README March 30, 1999 BIOMOC A multispecies solute-transport model with biodegradation BIOMOC - Version 1.0 1999/03/10 Instructions for installation, execution, and testing are provided below. After installation, see the file doc\biomoc.txt in the BIOMOC installation directory for summary information on BIOMOC, including documentation references. For assistance, enhancement requests, or to report bugs, contact the Hydrologic Analysis Software Support Program by sending e-mail to h2osoft@usgs.gov. TABLE OF CONTENTS A. DISTRIBUTION FILES B. EXTRACTING FILES C. COMPILING D. INSTALLING E. RUNNING THE SOFTWARE F. TESTING A. DISTRIBUTION FILES The following distribution files (containing the software, test data sets, and information files) are currently available for UNIX systems: biomoc1.0.DGUX.tar.gz - Compiled for Data General AViiON under DG/UX 4.11 biomoc1.0.Solaris.tar.gz - Compiled for Sun UltraSPARC-II under Solaris 2.6 biomoc1.0.SGI.tar.gz - Compiled for Silicon Graphics Indigo (32-bit) under Irix 6.2 biomoc1.0.source.tar.gz - Source code only B. EXTRACTING FILES The compressed tar file, named biomoc1.0.OS.tar.gz, contains all the files needed to install and test BIOMOC on a computer with a particular operating system, where OS is a string indicating the operating system the distribution is intended for. If a version is not available for your operating system, the file biomoc1.0.source.tar.gz contains the source code and all other files needed to compile, install, and test the software on a UNIX-based computer. For either type of distribution, the directory biomoc1.0 is created (or overwritten) when the files are extracted from the tar file. If the biomoc1.0 directory already exists, you may want to delete or rename it before extracting the files. The following are the steps to extract the files from a distribution tar file. 1. If the tar file is not already in the directory under which you want the distribution installed, move it there. For example: mv biomoc1.0.____.tar.gz /usr/opt/wrdapp 2. If you are not in the directory where the tar file is located, go there. For example: cd /usr/opt/wrdapp 3. Uncompress the distribution file. For example: gunzip biomoc1.0.____.tar.gz 4. Extract the distribution files from the tar file. For example: tar -xvpof biomoc1.0.___.tar This creates the following directory structure (the contents of each directory are shown to the right): biomoc1.0 ; copy of this README file `-----bin ; compiled executable `-----doc ; documentation files `-----src ; Makefile and source code `-----test ; scripts to run verification tests `-----data ; standard data sets used in verification tests Notes: a) The bin directory is not included in the biomoc1.0.source.tar.gz distribution (it is created during compilation). b) Source code is included only with the biomoc1.0.source.tar.gz distribution. c) It is recommended that no user files be kept in the biomoc1.0 directory structure. If you do plan to put files in the biomoc1.0 directory structure, do so only by creating subdirectories of biomoc1.0. C. COMPILING If a compiled version of the software is not available for your computer, or if you want to build the executable yourself, follow the instructions in this section. If you have retrieved a pre-compiled distribution of the software, skip to the Installing section below. The source code is provided in the biomoc1.0.source.tar.gz distribution so that users can generate the executable themselves. No support can be provided for users generating their own versions of the software. In general, the requirements are a Fortran compiler and a minimal level of knowledge of the compiler and the UNIX operating system. As provided, the Makefile and source code are set up for use on Data General AViiON workstations running the DG/UX operating system. To generate a new executable, do the following: 1. Change directory to the source directory: cd biomoc1.0/src 2. Modify the beginning of the file named Makefile to correctly specify system-dependent variables: F77 Fortran compiler name FFLAGS Fortran compiler flags 3. Use the make program to initiate compilation of the source code and installation of the software: make [BINDIR=directory_for_links] See the Installing instructions below for an explanation of BINDIR. The make will: a. create the directories biomoc1.0/bin and BINDIR if they do not already exist, b. compile the source code, c. place the executable (biomoc) in biomoc1.0/bin, and d. place a link to the executable in BINDIR if specified. D. INSTALLING To make the executable (biomoc) easy to use, it should be installed in a directory included in the user's search path. The Makefile (input instructions to the UNIX make program--located in biomoc1.0/src) contains instructions to optionally place a link in a specified directory to the executable contained in biomoc1.0/bin. Use the following two