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 should be applicable for Anaconda command line usage, but we do not provide Anaconda support for EMAN development. If you are interested in using Anaconda, please, go to Anaconda.

Linux Clusters

The approach below 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.

Setup Development Environment with Conda

1. If you have an existing Miniconda2/Anaconda2 installation,

   1. Remove miniconda/anaconda entries from PATH.

   2. If you want to make use of your cached packages, move your pkgs/ and envs/ folders out of your current installation to another location.

         1   mkdir -p <path-to-conda-cache-directory>
         2 # mkdir -p ~/conda-global-cache
         3 
         4 mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cache-directory>
         5 mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cache-directory>
      

1. ??? Make sure that you have added miniconda2/bin as the first element in your PATH, and that 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 EMAN2/miniconda.

2. Download Miniconda3 for Linux or MacOSX.

1. Install Miniconda3.

      1 bash <Miniconda3-installer>
      2 
      3 # See command help for supported options
      4 bash <Miniconda3-installer> --help
   

   and follow the prompts.

2. Specify package and environment directories outside of the miniconda installation. These are the directories where conda environments and extracted packages will live. If you need to reinstall miniconda, you won't have to re-create your environments and re-download and re-extract all the packages. Reinstallation will only reset the base environment. First, create the cache directory, if it doesn't exist.

      1   mkdir -p <path-to-conda-cache-directory>
      2 # mkdir -p ~/conda-global-cache
      3 
      4   conda config --add pkgs_dirs <path-to-conda-cache-directory>/pkgs
      5 # conda config --add pkgs_dirs ~/conda-global-cache/pkgs
      6 
      7   conda config --add envs_dirs <path-to-conda-cache-directory>/envs
      8 # conda config --add pkgs_dirs ~/conda-global-cache/envs
      9 
   

3. Configure conda.

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

         1 conda config --set auto_update_conda False
      

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

         1 conda config --set auto_activate_base False
      

4. Install conda 4.6.14.

      1 conda install conda=4.6.14 -c defaults
   

5. Initialize conda for shell interaction.

      1 conda init bash
      2 
      3 # See command help for supported shells
      4 conda init --help
   

Development Environments

Do not install anything into the base environment, do not use the base environment for development, use non-base environments.

1. Create a new environment.

      1 conda create -n eman-deps-14.1 eman-deps=14.1 -c cryoem -c defaults -c conda-forge
   

   OR choose a simpler name for the environment, eman-env or eman.

      1 conda create -n eman-env eman-deps=14.1 -c cryoem -c defaults -c conda-forge
   

2. Activate the environment.

      1 conda activate eman-deps-14.1
   

   OR

      1 conda activate eman-env
   

3. Navigate to your source directory. Checkout a branch and pull updates from the remote.

      1 cd <source-directory>
      2 git checkout <branch>
      3 git pull --rebase
   

4. Navigate to your build directory, build and install.

      1 cd <build-directory>
      2 cmake <eman-source-directory>
      3 make
      4 make install
   

Current Development Environment

After PR: Upgrade CMake to 3.14 is merged.

1. Create a new environment, if it doesn't exist.

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

2. Activate your environment.

      1 conda activate eman-deps-15.1
   

3. Get EMAN2 code if you don't have it from GitHub:cryoem/eman2.

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

4. Checkout branch. Navigate to your source directory. Checkout a branch and pull updates from the remote.

      1 cd <source-directory>
      2 git checkout master
      3 git pull --rebase
   

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

      1 mkdir <build-directory> # eg- $HOME/src/eman2-build
      2 cd <build-directory>
      3 cmake <source-directory>   # - eg $HOME/src/eman2. On linux, also add -DENABLE_OPTIMIZE_MACHINE=ON
      4 
   

• ??? If conda is not found in PATH, set CONDA_PREFIX to your conda environment directory. It could be the main installation or an environment. This step most likely will be needed only if you use cmake-gui.

• ??? If you set CONDA_PREFIX to an environment, make sure to delete any cmake variables that cmake already found, variables like *_LIBRARY or similar, *_INCLUDE_PATH or similar.

• Rerun cmake.

1. Build EMAN2

   make -j
   make install

2. You may also wish to run

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

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

      1 conda deactivate
   

Miniconda2

1. Make sure that you have added miniconda2/bin as the first element in your PATH, and that you do not have LD_LIBRARY_PATH or PYTHONPATH 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 EMAN2/miniconda.

2. Install dependencies, click here for conda dependencies

   conda install cmake=3.9 -c defaults
   conda install eman-deps=14 -c cryoem -c defaults -c conda-forge

3. Checkout EMAN2 code from GitHub:cryoem/eman2.

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

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

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

   • If conda is not found in PATH, set CONDA_PREFIX to your conda environment directory. It could be the main installation or an environment. This step most likely will be needed only if you use cmake-gui.

     • If you set CONDA_PREFIX to an environment, make sure to delete any cmake variables that cmake already found, variables like *_LIBRARY or similar, *_INCLUDE_PATH or similar.
     • Rerun cmake.

5. Build EMAN2

   make -j
   make install

6. You may also wish to run

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