!!! UNDER CONSTRUCTION !!!

All platforms

Mac OS X

To install:

1. Download the appropriate file.

2. Type the following command and follow the instructions. You will be prompted for a location to install EMAN2 and if you want to add  export PATH=...  to your .profile file.

      bash <path to EMAN2 installer>

3. If you choose to update your .profile file, restart your terminal program for a fresh shell. Or, you can manually run the export command that is printed at the end of the installation.

Linux

To install:

1. Download the appropriate file.

2. Type the following command and follow the instructions. You will be prompted for a location to install EMAN2 and if you want to add  export PATH=...  to your .bashrc file.

      bash <path to EMAN2 installer>

3. If you choose to update your .bashrc file, restart your terminal program for a fresh shell. Or, you can manually run the export command that is printed at the end of the installation.

Cluster installations

Important note for Linux Cluster use:

If you are using EMAN2/SPARX/SPHIRE on a cluster, the version of OpenMPI we provide may not work with your batch queueing system, meaning you would not be able to run jobs on more than one node at a time. If that is the case or system OpenMPI can't be used for any reason, EMAN2 installation can be tweaked to work with the existing system OpenMPI or OpenMPI can be installed from source. There are some scripts included in the binary distribution intended to help with these situations. The scripts run conda build/install commands with appropriate options. If desired, additional valid conda-build and conda-install options can be passed to scripts. Please, refer to corresponding command documentation for more details. Some situations can be dealt with by rebuilding Pydusa, some may require rebuilding EMAN2. The version of NumPy that EMAN2 is built against and bundled in the binary distribution is 1.8.

Use system OpenMPI and NumPy v1.8

1. Remove the OpenMPI we provided.

       bash <path to EMAN2 directory>/utils/uninstall_openmpi.sh

2. Make sure that the correct OpenMPI for your cluster is in your path. You should be able to run 'mpicc' and get a message like 'gcc: no input files'(note that it is critical that OpenMPI be compiled with '--disable-dlopen', which may or may not be true on your cluster. You may need to consult a sysadmin.)

3. Rebuild and install Pydusa using the system installed OpenMPI.

       bash <path to EMAN2 directory>/utils/build_pydusa_numpy.sh 1.8
       bash <path to EMAN2 directory>/utils/install_pydusa_numpy.sh 1.8

Rebuild and install OpenMPI, use NumPy v1.8

1. Remove the OpenMPI we provided.

       bash <path to EMAN2 directory>/utils/uninstall_openmpi.sh

2. Rebuild OpenMPI.

       bash <path to EMAN2 directory>/utils/build_and_install_openmpi.sh

3. Rebuild and install Pydusa using the system installed OpenMPI.

       bash <path to EMAN2 directory>/utils/build_pydusa_numpy.sh 1.8
       bash <path to EMAN2 directory>/utils/install_pydusa_numpy.sh 1.8

Build against a version of NumPy other than the bundled version, v1.8

OpenMPI doesn't depend on NumPy, so changing to a different NumPy version doesn't require OpenMPI to be rebuilt. However, Pydusa and EMAN2 need to be rebuilt.

1. Rebuild and install Pydusa against the desired NumPy version.

       bash <path to EMAN2 directory>/utils/build_pydusa_numpy.sh   <list of NumPy version(s)>
       bash <path to EMAN2 directory>/utils/install_pydusa_numpy.sh <NumPy version>
       bash <path to EMAN2 directory>/utils/build_eman_numpy.sh     <list of NumPy version(s)>
       bash <path to EMAN2 directory>/utils/install_pydusa_numpy.sh <NumPy version>

Windows

1. Download and install EMAN2 binary.

2. Install Python Launcher.

Bash On Windows

1. Install "Bash on Windows 10", https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/.

2. When prompted to set a user name, enter root. This should give you an account without a password.

Install OpenGL and X Server, set environment variables

1. Install OpenGL.

    sudo apt-get update
    sudo apt-get install libsm-dev \
                         libxrender-dev \
                         build-essential \
                         libgl1-mesa-dev \
                         mesa-utils \
                         mesa-common-dev
    sudo apt-get autoremove

2. Install Xming X Server for Windows.

3. Set environment variables.

    export DISPLAY=:0
    glxinfo | grep OpenGL
    export KMP_AFFINITY=disabled # per https://github.com/Microsoft/BashOnWindows/issues/785#issuecomment-238079769

4. Download and install eman2.2.linux64.centos7.sh.

5. Start X Server before running eman2.

Testing

After installing on any of the systems below, you should test to make sure it's working by running the following 4 basic tests:

• e2version.py (make sure the displayed version is what you expect, including the timestamp. If you have any problems we need you to include the output from this command in your message)
• e2speedtest.py (will also give you the relative speed to expect from your machine)
• e2projectmanager.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)