commands to do this: cd biomoc1.0/src make install [BINDIR=directory_for_links] If BINDIR is specified, a link to the executable is placed in the specified directory. For example, if your search path consists of: /usr/bin:/usr/opt/bin:/usr/local/bin use the command: make install BINDIR=/usr/local/bin to make the executable accessible from any directory without requiring the full pathname of the software's location. Notes: a) Brackets "[xxx]" are used to indicate optional arguments to commands. b) To create and delete a link to the biomoc executable, the installer must have sufficient rights in the directory that BINDIR is set to. E. RUNNING THE SOFTWARE After BIOMOC is properly installed in a directory that is included in your PATH, it can be executed with the command "biomoc". Input data for the BIOMOC model is read from the file named "input.dat". Output is written to predefined output file names, all bearing the suffix ".out". F. TESTING Test data sets are provided to verify that the program is correctly installed and running on the system. The tests may also be looked at as examples of how to use the program. The directory biomoc1.0/test contains the scripts to run the tests. The directory biomoc1.0/data contains the input data and expected results for each test. Tests are usually run in the directory biomoc1.0/test, but they can be run in any user directory if the installation procedure was completed (make install performed). Run the tests using any of the commands in the table below. To test the installation, change to the biomoc1.0/test directory and type the command: ./test.sh [m [n]] If running from another directory, specify the full path to the script; for example: /usr/opt/wrdapp/biomoc1.0/test/test.sh [m [n]] where: m = the number of the first test to perform, default=1 n = the number of the last test to perform, default=3 For example: command what happens ------------------ ------------------------------------ ./test.sh runs all of the tests ./test.sh n runs test 'n' through the last test ./test.sh n m runs test 'n' through 'm' After the tests are completed, the results are compared to the expected results. If all goes well, there should be no differences. To clean up after the tests, type the command: ./clean.sh NOTE: the standard data sets included with the source code in biomoc1.0.source.tar.gz were created on a Data General AViiON workstation. You may notice slight numeric differences in the results on other computers. These are generally due to different round-off algorithms and the different architecture of the central processing unit chip. Also, slight differences in output formats may occur on other computers. The tests are described in the table below. Test is the test number and the usage column indicates how a file is used, with i for input and o for output. Note that the normal file suffixes of the input and output files have been replaced with "t1," "t2," and "t3" to indicate the test to which each set of files corresponds; the input file is normally named "input.dat" and the output files normally bear a ".out" suffix. test description of test and files file name & usage ---- ------------------------------------- ----------------- 1 Steady-state zero- and first-order decay BIOMOC input file input.t1 i summary of processed data biomoc.t1 o final heads biohead.t1 o grid block velocities biovel.t1 o final concentrations for solute 1 biocon1.t1 o final concentrations for solute 2 biocon2.t1 o final concentrations for population 1 biopop1.t1 o observation location 1 concentrations bioobs1.t1 o observation location 2 concentrations bioobs2.t1 o observation location 3 concentrations bioobs3.t1 o observation location 4 concentrations bioobs4.t1 o observation location 5 concentrations bioobs5.t1 o concentration profiles bioprof.t1 o 2 Transient zero- and first-order decay BIOMOC input file input.t2 i summary of processed data biomoc.t2 o final heads biohead.t2 o grid block velocities biovel.t2 o final concentrations for solute 1 biocon1.t2 o final concentrations for solute 2 biocon2.t2 o final concentrations for population 1 biopop1.t2 o observation location 1 concentrations bioobs1.t2 o observation location 2 concentrations bioobs2.t2 o observation location 3 concentrations bioobs3.t2 o observation location 4 concentrations bioobs4.t2 o observation location 5 concentrations bioobs5.t2 o concentration profiles bioprof.t2 o 3 Aerobic degradation of toluene and benzene BIOMOC input file input.t3 i summary of processed data biomoc.t3 o final heads biohead.t3 o grid block velocities biovel.t3 o final concentrations of toluene biocon1.t3 o final concentrations of benzene biocon2.t3 o final concentrations of oxygen biocon3.t3 o final conc. of toluene degraders biopop1.t3 o final conc. of benzene degraders biopop2.t3 o outflow concentrations bioobs1.t3 o concentration profiles bioprof.t3 o