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FOQUS
(Framework for Optimization, Quantification of
Uncertainty and Sensitivity)
INSTALL MANUAL
Version 2015.3.0
March 24, 2015

FOQUS Installation Manual

This Material was produced under the DOE Carbon Capture Simulation Initiative
(CCSI), and copyright is held by the software owners: ORISE, LANS, LLNS,
LBL, PNNL, CMU, WVU, et al. The software owners and/or the U.S. Government
retain ownership of all rights in the CCSI software and the copyright and patents
subsisting therein. Any distribution or dissemination is governed under the terms
and conditions of the CCSI Test and Evaluation License, CCSI Master NonDisclosure Agreement, and the CCSI Intellectual Property Management Plan. No
rights are granted except as expressly recited in one of the aforementioned
agreements.

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Rev. 0

Table of Contents
1.

Read This First ............................................................................................................. 1-1

2.

Introduction................................................................................................................. 2-1

3.

4.

5.
6.

Third-Party Packages ................................................................................................... 3-1

3.1.
3.2.
3.3.
3.4.
3.5.
3.6.
3.7.
3.8.
3.9.
3.10.
3.11.
3.12.
3.13.
3.14.
3.15.
3.16.
3.17.
3.18.

Optional Packages ....................................................................................................... 4-6

4.1.
4.2.
4.3.
4.4.
4.5.
4.6.
4.7.
4.8.

GAMS ............................................................................................................................... 4-6
Java .................................................................................................................................. 4-7
Apache Ant ...................................................................................................................... 4-7
Git .................................................................................................................................... 4-7
CMA ................................................................................................................................. 4-7
NLopt ............................................................................................................................... 4-8
Alfresco OpenCMIS Extension .......................................................................................... 4-8
Apache Chemistry ............................................................................................................ 4-8

CCSI Software Dependencies........................................................................................ 5-8
Windows Installation Proceedure ................................................................................ 6-9
6.1.
6.2.

7.

Python ............................................................................................................................. 3-2
PySide .............................................................................................................................. 3-2
Numpy ............................................................................................................................. 3-2
SciPy ................................................................................................................................ 3-2
Matplotlib ........................................................................................................................ 3-3
pyparsing ......................................................................................................................... 3-3
pywin32 (Windows only) .................................................................................................. 3-3
Python-Dateutils .............................................................................................................. 3-3
Python-ntlm ..................................................................................................................... 3-4
Py4J ................................................................................................................................. 3-4
networkx.......................................................................................................................... 3-4
pycrypto ........................................................................................................................... 3-4
adodbapi .......................................................................................................................... 3-5
GitPython ......................................................................................................................... 3-5
GitDB ............................................................................................................................... 3-5
D3 .................................................................................................................................... 3-5
SLF4J ................................................................................................................................ 3-6
JSON.org .......................................................................................................................... 3-6

Install ............................................................................................................................... 6-9
Uninstall .......................................................................................................................... 6-9

Manual Installation Procedure ..................................................................................... 7-9

7.1.
7.2.

Installation ...................................................................................................................... 7-10
Uninstall ......................................................................................................................... 7-11

8.

Running FOQUS from an svn checkout ........................................................................8-11

9.

Building a Windows installer .......................................................................................9-11
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10.

Optimziation Plug-ins ............................................................................................ 10-12

11.

Testing .................................................................................................................. 11-12

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1. READ THIS FIRST
Most users should not need this manual. The best way to install FOQUS is to use the
FOQUS Bundle installer, which in addition to installing FOQUS, installs TurbineLite,
SimSinter, and PSUADE. This installation manual provides additional information about the
FOQUS installer and installation on non-windows operating systems like Linux and OS X. This
manual also contains information useful to developers of FOQUS, and users wishing to build a
custom installer with different versions of third-party libraries.

2. INTRODUCTION
There are two methods of installation. The first method is to use the Windows installer. The
installer provides FOQUS and all third-

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3.1. Python
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

Python
2.7.3 or higher (not Python 3) (32-bit recommended on Windows)
Copyright (c) 2001-2013 Python Software Foundation
Needed for FOQUS and the graphical interface
http://python.org
http://python.org/download/
Python interpreter
http://docs.python.org/2/license.html

3.2. PySide
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

PySide
1.2.1 or higher (32-bit recommended on Windows)
Copyright (C) 2013 Digia Plc and/or its subsidiaryies
Provides a graphical user interface (GUI) toolkit
http://qt-project.org/wiki/Category:LanguageBindings::PySide
http://qt-project.org/wiki/PySide_Binaries_Windows
A python interface for the Qt graphical interface library. On Windows PySide
provides the Qt libraries. On other platforms such as Linux PySide and Qt may
be packaged separately.
LGPL version 2.1, see http://qt-project.org/wiki/About-PySide

