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Installation Instructions for precompiled MSMBuilder

Supported systems
Linux (tested on Ubuntu 10, openSUSE 10.2, and Centos 5)
Mac OSX

Required software
Python 2.5 or 2.6 (Python 3.x may not work)
NumPy
A C compiler

Optional software (recommended)
Matplotlib (also referred to as Pylab) for use with visualization scripts included with the tutorials. This is what we will be showing in the workshop, but you can also use any other software that can visualize a series of files containing columns of data (i.e., Gnuplot, Xmgrace, Matlab…)

Installation instructions

Installing the software needed by MSMBuilder (includes instructions for recommended but optional matplotlib)

Mac OS X:

1) Open a terminal window: Go to Applications -> Utilities -> Terminal

2) You will need Python and NumPy. MSMBuilder will work with the native Python that comes with Mac Leopard. However, if you wish to use the provided plotting scripts provided with the examples and/or want to upgrade to NumPy 1.1, you will need to get a new Python installation.

a. Determine what version of Python is installed (if any). Assuming you want to use the plotting scripts, you will need Python 2.5.4 (not higher). To check what version of Python you have (if any), in your terminal window, type:

python

If you have Python, the first line that prints will provide the version number, e.g., Python 2.4.3. If you do not have Python, you will get an error message. Press ctrl-D to exit.

b. If you need a new version of Python, go to http://python.org/download/releases/ and click on ”Python 2.5.4.” Download python-2.5.4-macosx.dmg and install.

c. Check what version of NumPy you have (if any):

python
>> import numpy.version
>> numpy.version.version

If you have NumPy, this will print the version number, otherwise you will receive an error. (Commands preceded by >> are to be entered into the python interpreter). Press ctrl-D to exit.

d. We recommend NumPy version 1.3.0, so that you can run the visualization scripts. If you need a new version of NumPy, go to http://numpy.scipy.org. Click on the “Download NumPy” link on the left and get numpy-1.3.0-py2.5-macosx10.5.dmg. Just double click the .dmg file to open the installation wizard and follow the instructions

3) We recommend that you install matplotlib so that you can run the visualization scripts. This is useful for understanding what MSMBuilder is doing. To install matplotlib:

a. Goto http://sourceforge.net/project/showfiles.php?group_id=80706&package_id=278194&release_id=646644

b. Download and uncompress matplotlib-0.98.5.3-py2.5-macosx10.5.zip.

c. Double-click on the package and install.

Linux:

The best option is to use your system’s package manager to get Python 2.5 or 2.6, NumPy 1.2 or later, and matplotlib (also referred to as Pylab) and then to skip down to the section on installing MSMBuilder. However, if you want to install from source you can follow the instructions below.

1) Open a terminal window: Go to Applications -> Utilities -> Terminal

2) You will need Python 2.5 or 2.6 and NumPy (We recommend version 1.2 or later. Earlier versions may work. If you intend to use matplotlib, you will need version 1.1 or later).
a. Determine what version of Python is installed (if any). To check what version of Python you have (if any), in your terminal window, type:

python

If you have Python, the first line that prints will provide the version number, e.g., Python 2.4.3. If you do not have Python, you will get an error message. Press ctrl-D to exit.

b. If you need a new version of Python, go to http://python.org/download/releases/ and click on the compressed source tarball file for the version you want.

1. Navigate to the location where you saved this file, e.g.,:
cd /home/user_name

2. Uncompress the file by typing:
tar xvf Python-2.6.2.tgz

3. Navigate to the Python folder:
cd Python-2.6.2

4. Configure Python to be built on your machine. We recommend doing a local installation (in your own directory, i.e., $HOME). You can do this by typing:
./configure -prefix=$HOME

5. Then, build Python by typing:

make
make install

6. If you do a local installation, you will need to add the $HOME/bin directory to your PATH. If you’re running BASH, you can try doing this by adding the following lines to your .bashrc file:

PATH=$HOME/bin:$PATH
export PATH

Load in the updated .bashrc file:

source $HOME/.bashrc

7. Check that you are calling the version of Python that you just installed. Type:

python

Check the first line for the version number. If it does not match the version that you just installed, check that your path has been updated to include the directory for the new python command:

echo $PATH

c. Check what version of NumPy you have (if any). Note that you need to provide the full path to call the new version of Python, since we did not overwrite the default Python in our installation process, i.e.,

python
>> import numpy.version
>> numpy.version.version

If you have NumPy, this will print the version number, otherwise you will receive an error. (Commands preceded by >> are to be entered into the python interpreter). Press ctrl-D to exit.

d. We recommend NumPy version 1.2 or higher (Earlier versions may work. If you intend to use matplotlib, you will need version 1.1 or later). If you need a new version of NumPy, go to http://numpy.scipy.org. Click on the “Download NumPy” link on the left and get the desired version of the .tar.gz file.

