CRC Software and Libraries

From CRCwiki

Contents 1 License Servers 2 High Performance Visualization (HPV) softwares 3 Mathematical Libraries 4 Installed Programs and Applications 4.1 Abaqus 4.2 Amber 4.3 ARB 4.4 Biosym 4.5 BLAST 4.6 Chemkin 4.7 FrameMaker (Sun Sparc) 4.8 Gamess 4.9 Gaussian 4.10 Gaussview 4.11 GROMACS 4.12 hdf5 4.13 HPC Cluster Tools 4.14 Intel Compilers 4.15 Interactive Data Language (IDL) 4.16 IMSL 4.17 InsightII 4.18 Jaguar (See Schrodinger Website) 4.19 Jmol 4.20 LAM/MPI 4.21 LAMMPS 4.22 MacroModel (See Schrodinger Website) 4.23 Maple 4.24 Mathematica 4.25 Matlab 4.26 Message Passing Tools 4.27 MPI 4.28 MPICH 4.29 NAMD 4.30 NWChem 4.31 OpenAFS 4.32 PathScale Compilers 4.33 Portland Group Compiler (Cluster Development Kit - CDK) 4.34 ProEngineer Wildfire 4.35 Rasmol 4.36 SAS - ND Faculty/Staff/Grad Students ONLY 4.37 Schrodinger 4.38 S-Plus 4.39 Sun Studio Compilers 4.40 Towhee 4.41 TotalView 4.42 Vis5D 4.43 VMD 4.44 XMGrace

License Servers

License Servers

High Performance Visualization (HPV) softwares

HPV system and software

Mathematical Libraries

All mathematical libraries are located in /opt/und/mathlib. The general tree architecture is: /opt/und/mathlib/library_name/cpu_architecture/library. The previous directory is a link to the lastest ACML version installed. Previous versions still can be accessed in the directory /opt/und/mathlib/library_name/cpu_architecture/library_version.

• ACML http://developer.amd.com/acml.jsp

ACML consists of the following main components:

1. A full implementation of Level 1, 2 and 3 Basic Linear Algebra Subroutines (BLAS), with key routines optimized for high performance on AMD Opteron™ processors.
2. A full suite of Linear Algebra (LAPACK) routines. As well as taking advantage of the highly-tuned BLAS kernels, a key set of LAPACK routines has been further optimized to achieve considerably higher performance than standard LAPACK implementations.
3. A comprehensive suite of Fast Fourier Transforms (FFTs) in both single-, double-, single-complex and double-complex data types.
4. Fast scalar, vector, and array math transcendental library routines optimized for high performance on AMD Opteron processors.
5. Random Number Generators in both single- and double-precision.

Depending on the compiler used and the architecture of the CPU, there is a corresponding library for each of them.

Four compilers are currently supported: Gfortran/GCC, Intel Ifort/ICC, Pathscale pathf90/pathcc, Portland pgf90/pgcc. For instance, gfortran64 directory contains ACML library to be linked with Gfortran compiler on a 64bits machine. pgi64_mp directory contains ACML library to be linked with Pathscale compiler on a 64bits using OpenMP directives.

To access DYNAMICALLY the library using Portland compiler from a Fortran program on a 64bits machine:

pgf90 -Wl,-rpath,/opt/und/mathlib/acml/x86_64/acml/pgi64/lib my_fortran_program.f90 -lacml

To access STATICALLY the library using Pathscale compiler from a Fortran program on a 64bits machine:

pathf90 /opt/und/mathlib/acml/x86_64/acml/pathscale64/libacml.a my_fortran_program.f90

The advantage to compile dynamically the library is that you will not have to recompile your program when the library will be updated.

For more information, please refer to the documentation in /opt/und/mathlib/acml/x86_64/acml/Doc or http://developer.amd.com/assets/acml_userguide.pdf

• Atlas: http://math-atlas.sourceforge.net/

• Blacs: http://www.netlib.org/blacs/

• Blas: http://www.netlib.org/blas/index.html

• FFTW: http://www.fftw.org

FFTW ("Fastest Fourier Transform in the West") is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).

• Goto: http://www.tacc.utexas.edu/resources/software/gotoblasfaq.php

The GotoBLAS codes are currently the fastest implementations of the Basic Linear Algebra Subroutines.

• Lapack : http://www.netlib.org/lapack/lug/index.html

• Linpack: http://www.netlib.org/linpack

• MKL: http://www3.intel.com/cd/software/products/asmo-na/eng/307757.htm

Intel® Math Kernel Library (Intel® MKL) offers highly optimized, extensively threaded math routines for scientific, engineering, and financial applications that require maximum performance.

1. Linear Algebra - BLAS and LAPACK

   Deploy BLAS and LAPACK routines that are highly optimized for Intel processors, and that provide significant performance improvements over alternative implementations. Intel MKL 9.1 is compliant with the new 3.1 release of LAPACK.

