Commit 3abedd8d authored by gsell's avatar gsell

build-blocks:

- modulefiles added
parent e01e8cac
#%Module1.0
set whatis "visualization tool for H5hut files"
set url "http://amas.psi.ch/"
set license "PSI"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "optimized BLAS and LAPACK library."
set url "http://www.openblas.net/"
set license "BSD"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
The BLAS (Basic Linear Algebra Subprograms) are routines that provide
standard building blocks for performing basic vector and matrix operations.
The Level 1 BLAS perform scalar, vector and vector-vector operations, the
Level 2 BLAS perform matrix-vector operations, and the Level 3 BLAS perform
matrix-matrix operations. Because the BLAS are efficient, portable, and
widely available, they are commonly used in the development of high quality
linear algebra software, LAPACK for example.
LAPACK (Linear Algebra PACKage) is written in Fortran 90 and provides
routines for solving systems of simultaneous linear equations, least-
squares solutions of linear systems of equations, eigenvalue problems,
and singular value problems. The associated matrix factorizations (LU,
Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are
related computations such as reordering of the Schur factorizations and
estimating condition numbers. Dense and banded matrices are handled, but
not general sparse matrices. In all areas, similar functionality is
provided for real and complex matrices, in both single and double precision.
"
source $env(PSI_LIBMODULES)
setenv BLASLIB $PREFIX/libopenblas.a
#%Module1.0
set whatis "optimized BLAS and LAPACK library compiled with OpenMP."
set url "http://www.openblas.net/"
set license "BSD"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
The BLAS (Basic Linear Algebra Subprograms) are routines that provide
standard building blocks for performing basic vector and matrix operations.
The Level 1 BLAS perform scalar, vector and vector-vector operations, the
Level 2 BLAS perform matrix-vector operations, and the Level 3 BLAS perform
matrix-matrix operations. Because the BLAS are efficient, portable, and
widely available, they are commonly used in the development of high quality
linear algebra software, LAPACK for example.
LAPACK (Linear Algebra PACKage) is written in Fortran 90 and provides
routines for solving systems of simultaneous linear equations, least-
squares solutions of linear systems of equations, eigenvalue problems,
and singular value problems. The associated matrix factorizations (LU,
Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are
related computations such as reordering of the Schur factorizations and
estimating condition numbers. Dense and banded matrices are handled, but
not general sparse matrices. In all areas, similar functionality is
provided for real and complex matrices, in both single and double precision.
"
source $env(PSI_LIBMODULES)
setenv OMP_NUM_THREADS 1
setenv BLASLIB $PREFIX/libopenblas.a
#%Module1.0
set whatis "library for direct solution of large, sparse, nonsymmetric systems of linear equations."
set url "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
set license "BSD, see \$SUPERLU_DIR/share/doc/SuperLU/README"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
SuperLU is a general purpose library for the direct solution of large,
sparse, nonsymmetric systems of linear equations on high performance
machines. The library is written in C and is callable from either C or
Fortran. The library routines will perform an LU decomposition with
partial pivoting and triangular system solves through forward and back
substitution. The LU factorization routines can handle non-square
matrices but the triangular solves are performed only for square
matrices. The matrix columns may be preordered (before factorization)
either through library or user supplied routines. This preordering for
sparsity is completely separate from the factorization. Working
precision iterative refinement subroutines are provided for improved
backward stability. Routines are also provided to equilibrate the
system, estimate the condition number, calculate the relative backward
error, and estimate error bounds for the refined solutions.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "routines for solving unsymmetric sparse linear systems using the Unsymmetric MultiFrontal method."
set url "https://www.cise.ufl.edu/research/sparse/umfpack/"
set license "GNU GPL"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
UMFPACK is a set of routines for solving unsymmetric sparse linear systems,
Ax=b, using the Unsymmetric MultiFrontal method. Written in ANSI/ISO C, with
a MATLAB (Version 6.0 and later) interface. Appears as a built-in routine
(for lu, backslash, and forward slash) in MATLAB. Includes a MATLAB
interface, a C-callable interface, and a Fortran-callable interface. Note
that "UMFPACK" is pronounced in two syllables, "Umph Pack". It is not "You
Em Ef Pack".
