How to obtain EMAN2/SPARX

Stable releases of SPARX are here: Downloads.

To download the daily release (snapshots taken at noon CT US time) of EMAN2/SPARX please visit the EMAN2 website:

where you can find links to the source code and the binary distributions for Linux, Mac OS X and Windows.

How to install EMAN2/SPARX on a Mac OS

Select the dmg file from the download location. After downloading the binary it will be located in the Downloads subdirectory. Simply double click the dmg image file and follow the instructions found in the install.txt file. In order to verify success of the EMAN2/SPARX install run this command from a terminal window: e2version.py. The response should indicate the version of python on the system.

The next step requires clicking this link MPI-installation and following the instructions for a Mac installation. One caveat to the instructions is that it will not be necessary to unzip the tar file using the command line, a double click on the downloaded file will unzip the file and create the expected subdirectories.

How to install EMAN2/SPARX

The easiest way of installing EMAN2/SPARX is to install the binary distribution, which is also strongly recommended. If you are interested in knowing the details of implementation or plan to write/revise low-level C++ codes, you may also build EMAN2/SPARX from the source code, but it will be considerably more difficult.

Install the binary distribution

It is suggested to install EMAN2/SPARX under your home directory.

If you are using Linux, download the file which fits your platform, the current file name is eman2.daily.linux.gcc4.tar.bz2 (may change in the future), save it in the home directory, then use the following commands:

    cd $HOME
    tar --bzip2 -xvf eman2.daily.linux64.gcc4.tar.bz2
    cd EMAN2
    ./eman2-installer

The installer will ask you about the version of python your are using. Then it will generate a file named eman2.bashrc. By running source eman2.bashrc the environmental variables will be set correctly.

bdb cache was permanently disabled on 07/07/2013

After that please follow the instruction of MPI-installation to install the MPI-python binding and enable the MPI version of sparx.

NOTE: the new version (05/27/2014) will determine whether the system has access to windows display and if not, it will be disabled automatically.

Verify the release date

   sx.py
   Util.version()
   quit

Problem with memory fragmentation under Linux

Due to a recent change of memory management algorithm in Linux kernel SPARX will tend to occupy an increasing amount of memory and the program may eventually crash. This is caused by a new memory defragmentation algorithm implemented recently (~2010?) in Linux kernel. We determined that one can all but eliminate the problem by changing a setting of this algorithm, which requires addition to cshell (or, equivalently, to bash), of either of the following statements:

setenv MALLOC_MMAP_THRESHOLD_ 32768

export MALLOC_MMAP_THRESHOLD_=32768

Problem with annoying halting responses during interactive sessions on Mac Mavericks

Please type the following command to disable Mavericks new AppNap feature

defaults write org.python.python NSAppSleepDisabled -bool YES

Install from the source code

Detailed step-by-step instructions can by found in SourceCodeInstallation.

Installer (last edited 2017-01-17 00:19:37 by penczek)