1. Navigate to the location where you saved this file, e.g.,:
cd /home/user_name

2. Uncompress the file by typing:
tar xvf numpy-1.3.0.tar.gz

3. Navigate to the NumPy folder:
cd numpy-1.3.0

4. Install NumPy by typing: (Again, make sure you are calling the latest Python version)

python setup.py install

3) We recommend that you install matplotlib so that you can run the visualization scripts. This is useful for understanding what MSMBuilder is doing, but is optional. To install matplotlib:

a. Goto http://sourceforge.net/project/showfiles.php?group_id=80706&package_id=278194&release_id=646644

b. Download and uncompress matplotlib-0.98.5.3.tar.gz:

tar xvf matplotlib-0.98.5.3.tar.gz

c. Go to the matplotlib folder:

cd matplotlib-0.98.5.3

d. Type (remember to use the correct version of Python):

python setup.py build
python setup.py install

Installing MSMBuilder

Instructions below describe how to install the pre-compiled versions of MSMBuilder. For installing from source, please refer to the README and INSTALL files in msmbuilder-0.1beta.tar.gz.

1) Download MSMBuilder for your platform from http://simtk.org/home/msmbuilder. Click on “Downloads” and select either msmbuilder_linux-0.1beta.tar.gz or msmbuilder_mac-0.1.beta.tar.gz.

2) Navigate to the location where this file was saved (on Mac, the default locations are on the Desktop or in your Downloads directory) and uncompress it. Note that on the Mac, you can also just double-click the file to uncompress it.

cd /home/user_name

tar xvf msmbuilder_linux-0.1beta.tar.gz
      or
tar xvf msmbuilder_mac-0.1beta.tar.gz

3) Move the folder to a permanent location (i.e., $HOME on Linux, /Developer on Mac) and rename the folder to msmbuilder. On the Mac, by dragging and dropping the file. Remember to rename the file to msmbuilder. On Linux, in the terminal window, you would type:

mv msmbuilder_linux $HOME/msmbuilder

4) Set environment variables so your computer knows where to find these tools. The command depends on your operating system, but you should set variables for the locations of each of the 3 folders you moved. For example, on Linux with a Bash shell:

export LD_LIBRARY_PATH=$HOME/msmbuilder/Clusterer/lib:$LD_LIBRARY_PATH
export PATH=$HOME/msmbuilder/Clusterer/bin:$PATH
export MSMBUILDERHOME=$HOME/msmbuilder
export PH=$HOME/msmbuilder/PythonTools_V2

On Mac OS X:
export DYLD_LIBRARY_PATH=/Developer/msmbuilder/Clusterer/lib:$DYLD_LIBRARY_PATH
export PATH=/Developer/msmbuilder/Clusterer/bin:$PATH
export MSMBUILDERHOME=/Developer/msmbuilder
export PH=/Developer/msmbuilder/PythonTools_V2

Add these lines to your .bash_profile file to make the changes permanent

5) Do a simple check of your installation. In your terminal window, type: (make sure you are calling the right version of Python, if you have multiple versions installed)

python $PH/BuildMSMsAsVaryLagTime.py -h

You should see a brief description of this command, along with a list of options for it.

Also try typing:

doFastGromacsClustering -h

You should see a brief description of this command, along with a list of options for it.

Installation instructions are coming soon.

