biopse ncrr scirun: getting started installation and configuration j. davison de st. germain...

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SCIRun: Getting StartedSCIRun: Getting Started

Installation and ConfigurationInstallation and Configuration

J. Davison de St. GermainJ. Davison de St. [email protected]

(801) 581-4078(801) 581-4078

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SCIRun: Install and ConfigureSCIRun: Install and Configure

• System Specs and RequirementsSystem Specs and Requirements• Third Party CodesThird Party Codes• Getting and Configuring SCIRunGetting and Configuring SCIRun• Environment VariablesEnvironment Variables• Using a Single Shared SCIRunUsing a Single Shared SCIRun• Using CVS LocallyUsing CVS Locally

http://software.sci.utah.edu/scirun.htmlhttp://software.sci.utah.edu/scirun.html

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System Specs and RequirementsSystem Specs and Requirements

Required OS and Build ToolsRequired OS and Build Tools• SGISGI• IRIX 6.5IRIX 6.5• MIPSPro Compilers (CC) 7.3.1.1mMIPSPro Compilers (CC) 7.3.1.1m

• LinuxLinux• Kernel 2.2.17Kernel 2.2.17• GCC 2.95.3GCC 2.95.3

• BothBoth• GNU Make 3.79.1GNU Make 3.79.1

http://software.sci.utah.edu/doc/TechnicalGuide/p1c1.htmlhttp://software.sci.utah.edu/doc/TechnicalGuide/p1c1.html

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Minimum System RequirementsMinimum System Requirements

Tested Systems: Gateway, Micron, Dell.Tested Systems: Gateway, Micron, Dell.http://software.sci.utah.edu/tested_systems/tested_systems.htmlhttp://software.sci.utah.edu/tested_systems/tested_systems.html

Processor(s)Processor(s) Main MemoryMain Memory Other HW/SWOther HW/SW

SGISGI250 MHz250 MHz

R10KR10K256 MB256 MB Texture Mapping Texture Mapping

Hardware/MemoryHardware/Memory

LinuxLinux700 MHz700 MHz

Pentium IIIPentium III256 MB256 MB

NVIDIA GeForce3 Graphics NVIDIA GeForce3 Graphics Card, XFree86 drivers Card, XFree86 drivers

version 1.0-1541version 1.0-1541


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Third Party SoftwareThird Party Software

• RequiredRequired• Tcl, Tk, Itcl, Itk, BLT, XercesTcl, Tk, Itcl, Itk, BLT, Xerces

• OptionalOptional• MPEGe LibMPEGe Lib• MPEG EncoderMPEG Encoder• LibimageLibimage• teemteem


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Third Party CodesThird Party Codes

• You can install all the third party You can install all the third party codes yourself, but we codes yourself, but we highlyhighly recommend using the SCIRun recommend using the SCIRun Thirdparty TarballThirdparty Tarball• Stable BuildStable Build• Build - v1.4.2 - Mar 16, 2002Build - v1.4.2 - Mar 16, 2002

• Development BuildDevelopment Build• Build - v1.5.1 - Apr 24, 2002Build - v1.5.1 - Apr 24, 2002

http://software.sci.utah.edu/downwiz/scirun-biopse/http://software.sci.utah.edu/downwiz/scirun-biopse/scirun-biopse_bundles.xml?package=fullscirun-biopse_bundles.xml?package=full

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Third Party Codes Cont.Third Party Codes Cont.

• Download tarball: Download tarball: Thirdparty_install.x.x.x.tar.gzThirdparty_install.x.x.x.tar.gz• Gunzip / untarGunzip / untar• cd Thirdparty_install.x.x.xcd Thirdparty_install.x.x.x• Set your compilers (must match SCIRun Set your compilers (must match SCIRun

compilers):compilers):• setenv CC gccsetenv CC gcc• setenv CXX g++setenv CXX g++• setenv TAR gtar # Need a gnu compatible tarsetenv TAR gtar # Need a gnu compatible tar


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Third Party Codes Cont.Third Party Codes Cont.