3.3. Numpy
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

Numpy
1.7 or higher (32-bit recommended on Windows)
Copyright (c) 2005-2013, NumPy Developers
Needed for the optimization framework
http://www.numpy.org/
http://sourceforge.net/projects/numpy/files/
Array processing/mathematics module for Python
http://www.numpy.org/license.html

3.4. SciPy
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

SciPy
0.12.0 or higher (32-bit recommended on Windows)
Copyright (c) 2003-2013, SciPy Developers
Needed for some optimization solvers and some UQ GUI components
http://www.scipy.org/
http://sourceforge.net/projects/scipy/files/
Common numerical methods for Python
http://www.scipy.org/scipylib/license.html

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3.5. Matplotlib
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

Matplotlib
1.3.0 or higher (32-bit recommended on Windows)
Copyright (c) 2013, Matplotlib Development Team
Needed to visualize optimization and UQ results
http://matplotlib.org/
http://matplotlib.org/downloads.html (Windows 32 bit)
A Python plotting library
http://matplotlib.org/users/license.html

3.6. pyparsing
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

pyparsing
2.0.1
Copyright (c) 2003-2013, Paul T. McGuire
Needed by Matplotlib
http://pyparsing.wikispaces.com/
http://sourceforge.net/projects/pyparsing/
For parsing expressions
http://pyparsing.wikispaces.com/share/view/5698048?replyId=5724804

3.7. pywin32 (Windows only)
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

pywin32
Build 218
Copyright (c) 1994-2008, Mark Hammond
Needed to determine short names for Window files in UQ module
http://sourceforge.net/projects/pywin32/
http://sourceforge.net/projects/pywin32/files/pywin32/
Python for Windows extensions
Python Software Foundation License

3.8. Python-Dateutils
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

Python-Dateutils
1.5
Copyright (c) 2003-2011, Gustavo Niemeyer
Used by the Turbine client software and Matplotlib
http://labix.org/python-dateutil
http://labix.org/python-dateutil
Dateutils is used by Matplotlib and the Turbine Client libraries
Python Software Foundation License

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3.9. Python-ntlm
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

Python-ntlm
1.0.1
Copyright (c) 2001 Dmitry A. Rozmanov
Used by the Turbine client software
https://code.google.com/p/python-ntlm/
https://code.google.com/p/python-ntlm/source/checkout
Python-ntlm is used for authentication features in the Turbine Client library
LGPL v3

3.10. Py4J
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

Py4J
0.8.1
Copyright (C) 2009, Barthelemy Dagenais
Used by the data management framework
http://py4j.sourceforge.net/
http://py4j.sourceforge.net/download.html
Allows Java objects to be used in Python
BSD

3.11. networkx
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

networkx
1.91
Copyright (C) 2004-2012, NetworkX Developers
Used by the data management framework for display dependencies
https://networkx.github.io/
https://networkx.github.io/download.html
Graph and Graph visualization software
BSD type, https://networkx.github.io/documentation/latest/reference/legal.html

3.12. pycrypto
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

pycrypto
2.6.1
Mostly Public Domain, HMAC.py is Copyright Python Foundation
Used by data management framework
https://www.dlitz.net/software/pycrypto/
https://www.dlitz.net/software/pycrypto/
Python cryptography module.
Mostly Public Domain, HMAC.py has Python License and was derived from
Python 2.2

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3.13. adodbapi
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

adodbapi
2.6.0.6
Copyright (C) 2002 Henrik Ekelund, versions 2.1 and later by Vernon Cole
Direct access to TurbineLite database
http://adodbapi.sourceforge.net/
http://sourceforge.net/projects/adodbapi/
Module for ADO database interface
LGPL 2.1 or optionally a later version

3.14. GitPython
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

GitPython
1.0.1
Copyright (C) 2008, 2009 Michael Trier and contributors, 2010-2015
Sebastian Thiel
For performing Git operations in DMF
https://pypi.python.org/pypi/GitPython/1.0.1
https://pypi.python.org/pypi/GitPython/1.0.1
Module for interfacing with Git
BSD (https://github.com/gitpython-developers/GitPython/blob/master/LICENSE)

3.15. GitDB
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

gitdb
0.6.4
Copyright (C) 2011, Sebastian Thiel
For performing Git operations in DMF
https://pypi.python.org/pypi/gitdb
https://pypi.python.org/pypi/gitdb
GitPython dependency
BSD (https://github.com/gitpython-developers/gitdb/blob/master/LICENSE)

