User’s Guide on Software at UoW HPC Cluster Information Technology Services University of Wollongong ( Last updated on October 10, 2011) Contents 1 Requests for Software4 2 Environment Modules4 3 Software List4 4 How to Use7 4.1 Parallel Programming Libraries/Tools...................7 4.1.1 LAM/MPI.............................7 4.1.2 MPICH...............................7 4.1.3 MPICH2..............................7 4.1.4 OpenMPI..............................7 4.2 Compilers..................................8 4.2.1 GNU Compiler Collection (GCC).................8 4.2.2 Intel Fortran Compiler.......................8 4.2.3 Intel C Compiler..........................8 4.2.4 CMake...............................9 4.3 Scripting Languages............................9 4.3.1 Python...............................9 4.3.2 Perl.................................9 4.3.3 Java.................................9 4.4 Editors....................................9 4.4.1 Emacs................................9 4.4.2 Nano................................ 10 4.5 Math Libraries............................... 10 CONTENTS CONTENTS 4.5.1 FFTW................................ 10 4.5.2 FFTW3............................... 10 4.5.3 Intel Math Kernel Library (IMKL)................. 10 4.5.4 Basic Linear Algebra Subroutines (BLAS)............ 11 4.5.5 Linear Algebra PACKage (LAPACK)............... 11 4.5.6 Basic Linear Algebra Communication Subprograms (BLACS).. 12 4.5.7 Scalable LAPACK (ScaLAPACK)................. 12 4.5.8 Automatically Tuned Linear Algebra Software (ATLAS)..... 13 4.5.9 AMD Core Math Library (ACML)................. 13 4.5.10 GotoBLAS2............................ 14 4.6 Debuggers, Profilers and Simulators.................... 14 4.6.1 Valgrind............................... 14 4.6.2 Intel Debugger........................... 14 4.7 Graphics................................... 15 4.7.1 GNUPlot.............................. 15 4.8 Statistics and Mathematics Environments................. 15 4.8.1 R.................................. 15 4.9 Computational Chemistry.......................... 15 4.9.1 Quantum ESPRESSO....................... 15 4.9.2 GROMACS............................. 16 4.9.3 GAUSSIAN............................ 17 4.9.4 VMD................................ 18 4.9.5 NAMD............................... 18 4.9.6 ABINIT............................... 19 4.9.7 CPMD............................... 20 4.9.8 XCrySDen............................. 21 4.9.9 PSI3................................. 21 4.9.10 TINKER.............................. 22 4.9.11 MOPAC 2009............................ 23 4.9.12 DOCK............................... 23 4.9.13 NWChem.............................. 24 4.9.14 GAMESS.............................. 25 4.9.15 OpenBabel............................. 26 4.10 Informatics................................. 26 4.10.1 GhostScript............................. 26 4.10.2 ImageMagick............................ 26 4.11 Engineering................................. 26 CONTENTS CONTENTS 4.11.1 MATLAB.............................. 26 4.11.2 ANSYS............................... 31 4.11.3 ABAQUS.............................. 31 4.11.4 Ansoft Maxwell.......................... 31 4.11.5 LAMMPS.............................. 31 4.11.6 Materials Studio.......................... 32 4.12 Biology................................... 32 4.12.1 MrBayes.............................. 32 4.12.2 ATSAS............................... 33 3 SOFTWARE LIST 1 Requests for Software If you require software that is not installed on the UoW HPC cluster please send an email to the ITS admin team at hpc [email protected]. Please note: As there is currently no central budget for software licenses, any costs incurred for the requested software must be covered by user’s research group or the department of the university that the user is employed by. Please see the Section3 (Software List) for the details of the available software. 2 Environment Modules Package Environment Modules provide a great way to easily customize your shell environment to the requirements of whatever software you wish to use. They are available on the whole system. Always put the following line in your job script to active the environment modules: source /etc/profile.d/00-modules.sh 3 Software List Some software installed on the UoW HPC cluster is licensed and paid for by various departments and research groups on campus. The * under the ‘Prerequisite’ column indicates software that requires some discussion with the HPC admin to be able to access. Read the ‘How to Use’ section of this guide for more details. Please Note: All software installed on the UoW HPC cluster has passed the standard test suite (if existing). However, it is a