-  ⇤ ← Revision 2 as of 2010-09-21 20:58:33 → 
  Size: 8927
  Editor: gbowman
  Comment:
+   ← Revision 3 as of 2010-11-20 06:05:29 → ⇥
  Size: 98
  Editor: gbowman
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
-Installation Instructions for precompiled MSMBuilder
-Line 6:
+Line 5:
-Supported systems  
Linux (tested on Ubuntu 10, openSUSE 10.2, and Centos 5)
Mac OSX

Required software
Python 2.5 or 2.6  (Python 3.x may not work) 
NumPy 
A C compiler

Optional software (recommended)
Matplotlib (also referred to as Pylab) for use with visualization scripts included with the tutorials.  This is what we will be showing in the workshop, but you can also use any other software that can visualize a series of files containing columns of data (i.e., Gnuplot, Xmgrace, Matlab…)


Installation instructions

Installing the software needed by MSMBuilder (includes instructions for recommended but optional matplotlib)

Mac OS X:

1)	Open a terminal window:  Go to Applications -> Utilities -> Terminal  

2)	You will need Python and NumPy.  MSMBuilder will work with the native Python that comes with Mac Leopard.  However, if you wish to use the provided plotting scripts provided with the examples and/or want to upgrade to NumPy 1.1, you will need to get a new Python installation.

a.	Determine what version of Python is installed (if any).  Assuming you want to use the plotting scripts, you will need Python 2.5.4 (not higher).  To check what version of Python you have (if any), in your terminal window, type:

python
  
If you have Python, the first line that prints will provide the version number, e.g., Python 2.4.3.  If you do not have Python, you will get an error message.  Press ctrl-D to exit.

b.	If you need a new version of Python, go to http://python.org/download/releases/  and click on ”Python 2.5.4.”  Download python-2.5.4-macosx.dmg and install.

c.	 Check what version of NumPy you have (if any):

python
>> import numpy.version
>> numpy.version.version

If you have NumPy, this will print the version number, otherwise you will receive an error.  (Commands preceded by >> are to be entered into the python interpreter).  Press ctrl-D to exit.

d.	We recommend NumPy version 1.3.0, so that you can run the visualization scripts.  If you need a new version of NumPy, go to http://numpy.scipy.org.  Click on the “Download NumPy” link on the left and get numpy-1.3.0-py2.5-macosx10.5.dmg.  Just double click the .dmg file to open the installation wizard and follow the instructions

3)	 We recommend that you install matplotlib so that you can run the visualization scripts.  This is useful for understanding what MSMBuilder is doing.  To install matplotlib:

a.	Goto  http://sourceforge.net/project/showfiles.php?group_id=80706&package_id=278194&release_id=646644

b.	Download and uncompress matplotlib-0.98.5.3-py2.5-macosx10.5.zip.

c.	Double-click on the package and install.


Linux:

The best option is to use your system’s package manager to get Python 2.5 or 2.6, NumPy 1.2 or later, and matplotlib (also referred to as Pylab) and then to skip down to the section on installing MSMBuilder.  However, if you want to install from source you can follow the instructions below.

1)	Open a terminal window:  Go to Applications -> Utilities -> Terminal  

2)	You will need Python 2.5 or 2.6 and NumPy (We recommend version 1.2 or later.  Earlier versions may work.  If you intend to use matplotlib, you will need version 1.1 or later).  
a.	Determine what version of Python is installed (if any).  To check what version of Python you have (if any), in your terminal window, type:

python
  
If you have Python, the first line that prints will provide the version number, e.g., Python 2.4.3.  If you do not have Python, you will get an error message.  Press ctrl-D to exit.

b.	If you need a new version of Python, go to http://python.org/download/releases/  and click on the compressed source tarball file for the version you want.

1.	Navigate to the location where you saved this file, e.g.,:
cd /home/user_name

2.	Uncompress the file by typing:    
tar xvf Python-2.6.2.tgz

3.	Navigate to the Python folder:
cd Python-2.6.2

4.	Configure Python to be built on your machine.  We recommend doing a local installation (in your own directory, i.e., $HOME).  You can do this  by typing:
./configure -prefix=$HOME

5.	Then, build Python by typing:  

make 
make install

6.	If you do a local installation, you will need to add the $HOME/bin directory to your PATH.  If you’re running BASH, you can try doing this by adding the following lines to your .bashrc file:


PATH=$HOME/bin:$PATH 
export PATH

Load in the updated .bashrc file:

source $HOME/.bashrc

7.	Check that you are calling the version of Python that you just installed.  Type:

python
  
Check the first line for the version number.  If it does not match the version that you just installed, check that your path has been updated to include the directory for the new python command:

echo $PATH

c.	Check what version of NumPy you have (if any).  Note that you need to provide the full path to call the new version of Python, since we did not overwrite the default Python in our installation process, i.e., 

python
>> import numpy.version
>> numpy.version.version

If you have NumPy, this will print the version number, otherwise you will receive an error.  (Commands preceded by >> are to be entered into the python interpreter).  Press ctrl-D to exit.

d.	We recommend NumPy version 1.2 or higher (Earlier versions may work.  If you intend to use matplotlib, you will need version 1.1 or later).   If you need a new version of NumPy, go to http://numpy.scipy.org.  Click on the “Download NumPy” link on the left and get the desired version of the .tar.gz file.

1.	Navigate to the location where you saved this file, e.g.,:
cd /home/user_name

2.	Uncompress the file by typing:    
tar xvf numpy-1.3.0.tar.gz

3.	Navigate to the NumPy folder:
cd numpy-1.3.0

4.	Install NumPy by typing:  (Again, make sure you are calling the latest Python version)

python setup.py install 


3)	 We recommend that you install matplotlib so that you can run the visualization scripts.  This is useful for understanding what MSMBuilder is doing, but is optional.  To install matplotlib:

a.	Goto  http://sourceforge.net/project/showfiles.php?group_id=80706&package_id=278194&release_id=646644

b.	Download and uncompress matplotlib-0.98.5.3.tar.gz:

tar xvf matplotlib-0.98.5.3.tar.gz

c.	Go to the matplotlib folder:

cd matplotlib-0.98.5.3

d.	Type (remember to use the correct version of Python):

python setup.py build
python setup.py install



Installing MSMBuilder

Instructions below describe how to install the pre-compiled versions of MSMBuilder.  For installing from source, please refer to the README and INSTALL files in msmbuilder-0.1beta.tar.gz.

1)	Download MSMBuilder for your platform from http://simtk.org/home/msmbuilder.  Click on “Downloads” and select either msmbuilder_linux-0.1beta.tar.gz or msmbuilder_mac-0.1.beta.tar.gz.

2)	Navigate to the location where this file was saved (on Mac, the default locations are on the Desktop or in your Downloads directory) and uncompress it.  Note that on the Mac, you can also just double-click the file to uncompress it.  

cd /home/user_name

tar xvf msmbuilder_linux-0.1beta.tar.gz
      or    
tar xvf msmbuilder_mac-0.1beta.tar.gz

3)	 Move the folder to a permanent location (i.e., $HOME on Linux, /Developer on Mac) and rename the folder to msmbuilder.  On the Mac, by dragging and dropping the file.  Remember to rename the file to msmbuilder.  On Linux, in the terminal window, you would type:

mv msmbuilder_linux $HOME/msmbuilder

4)	Set environment variables so your computer knows where to find these tools.  The command depends on your operating system, but you should set variables for the locations of each of the 3 folders you moved.  For example, on Linux with a Bash shell:

export LD_LIBRARY_PATH=$HOME/msmbuilder/Clusterer/lib:$LD_LIBRARY_PATH
export PATH=$HOME/msmbuilder/Clusterer/bin:$PATH
export MSMBUILDERHOME=$HOME/msmbuilder
export PH=$HOME/msmbuilder/PythonTools_V2


On Mac OS X:
export DYLD_LIBRARY_PATH=/Developer/msmbuilder/Clusterer/lib:$DYLD_LIBRARY_PATH
export PATH=/Developer/msmbuilder/Clusterer/bin:$PATH
export MSMBUILDERHOME=/Developer/msmbuilder
export PH=/Developer/msmbuilder/PythonTools_V2


Add these lines to your .bash_profile file to make the changes permanent

5)	Do a simple check of your installation.  In your terminal window, type:  (make sure you are calling the right version of Python, if you have multiple versions installed)

python $PH/BuildMSMsAsVaryLagTime.py -h

You should see a brief description of this command, along with a list of options for it.

Also try typing:

doFastGromacsClustering -h
 
You should see a brief description of this command, along with a list of options for it.
+Installation instructions are coming soon.