EPA/600/B-15/276
Quantitative Microbial Risk Assessment Tutorial
Installation of Software for Watershed Modeling in Support of
QMRA
Gene Whelan
Kurt Wolfe
Rajbir Parmar
Michael Galvin
U.S. Environmental Protection Agency
Office of Research and Development
National Exposure Research Laboratory
Athens, GA
Keewook Kim
University of Idaho
Idaho National Laboratory
Center for Advanced Energy Studies
Idaho Falls, Idaho
11/25/15
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Summary
This tutorial provides instructions for accessing, retrieving, and downloading the following software to
install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling:
SDMProjectBuilder (which includes the Microbial Source Module as part of the installation)
BASINS (including WinHSPF and WinHSPFIt)
SARA Timeseries Utility
HSPF_PEST_flow and HSPF_PEST_microbe
FORTRAN Library
PEST
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Installation of Software for Watershed Modeling in Support of QMRA
PURPOSE
Consolidate information for gaining access to software used in support of Quantitative Microbial Risk
Assessment (QMRA) modeling.
OBJECTIVE
Provide instructions for accessing, retrieving, and downloading software in support of Quantitative
Microbial Risk Assessment modeling to install on a host computer.
DEMONSTRATION
This tutorial provides instructions on how to access, retrieve, download, and install the following
software:
SDMProjectBuilder (which includes the Microbial Source Module as part of the installation)
BASINS (including WinHSPF and WinHSPFIt)
SARA Timeseries Utility
HSPF_PEST_flow and HSPF_PEST_microbe
FORTRAN Library
PEST
SOFTWARE ACCESS, RETRIEVAL, DOWNLOAD, AND INSTALLATION
Users should execute installation instructions on only those software products that
have not been previously installed or
have been previously installed, but require an updated version.
The software should be removed using the Microsoft Windows Add/Remove feature, except
"HSPF_PEST_flow.exe", "Inputjlow.in", "HSPF_PEST_microbe.exe", and "lnput_microbe.in".
"HSPF_PEST_flow.exe", "Inputjlow.in", "HSPF_PEST_microbe.exe", and "lnput_microbe.in" can be
removed by simply deleting them. If software does NOT need to be installed again, skip to the
appropriate point in the installation instructions.
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SDMProjectBuilder
The SDMProjectBuilder installation also includes installation of the Microbial Source Module (MSM),
even though they are separate software products. Documentation on the MSM is by Whelan et al.,
(2015a). If users have already downloaded SDMProjectBuilder, skip this step; otherwise, proceed with
installation.
1. The SDMProjectBuilder software contained in the zip file and titled "SDMPB.zip" can be
retrieved at:
O:\Public\QMRA\Software for Download\SDMPB
2. Download "SDMPB.zip".
The zip file contains Setup.exe and InstallSDMPB.msi. Setup.exe is the InstallShield
installation executable and InstallSDMPB.msi is the SDMPB Windows installer package.
Unzip the files to your computer. It is recommended to locate the files in a folder where you
have administrative privileges such as your user's folder (C:\Users\).
3. After downloading, run Setup.exe, and follow the installation instructions.
4. A Setup window will appear.
Welcome to the SDMPB Setup Wizard
The installer will guide you through the steps required to install SDMPB on your computer.
WARNING: This computer program is protected by copyright law and international treaties.
Unauthorized duplication or distribution of this program, or any portion of it may result in severe civil
or criminal penalties, and will be prosecuted to the maximum extent possible underthe law.
-------
5. Click "Next", and the "Select Installation Folder" window will appear. Select the folder path with
administrative privileges where you will install SDMProjectBuilder, such as the user's folder
(C:\Users\). In the example below, SDMProjectBuilder will be installed in
"C:\SDMPB\".
Select Installation Folder
The installer will install SDMPB to the following folder.
To install in this folder, click "Next". To install to a different folder, enter it below or click "Browse".
FnlHpr
Browse..
Disk Cost...
Install SDMPB for yourself, or for anyone who uses this computer:
@| Everyone
Just me
Cancel
6. Click "Next" and the "Confirm Installation" page will appear.
Confirm Installation
The installer is ready to install SDMPB on your computer.
Click "Next" to start the installation.
Cancel
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7. Click "Next" and SDMProjectBuilder will be installed.