user’s responsibility to check the correctness and validity of the software installed on the cluster prior to publishing any result by using them. Table 1: List of software Name Version Site Prerequisite 1. Parallel Programming Libraries/Tools (Sec. 4.1) LAMMPI 7.1.4 System MPICH 1.2.7 System MPICH2 1.3.1 System OpenMPI 1.3; 1.4.2; 1.4.3 System 2. Compilers (Sec. 4.2) GCC 4.1.2;4.5.2 System Intel Fortran Compiler 10.1.023; 11.1.046 System Intel C/C++ Compiler 10.1.023 System Continued on next page 4 3 SOFTWARE LIST Table 1 – continued from previous page Name Version Site Prerequisite CMake 2.8.3; 2.8.5 System 3. Scripting Languages (Sec. 4.3) Python 2.4.3 System Perl 5.12.2 System Java 1.6.0 17 Head-node 4. Editors (Sec. 4.4) Emacs 23.2.1 System Nano 2.2.6 System 5. Math Libraries (Sec. 4.5) FFTW 2.1.5 System FFTW3 3.2.2 System Intel MKL 10.2 System BLAS — System LAPACK 3.2.2 System BLACS — System SCALAPACK 1.8.0 System ATLAS 3.9.32 System ACML 4.4.0 System GotoBLAS2 1.13 System 6. Debuggers,Profilers and Simulators (Sec. 4.6) Valgrind 3.2.1 Head-node Intel Debugger 11.1.046 Head-node 7. Graphics (Sec. 4.7) GNUPlot 4.0 Head-node 8. Statistics and Mathematics Environments (Sec. 4.8) R 2.12.0 System 9. Computational Chemistry (Sec. 4.9) Quantum Espresso 4.2.1; 4.3 System GROMACS 4.5.1 System GAUSSIAN g03e01; g09a02 System * VMD 1.8.7; 1.9 System * NAMD 2.7b4; 2.7; 2.8 System * ABINIT 6.4.1 System CPMD 3.13.2; 3.15.1 System * Continued on next page 5 3 SOFTWARE LIST Table 1 – continued from previous page Name Version Site Prerequisite XCrySDen 1.5.21 System PSI3 3.4 System TINKER 5.0.19 System MOPAC2009 11.053 System DOCK 6.5 System * NWChem 6.0 System GAMESS 1Oct2010 System * OpenBabel 2.3.0 System 10. Informatics (Sec. 4.10) GhostScript 8.15 System ImageMagick 6.6.4-10 System 11. Engineering (Sec. 4.11) MATLAB R2010b; R2011a System ANSYS 12,13 System * ABAQUS 6.91 System * Ansoft Maxwell 14.0 System * LAMMPS 05Nov10 System Materials Studio 5.5 System * 12. Biology (Sec. 4.12) MrBayes 3.1.2 System ATSAS 2.4.1-4 System 6 4 HOW TO USE 4 How to Use 4.1 Parallel Programming Libraries/Tools 4.1.1 LAM/MPI To use LAM/MPI version 7.1.4 in the current shell, do %module load mpi/lam-7.1.4 NOTE: ‘%’ represents command line prompt all through this paper. 4.1.2 MPICH To use MPICH version 1.2.7 (gcc build) in the current shell, do %module load mpich/1.2.7-gcc 4.1.3 MPICH2 To use MPICH2 version 1.3.1 (gcc build) in the current shell, do %module load mpi/mpich2-1.3.1-gcc To use Intel Compiler build of MPICH2 %module load mpich2/1.3.1-itl 4.1.4 OpenMPI To use OpenMPI version 1.3 in the current shell, do %module load mpi/openmpi-1.3 To use OpenMPI version 1.4.2 in the current shell, do %module load mpi/openmpi-1.4.2 To use OpenMPI version 1.4.3 in the current shell, do %module load mpi/openmpi-1.4.3 OpenMPI 1.4.3 is RECOMMENDED as your default MPI environment. NOTE: MPI environment can be set for future shells by using environment switcher package. Please refer to ‘UOW HPC Cluster User Guide’ for further detail. 7 4.2 Compilers 4 HOW TO USE 4.2 Compilers 4.2.1 GNU Compiler Collection (GCC) GCC 4.1.2 is installed in system path which can be used directly. To use GCC version 4.5.2, do %module load gcc/4.5.2 in the command line or in your job script. 4.2.2 Intel Fortran Compiler The Intel Fortran Compiler is called ifort. To use Intel Fortran Compiler version 11.1.046, do %module load intel-fc/11.1.046 in the command line or add it in your job script. NOTE: This version is incompatible with intel-cc/10.1.023. To use Intel Fortran Compiler version 10.1.023, do %module load intel-fc/10.1.023 This version is compatible with intel-cc/10.2.023. To see all other versions of the compiler available do %module avail intel-fc Note that the debugger idb is now the graphical debugger. To use the non-graphical interface use idbc command. 4.2.3 Intel C Compiler The Intel C/C++ Compiler is called as icc and the C++ compiler is icpc. To use Intel C/C++ Compiler version 10.1.023, do %module load intel-cc/10.1.023 NOTE: This version is incompatible with intel-fc/11.1.046. To see all installed versions do %module avail intel-cc 8 4.3 Scripting Languages 4 HOW TO USE 4.2.4 CMake The cross-platform, open-source build system CMake is a family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and workspaces that can be used in the compiler environment of your choice. To use CMake, type module load cmake/2.8.3 or module load cmake/2.8.5 in the command line. 4.3 Scripting Languages 4.3.1 Python Python is installed system wide (which means user can submit python based applications to the queue system). To use python, do %python 4.3.2 Perl To use Perl, do module load perl/5.12.2 in your job script.