3.16. D3
Package:
Version:
Copyright:
Purpose:
Homepage:
Download:
Description:
License:

D3
3.5.6
Copyright (C) 2015 Mike Bostock
Used by DMF to display data dependencies
http://d3js.org/
http://d3js.org/
Visualization library
BSD (https://github.com/mbostock/d3/blob/master/LICENSE)

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3.17. SLF4J
Package:
Version:
Purpose:
Homepage:
Download:
Description:
License:

slf4j
1.7.10
Logging in DMF Java code
http://www.slf4j.org
http://www.slf4j.org/download.html
Java logging library jar
MIT (http://www.slf4j.org/license.html)

3.18. JSON.org
Package:
Version:
Purpose:
Homepage:
Download:
Description:
License:

json.org
20150729
Creation and processiong of JSON data objects in Java for DMF
http://www.json.org/java/index.html
http://www.json.org/java/index.html
Java JSON data object library
Custom (http://www.json.org/license.html)

4. OPTIONAL PACKAGES
The following packages are optional and may be installed before or after installing FOQUS.
These generally operate as separate programs. FOQUS will function without these packages,
however some feature may not work. The need for these packages depends on how you want to
use FOQUS.
These packages are not provided with the Windows FOQUS or FOQUS Bundle installers
and must be downloaded and installed separately.

4.1. GAMS
Package:
Version:
Purpose:
Homepage:
Download:
Description:

License:

GAMS
24.1.3 (32-bit)
Needed to run the heat integration
http://www.gams.com/
http://www.gams.com/download/ (Windows 32 bit)
The General Algebraic Modeling System (GAMS) is a high-level modeling
system for mathematical programming and optimization, which consists of a
language compiler and a stable of integrated high-performance solvers. The heat
integration tool is modeled and implemented in GAMS.
The purchase information for user licenses can be found in
http://www.gams.com/sales/sales.htm.

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4.2. Java
Package:
Version:
Purpose:
Homepage:
Download:
Description:
License:

Java
Oracle Java 8 or higher
Needed to run the data management framework and iREVEAL plug-in
https://www.java.com/en/
https://www.java.com/en/
http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads2133151.html (JDK 8)
Java runtime environment to execute Java code. Java JDK for compilation of
additional dependencies in for server based DMF.
http://www.oracle.com/technetwork/java/javase/downloads/jre-6u21-license159054.txt

4.3. Apache Ant
Package:
Version:
Purpose:
Homepage:
Download:
Description:
License:

Apache Ant
1.9.6
To compile additional dependencies in the server based DMF.
http://ant.apache.org/index.html
http://ant.apache.org/srcdownload.cgi
Java library and command line tool for building Java applications.
http://www.apache.org/licenses/LICENSE-2.0.html (Apache Version 2.0)

4.4. Git
Package:
Version:
Purpose:
Homepage:
Download:
Description:
License:

Git
2.6.0 or higher
Needed to run the data management framework lite
https://git-scm.com/
https://git-scm.com/
Git used as a repository to store data for the DMF lite
https://github.com/git/git (GPLv2)

4.5. CMA
Package:
Version:
Copyright:
Author:
Purpose:
Homepage:
Download:
Description:

CMA
1.1.02
Copyright (c) 2014 Inria
Nikolaus Hansen
Derivative free optimization algorithm (included in FOQUS, no need to install)
https://www.lri.fr/~hansen/cmaesintro.html
https://www.lri.fr/~hansen/cmaes_inmatlab.html#python
Python module for CMA-ES. This is the only fully functional derivative-free
optimization (DFO) algorithm currently implemented. This module can be used
with parallel objective function evaluation and can be restarted if optimization is
interrupted or more iteration is desired.

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License:

BSD 3-Clause (included in cma.py comments)

4.6. NLopt
Package:
Version:
Purpose:
Homepage:
Download:
Description:
License:

NLopt
2.4.2
Optional DFO solvers, contains gradient methods, but not supported by FOQUS
http://ab-initio.mit.edu/wiki/index.php/NLopt
http://ab-initio.mit.edu/wiki/index.php/NLopt
A selection of optimization solvers currently does not support parallel objective or
check pointing.
LGPL, some solvers have less restrictive licensing

4.7. Alfresco OpenCMIS Extension
Package:
Version:
Purpose:
Homepage:
Download:
Description:
License:

alfresco-opencmis-extensions
0.7
Used by the DMF to communicate with Alfresco
https://code.google.com/a/apache-extras.org/p/alfresco-opencmis-extension/
https://code.google.com/a/apache-extras.org/p/alfresco-opencmisextension/downloads/list
Java library dependency for communicating with Alfresco CMIS interface
Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)