"
source $env(PSI_LIBMODULES)
#%Module1.0
source $env(PSI_LIBMODULES)
set whatis "efficient BLAS and partial LAPACK implementation"
set url "http://math-atlas.sourceforge.net/"
set license "BSD-style license"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
The ATLAS (Automatically Tuned Linear Algebra Software) project is an
ongoing research effort focusing on applying empirical techniques in
order to provide portable performance. At present, it provides C and
Fortran77 interfaces to a portably efficient BLAS implementation, as
well as a few routines from LAPACK.
"
#%Module1.0
set whatis "C++ libraries"
set url "http://www.boost.org"
set license "Boost Software License"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
Boost is a set of libraries for the C++ programming language that provide
support for tasks and structures such as linear algebra, pseudorandom number
generation, multithreading, image processing, regular expressions, and unit
testing. It contains over eighty individual libraries.
(Wikipedia)
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "GNU Scientific Library"
set url "http://www.gnu.org/software/gsl/"
set license "GNU GPL"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
The GNU Scientific Library (GSL) is a numerical library for C and C++
programmers.
The library provides a wide range of mathematical routines such as random
number generators, special functions and least-squares fitting. There are
over 1000 functions in total with an extensive test suite.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "Hierachical Data Format 5"
set url "http://www.hdfgroup.org/HDF5"
set license "HDF license (BSD-like)"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
HDF5 is a data model, library, and file format for storing and managing
data. It supports an unlimited variety of datatypes, and is designed for
flexible and efficient I/O and for high volume and complex data. HDF5 is
portable and is extensible, allowing applications to evolve in their use
of HDF5. The HDF5 Technology suite includes tools and applications for
managing, manipulating, viewing, and analyzing data in the HDF5 format.
"
source $env(PSI_LIBMODULES)
set-family HDF5_serial
conflict hdf5
#%Module1.0
set whatis "a high performance implementation of the MPI standard."
set url "http://www.mpich.org/"
set license "BSD-like"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
MPICH is a high-performance and widely portable implementation of the
MPI Standard, designed to implement all of MPI-1, MPI-2, and MPI-3 (in-
cluding dynamic process management, one-sided operations, parallel I/O,
and other extensions).
"
source $env(PSI_LIBMODULES)
set-family MPI
setenv MPICC $PREFIX/bin/mpicc
setenv MPICXX $PREFIX/bin/mpicxx
setenv MPIF77 $PREFIX/bin/mpif77
setenv MPIF90 $PREFIX/bin/mpif90
setenv MPIFC $PREFIX/bin/mpif90
setenv MPIFORTRAN $PREFIX/bin/mpif90
setenv MPIEXEC $PREFIX/bin/mpiexec
setenv MPIRUN $PREFIX/bin/mpirun
#%Module1.0
module-whatis "open source MPI-2 implementation"
module-url "http://www.open-mpi.org/"
module-license "See \$OPENMPI_DIR/share/doc/openmpi/LICENSE"
module-maintainer "Achim Gsell <achim.gsell@psi.ch>"
module-help "
The Open MPI Project is an open source MPI-2 implementation that is
developed and maintained by a consortium of academic, research, and
industry partners. Open MPI is therefore able to combine the expertise,
technologies, and resources from all across the High Performance Computing
community in order to build the best MPI library available. Open MPI offers
advantages for system and software vendors, application developers and
computer science researchers.
"
module-addgroup MPI
setenv MPICC $PREFIX/bin/mpicc
setenv MPICXX $PREFIX/bin/mpicxx
setenv MPIF77 $PREFIX/bin/mpif77
setenv MPIF90 $PREFIX/bin/mpif90
setenv MPIFC $PREFIX/bin/mpif90
setenv MPIFORTRAN $PREFIX/bin/mpif90
setenv MPIEXEC $PREFIX/bin/mpiexec
setenv MPIRUN $PREFIX/bin/mpirun
#%Module1.0
set whatis "CERN root"
set url "http://root.cern.ch/"
set license "GNU LGPL v2"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
ROOT is an object-oriented framework aimed at solving the data analysis
challenges of high-energy physics. There are two key words in this
definition, object oriented and framework. First, we explain what we
mean by a framework and then why it is an object-oriented framework.