2. Linear Algebra - ScaLAPACK

   Available in the Cluster Edition only. The Intel MKL implementation of ScaLAPACK can provide significant performance improvements over the standard NETLIB implementation.

3. Linear Algebra- Sparse Solvers

   Solve large, sparse linear systems of equations with the PARDISO Direct Sparse Solver – an easy-to-use, thread-safe, high-performance, and memory-efficient software library licensed from the University of Basel. Intel MKL also includes Conjugate Gradient and FGMRES iterative sparse solvers.

4. Fast Fourier Transforms (FFT)

   Employ multi-dimensional FFT routines (1D up to 7D) with mixed radix support and a modern, easy-to-use C/Fortran interface. Intel MKL also provides a set of C routines ("wrappers") that mimic the FFTW 2.x and 3.0 interfaces making it easy for current FFTW users to compare performance with Intel MKL.

5. Fast Fourier Transforms for Distributed Memory Multiprocessors (Clusters)

   Available in the Cluster Edition only. Improve your FFT performance even more by distributing the work over a large number of processors.

6. Vector Math Library

   Increase application speeds with vectorized implementations of computationally intensive core mathematical functions (power, trigonometric, exponential, hyperbolic, logarithmic, and so on).

7. Vector Random Number Generators

   Speed up your simulations using our vector random number generators, which can provide substantial performance improvements over scalar random number generator alternatives.

8. LINPACK Benchmark

   Intel provides free LINPACK benchmark packages to help you obtain the highest possible benchmark results for your Intel® architecture-based systems.

• Petsc: http://www-unix.mcs.anl.gov/petsc/petsc-as/

PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication.

• Sundials: http://www.llnl.gov/CASC/sundials/

SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers) consists of the following four solvers:

1. CVODE solves initial value problems for ordinary differential equation (ODE) systems.
2. CVODES solves ODE systems and includes sensitivity analysis capabilities (forward and adjoint).
3. IDA solves initial value problems for differential-algebraic equation (DAE) systems.
4. KINSOL solves nonlinear algebraic systems.

Installed Programs and Applications

Abaqus

A finite element analysis for Engineering applications.

Amber

Assisted model building energy refinement.

ARB

The ARB (from Latin arbor, tree) program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

Biosym

See InsightII

BLAST

BLAST is used to match DNA sequences.

Chemkin

Chemkin is used to model chemical reactions.

FrameMaker (Sun Sparc)

Adobe FrameMaker is a word processor and document publishing package.

Gamess

General Atomic Molecular Electronic Structure Systems

Gaussian

Gaussian is an ab initio molecular modeling package.

Gaussview

Gaussview is a full-featured graphical user interface for Gaussian 98. With GaussView you can construct molecular systems of interest quickly and efficiently using its molecule building facility. You can also set up and run Gaussian calculations right from the interface, and monitor their progress as they run. When a calculation has completed, you can use GaussView to examine a variety of results graphically via its advanced visualization facilities.

GROMACS

hdf5

hdf5 is a general purpose library and file format for storing scientific data.

HPC Cluster Tools

MPI Tool Kit for Sun Sparc architecture

Intel Compilers

Interactive Data Language (IDL)

The IDL package is used for data viusualization, data reduction, and analysis.

IMSL

The IMSL libraries for math and statistics.

InsightII

MSI InsightII (aka Biosym) is used for the simulation of large molecular/biopolymer systems.

Jaguar (See Schrodinger Website)

Jaguar is an ab initio molecular modeling package.

Jmol

Jmol is a used to view and edit molcules in 3D.

LAM/MPI

LAMMPS

LAMMPS is classical molecular dynamics code, which stands for Large-scale Atomic/Molecular Massively Parallel Simulator.

MacroModel (See Schrodinger Website)

MacroModel is used to model molecules.

Maple

Maple is a symbolic math package.

Mathematica

Mathematica is a symbolic math package.

Matlab

MATLAB is an integrated mathematical computing, visualization package.

Message Passing Tools

MPT libraries and commands support parallel programming using MPI, pbm, and SHMEM.

MPI

See Message Passing Tools.

MPICH

NAMD

NAMD is a parallel, object-oriented molecular dynamics program designed for high-performance simulation of large biomolecular systems.

NWChem

NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction Project.

OpenAFS

OpenAFS is the Networked File System used for programs and user data at Notre Dame.

PathScale Compilers

Portland Group Compiler (Cluster Development Kit - CDK)

man pages also available for pgCC, pgcc, pgdbg, pgf77, pgf90, pghpf, pgprof

ProEngineer Wildfire

Rasmol

SAS - ND Faculty/Staff/Grad Students ONLY

Notre Dame has a site license for installation of SAS on institutionally and personally-owned machines.

Schrodinger

See Jaguar and MacroModel

S-Plus

Sun Studio Compilers

Towhee

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases.

TotalView

TotalView is a multiprocess debugger.

Vis5D

VMD

Visual Molecular Dynamics

XMGrace

XMGrace is a 2D plotting/graphing package. It can read text and netCDF files and output in several formats including PDF.