All platforms

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 developers. Instead, we suggest just running the following 4 basic tests:

Mac OS X

Mac OS X versions 10.7 and higher are supported for EMAN2 nightly builds (10.6 is only supported in older, pre 2.1 releases). To install:

  1. Download the appropriate '.dmg' file from the nightly build page and copy the "EMAN2" folder into "/Applications".
  2. If you use the bash shell, add the following line to your ".profile" file: 
    test -r /Applications/EMAN2/eman2.bashrc && source /Applications/EMAN2/eman2.bashrc
    Similarly, if you use the csh or tcsh shell, add the following line to ".cshrc": 
    test -r /Applications/EMAN2/eman2.cshrc && source /Applications/EMAN2/eman2.cshrc
  3. Restart your terminal program for a fresh shell. EMAN2 should now be installed and function properly.

Notes:

Linux

In the following installation instruction, we assume you are installing EMAN2 in your home directory (no root privileges required), it can also be installed system-wide, in which case each user needs to source the eman2.bashrc file.

There are 2 Linux binaries:

If you are upgrading from a previous version of EMAN2, please rename or completely remove the old EMAN2 directory before installing the new version. Unpacking the new version on top of an older version can sometimes cause problems. It is critical that you re-run the installer after unpacking the new version, and insure that your .bashrc or other login file is updated. This is the suggested sequence: 

rm -rf EMAN2.old
mv EMAN2 EMAN2.old
tar xvzf eman2.daily.linux64.tar.gz
cd EMAN2
./eman2-installer

When the installer is done (takes only a few seconds), it will display an instruction to add eman2.bashrc to your login script (or similar, depending on what shell you use).

If you are familiar with Linux, this instruction should be clear. Just make sure you open a new terminal window to test the installation.

If you are a Linux novice, you need to understand that there are several different 'shells' you can use within your terminal window. The 'shell' is what provides the terminal prompt and what interprets the commands you type. Why there are different ones is a long story, but the default shell for most linux installations is called BASH. Every time you open a new terminal window or log in to the computer with something like SSH, the shell initializes itself by reading a file called .bashrc. EMAN2 has some additions to this file to tell the shell where you installed it, so it can find all of the e2* commands when you run them. You also need to know that on Linux, files starting with '.' are considered hidden files, so if you do an 'ls' you won't see this file, and it may be hidden in your file browser. If you do an 'ls -al', you will see the hidden files too. An easy way to add a line of text to the end of a file, is to (replace text with the line you need to add): 

echo text >>.bashrc

If you see an error like: Cannot mix incompatible Qt library (version 0x40806) with this library (version 0x40804). This means the Qt installed on your computer is conflicting with the Qt distributed with EMAN2. In most cases, if you just remove the Qt that comes with EMAN2 from extlib/lib, eg - rm -rf EMAN2/extlib/lib/libQt*. If this doesn't solve the problem, take note of the new error message, and ask for help!

This completes the installation. Follow the testing instructions above. If there are problems, please use EMAN2 Google Group. If you cannot use the Google Group for some reason, please feel free to email sludtke@bcm.edu .

Additional tips:

Conflicts between software packages:

In a perfect world no software would interfere with each other and the world would be a happy place. When things are distributed as source, and compiled on your computer, or similarly if they come with the package manager on your computer, then all of the different software share access to a common set of dependencies (shared libraries). For example, FFTW, Qt, libGSL, etc. However, if you are a developer and want to distribute a single binary package that will run on any version of linux from the last 5 years, you pretty much have to include one specific version of each library along with the binary package. This is a pretty common practice. While it's inefficient, most scientific software projects simply lack the manpower to compile different binary packages for every different linux distribution. Unfortunately that means that, for example, if you install EMAN2 and IMOD in the same account and the two packages use different versions of some specific libraries, you can get conflicts and one of the two packages will not work properly. Here is an example: 

Traceback (most recent call last):
  File "/t2/home/EMAN2/bin/e2projectmanager.py", line 34, in <module>
    from PyQt4 import QtCore, QtGui
ImportError:
/t2/home/EMAN2/extlib/lib/python2.7/site-packages/PyQt4/QtCore.so:
undefined symbol: _ZN7QLocale14scriptToStringENS_6ScriptE

