1. Advanced BioPSE NCRR How to Install and Configure J. Davison de St. Germain Chief Software Engineer SCI Institute 801-581-4078 December 2003 J. Davison de St. Germain Chief Software Engineer SCI Institute 801-581-4078 December 2003 dav@sci.utah.edu

2. Advanced BioPSE NCRR Installation Steps 1.Download software RPM (Linux) - Has everything Or... (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 datasets For Source Install only: 2.Install Thirdparty 3.Configure/Compile SCIRun

3. Advanced BioPSE NCRR Downloading 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

4. Advanced BioPSE NCRR Common 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 )

5. Advanced BioPSE NCRR Linux 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!

6. Advanced BioPSE NCRR 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

7. Advanced BioPSE NCRR Thirdparty 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)

8. Advanced BioPSE NCRR 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

9. Advanced BioPSE NCRR Other 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 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

10. Advanced BioPSE NCRR Machine 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

11. Advanced BioPSE NCRR OS 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

12. Advanced BioPSE NCRR Configure 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/thirdparty CC=gcc CXX=g++

13. Advanced BioPSE NCRR Common 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.

14. Advanced BioPSE NCRR Debugging 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).

15. Advanced BioPSE NCRR Config.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 | | int | main () | { | ; | return 0; | } configure:12327: result: not found

16. Advanced BioPSE NCRR Compiling 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.

17. Advanced BioPSE NCRR 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.

18. Advanced BioPSE NCRR Documentation Use the docs. They cover all of this in more detail… - http://software.sci.utah.edu/doc http://software.sci.utah.edu/doc But more importantly… - Let us know if you find any problems with them.

19. Advanced BioPSE NCRR 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.)

20. Advanced BioPSE NCRR