All platforms

When upgrading to a newer version, BEFORE downloading/untaring the new version, you MUST run

e2bdb.py -c

This will clean up the cache and make sure you don't have any running EMAN2 jobs while you do the upgrade. While unlikely, failing to do this could result in corruption of some files. If you do forget, and don't want to reinstall the old version, you will need to 'rm -rf /tmp/eman2db-*' to remove all old cache files. Normally this will be safe as long as no EMAN2 programs are actively running, and nothing crashed.

Note for International use - We lack sufficient manpower at present for any real internationalization support. In particular some users have reported problems with the use of ',' rather than '.' in numbers. The only known solution at present is to set English to your language.

Testing

After installing on any of the systems below, you should test to make sure it's working. While we have unit testing, it is mainly for those compiling from source. Instead, we suggest just running the following 3 basic tests:

• e2speedtest.py (will also give you the relative speed to expect from your machine)
• e2workflow.py (if the GUI pops up, it's working)
• e2proc2d.py anyimagefile bdb:test (anyimagefile is any 2d image or stack supported by eman2, this will make sure the database works)

Mac OS X

Mac OS X 10.5 and 10.6 are supported for EMAN2 nightly builds. The build is fully 64 bit on 10.6, and this package is recommended and tested more regularly. Download the appropriate dmg from the nightly build page, copy "EMAN2" to your "/Applications" folder. Instructions on loading the environment variable init script are included in the README.txt file.

There is a visual installation guide that explains the process with screenshots.

Linux

Note: In the following installation instruction, I assume you are installing EMAN2 in your home directory. So I use my home directory "/home/gtang" as an example. EMAN2 provides four nightly builds for Linux: eman2.nightly.linux.tar.bz2 and eman2.daily.linux.tar.bz2 are for 32 bit Linux (i386). eman2.daily.linux64.tar.bz2 and eman2.daily.linux64.gcc4.tar.bz2 are for 64 bit Linux (x86_64). The gcc4 version requires glibc version at least 2.5. We recommend you install the gcc4 version of EMAN2 unless your linux release is several years out of date. If you are not sure, you can check your glibc version by typing '/sbin/ldconfig -V'. If you are not sure if your linux is 32 bit or 64 bit. You can check with command 'uname -r'. If you see x86_64 that means your linux is 64 bit. Otherwise it's 32 bit linux. To install this binary release, for example, on 64 bit Linux: download eman2.daily.linux64.gcc4.tar.bz2 to your home directory.

$tar xvjf eman2.daily.linux64.gcc4.tar.bz2
$cd EMAN2
$./eman2-installer

When the installer is done (takes only a few seconds):

Please add the following line to the end of your /home/gtang/.bashrc
source /home/gtang/EMAN2/eman2.bashrc

This eman2.bashrc just provides some environment variables for EMAN2 and sparx. You can either add the source line to your .bashrc, or copy all the environment variable setting in eman2.bashrc into your.bashrc file:

$gedit /home/gtang/.bashrc

Then add the given source line to the file. Note: if you are using some kind of c shell, you will see the eman2.chsrc file.

NOTE: If you are also using EMAN1, you should put the EMAN2 'source' after the EMAN1 'source' in your .bashrc file.

This completes the installation. You can try running 'e2speedtest.py' and 'e2display.py' in a new terminal window. If they both work, everything should be installed properly. If they do not work, please report the problem either to sludtke@bcm.edu, or check the EMAN2 Google Group.

NOTE: EMAN2 on Linux ships with its own Python interpreter. The eman2-installer will automatically change the python interpreter in the EMAN2 python files to use this version of Python. For example:

#!/home/username/EMAN2/python/Python-2.6.5-ucs4/bin/python

If you wish to write your own EMAN2 scripts, you will need to use this same Python interpreter, or 'import EMAN2' will fail !

NOTE: Ubuntu users A package called 'freeglut' is not always installed on Ubuntu machines, and may be required for 2-D plots (such as interactive CTF tuning). If you see blank windows when you expect to see plots, please use the package manager to install freeglut.