• Run Run (must have Python version 1.5.2 or higher!)(must have Python version 1.5.2 or higher!)• python install <base-path> <architecture> <compiler> python install <base-path> <architecture> <compiler>

<bit-size> [# procs]<bit-size> [# procs]

• E.g.: E.g.: • python install /usr/local/SCIRun_Thirdparty linux gcc-python install /usr/local/SCIRun_Thirdparty linux gcc-

3.0.4 32 43.0.4 32 4

• Creates directory structure:Creates directory structure:• /usr/local/SCIRun_Thirdparty/<version #>/<OS>/<compiler>//usr/local/SCIRun_Thirdparty/<version #>/<OS>/<compiler>/

bin, include, lib, man, srcbin, include, lib, man, src


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Getting and Configuring SCIRunGetting and Configuring SCIRun

• Go to sci websiteGo to sci website• Software: Software: www.sci.utah.edu/software• Documentation: Documentation: www.sci.utah.edu/doc

• Use configureUse configure• Configure verifies that your system has Configure verifies that your system has

the proper libraries, etc to build and run the proper libraries, etc to build and run SCIRunSCIRun


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SCIRun Directory StructureSCIRun Directory Structure

• Tarball creates (src files):Tarball creates (src files):

./SCIRun/src/./SCIRun/src/

Packages/Packages/

BioPSEBioPSE

CoreCore

DataflowDataflow

… …• User Creates (obj files):User Creates (obj files):

./SCIRun/sgi32opt./SCIRun/sgi32opt

sgi64dbgsgi64dbg

linux32opt linux32opt

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Using ConfigureUsing Configure

configure <options>configure <options>--with-thirdparty= --with-thirdparty=

/usr/local/SCIRun_Thirdparty/1.5.2/aix51/xlC-32bit/usr/local/SCIRun_Thirdparty/1.5.2/aix51/xlC-32bit--enable-package=“BioPSE Uintah”--enable-package=“BioPSE Uintah”--enable-optimize[=“your flags”] (default: –O2)--enable-optimize[=“your flags”] (default: –O2)--enable-debug--enable-debug--enable-64bit (or 32bit)--enable-64bit (or 32bit)--enable-sci-malloc (--disable-sci-malloc)--enable-sci-malloc (--disable-sci-malloc)--enable-assertion-level=X (X=0..3, default = 3)--enable-assertion-level=X (X=0..3, default = 3)--with-<other packages>=/path/to/package--with-<other packages>=/path/to/package--enable-verbosity (Use this before calling --enable-verbosity (Use this before calling ))


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Using Configure Cont.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

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Using Configure Cont.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

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Environment VariablesEnvironment 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

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Environment Variables Cont.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”

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Environment Variables Cont.Environment Variables Cont.

• Locations searched for data:• SCIRUN_DATA (directory path)• SCI_DATA (directory path)• PSE_DATA (directory path)

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Sharing a Single SCIRunSharing 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

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Using CVS LocallyUsing 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.htmlhttp://www.cvshome.org/docs/manual/cvs_13.html

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Install and Configure: QuestionsInstall and Configure: Questions

Questions?Questions?

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Using CVSUsing CVS

cvs checkout <SCIRun|BioPSE>cvs checkout <SCIRun|BioPSE>- Done onceDone once

cvs update –Pd [file/dir names]cvs update –Pd [file/dir names]- P => prune empty directoriesP => prune empty directories- d => include new directoriesd => include new directories- r <tag> => update to specified tag/revision r <tag> => update to specified tag/revision

number (sticky)number (sticky)- A => clear sticky tagsA => clear sticky tags- D <“04/15/02”> => update to this dateD <“04/15/02”> => update to this date

http://www.cvshome.org/docs/manual/http://www.cvshome.org/docs/manual/

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Using CVS Cont.Using CVS Cont.

cvs diff filenamecvs diff filename•What has changed in the fileWhat has changed in the file

cvs log filenamecvs log filename•Comments stored with each update Comments stored with each update to the fileto the file

cvs annotate filenamecvs annotate filename•Who “owns” each line in the fileWho “owns” each line in the file

biopse ncrr scirun: getting started installation and configuration j. davison de st. germain...

Documents

biopse ncrr scirun

scirun compilers

biopse ncrr system specs

party codesthird party

scirun thirdparty tarballyou

thirdparty usrlocalscirun

thirdparty linux gcc

src http