"
source $env(PSI_LIBMODULES)
setenv ROOTSYS $PREFIX
#%Module1.0
set whatis "Visualization ToolKit"
set url "http://www.vtk.org"
set license "Kitware, Inc., Insight Software Consortium (BSD-like)"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
The Visualization Toolkit (VTK) is an open-source, freely available
software system for 3D computer graphics, image processing and
visualization. VTK consists of a C++ class library and several
interpreted interface layers including Tcl/Tk, Java, and Python.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "HDF5 utility toolkit"
set url "http://amas.psi.ch/H5hut"
set license "BSD-like"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
H5hut is a veneer API for HDF5: H5hut files are also valid HDF5 files
and are compatible with other HDF5-based interfaces and tools. For
example, the h5dump tool that comes standard with HDF5 can export H5hut
files to ASCII or XML for additional portability. H5hut also includes
tools to convert H5hut data to the Visualization ToolKit (VTK) format
and to generate scripts for the GNUplot data plotting tool.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "Network Common Data Form"
set url "http://www.unidata.ucar.edu/software/netcdf/"
set license "BSD-like, see \${NETCDF_DIR}/share/doc/netcdf/COPYRIGHT"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
NetCDF is a set of software libraries and self-describing, machine-
independent data formats that support the creation, access, and
sharing of array-oriented scientific data.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "HDF5 utility toolkit"
set url "http://amas.psi.ch/H5hut"
set license "BSD-like"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
H5hut is a veneer API for HDF5: H5hut files are also valid HDF5 files
and are compatible with other HDF5-based interfaces and tools. For
example, the h5dump tool that comes standard with HDF5 can export H5hut
files to ASCII or XML for additional portability. H5hut also includes
tools to convert H5hut data to the Visualization ToolKit (VTK) format
and to generate scripts for the GNUplot data plotting tool.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "library and utilities for processing GIFs"
set url "http://sourceforge.net/projects/giflib/"
set license "X Consortium-like open-source license"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
giflib is a library for reading and writing gif images. It is API and ABI
compatible with libungif which was in wide use while the LZW compression
algorithm was patented.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "GNU Multiple Precision Arithmetic Library"
set url "http://gmplib.org/"
set license "GNU GPL v3 / GNU LGPL v3"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
GMP is a free library for arbitrary precision arithmetic, operating on
signed integers, rational numbers, and floating-point numbers. There is
no practical limit to the precision except the ones implied by the available
memory in the machine GMP runs on. GMP has a rich set of functions, and the
functions have a regular interface.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "library and utilities for processing GIFs"
set url "http://sourceforge.net/projects/giflib/"
set license "X Consortium-like open-source license"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
giflib is a library for reading and writing gif images. It is API and ABI
compatible with libungif which was in wide use while the LZW compression
algorithm was patented.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "GNU Mpc"
set url "http://www.multiprecision.org"
set license "GNU LGPL v3"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
Gnu Mpc is a C library for the arithmetic of complex numbers with
arbitrarily high precision and correct rounding of the result.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "GNU Multiple-Precision Floating-point library with correct Rounding"
set url "http://www.mpfr.org/"
set license "GNU GPL v3 / GNU LGPL v3"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
The main goal of MPFR is to provide a library for multiple-precision
floating-point computation which is both efficient and has a well-
defined semantics. It copies the good ideas from the ANSI/IEEE-754
standard for double-precision floating-point arithmetic (53-bit
significand).
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "set of C functions that support the manipulation of TIFF image files."
set url "http://www.libtiff.org/"
set license "BSD-like, see: http://libtiff.org/misc.html"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
This software provides support for the Tag Image File Format (TIFF), a
widely used format for storing image data. The latest version of the TIFF
specification is available on-line in several different formats, as are a
number of Technical Notes (TTN's).