Installing SDMPB
SDMPB is being installed
Please wail...
8. Once installation is finished, the "Installation Complete" page will appear.
Installation Complete
SDMPB has been successfully installed.
Click "Close" to exit.
Please use Windows Update to check for any critical updates to the .NET Framework.
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11. The user will need to have "Full control" on the folder where SDMProjectBuilder is installed. To
confirm user control, right-click on the folder where SDMProjectBuilder was installed (in this
example "C:\SDMPB\"), and select "Properties".
Restore previous versions
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12. The "Properties" window will appear, and select the "Security" tab.
SDMPB Propertie
General j Sharing | Secmity | Previous Versions | Customize |
SDMPB
Type: File folder
Location: C:\
Size: 438 MB (460,084.694 bytes)
Size on disk: 440 MB (461.451.264 bytes)
Contains: 626 Files. 52 Folders
Created:
Today. October 19.2015. 3 minutes ago
Attributes: 'f Read-only (Only applies to files in folder)
D Hidden
OK
Cancel
Apply
-------
13. Select "Users" in the "Group or user names" section, and click "Edit".
General | Sharing | Security | Previous Versions | Customize
Object name: C:\SDMPB
Group or user names:
^.Authenticated Users
&. SYSTEM
^.AdministratorsflVIERCEDESVAdministrators)
H Users (MERCEDES\Users
To change permissions, click Edit
Permissions for Users
Allow
Deny
Full control
Modify
Read & execute
List folder contents
Read
Write
For special permissions or advanced settings.
click Advanced.
Learn aboutaccess control and permissions
OK
Cancel
14. The "Permissions" for SDMPB folder will appear. In the window, select "Users" in "Group or user
names" section, and ensure "Allow" for "Full control" under the "Permissions for Users" section
is checked. Then, click "OK".
Security
Objectname: C:\SDMPB
Group or user names:
-^Authenticated Users
%SYSTEM
a.Administrators (MERCEDES\Administrators)
Si, Users (MERCEDES\Users)
Add...
Remove
Permissions for Users
Allow
Deny
Full control
Modify
Read & execute
List folder contents
Read
fn *
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Learn about access control and permissions
OK Cancel
Apply
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BASINS, WinHSPFS.O, and WinHSPFIt
If BASINS, WinHSPFS.O, and WinHSPFIt have already been downloaded to the computer, skip this step;
otherwise, proceed with the installation.
The BASINS installation package includes both forms of the HSPF model: WinHSPFS.O, the Windows
version with a user-friendly, user interface and WinHSPFIt, the "lite" version associated with batch
simulation for model calibration.
The version of BASINS being used with this workflow is one that has NOT been released through the
BASINS download web site (i.e., http://water.epa.gov/scitech/datait/models/basins/download.cfm). as
of yet. Hence, a beta version of the latest updates is available as an executable version, located at
O:\Public\QMRA\Software for Download\BASINS-WinHSPF-HSPFIt.
1. The BASINS, WinHSPFS.O, and WinHSPFIt software can be retrieved at:
O:\Public\QMRA\Software for Download\BASINS-WinHSPF-HSPFIt
2. Download "BASINS4.1.Updatela.2015.01.exe" to your computer, locating the file in a folder
where you have administrative privileges, such as your user's folder (C:\Users\).
BASINS4.1.Updatela.2015.01.exe is the InstallShield installation executable.
3. After downloading, run "BASINS4.1.Updatela.2015.01.exe", and follow the installation
instructions.
4. The following setup window will appear.
Setup - BASINS
*
^*
Welcome to the BASINS Setup
Wizard
This will install BASINS 4,1.1,2015.01 on your computer.
It is recommended that you dose all other applications before
continuing.
Click Next to continue, or Cancel to exit Setup.
Next>
Cancel
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5. Click "Next" and the following information page will appear.
If Setup - BASINS i t=>i|*=*
Information
Please read the following important information before continuing.
tyhen you are ready to continue with Setup, dick Next.
BASINS 4. 1 Update 1 - 20 1 5-0 1-12
Any previous version of BASINS 4.x should be uninstalled before proceeding.
