Anaconda based Build, All Platforms

Note: Along with upgrading NumPy to 1.13, we are also upgrading conda to 4.4 and conda-build to 3. Please, pay attention to PATH related instructions as there is no need to manipulate PATH anymore.

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 6-7 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 approaches you can use for the installation. One uses 'Miniconda' and the other uses full 'Anaconda'. Miniconda is a much smaller (~30 MB) install, provides everything EMAN2 needs, and can be expanded with more packages as you like. Anaconda is a much more complete environment (~300 MB), including useful tools such as the Jupyter notebook, but will require the use of a conda environment to make EMAN2 work properly at present.

Linux Clusters

The approaches below will install EMAN2 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. https://github.com/cryoem/eman2/pull/167

Miniconda2

1. Download and install Miniconda2-4.4.10 for Linux or Mac OSX.

   1. For existing installations install conda 4.4.

      conda install conda=4.4 -c defaults

2. Remove any miniconda2/bin entries from your PATH and run

   . <miniconda2-path>/etc/profile.d/conda.sh

   • or, if you have a line reading

    export PATH=<miniconda2-path>/bin:$PATH

   in your .bashrc or .profile, replace it with

   . <miniconda2-path>/etc/profile.d/conda.sh

3. Make sure 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.

4. Install dependencies

   conda install cmake=3.9 -c defaults
   conda install eman-deps=8 -c cryoem -c defaults -c conda-forge

5. 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

6. 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.

7. Build EMAN2

   make -j
   make install

8. 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

Anaconda2

1. Download and install Anaconda2-5.1.0 for Linux or Mac OSX.

   1. For existing installations install conda 4.4.

      conda install conda=4.4 -c defaults

2. Remove any anaconda2/bin entries from your PATH and run

   . <anaconda2-path>/etc/profile.d/conda.sh

   • or, if you have a line reading

    export PATH=<anaconda2-path>/bin:$PATH

   in your .bashrc or .profile, replace it with

   . <anaconda2-path>/etc/profile.d/conda.sh

3. Make sure 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 Anaconda. Alternatively, you may set up a shell script or alias to make these environment changes on demand when you want to use EMAN2/anaconda.

4. Install dependencies

   conda create -n eman-env cmake=3.9 -c defaults
   conda install -n eman-env eman-deps=8 -c cryoem -c defaults -c conda-forge
   
   conda activate eman-env

5. Note that you will need to run  conda activate eman-env  once in each shell before being able to run EMAN2 commands.

6. 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

7. 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.

8. Build EMAN2

   make -j
   make install

9. 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