Anaconda based Build, All Platforms (except Windows)

EMAN source lives on GitHub, downloading the source is part of the instructions below. Since EMAN uses Anaconda for its base environment, please follow the instructions below for a painless compile from source. If you go 'off script' you're on your own!

Note that even with a source build it may be difficult to get this working on systems with very old operating system installs. We normally try to support OS versions as much as 5-7 years old. Please report any problems.

GPU Support

For features which support the GPU, please complete the source install instructions below, then follow the GPU instructions from the binary installation page.

Mac OS X, Linux

There are two installer options you can choose from for the installation. One is 'Miniconda' and the other is full 'Anaconda'. Miniconda is a much smaller (~30 MB) installer, provides a minimal conda environment. Anaconda is a much more complete environment (~300 MB), including useful tools such as the Jupyter notebook. The installation and environment setup instructions for Miniconda and Anaconda are similar, the only difference is the installer used.

Initial Setup

1. If you do not have Anaconda/Miniconda (or another copy of EMAN2/SPARX/SPHIRE) already installed in your account, skip to the next step. If you DO have Anaconda or Miniconda installed in your account, these instructions will be installing a new complete copy of Miniconda, so you must insure that any existing install you have is not active in your shell (not in PATH, no LD_LIBRARY_PATH or PYTHONPATH set). While it may also be possible to set up an environment for EMAN2 in your existing install, you would need to adapt these instructions to your own situation to attempt that.

      1 echo $PATH
      2 # make sure no Anaconda/Miniconda/EMAN2 entries
      3 echo $LD_LIBRARY_PATH
      4 echo $PYTHONPATH
      5 # ideally, both return nothing. If it set to something it is possible that it may interfere with Anaconda
      6 # strongly suggest at least during the install, ''unset'' both of these. After installation you can test
      7 # to see if they cause any issues
      8 
   

2. Download and install this version of Miniconda for Linux or MacOSX.

      1 bash <Miniconda-installer>
      2 
      3 # See command help for supported options
      4 bash <Miniconda-installer> --help
   

   and follow the prompts.
3. Make sure that:

   1. You do not have any <miniconda/anaconda>/bin entries in PATH added by your shell initialization files.

   2. You do not have LD_LIBRARY_PATH or PYTHONPATH (or PYTHONHOME for some very old python versions) set in your shell.

   If you need these settings for other software, you can still try to proceed, and hope they do not conflict with Miniconda. Alternatively, you may set up a shell script or alias to make these environment changes on demand when you want to use EMAN.
4. Initialize conda for shell interaction, if you haven't done it during installation. At this point, if you have cleaned up your shell initialization files and started a new terminal session, you shouldn't be able to use conda. If that is not the case and you have a working conda, run the following

      1 conda init
   

   If you can't run conda, run

      1 source <miniconda-path>/etc/profile.d/conda.sh
      2 conda init
   

   For more information on conda-init and activation, see https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment.

   MacOSX Users

   On MacOSX, this modifies ~/.bash_profile. If you have ~/.profile as startup file, only ~/.bash_profile will be read. So, if you want ~/.profile as your startup file, move the contents of ~/.bash_profile into ~/.profile or move contents of ~/.profile into ~/.bash_profile and delete the empty file.

   For differences between login- and non-login shells and order of reading the startup files on Mac OSX, see, https://www.anintegratedworld.com/basics-of-osx-bashrc-v-profile-v-bash_profile/.

5. Configure conda.

   1. Do not update conda automatically. (Strongly recommended)

         1 conda config --set auto_update_conda False
      

      This is to prevent automatic upgrades of conda which sometimes introduce breaking changes. The latest version known to work with EMAN is conda 4.6.14.

   2. If you don't want conda's base environment to be activated automatically. (Optional)

         1 conda config --set auto_activate_base False
      

      The current default behavior is to automatically activate the base environment. This adds the base environment to PATH and the shell prompt displays the name of the environment. If these are not desired, turn the auto activation off.

6. Create a new environment with the dependencies. For the list of conda dependencies that eman-deps is built from, click here.

      1 conda create -n eman eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
   

7. Get EMAN code from GitHub:cryoem/eman2.

      1 cd <path-where-you-want-eman2-source>   # eg - $HOME/src
      2 git clone https://github.com/cryoem/eman2.git # this will create an eman2 folder containing the current source code from the master branch
      3 
   

8. Create a build directory (out-of-source builds are recommended).

      1 mkdir <build-directory> # eg- $HOME/src/eman2-build
      2 
   

EMAN Daily Development

1. Activate your environment.

      1 conda activate eman
   

2. Checkout source code and pull from the remote.

      1 cd <source-directory>  # <path-where-you-want-eman2-source>/eman2
      2 git checkout <branch>
      3 git pull --rebase
   

3. Build EMAN

      1 cd <build-directory>
      2 cmake <source-directory>   # - eg $HOME/src/eman2. On linux, also add -DENABLE_OPTIMIZE_MACHINE=ON
      3 
   

   • If you use cmake-gui, since conda is not in PATH anymore, cmake will fail to find the environment directory. In that case set CONDA_PREFIX to your conda environment directory manually.

   • Make sure to delete any cmake variables that cmake already found, variables like *_LIBRARY or similar, *_INCLUDE_PATH or similar, CONDA_EXECUTABLE, CMAKE_INSTALL_PREFIX and any variables that are expected to contain conda environment related values.
   • Configure and generate in cmake.

      1 make -j
      2 make install
   

4. You may also wish to run

      1 make test          # if everything passes you are fine, if there are failures, you are welcome to ask
      2 make test-verbose  # verbose test output to help to identify specific failures
      3 
   

5. To switch to another conda environment, first deactivate your current environment.

      1 conda deactivate
   

Linux Clusters

The approach above will install EMAN with a precompiled version of OpenMPI, which may or may not work with the batch queuing system on your cluster. If it does not work, the symptom will be that MPI parallel jobs will use only a single node, no matter how many you have allocated in your job. If this happens please see the linux cluster installations on the binary install page. Those instructions should also work with either of the source-based installations below.