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "block-structured AMR framework"
set url "https://ccse.lbl.gov/BoxLib/index.html"
set license "BSD"
set licensefile "license.txt"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
BoxLib contains all the functionality needed to write a parallel,
block-structured AMR application. The fundamental parallel abstraction is
the MultiFab, which holds the data on the union of grids at a level. A
MultiFab is composed of FAB's; each FAB is an array of data on a single
grid. During each MultiFab operation the FAB's composing that MultiFab are
distributed among the cores. MultiFab's at each level of refinement are
distributed independently. The software supports two data distribution
schemes, as well as a dynamic switching scheme that decides which approach
to use based on the number of grids at a level and the number of processors.
The first scheme is based on a heuristic knapsack algorithm; the second is
based on the use of a Morton-ordering space-filling curve. MultiFab
operations are performed with an owner computes rule with each processor
operating independently on its local data. For operations that require data
owned by other processors, the MultiFab operations are preceded by a data
exchange between processors. Each processor contains meta-data that is
needed to fully specify the geometry and processor assignments of the
MultiFab's. At a minimum, this requires the storage of an array of boxes
specifying the index space region for each AMR level of refinement. The
meta-data can thus be used to dynamically evaluate the necessary
communication patterns for sharing data amongst processors, enabling us to
optimize communications patterns within the algorithm. One of the advantages
of computing with fewer, larger grids in the hybrid OpenMP--MPI approach
is that the size of the meta-data is substantially reduced.
"
source $env(PSI_LIBMODULES)
#%Module1.0
# OPAL_PREFIX is also used by OpenMPI!
set dont-setenv { OPAL_PREFIX }
set whatis "Object Oriented Particle Accelerator Library"
set url "http://amas.psi.ch/OPAL"
set license "PSI"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
OPAL is a C++ framework for general particle accelerator simulations. It
includes various beam line element descriptions and methods for single
particle optics, namely maps up to arbitrary order, symplectic integration
schemes and lastly time integration. OPAL is based on IPPL (Independent
Parallel Particle Layer) which adds parallel capabilities. Main functions
inherited from IPPL are: structured rectangular grids, fields and parallel
FFT and particles with the respective interpolation operators. Other
features are, expression templates and massive parallelism (up to 65000
processors) which makes is possible to tackle the largest problems in the
field. A new iterative solver handles arbitrary complex boundary conditions
and benefiting from the new geometry class.
"
source $env(PSI_LIBMODULES)
setenv OPAL_EXE_PATH "${PREFIX}/bin"
set-family OPAL
#%Module1.0
set whatis "SuperLU_DIST - A library for direct solution of large, sparse, nonsymmetric systems of linear equations."
set url "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
set license "BSD"
set licensefile "README"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
SuperLU is a general purpose library for the direct solution of large,
sparse, nonsymmetric systems of linear equations on high performance
machines. The library is written in C and is callable from either C or
Fortran. The library routines will perform an LU decomposition with
partial pivoting and triangular system solves through forward and back
substitution. The LU factorization routines can handle non-square
matrices but the triangular solves are performed only for square
matrices. The matrix columns may be preordered (before factorization)
either through library or user supplied routines. This preordering for
sparsity is completely separate from the factorization. Working
precision iterative refinement subroutines are provided for improved
backward stability. Routines are also provided to equilibrate the
system, estimate the condition number, calculate the relative backward
error, and estimate error bounds for the refined solutions.
"
source $env(PSI_LIBMODULES)
#%Module1.0
module-whatis "plane wave/pseudopotential implementation of Density Functional Theory"
module-url "http://cpmd.org/"
module-license "?"
module-maintainer "Achim Gsell <achim.gsell@psi.ch>"
module-help "
The CPMD code is a parallelized plane wave / pseudopotential implementation
of Density Functional Theory, particularly designed for ab-initio molecular
dynamics.
