How to Install and Configure
Advanced BioPSE
J. Davison de St. Germain
Chief Software Engineer
SCI Institute
801-581-4078
dav@sci.utah.edu
December 2003
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Installation Steps
1.
Download software
Advanced BioPSE
•
RPM (Linux) - Has everything
Or... (for source install (Mac, SGI, Linux):
•
Thirdparty
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We provide: Tcl/Tk, Xerces, MPEG, etc
We do not provide: Insight, PETSc, Matlab
•
SCIRun
•
Packages (BioPSE,Teem,Insight,etc)
•
Get example datasets
For Source Install only:
2.
3.
Install Thirdparty
Configure/Compile SCIRun
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Downloading SCIRun
• software.sci.utah.edu
Advanced BioPSE
• Register the 1st time
• Click on “Enter”
• Select SCIRun/BioPSE
• Agree to License
• Join Mailing List
(scirun-users@sci.utah.edu)
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Common to SGI/Mac/Linux
Advanced BioPSE
• 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.1.20.0to-1.20.1-update.tar.gz)
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Linux
Advanced BioPSE
• 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)
Advanced BioPSE
• 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 Software
Advanced BioPSE
• 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)
Advanced BioPSE
• 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 Get
Advanced BioPSE
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 Recommendations
Advanced BioPSE
• 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 Recommendations
• Mac
Advanced BioPSE
- 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 Friend
• mkdir ./SCIRun/darwin32dbg
• cd darwin32dbg
Advanced BioPSE
- 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/thirdparty
CC=gcc
CXX=g++
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Common Reasons Configure Fails
• Thirdparty moved
Advanced BioPSE
- 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 Configure
Advanced BioPSE
• 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.log
Advanced BioPSE
• 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-3.132bit/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"
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| /* 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 SCIRun
• Once configure is done…
Advanced BioPSE
 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)
• Files worth knowing about:
Advanced BioPSE
- 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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Documentation
Advanced BioPSE
• 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?
Advanced BioPSE
• 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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Advanced BioPSE
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