Upload page content

You can upload content for the page named below. If you change the page name, you can also upload content for another page. If the page name is empty, we derive the page name from the file name.

File to load page content from
Page name


The SPARX source installer installs SPARX, EMAN2 and the SPARX gui, along with all third-party programs they require. Everything is put into a user-chosen directory; the installer does NOT require administrator (root) privileges, does not touch anything outside that directory, and it does not interfere with other installed libraries.

The list of third-party programs included is found here. The third-party programs are all open source/free software released under various licences.

The idea behind the installer is that third-party programs are updated infrequently, while SPARX / EMAN2 are updated frequently. The first time the source installer is used, all packages are compiled, which can take several hours. Updating SPARX / EMAN2 from this first installation takes much less time, typically minutes.

Instructions for the first (full) installation are found below, followed by instructions for updating SPARX/EMAN2 .

Platform Notes


sparx is developed on various linux systems, and the installer should work on these:

Fedora Core 4 has some problems with EMAN2. There are many unit test failures, so Fedora Core 4 is not recommended as a platform for sparx/eman2.

macos x

The macos port is incomplete.


The windows port is incomplete.


The SPARX installer lives in a single subdirectory chosen by the user; in the following instructions, this is /your/installer/path. In this directory, all needed packages are built.

The packages are "installed" under a second user-chosen directory, here named /your/sparxroot.

The installer does NOT touch anything outside those two directories, and it does not interfere with other installed libraries. It only uses basic system libraries, so it should work on any Linux system. If it fails to build, let me (mhhohn@lbl.gov) know.


The installer checks for required packages when it is run and reports missing ones. For reference, the currently needed packages include:

For full installation including the graphical parts, you must also have

Installation from source

This takes substantially longer than a binary installation but


    mkdir /your/installer/path
    cd /your/installer/path

Then, preferably:

    svn co svn://cci.lbl.gov/sparx-installer/trunk \

If you do not have subversion, and don't mind reinstalling everything occasionally, you can instead use this:

    wget http://cci.lbl.gov/~hohn/sparx-installer.tar.gz
    tar zxvf sparx-installer.tar.gz

If you don't have wget, try curl instead:

curl http://cci.lbl.gov/~hohn/sparx-installer.tar.gz -o sparx-installer.tar.gz


    cd sparx-installer
    ./configure /your/sparxroot

The last step (./configure) will print a summary. If there are any errors, your system is missing the listed prerequisite(s).

The full install is done via


For headless machines (like cluster nodes), you can use


which is a much smaller build that doesn't require X11.

After running the install script, you must follow the update instructions below before running sparx.

Type ./configure -h for help.

Some compilation times






./install -j 8

distcc, 8 x Intel(R) Xeon(TM) CPUs (4 physical), 2.80GHz


./install -j 12

distcc, 16 x Intel(R) Xeon(TM) CPUs (8 physical), 2.80GHz


./install -j 8

8 x AMD Opteron(tm) Processor 8347, 1.9GHz, using tmpfs

Current version, ./install-no-gui.




4 x Dual Core AMD Opteron(tm) Processor 285, 2.6GHz

Minimal tests

Assuming the ./install command finished successfully, you should try the following tests.

    cd /your/sparxroot/
    .  ./sparx.setpath  
    # or 
    source sparx.setpath.csh

    # This should just exit successfully
    sparx.python -c '"import EMAN2"'

    # Try a test.
    pushd ./eman2/install/test/rt
    sparx.python test_emdata.py 

    # Try the gui 

    # Try sparx console
    # cctbx
    sparx.python -c '"import iotbx.pdb"'

    # iotbx

    # EMAN2 2-D image viewer
    pushd sparx/test/
    e2display.py  test.spi

To run

The SPARX commands must be made available before they can be used. There are two choices, depending on your shell:


Once the .setpath is sourced, some new commands available are:

To update SPARX and EMAN2

Developers with access to the sources can update as described here.

Others can use the following scripts to get the morning snapshot.

. /your/sparxroot/sparx.setpath

Typical output should look like this:

$ sparx.update-sparx 
* Archive old install
* Get new sources.
* Remove old source.
* Extract.
* Post-install.
* Done.

The archive is formed in case the update fails, or in case the updated package produces odd results. For sparx, restoring an old version could be done via e.g.

\rm -fR sparx
tar zxf archive/sparx-05.02.07-4312.tar.gz