"
#%Module1.0
source $env(PSI_LIBMODULES)
set whatis "GROMACS is a versatile package to perform molecular dynamics"
set url "http://www.gromacs.org/"
set license "See PREFIX/share/doc/COPYING"
set maintainer "Antonio Benedetto <antonio.benedetto@psi.ch>"
set help "
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
particles.
It is primarily designed for biochemical molecules like proteins, lipids and
nucleic acids that have a lot of complicated bonded interactions, but since
GROMACS is extremely fast at calculating the nonbonded interactions (that
usually dominate simulations) many groups are also using it for research on
non-biological systems, e.g. polymers.
"
set-family MPI
#%Module1.0
set whatis "Hierachical Data Format 5"
set url "http://www.hdfgroup.org/HDF5"
set license "HDF license (BSD-like)"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
HDF5 is a data model, library, and file format for storing and managing
data. It supports an unlimited variety of datatypes, and is designed for
flexible and efficient I/O and for high volume and complex data. HDF5 is
portable and is extensible, allowing applications to evolve in their use
of HDF5. The HDF5 Technology suite includes tools and applications for
managing, manipulating, viewing, and analyzing data in the HDF5 format.
"
source $env(PSI_LIBMODULES)
conflict hdf5_serial
set-family HDF5
#%Module1.0
set whatis "the Independent Parallel Particle Layer"
set url "http://amas.psi.ch/IPPL"
set license "PSI"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
IPPL is an object-oriented framework for particle based applications in
computational science requiring high-performance parallel computers. It
is a library of C++ classes designed to represent common abstractions in
these applications. IPPL is based on data-parallel programming at the
highest abstraction layer. Codes developed on serial workstations port
to all supported architectures, including parallel processors.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "ParMETIS - Parallel Graph Partitioning and Fill-reducing Matrix Ordering"
set url "http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview"
set license "See: \$PARMETIS_DIR/share/doc/parmetis/LICENSE.txt"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
ParMETIS is an MPI-based parallel library that implements a variety of
algorithms for partitioning unstructured graphs, meshes, and for computing
fill-reducing orderings of sparse matrices. ParMETIS extends the functioni-
ality provided by METIS and includes routines that are especially suited
for parallel AMR computations and large scale numerical simulations. The
algorithms implemented in ParMETIS are based on the parallel multilevel
k-way graph-partitioning, adaptive repartitioning, and parallel multi-
constrained partitioning schemes developed in our lab.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "Object-Oriented Solver Framework"
set url "http://trilinos.sandia.gov/"
set license "BSD-like"
set licensefile "Copyright.txt"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
Trilinos is a collection of open source software libraries, called packages,
intended to be used as building blocks for the development of scientific
applications. The word \"Trilinos\" is Greek and conveys the idea of \"a string
of pearls,\" suggesting a number of software packages linked together by a
common infrastructure. Trilinos was developed at Sandia National Laboratories
from a core group of existing algorithms, and utilizes the functionality of
software interfaces such as the BLAS, LAPACK, and MPI.
(Wikipedia)
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "opt-pilot"
set url "http://amas.psi.ch/OPAL"
set license "PSI"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "scripting language."
set url "http://www.python.org/"
set license "Python Software Foundation license (GPL-compatible)"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
Python is an easy to learn, powerful programming language. It has
efficient high-level data structures and a simple but effective
approach to object-oriented programming. Python’s elegant syntax
and dynamic typing, together with its interpreted nature, make it
an ideal language for scripting and rapid application development
in many areas on most platforms.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "a very powerful, easy to learn programming language"
set url "http://www.tcl.tk"
set license "BSD-lik"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic
programming language, suitable for a very wide range of uses, including
web and desktop applications, networking, administration, testing and many
more. Open source and business-friendly, Tcl is a mature yet evolving
language that is truly cross platform, easily deployed and highly
extensible.
"
source $env(PSI_LIBMODULES)
#%Module1.0
set whatis "graphical user interface toolkit"
set url "http://www.tcl.tk"
set license "BSD-like"
set maintainer "Achim Gsell <achim.gsell@psi.ch>"
set help "
Tk is a graphical user interface toolkit that takes developing desktop