Major Changes for Update 1:
- Updates the BASINS HSPF installation to version 12. 4r providing new dynamic
wave routing options in RCHRES and binary output options from BMPRAC
- Integrates the HSPF BMP Toolkit for representation of Low Impact Development
(LID) controls and a Sewer and Open Channel Design Tool, both of which
calculate FTABLES for the HSPF model, within WinHSPF 3.0.
- Provides an advanced wetiands setup capability within the BASINS HSPF setup
tool, with which a user can choose to represent wetiands as separate RCHRES
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6. Click "Next", and the "Select Destination Location" window will appear.
7. Choose the folder location where you would like BASINS to be installed. It is typically installed in
in "C:\BASINS41", as illustrated in the example below. If you only have administrative privileges
in special locations on your computer (e.g., C:\Users\), you may want to install the
software there.
|| Setup - BASINS
Select Destination Location
Where should BASINS be installed?
Setup will install BASINS into the following folder,
To continue, dick Next. If you would like to select a different folder, dick Browse.
Browse...
At least 493.9 MB of free disk space is required.
Cancel
-------
8. Click "Next" and you can specify a Start menu folder where the program's shortcuts will be
located.
Setup - BASINS
Select Start Menu Folder
Where should Setup place the program's shortcuts?
Setup will create the program's shortcuts in the following Start Menu folder.
To continue, dick Next. If you would like to select a different folder, dick Browse.
Browse...
^] Don't create a Start Menu folder
Cancel
9. Click "Next", and the following "Ready to Install" screen will appear:
Ready to Install
Setup is now ready to begin installing BASINS on your computer.
Click Install to continue with the installation, or dick Back if you want to review or
change any settings.
Destination location:
Setup type:
Full installation
Selected components:
BASINS Core Components
Tiles plug-in: View web map background layer from OpenStreetMap
HSPF and Related Programs
SWAT Databases
GWLF-E
Desktop Icons
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10. Click "Next", and then "Install". BASINS will be installed with HSPF.
H Setup - BASINS
Installing
Please wait while Setup installs BASINS on your computer.
Extracting files...
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11. Once the BASINS installation is finished, shortcut icons for BASINS 4.1, WinHSPF 3.0, and
WinHSPFIt will appear on your computer's Desktop.
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WinHSPFIt is a "lite" version of WinHSPF 3.0 and can runs HSPF on a Command window (e.g., batch
runs). WinHSPF 3.0 can run HSPF only through a user interface. WinHSPFIt is frequently coupled with
other software such as PEST, FRAMES, etc.
If the icons do not appear on the Desktop, locate the following executables- BASINS.exe, WinHSPF.exe,
and WinHSPFIt.exe - on the hard drive, where they are typically found in \BASINS41\bin,
\BASINS41\models\WinHSPF30\bin, and \BASINS41\models\HSPF\bin, respectively.
11
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SARA Timeseries Utility
Prior to installation, un-install any prior version of SARA Timeseries Utility tool. If asked whether to
remove shared components, answer Yes.
1. The SARA Timeseries Utility software product and an associated WDM file can be retrieved
from:
O:\Public\QMRA\Softwarefor Download\SARA Timeseries Utility
2. Download the following zip file to the folder of your choice:
SARA_Timeseries_Utility.zip.
The zip file contains two files:
o The executable saves text output as UTF-8, omits the Byte Order Marker at the
beginning of the file, skips the title line in the file if the title is blank, and skips
the date column if all date and time components are hidden.
o The WDM file, O40301010406.wdm, is used in the tutorial, which demonstrates
how a concentration time series is converted to a txt file (Whelan et al., 2015b).
Typically, the wdm is located in the HSPF folder within the working folder (e.g.,
\HSPF\).
In this example, it was saved to:
C:\Users\gwhelan\iemTechnologies\SARATimeSeriesUtility
ti*l - Mf * CDrflPuter * OSDisk (C:) ^ Users * gwhe an * TimeSeriesUtility f
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Name Date modified ~fype ^'ze
^[ SARA_Times_Series_Utility.zip 9/30/2015 2:01 PM WinZip File 3,308 KB
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12
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2. Open the SARA_Timeseries_Utility.zip file by double-clicking on it, and choose the Unzip button.