4.8. Apache Chemistry
Package:
Version:
Purpose:
Homepage:
Download:
Description:
License:

Apache Chemistry
0.10.0
Used by the DMF to communicate with Alfresco
https://chemistry.apache.org/
https://chemistry.apache.org/java/download.html
Java library dependency for communicating with CMIS repositories
Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)

5. CCSI SOFTWARE DEPENDENCIES
There are several other CCSI software packages that FOQUS depends upon for full functionality.
The easiest way to install these is to use the FOQUS Bundle installer, which installs everything
needed to run FOQUS. These packages may also be downloaded and install individually form
the CCSI web site.
• TurbineLite – Job queuing system from simulation jobs
•

SimSinter – Standard .NET interface to simulation software, and graphical interface for
configuration files that define simulation inputs and outputs

•

PSUADE – Needed for UQ portions of FOQUS.

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The following CCSI packages are not currently provided by the FOQUS Bundle, but provide
additional surrogate model functionality to FOQUS. They can be downloaded from the CCSI
website:
•

ALAMO – build simple algebraic surrogate models

•

iREVEAL – Surrogate models for CFDs

6. WINDOWS INSTALLATION PROCEEDURE
This is officially supported and tested for Windows 7, 32 and 64 bit. It may also work on other
versions of Windows; however it has not been fully tested. This section provides information
about the FOQUS windows installer. The best way to install FOQUS is to use the FOQUS
Bundle installer, which provides additional required CCSI software.

6.1. Install
1. Uninstall any previously installed version of FOQUS (see Section 4.2)
2. Download the MSI file from
https://www.acceleratecarboncapture.org/drupal/product/foqus
3. In the Windows file explorer double click the installer
4. The installation will proceed without asking any questions
5. The working directory for a user is set the first time you run FOQUS. This setting is
stored in $HOME/.foqus.cfg on Linux or Mac, and %APPDATA%.foqus.cfg on
Windows. The working directory can be changed in the FOQUS settings, or be editing
the confutation file.
6. Install optional software.
7. See Section 10 for testing the installation.
The install location is generally C:\Program Files\FOQUS\foqus_version\ or C:\Program Files
(x86)\FOQUS\foqus_version\
Start menu items are created for documentation and starting FOQUS. The Turbine_console
menu item sets up an environment with the Turbine client scripts in the PATH for easy use.

6.2. Uninstall
1.
2.
3.
4.

Open the Windows Control Panel
Select programs
Select uninstall a program
Right click on FOQUS and select uninstall

7. MANUAL INSTALLATION PROCEDURE
This procedure should work on platforms that support Python and PySide. This should work on
Linux and Mac, however these platforms are not as well tested as Windows 7. The Windows
MSI installer is generally the preferred install method. On Linux most of the third party Python
modules are packaged by the distribution maintainers, and can be installed through the
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distribution’s package manager. TurbineLite and SimSinter only run on Windows, so FOQUS
running on non-windows platforms will either not run windows based simulators or run them on
remote machines.

7.1. Installation
1. Install Python 2.7.3 (or higher in the 2.7 series) (http://python.org/download/). There are
also several Python distributions that will provide most or all of the required packages
(See http://www.scipy.org/install.html for a list of additional Python distributions). In
Linux Python is generally available through the standard package manager.
2. Install the required packages. Download information is provided, but you will need to
select the appropriate package and version for your system. For a Linux install, these
packages should be available in the distributions package management system.
§

Install PySide version 1.2 or higher (http://qtproject.org/wiki/PySide_Binaries_Windows)

§

Install Numpy version 1.7 or higher (http://sourceforge.net/projects/numpy/files/)

§

Install SciPy version 0.12 or higher (http://sourceforge.net/projects/scipy/files/)

§

Install Matplotlib version 1.3 or higher (http://matplotlib.org/downloads.html)

§

Install pywin32 (windows only)
http://sourceforge.net/projects/pywin32/files/pywin32/

§

Install Python-requests

§

Install networkx

§

Install py4j

§

Other required third-party packages are automatically installed

3. Install FOQUS. The install may require admin or root privileges.
§
§

Download the FOQUS source zip from
https://www.acceleratecarboncapture.org/drupal/product/sim-based_optimize
Extract the files to a convenient directory.

§

Open a terminal or command prompt Window.

§

At the command prompt change to the directory of the install files.

§

Change to the foqus subdirectory

§

Type “setup.py install” in Windows or “python setup.py install” in Linux. You
may need to install as root in Linux or have admin privileges in Windows. The
install argument is important, without it nothing will be installed. If you do not
have root privileges, you may use the “setup.py install --user” command.

