefano Maiolatesi
|
|
|
|
|
Dario Pascucci
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