Is^rV-^^ * Computer > OSDisk [C:] * Users > gwhelan > TimeSeriesUtility > SARA_Times_Series_Utilrty
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USEPA
Name Date modified Type Size
ฃ O40301010406.wdm 10/6/2014 6:08 PM WDM File 1,400KB
ฃ SARA_Timeseries_Utility_2015-Q8-13.exe 8/13/2015 11:31 AM Application 2,768 KB
3; 1 5, r ' > 1 WinZip - SARA_Times_Series_Utility.zip
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3. Run the installer titled SARA Timeseries Utility2015-08-13.exe by double-clicking on it, either
from the folder
> Computer > OSDisk (C:) > Users > gwhelan > iemTechnologies > SARATimeSeriesUtility > SARA_Timeseries_Utility_2015-08-l:
File Edit View Tools Help
Organize1' Extract all files
pestl3
* Jj SARATimeSeriesUtility
SARA_Timeseries.Utility_2015-08-13,zip
> ^ SDMPB
SDMProjectBuilder.100214
!> . SDMProjectBuilder_101714
inMPrniprtRnnHpr 111314
Name
H5ARA_Timeseries_Utility_2015-08-13.exe
Type
Application
or from within the zip file.
I 3ฃ ~ i - I WinZip-SARA_Timeseries_Utility_2015-08-13.zip
zip Edit Share Backup Tools Settings View Help Upgrade
SA.RA_Timesene5_Utility_ 2015-08-13
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Selected 0 files, 0 bytes
Total 1 file, 2,768KB
13
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4. Running the installer as an Administrator may be required, depending on security settings and
the chosen installation location. Place it in the file location you created earlier. A Shortcut icon
for SARA Timeseries Utility should now be on your computer screen:
14
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HSPF-PEST
If the user has already downloaded the correct version of "HSPF_PEST_flow.exe", "lnput_flow.in",
"HSPF_PEST_microbe.exe," and "lnput_microbe.in" to the computer, skip this step; otherwise, proceed
with the installation. "HSPF_PEST_flow.exe" and "HSPF_microbe.exe" are executables compiled with
FORTRAN that prepares the inverse model PEST input files for HSPF flow and microbial parameter
calibrations. "lnput_flow.in" and "lnput_microbe.in" are default input files that contain folder locations
of HSPFIt [batch (or light) version of HSPF], observed data used in the calibration, and PEST. Users should
place these files in a folder where they have administrative privileges.
1. "HSPF_PEST_flow.exe", "Inputjlow.in", "HSPF_PEST_microbe.exe," and "lnput_microbe.in" are
located in a zip file, titled "HSPF-PEST.zip", which can be retrieved from:
O:\Public\QMRA\Software for Download\HSPF-PEST
2. Download "HSPF-PEST.zip" to any folder where the user has administrative privileges.
"HSPF_PEST_flow.exe" and "Inputjlow.in" MUST be in the same folder.
"HSPF_PEST_microbe.exe," and "lnput_microbe.in" MUST be in the same folder.
In this example, the files were placed in "C:\Temp\SDMProject\Manitowoc\HSPF-PEST".
ซ SDMProject > Manitowoc > HSPF_PEST
File Edit View Jools Help
Include in library ป Share with ป Burn New folder
s1 Temp
. pb48sc
^ SDMProject
Manitowoc
HSPF_PEST
Ji USEPA
. Users
a
Name Date modified
I' HSPF-PEST.iip 11/25/201512:32...
Type Size
WinZip File 69 KB
1 item
_ I Computer
3. Unzip the file.
ซ SDMProject > Manitowoc > HSPF_PEST t HSPF-PEST
File Edit View lools Help
Organize
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New folder
i=' a 9
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Manitowoc
. HSPF_PEST
HSPF-PEST
- HSPF-PEST.zip
4 items
Name
B! HSPF_PEST_flow.exe
B HSPF_PEST_microbe.exe
, , Inputjlow.in
, , Inp'Ut_microbe,in
w Date modified
Type
Size
9/16/2015 1:26 PM Application
10AO/2015 1:44 AM Application
11/25/2015 12:26 ... IN File
11/25/2015 12:26 ... IN File
85KB
108KB
1KB
1KB
15
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FORTRAN Library
To properly execute PEST input files for HSPF parameter calibration which is an executable, the
appropriate FORTRAN Library must be on the user's machine: "Intelฎ Visual Fortran Redistributables on
IA-32". If this software already exists on the machine, skip this install; otherwise, proceed with this
download to install.