4. The working directory is set the first time you run FOQUS. This setting is stored in
$HOME/.foqus.cfg in Linux or Mac, and %APPDATA%.foqus.cfg in windows. The
working directory can be changed in the FOQUS settings.
5. Install optional software.
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6. See Section 10 for information about testing the install.

7.2. Uninstall
The following steps can be used to uninstall FOQUS, if it was installed manually by the above
procedure. You may wish to leave the Turbine Client files, if you want to uninstall FOQUS but
not the Turbine Client.
• Determine the directory where the python packages are installed. On a standard
Windows install this would be C:\Python27\Lib\site-packages.
• Go to the site packages directory.
• Delete the FOQUS files and directories.
o Delete foqus_*
• Delete the Turbine client egg file (TurbineCient-*.egg).
• Open the easy-install.pth file in WordPad (NotePad will not properly recognize the line
breaks).
• Delete lines for FOQUS and the Turbine Client
o ./turbineclient*
o ./foqus_*
• In the Windows file explorer go to the Python scripts directory (Usually
c:\Python27\Scripts).
• Delete the file foqus.py
• Delete the turbine client scripts turbine_*

8. RUNNING FOQUS FROM AN SVN CHECKOUT
1. Install Python and Modules from Section 3. Python 2.7.x is required, but newer versions
of the listed modules are most likely fine.
2. Install TurbineClient
a. Check the TurbineClient out from svn.
b. Install using setup.py script and follow instructions provide with TurbineClient
3. Check out the FOQUS project from svn/
4. You should now be able to run the foqus.py script without installing FOQUS.
5. (Optional) Install any optional modules from Section 4 that you need

9. BUILDING A WINDOWS INSTALLER
The following section provides instructions for building Windows installer MSI file. Py2exe and
WiX are used to create a windows MSI installer that does not require separate installation of
third-party software. Py2exe bundles everything into a self-contained directory including the
python interpreter, modules, the Turbine Client, and FOQUS. This is packaged for installation
by WiX.
1. Two additional pieces of software are required to build the MSI file. Both are freely
available.

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a. Py2exe creates the exe files and bundles the required Python modules. It can be
downloaded from http://www.py2exe.org/
b. WiX creates Windows installer MSI files and can be downloaded from
http://wixtoolset.org/
2. Install Python and the required modules. See the procedure in section 5.1 steps 1 and 2.
3. Run the “python setup.py wix” from the command line, in the same directory as the batch
file.
4. The above step should have created an MSI called foqus_installer.msi.

10. OPTIMZIATION PLUG-INS
The FOQUS working directory contains a subdirectory called user_plugins. This directory
contains Python code for user provided optimization plug-ins. FOQUS will check this directory
when it starts to see what optimization methods are available. If you have not set the FOQUS
working directory, you should run FOQUS once and exit before installing plugins to create the
directory structure, or you can create the user_plugins subdirectory yourself to add plugins
before starting FOQUS the first time.
At this early development stage, only the CMA-ES plug-in is fully functional. This plug-in
requires a third party Python module that is made available by Nikolaus Hansen
(https://www.lri.fr/~hansen/) under a BSD style license. This module is included with the
FOQUS installer. If you are using an older version of FOQUS and have installed cma.py in your
user_plugins directory, you should delete it.

11. TESTING
This section provides a simple test procedure to see if FOQUS was installed properly. This
method assumes you used the Windows MSI installer, but a similar procedure can be used to test
other install methods.
The Turbine Gateway installation is required to run simulations, but the FOQUS installation can
be tested on some provided example problems without it. This test does not require turbine.
1. From the Windows start menu select the CCSI Tools -> FOQUS folder, and then select
FOQUS.
2. The first time FOQUS start you will be asked to select a working directory. This is the
directory where FOQUS will store its files. This directory should be dedicated to
FOQUS, and used for nothing else. The directory selection dialog will allow you to
create new directories.
3. From the FOQUS home screen select Open.
4. A file selection dialog will open.
a. The example files will be in the examples folder in the location where FOQUS
was installed.
b. Browse to {FOQUS install location}\examples\optimization\Rosenbrock.json
c. Open the Rosenbrock.json example file
5. Click the optimization icon at the top of the window.
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6. Click the Run tab, and push the start button
7. The optimization should complete in 10 to 40 seconds.
8. If errors occur, refer to the debugging section of the user’s manual and contact ccsisupport@acceleratecarboncapture.org.

Protected under CCSI MASTER NDA-1107306

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