SCIRun: Getting Started
BioPSE
Installation and Configuration
J. Davison de St. Germain
dav@cs.utah.edu
(801) 581-4078
NCRR
SCIRun: Install and Configure
BioPSE
• 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
NCRR
System Specs and Requirements
Required OS and Build Tools
• SGI
BioPSE
• 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
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Minimum System Requirements
BioPSE
Processor(s)
Main Memory
Other HW/SW
SGI
250 MHz
R10K
256 MB
Texture Mapping
Hardware/Memory
Linux
700 MHz
Pentium III
256 MB
NVIDIA GeForce3 Graphics
Card, XFree86 drivers
version 1.0-1541
http://software.sci.utah.edu/doc/TechnicalGuide/p1c2.html
Tested Systems: Gateway, Micron, Dell.
http://software.sci.utah.edu/tested_systems/tested_systems.html
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Third Party Software
• Required
BioPSE
• Tcl, Tk, Itcl, Itk, BLT, Xerces
• Optional
• MPEGe Lib
• MPEG Encoder
• Libimage
• teem
http://software.sci.utah.edu/doc/TechnicalGuide/p1c1.html
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Third Party Codes
BioPSE
• 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/scirunbiopse/scirun-biopse_bundles.xml?package=full
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Third Party Codes Cont.
BioPSE
•
•
•
•
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
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Third Party Codes Cont.
BioPSE
• 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 gcc3.0.4 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
NCRR
Getting and Configuring SCIRun
BioPSE
• 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
NCRR
SCIRun Directory Structure
• Tarball creates (src files):
./SCIRun/src/
Packages/
BioPSE
Core
Dataflow
…
• User Creates (obj files):
./SCIRun/sgi32opt
sgi64dbg
linux32opt
BioPSE
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Using Configure
BioPSE
 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
NCRR
Using Configure Cont.
• Important configure files
BioPSE
• 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.
BioPSE
• 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 Variables
BioPSE
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
NCRR
Environment Variables Cont.
• MALLOC_STATS (filename)
BioPSE
• 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”
NCRR
Environment Variables Cont.
• Locations searched for data:
BioPSE
• SCIRUN_DATA (directory path)
• SCI_DATA (directory path)
• PSE_DATA (directory path)
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Sharing a Single SCIRun
• Mostly for Groups of Users
BioPSE
• (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 Locally
BioPSE
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
NCRR
Install and Configure: Questions
BioPSE
Questions?
NCRR
Using CVS
BioPSE
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/
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Using CVS Cont.
BioPSE
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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