1. Go to https://software.intel.com/en-us/articles/redistributable-libraries-of-the-intel-c-and-
fortran-compiler-for-windows.
2. Under "Links to the redistribution packages", download "Intel Visual Fortran Compiler for
Windows 11.1 update 9 Redistribution library package for IA32" by clicking on "Redistribution
library package for IA32".
11.1.060 update 5
Redistributable library package for IA32
Redistributable library package (or Intel 64
Redistributable library package Tor IA-64
Intel C++ Compiler for Windows
11.1.065 update 6
Redistributable library package for IA32
Redistributable library package for Intel 64
Redistributable library package Tor IA-64
Intel C++ Compiler for Windows
11.1.067 update 7
Redistributable library package Tor IA32
Redistributable library package Tor Intel 64
Redistributable library package Tor IA-64
Intel C++ Compiler for Windows
11.1.070 update 8
Redistributable library package Tor IA32
Redistributable library package Tor Intel 64
Redistributable library package Tor IA-64
Intel C++ Compiler for Windows
11.1 updates
Redistributable library package Tor IA32
Redistributable library package Tor Intel 64
Redistributable library package Tor IA-64
11.1.060 updates
Redistributable library package Tor IA32
Redistributable library package for Intel 64
Redistributable library package tor IA-64
Intel Visual Fortran Compiler for Windows
11.1.065 update S
Redistributable library package for IA32
Redistributable library package for Intel 64
- Redistributable library package for IA-64
Intel Visual Fortran Compiler for Windows
11.1.067 update 7
Redistributable library package for IA32
Redistributable library package for Intel 64
Redistributable library package for IA-64
Intel Visual Fortran Compiler for Windows
11.1.070 update 8
Redistributable library package for IA32
Redistributable library package for Intel 64
Redistributable library package for IA-64
Intel Visual Fortran Compiler for Windows
11.1 update 9
Cajdistributable library package for IA.3&
HeilidilUUUUIH HUIJli (JJlluyy lia Iulel64
Redistributable library package for IA-64
3. Select a folder where you have administrative privileges. In this example, the folder was
C:\Users\gwhelan\DLL download\Library Package IA32\
4. Execute "w_cprof_p_11.1.072_redist_ia32.exe".
5. An "Open File - Security Warning" window may appear. If so, click "Run", and a screen similar
to the following may appear.
16
-------
Do you wanl to run this file?
Name: ...sewook Kim\Desktop\w_cprof_p_11.1.072_redist_ia32.exe
Publisher: Intel (Ft) Software Products
Type: Application
From: C:\Users\Keewook Kim\Desktop\w_cprof_p_ll.l,072_redi...
Run
Cancel
0 Always ask before opening this file
While files from the Internet can be useful, this file type can potentially
harm your computer. Only run software from publishers you trust What's
the risk?
6. The "Preparing to Install..." window will appear, then disappear.
Preparing to Install...
Intel(R) Visual Fortran Redistributables for Windows* on IA-32
Setup is preparing the InstallShieid Wizard, which will guide you
through the program setup process. Please wait.
Extracting: Intel(R) Visual Fortran Redistributables tor Windows on
7. The InstallShieid window will appear.
Welcome to the InstallShieid Wizard for
Intel(R) Visual Fortran Redistributables for
Windows* on IA-32
The InstallShield(R) Wizard will install intel(R) Visual Fortran
Redistributables for Windows* on IA-32 on your computer. To
continue, click Next.
WARNING: This program is protected by copyright lav,' and
international treaties.
*0ther names and brands may be claimed as the property of
others.
ick Next 3
17
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8. Click "Next" and accept the license agreement.
Fortran Redistributable! for Windows* on IA-32 - InstallSh
^^m
License Agreement
Please read the following license agreement carefully.
IMPORTANT - READ BEFORE COPYING. DISTRIBUTING, INSTALLING OR
USING.
Do not copy, distribute, install, or use the Materials provided under this license
agreement ("Agreement"), until you have carefully read the following terms
and conditions.
By copying, distributing, installing, or otherwise using the Materials, you agree
to be bound by the terms of this Agreement. If you do not agree to the terms
of this Agreement, do not copy, distribute, install, or use the Materials.