NOTE: For SUSE users and users of some other KDE based platforms which refuse to work properly after installing EMAN2. EMAN2 ships with its own copy of the Qt libraries, which are not installed on all machines. If your distribution uses EXACTLY the same version of Qt that we provide, there may be a conflict which prevents KDE from working. Despite the version numbers being the same, Qt can be compiled with many different options, and if the options we used don't exactly match the options your OS used, then the EMAN2 libraries will conflict. There are two possible ways to resolve this: 1) remove all of the Qt libraries from EMAN2/lib, which will force EMAN2 to use the system libraries. There is a chance that EMAN2 will not work with the system libraries. 2) Remove the EMAN2 bashrc file from your .bashrc file, and when you want to use EMAN2, set up an alias to source the bashrc from the shell you want to run EMAN2 from. This will make it so only those shells will use EMAN2's libraries, and it won't interfere with the rest of your system.

Windows

• If you have installed previous version of EMAN2. Please uninstall it and remove a directory called c:\tmp\eman2db-***.
• If you plan to install both EMAN1 and EMAN2, EMAN1 must be installed FIRST.

• For windows(XP/Vista/7 32/64), EMAN2 comes with it's own Python2.7, with preinstalled site-packages like PyQt4, PyOpenGL etc., So if you have your own Python installed, you may need uninstall it IF there is a conflict.

• After installation, you can open a command prompt and type e2.py.
  • If you get error like:

    • ImportError: DLL load failed: The application has failed to start because its side-by-side configuration is incorrect.

      ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem.

      please install Visual C++ 2008 Redistributable downloaded from Microsoft or from here Download Visual C++ 2008 redistributable runtime library here..

  • If you get a python prompt successfully, try typing 'display(test_image())'. You should see an s-shaped image appear on the screen. If so, EMAN2 is working.
• If you double click on one of the icons, and the application doesn't open properly, please try running it from the command-line instead. This will give better error information.

• EMAN2 uses PyQt4 as GUI toolkit. It has conflict with Matlab R2007b, you need uninstall Matlab or install it in a different account, i.e. not system wide install.

• Windows user please ignore this warning message, "WARNING: Using the out of date 'bsddb' module instead of bsddb3. Consider installing newer berkeleydb and bsddb3."

• EMAN2 may still have problems on specific windows machines. If you run into any, please report them to sludtke@bcm.edu

Environement Variable Setting For EMAN2 (All platforms)

In some rare cases, the EMAN2 installer will not be able to update your environment variables properly. In such cases, we need set up environment variables like PATH, LD_LIBRARY_PATH and PYTHONPATH for EMAN2 to work correctly. These environment variables should be automatically set when you run eman-installer script when you install binary EMAN release.

• For sh/bash like shells on Linux/UNIX system (suppose you install EMAN2 under your home directory):

export EMAN2DIR=${HOME}/EMAN2
export PATH=${PATH}:${EMAN2DIR}/bin
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
export PYTHONPATH=${PYTHON_PATH}:${EMAN2DIR}/lib

• For csh/tcsh like shell on Linux/UNIX system (suppose you install EMAN under your home directory):

setenv EMAN2DIR ${HOME}/EMAN2
setenv PATH ${PATH}:${EMAN2DIR}/bin
setenv LD_LIBRARY_PATH ${EMAN2DIR}/lib    #setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EMAN2DIR}/lib if you have LD_LIBRARY_PATH set
setenv PYTHONPATH ${EMAN2DIR}/lib         #setenv PYTHONPATH ${PYTHONPATH}:${EMAN2DIR}/lib  if you have PYTHONPATH set

• For windows users (suppose you install EMAN2 under C:\):

right click "my computer"->properties->Advanced->Environment Variables
in "system variables"edit the "path" entry, and add: 
C:\EMAN2\bin;C:\EMAN2\lib;C:\EMAN2\python\Python27;C:\EMAN2\python\Python27\Lib\site-packages\PyQt4\bin.

Create a new system variable PYTHONPATH, add: 
C:\EMAN2\lib;C:\EMAN2\bin. 
(note: In the example I suppose you installed EMAN2 into C:\ directory, change it accordingly if you install EMAN2 in other directory.)