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How to Install and ConfigureHow to Install and Configure

J. Davison de St. GermainChief Software Engineer

SCI Institute

801-581-4078

December 2003

J. Davison de St. GermainChief Software Engineer

SCI Institute

801-581-4078

December 2003

dav@sci.utah.edu

Advanced BioPSE

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Installation StepsInstallation Steps1. Download software• RPM (Linux) - Has everythingOr... (for source install (Mac, SGI, Linux):• Thirdparty• We provide: Tcl/Tk, Xerces, MPEG, etc• We do not provide: Insight, PETSc, Matlab

• SCIRun• Packages (BioPSE,Teem,Insight,etc)

• Get example datasetsFor Source Install only:

2. Install Thirdparty3. Configure/Compile SCIRun

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Downloading SCIRunDownloading SCIRun

• Register the 1st time• Click on “Enter”

• Select SCIRun/BioPSE• Agree to License• Join Mailing List (scirun-users@sci.utah.edu)

• software.sci.utah.edu

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Common to SGI/Mac/LinuxCommon to SGI/Mac/Linux

•Grab the example datasets:-SCIRunData.1.20.1.tar.gz

(If you downloaded previous datasets, you can get updates instead of downloading everything. Eg: SCIRunData.1.20.0-to-1.20.1-update.tar.gz)

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LinuxLinux

•Grab the rpm’s! But make sure you get the right one (RH8, RH9, or Mandrake 9).-SCIRun-1.20.1-rh8.0.i386.rpm-SCIRun-1.20.1-rh9.0.i386.rpm-SCIRun-1.20.1-mdk9.0.i586.rpm

• > rpm -i SCIRun-1.20.1-rh9.0.i386.rpm-Must be root to install- Comes with everything you need!

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Mac/SGI/Linux (Source Distribution)Mac/SGI/Linux (Source Distribution)

• Grab SCIRun.1.20.1.tar.gz- This is the core SCIRun code

• Grab BioPSE and Teem Packages- These build upon and add functionality

to the SCIRun PSE

• Grab Insight and/or MatlabInterface-More specific packages that add

functionality

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Thirdparty SoftwareThirdparty Software

• If more than one user will need the Thirdparty, install it in a global place.- Eg: RPM installs Thirdparty to:

/usr/local/SCIRun/Thirdparty

• If it is just you, your home dir will do.

• Installation:- Mac: ./install.sh install-dir 32- Linux/SGI: python install install-dir 32|64 (32|64 == Number of bits for build)

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Thirdparty Install (cont)Thirdparty Install (cont)

• Lots of stuff will scroll by… you can just ignore it… at the very end it will tell you whether everything installed correctly:

MPEG - SUCCESS

TCL - SUCCESS

TK - SUCCESS

ITCL - SUCCESS

BLT - SUCCESS

TEEM - SUCCESS

XERCES - SUCCESS

ImageMagick - SUCCESS

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Other S/W You Can GetOther S/W You Can Get

SCIRun supports the following, but they are not in the Thirdparty:• Insight- www.itk.org

• Petsc- ftp.mcs.anl.gov/pub/petsc/petsc.tar.gz

Instructions for installing these packages:- software.sci.utah.edu/doc/Installation/ Guide/sec.opt_inst.html

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Machine RecommendationsMachine Recommendations

• Something fairly modern…-Linux - 1.5 GHz, 512 MB, 2 GB Disk (Modern Nvidia/ATI)-Mac - 1.2 GHz, 512 MB, 2 GB Disk-SGI - MIPS R10000 (or better), 512 MB, 2 GB Disk

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OS RecommendationsOS Recommendations

• Mac- Panther 10.3- gcc

• Linux- Redhat 8, Redhat 9- Mandrake 9- gcc 3.1

• SGI- IRIX 6.5- Compiler: 7.3.1.3m

• Windows – Requesting Funding

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Configure Is Your FriendConfigure Is Your Friend

• mkdir ./SCIRun/darwin32dbg• cd darwin32dbg- You can have multiple binary directories (eg:

sgi64opt, linux32dbg, etc) all based on the same source tree.

• ../src/configure--enable-package=“BioPSE Teem”--enable-debug--enable-32bit--with-thirdparty=/path/to/thirdpartyCC=gccCXX=g++

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Common Reasons Configure FailsCommon Reasons Configure Fails

• Thirdparty moved- After compiling the Thirdparty software, you move it

someplace else.

• Missing libraries- Not installed or in unusual place.

• Conflicting libraries- Have old libraries system libraries that conflict with

upgraded libraries.

• LD_LIBRARY_PATH- Have libraries listed in this environment variable that

conflict with standard system libraries.

• Different compilers used- Compiled Thirdparty with a different compiler than you

compiled SCIRun with. Or some system libraries were compiled with a different compiler/OS.

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Debugging ConfigureDebugging Configure

• Edit config.log and search for the problem. - It will give you a compile line,-And the program it tried to compile.

• Try it by hand to see what is going on (see next slide).

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Config.logConfig.log• configure:9917: checking for required Tcl components......• configure:9958: checking for tcl library and headers (not-optional)• configure:10027: g++ -o conftest

-I/usr/sci/projects/SCIRun/Thirdparty/1.20/Darwin/gcc-3.1-32bit/include -I/usr/sci/projects/SCIRun/Thirdparty/1.20/Darwin/gcc-3.1-32bit/src/tcl/generic -g -fno-common -dynamic -fcoalesce-templates -Wno-long-double -L/usr/sci/projects/SCIRun/Thirdparty/1.20/Darwin/gcc-3.1-32bit/lib -L/usr/sci/projects/SCIRun/Thirdparty/1.20/Darwin/gcc-3.1-32bit/lib conftest.cc -ltcl >&5

• | #line 12276 "configure"• | /* confdefs.h. */• | #define HAVE_STRINGS_H 1• | #define HAVE_INTTYPES_H 1• | #define HAVE_STDINT_H 1• | /* end confdefs.h. */• | • | #include <tcl.h>• | • | int• | main ()• | {• | ;• | return 0;• | }• configure:12327: result: not found

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Compiling SCIRunCompiling SCIRun

• Once configure is done… gmake Can be run from anywhere in the object tree.Or... gmake -j# Where # is the number of processors to use to

compile. Helps to speed compilation up significantly… if you have multiple processors to spare.

Or... gmake lib/libPackages_BioPSE_Core_Datatypes.so

Useful to compile only what you are currently working on.

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Compiling (cont)Compiling (cont)• Files worth knowing about:- configVars.mk- Almost everything is defined in here: (Directory

paths to thirdparty, top of src tree, top of obj tree, compiler options, etc.)

- Makefile- Standard(ish) make file (uses configVars.mk)

- Sub.mk files- We use a single make file for the whole tree.

Each directory has a sub.mk file in it that will be pulled into the make. The sub.mk file specifies what to build in the given directory and any sub-directories that should be traversed by the make system.

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DocumentationDocumentation

•Use the docs. They cover all of this in more detail…- http://software.sci.utah.edu/doc

•But more importantly…-Let us know if you find any problems with them.

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Questions?Questions?

• dav@sci.utah.edu• 801-581-4078• (Hint: If you can display an

xterm remotely on my computer, we can usually solve your problem quickly.)

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