End User License Agreement for the Intel(R) Visual Fortran Compiler -
O I accept the terms in the license agreement
I do not accept the terms in the license agreement
9. Click "Next", and the "Ready to Install the Program" screen will appear.
: - Redistributable; for Windows* on IA-32-I-:., shie ' ::
Ready to Install the Program
The wizard is ready to begin installation.
Click Install to begin the installation.
If you want to review or change any of your installation settings, click Back. Click Cancel to exit
the wizard.
-, Install
10. Click "Install".
Installing Intel(R) Visual Fortran Redistributable? for Windows* on IA-32
The program features you selected are being installed.
Please v^ait while the InstallShield Wizard installs Intel(R) Visual Fortran
Re distributable s for Windows* on IA-32. This may take several minutes.
18
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11. If "User Account Control" window appears during the installation, click "OK".
12. When the installation is complete, click "Finish".
^^^^^^" ^^M^^^^^^^^^^^^^^^^^^^^^^^^^^"
J Intel(R) Visual Fortran Redistributables for Windows* on IA-32 - InstallShield Wiz...
InstallShield Wizard Completed
The InstallShield Wizard has successfully installed Intel(R) Visual
Fortran Redistributables for Windows* on IA-32. Click Finish to
exit the wizard.
: Back
Finish
Cancel
13. The FORTRAN Library is now on your machine.
19
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PEST
If the user has already downloaded PEST to the computer, skip this step; otherwise, proceed with the
installation.
1. Go to http://www.pesthomepage.org/Downloads.php. and under "PEST version 13.3",
download the zip file titled "pestl3.zip" by clicking "PC version of PEST".
Download the late
>T version 13.3
PC version of PEST..
Unzip the contents to a directory cited in the PATH environment variable. (This is very
important as, when undertaking SVD-assisted parameter estimation, PEST runs the
parcalc.exe and picalc.exe utility programs. It is essential that the operating system
knows where to find these).
Make sure that directories holding older versions of PEST are no longer in the PATH
string, as old versions of parcatc.exe and picalc.exe are not compatible with the new
PEST.
Download 64bit versions of certain programs of the PEST suite compiled using the
Intel(R) 64 bit compiler.
Download BEOPEST for Windows.
Download the latest Unix version of PEST.
Unzip the contents to find a tar file with PEST source code, makefile and examples.
Copy the tar file to a suitable directory on your machine, for example a directory
named /pest. Then extract its contents using the "-xvf" switch. Follow the instructions
provided in the documentation for Unix PEST (see the link in the "Documentation"
section above).
2.
Unzip "pestl3.zip" to a folder where you have administrative privileges, such as your user's
folder (C:\Users\).
In the example below, a folder named "PEST" was created on the C: drive, so the full
folder extension is "C:\PEST", to indicate where "pestl3.zip" was unzipped.
iฃ^\ Iv1, ^Computer > OS (C) > PEST~^
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Date modified
3/11/2015 3:23 PM
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*t Search PEST
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There is no required installation process for PEST. The user can copy "pest.exe" from the folder where
"pestl3.zip" was unzipped and place it in a folder where the user can run "pest.exe" in a Windows
Command Window. The PEST manual ("postman.pdf") can be found in the "doc" folder (see above
figure). Running PEST separately will not be necessary, as an executable has been developed
(HSPF_PEST_flow.exe) to automatically run PEST to calibrate flow parameters associated with an HSPF
simulation.
DISCLAIMER
This document has been reviewed in accordance with U.S. Environmental Protection Agency policy and
approved for publication.
REFERENCES
Whelan, G., R. Parmar, G.F. Laniak. 2015a. Microbial Source Module (MSM): Documenting the Science
and Software for Discovery, Evaluation, and Integration. EPA/600/B-15/315. U.S. Environmental
Protection Agency, Athens, GA.
Whelan, G., M. Gray, P. Duda, K. Wolfe, R. Parmar, M. Galvin, M. Molina. 2015b. Quantitative Microbial
Risk Assessment Tutorial: Publishing a Microbial Density Time Series as a Txt File. EPA/600/B-15/274.
U.S. Environmental Protection Agency, Athens, GA.
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