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SCIRun: Getting Started

Learn how to install and configure SCIRun software with step-by-step instructions. Includes system requirements, third-party codes, and environment variables.

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SCIRun: Getting Started

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  1. SCIRun: Getting Started • Installation and Configuration • J. Davison de St. Germain • dav@cs.utah.edu • (801) 581-4078

  2. SCIRun: Install and Configure • System Specs and Requirements • Third Party Codes • Getting and Configuring SCIRun • Environment Variables • Using a Single Shared SCIRun • Using CVS Locally http://software.sci.utah.edu/scirun.html

  3. System Specs and Requirements • Required OS and Build Tools • SGI • IRIX 6.5 • MIPSPro Compilers (CC) 7.3.1.1m • Linux • Kernel 2.2.17 • GCC 2.95.3 • Both • GNU Make 3.79.1 http://software.sci.utah.edu/doc/TechnicalGuide/p1c1.html

  4. Minimum System Requirements • Tested Systems: Gateway, Micron, Dell. • http://software.sci.utah.edu/tested_systems/tested_systems.html http://software.sci.utah.edu/doc/TechnicalGuide/p1c2.html

  5. Third Party Software • Required • Tcl, Tk, Itcl, Itk, BLT, Xerces • Optional • MPEGe Lib • MPEG Encoder • Libimage • teem http://software.sci.utah.edu/doc/TechnicalGuide/p1c1.html

  6. Third Party Codes • You can install all the third party codes yourself, but we highly recommend using the SCIRun Thirdparty Tarball • Stable Build • Build - v1.4.2 - Mar 16, 2002 • Development Build • Build - v1.5.1 - Apr 24, 2002 • http://software.sci.utah.edu/downwiz/scirun-biopse/scirun-biopse_bundles.xml?package=full

  7. Third Party Codes Cont. • Download tarball: Thirdparty_install.x.x.x.tar.gz • Gunzip / untar • cd Thirdparty_install.x.x.x • Set your compilers (must match SCIRun compilers): • setenv CC gcc • setenv CXX g++ • setenv TAR gtar # Need a gnu compatible tar http://software.sci.utah.edu/doc/TechnicalGuide/p1c3.html

  8. Third Party Codes Cont. • Run (must have Python version 1.5.2 or higher!) • python install <base-path> <architecture> <compiler> <bit-size> [# procs] • E.g.: • python install /usr/local/SCIRun_Thirdparty linux gcc-3.0.4 32 4 • Creates directory structure: • /usr/local/SCIRun_Thirdparty/<version #>/<OS>/<compiler>/ • bin, include, lib, man, src http://software.sci.utah.edu/doc/TechnicalGuide/p1c3.html

  9. Getting and Configuring SCIRun • Go to sci website • Software: www.sci.utah.edu/software • Documentation: www.sci.utah.edu/doc • Use configure • Configure verifies that your system has the proper libraries, etc to build and run SCIRun http://software.sci.utah.edu/doc/TechnicalGuide/p1c2.html

  10. SCIRun Directory Structure • Tarball creates (src files): • ./SCIRun/src/ • Packages/ • BioPSE • Core • Dataflow • … • User Creates (obj files): • ./SCIRun/sgi32opt • sgi64dbg • linux32opt

  11. Using Configure • configure <options> --with-thirdparty= /usr/local/SCIRun_Thirdparty/1.5.2/aix51/xlC-32bit --enable-package=“BioPSE Uintah” --enable-optimize[=“your flags”] (default: –O2) --enable-debug --enable-64bit (or 32bit) --enable-sci-malloc (--disable-sci-malloc) --enable-assertion-level=X (X=0..3, default = 3) --with-<other packages>=/path/to/package --enable-verbosity (Use this before calling ) http://software.sci.utah.edu/doc/TechnicalGuide/p1c2.html

  12. Using Configure Cont. • Important configure files • config.status • Includes the configure command used to configure this build • config.cache • Stores information about the current system that can speed the configure process • Warning: this can bite you if configure gets it wrong the first time! • config.log • Information about the configure run

  13. Using Configure Cont. • Configure creates a number of important files. Look in these to determine how your system is set up! • sci_defs.h • #define SCI_ASSERTION_LEVEL 3 • #define HAVE_MPI • #define SCI_32BITS • configVars.mk • Location of libs and include files for all supported packages • Compilers (CC,CXX,F77) • Compiler Flags • Basic build rules for .cc, .c, .f, etc • This file is used (included) in the Makefile

  14. Environment Variables • Helpful Enviroment Variables That Can Be Set Before Running SCIRun: • THREAD_NO_CATCH_SIGNALS • When using Pthreads, do not try to handle signals • SCI_DBXCOMMAND (“winterm –c dbx –p %d &”) • Debugger command to run on error • MALLOC_STRICT • Help catch bad memory references (only if using SCI malloc) • MALLOC_TRACE (filename) • Name of file to save malloc info in

  15. Environment Variables Cont. • MALLOC_STATS (filename) • Name of file to save malloc stats in • MALLOC_LAZY • Don’t audit memory all the time • SCI_SIGNALMODE (“ask”,”r”,”d”…) • What to do when an error occurs • SCI_DEBUG (stream:[+/-]) • List of debug output streams to turn on (file to write output to) • E.G.: “threadwatch:+,memwatch:+mem.out”

  16. Environment Variables Cont. • Locations searched for data: • SCIRUN_DATA (directory path) • SCI_DATA (directory path) • PSE_DATA (directory path)

  17. Sharing a Single SCIRun • Mostly for Groups of Users • (Not developers) • Single Shared Copy of SCIRun • Installed by main user or admin • Common location • Each SCIRun Installation can take up to 350+ MB • Permissions must be Set Correctly • Or pre-compile all dynamically compiled files initially • ./SCIRun/sgi64opt/on-the-fly-libs

  18. Using CVS Locally • You can set up a CVS repository locally to manage your changes to SCIRun code/modules. • Keep it in sync using the command… • > cvs import http://www.cvshome.org/docs/manual/cvs_13.html

  19. Install and Configure: Questions • Questions?

  20. Using CVS • cvs checkout <SCIRun|BioPSE> • Done once • cvs update –Pd [file/dir names] • P => prune empty directories • d => include new directories • r <tag> => update to specified tag/revision number (sticky) • A => clear sticky tags • D <“04/15/02”> => update to this date http://www.cvshome.org/docs/manual/

  21. Using CVS Cont. • cvs diff filename • What has changed in the file • cvs log filename • Comments stored with each update to the file • cvs annotate filename • Who “owns” each line in the file

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