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Experienced PHG Users
For those of you who have used the PHG in the past, you might want to skip ahead to installing version 2.9.2 to begin using the new software right away.
Please take the time to fill out our Registration Form. This will enable us to keep you informed of new developments, bug fixes, etc.
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Our software package (phg.2.9.2.tar.Z) and this web site (simsetweb.tar) are available for downloading via Web FTP. The following link will take you to a directory. From there, click to select the item you wish to download, then use "Save Target as" to save the file to your computer (the exact method for doing this will depend on your browser).
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This version introduces a few changes to the makefile: even experienced users of the PHG should follow the installation instructions carefully. However, installation has been made simpler for the most part, the one exception being that there are different instructions for compiling with 64-bit compilers.
To install SimSET, download the software package from
as described in Downloading above.
The software package is compressed. Many personal computers are configured to automatically decompress such files. Alternatively, the package may be decompressed using free software such as Adobe Reader, or from the command line on a computer running Unix or Linux:
From the UNIX prompt in the directory containing phg.2.9.2.tar.Z enter:
- anymachine% uncompress phg.2.9.2.tar.Z
- anymachine% tar -xvf phg.2.9.2.tar
When you extract the tar archive a directory structure will be setup which contains the SimSET software. The main level of this directory structure is named "2.9.2".
The directory structure will look like this:
There is also a shell script in the directory, make_all.sh.
In order to build the software you will need to edit simset.make. The file is found in the make.files directory. This has extensive internal consistency checking turned on and will be very helpful in verifying that the installation is valid. We don't recommend changing the makefile to reduce the debug-checks or using optimization, as it makes it more difficult to discover numerical issues. (Note, this can occur on different systems when prototypes for functions like "cos()" are not where we expect them to be; due to the brilliance of "C", these things are often not reported by the compiler but do result in unwanted numerical errors.)
Near the top of the make files you will find the following parameter which must be changed to point to the SimSET directory structure for your system:
- SIMSET_PATH = /Users/useruser/Desktop/2.9.2
You need to replace "/Users/useruser/Desktop/2.9.2" with your system's path structure.
There is also a "flag" variable and a compiler variable that must be set. The flag structure allows you to specify compiler options, while the compiler variable lets you specify precisely which C compiler is used on your system. SimSET has been compiled on the following system types:
- # SUN_OS
- # SGI_OS
- # SGI64_OS
- # ALPHA_OS
- # DEC_ULTRIX
- # DGUX
- # MPW
- # _MWERKS_
- # RS6000 (IBM)
- # HP_OS
- # WINNT
- # MAC_10
For example, the file is currently set to run on a Macintosh running the Macintosh Unix (Darwin) at the University of Washington (some comment lines deleted for clarity):
- # Suggested compiler flags for Macintosh Unix (Darwin)
OS_CFLAGS = -DDARWIN -g
- # LINUX
# Suggested compiler flags for LINUX
# OS_CFLAGS = -DGEN_UNIX -DLINUX
To compile on a Linux system, you would comment out (with a "#")
the Macintosh Unix (Darwin) OS_CFLAGS and de-comment (remove the "#") before the LINUX OS_CFLAGS:
If there are not specific compiler flags set for your system, try setting just the -DGEN_UNIX flag and work from there. Please share any discoveries about compiling on your system with us--and if you find you cannot get SimSET to compile, contact us.
one new change to be made for people using 64-bit compilers (which
seems to be most users these days). Go to the src directory (find
it at the top level of your SimSET directory) and edit the file
LbTypes.h. The line
/* #define LB_TYPE_USE_SYS_INTS */
should be decommented (i.e., remove the "/*" and "*/"):
Save the file and you're finished. We consider the 64-bit version to be a beta version, but we encourage people to use it and let us know if they run into problems.
After these changes have been made, you should be able to run the script "make_all.sh" at the top level of the SimSET directory structure. This script will remove any outdated object files that might exist and do a complete build. It will then create all of the symbolic links that you need to make in order to run all of the utilities. (Depending on your compiler settings, there may be many warnings. This is something we are working on reducing. These warnings do not usually cause run-time problems.)
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This can be a tricky operation. The nature of Monte Carlo simulations makes it difficult to verify that they are operating properly. A primary source for problems arises in the installation of the package. As noted above, small things like missing prototypes can throw a program off course without creating any warning flags.
The first form of validation is the compilation process. You should not receive any errors from the compiler. As noted above, there may be a number of warnings. For instance, in one of the "printf" routines we use an escape character that is not supported in some flavors of UNIX. The compiler will print a warning about this. The results of this situation do not cause data corruption, they just limit the beauty of the printed information.
The second form of validation comes from the sample data provided in the "samples" directory. In particular, we recommend that you run the fastTest simulation in the samples/fastTest subdirectory. Read samples/fastTest/%%ReadMe%% for more details on how to run the simulation and analyze the results. Successful completion of the fastTest simulation indicates that your installation performs as we expect. More subtle problems may still be present. For this reason, we strongly advise that you always approach your SimSET data with a critical eye, wary of the pitfalls of computer simulations.
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We are happy to provide support for your use of SimSET. Feel free to E-mail us at: firstname.lastname@example.org for any and all problems you encounter. We are currently a little short-staffed, so please allow ample time for us to respond!
This work supported by PHS Grant #CA42593 - Tumor Detection and Quantitation with Emission Tomography
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Last revised by: Robert Harrison Revision date: 24 January 2014