In this example, there is a problem with conflicting Qt libraries from two different sources. The most common way for a binary package to find the libraries distributed with it is via the LD_LIBRARY_PATH shell variable. Unfortunately, this is the root of the problem, because the path gets used in-order, so whatever appears first is what will be used. EMAN2 recently switched to the more modern approach, where the relative library paths are compiled into the programs/libraries themselves, so LD_LIBRARY_PATH isn't required, and EMAN2 should not interfere with any of your other software. However, if you have other software which uses LD_LIBRARY_PATH, it CAN interfere with EMAN2, but only if it uses exactly the same library version EMAN2 does and it was compiled with different options.

If you see an error like the one above, the first thing is to "unset LD_LIBRARY_PATH" (unsetenv in csh), and see if your EMAN2 programs start working. If they do, then there is some conflicting library somewhere in your path, and you should probably go back and re-add the LD_LIBRARY_PATH elements one at a time until it stops working again. This will tell you which package is conflicting, and you can then arrange to avoid the conflict (perhaps with a shell script to only add the offending path element when you need that particular package). You could also complain to the developer of the other package, and ask if they could switch to a distribution scheme which doesn't require LD_LIBRARY_PATH.

The alternative solution is to go through the modest pain of building from source. Packages built from source generally will never conflict with one another in this way.

NoMachine remote desktops

Some versions of NoMachine's remote desktop solution has significant OpenGL bugs which can cause a variety of annoying and odd artifacts. These are particularly noticeable in e2boxer, but may be seen in other programs as well. As far as we are aware, there is no good solution for this problem within that ecosystem. We have started using TurboVNC/VirtualGL for remote Linux desktop display instead. We have found no display glitches at all with this system, and due to the way it handles remote rendering, it is much faster for many operations as well.

Windows

Please note that EMAN2's Windows support is the "poor cousin" of the distributions. Like most open-source software EMAN2 was designed primarily for Unix-like environments (Mac/Linux) we expend substantial human effort to keep EMAN2 working on windows, and even with these efforts, some things still do not work optimally. If you have any other choice (Linux/Mac) you will generally have a much better experience on those platforms.

Here is a simple example: on windows 7 and above, the OS puts a priority on user interactivity, to the extent that if it detects a user event (mouse click, etc.) which isn't handled by the software within a second or two, it immediately kills the program. While clearly we strive for a good interactive user-experience, there are occasional places in EMAN2 where there may be a few second delay after you tell the program to do something before it will respond again (while it does what you asked it to do). If you happen to click on a window during this time, Win7+ will kill the program, often corrupting any files being processed at the time. Windows is the only platform with this issue. While we have tried to improve this issue in various places in EMAN2 it simply isn't practical to redesign the entire system around this arbitrary constraint, so the user has to be careful.

Anyway, if you're not deterred by my doom and gloom, we do try to make installation as simple as possible, and it IS possible to use EMAN2 effectively on Windows: 

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

or

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

Environment 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. 

export EMAN2DIR=${HOME}/EMAN2
export PATH=${PATH}:${EMAN2DIR}/bin
export PYTHONPATH=${PYTHON_PATH}:${EMAN2DIR}/lib
# export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib    # This line should no longer be used (with releases after 2.06)

setenv EMAN2DIR ${HOME}/EMAN2
setenv PATH ${PATH}:${EMAN2DIR}/bin
setenv PYTHONPATH ${EMAN2DIR}/lib         #setenv PYTHONPATH ${PYTHONPATH}:${EMAN2DIR}/lib  if you have PYTHONPATH set
#setenv LD_LIBRARY_PATH ${EMAN2DIR}/lib    # This line should no longer be used (with releases after 2.06)

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.)

Note that some windows machines may have so much software installed on them that the PATH and/or PYTHONPATH may exceed their maximum length. The only real solution to this that I'm aware of is to write little shell-scripts to adjust your environment for specific uses. This should be a very unusual situation, though.

EMAN2/Install/BinaryInstall (last edited 2017-12-27 01:56:26 by RJEdwards)