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Comment: no conda caching
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EMAN2 source lives on !GitHub, downloading the source is part of the instructions below. Since EMAN2 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! EMAN source lives on [[https://github.com/cryoem/eman2|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!
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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. The installation instructions for Anaconda cover only the command line usage and not the GUI interface that comes with the Anaconda installation.
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 to Anaconda command line usage, but we do not provide Anaconda support for EMAN development. If you are interested in using Anaconda, please, go to [[https://www.anaconda.com/distribution/|Anaconda]].
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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 [[EMAN2/Install/BinaryInstallAnaconda|binary install page]]. Those instructions should also work with either of the source-based installations below.
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 [[EMAN2/Install/BinaryInstallAnaconda|binary install page]]. Those instructions should also work with either of the source-based installations below.
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== Setup Development Environment with Conda ==
{{{#!wiki caution
'''TODO'''
 1. For difference between login- and non-login shells on Mac OSX, https://www.anintegratedworld.com/basics-of-osx-bashrc-v-profile-v-bash_profile/
 1. Review how to install new vs existing installations. How do you use conda-init, if conda is not on PATH?
  a. The installer seems to take care of it, if it is not used in batch mode.
  a. How do we handle it manually, if the installation was done in batch mode.
 1. Activation, conda init ... https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment
}}}
== Setup Conda ==
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  a. If you want to make use of your cached packages, move your '''pkgs/''' and '''envs/''' folders out of your current installation to another location.
  {{{#!highlight bash
  mkdir -p <path-to-conda-cache-directory>
# mkdir -p ~/conda-global-cache
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mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cache-directory>
mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cache-directory>
}}}
{{{#!wiki caution
'''???'''}}}
 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.
 1. Download '''Miniconda3''' for [[https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh|Linux]] or [[https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh|MacOSX]] or '''Anaconda3''' for ???links???. If you have installer related problems, the latest installers known to be working are ... and .....
{{{#!wiki caution
'''???'''}}}
 1. Install '''Miniconda3'''.		  1. Download and install '''Miniconda3''' for [[https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh|Linux]] or [[https://repo.continuum.io/miniconda/Miniconda3-4.6.14-MacOSX-x86_64.sh|MacOSX]].
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# See command help for supported options
bash <Miniconda3-installer> --help
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 1. 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. Make sure that:
  a. You do '''not''' have any miniconda/anaconda entries in '''PATH'''.
  a. 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.

 1. Initialize conda for shell interaction, if you haven't done it during installation.
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  mkdir -p <path-to-conda-cache-directory>
# mkdir -p ~/conda-global-cache		 conda init bash
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  conda config --add pkgs_dirs <path-to-conda-cache-directory>/pkgs
# conda config --add pkgs_dirs ~/conda-global-cache/pkgs		 # See command help for supported shells
conda init --help
}}}
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  conda config --add envs_dirs <path-to-conda-cache-directory>/envs
# conda config --add pkgs_dirs ~/conda-global-cache/envs		  If you can't run conda, because it is not in '''PATH''', run

  {{{#!highlight bash
source <miniconda-path>/etc/profile.d/conda.sh
conda init bash
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 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.

 {{{#!wiki caution
'''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/.
}}}
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 1. Install '''conda 4.6.14'''.
 {{{#!highlight bash
conda install conda=4.6.14 -c defaults
}}}
 1. Initialize conda for shell interaction.
 {{{#!highlight bash
conda init bash
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# See command help for supported shells
conda init --help

== EMAN Development Environment ==

{{{#!wiki warning
Do not install anything except conda-related packages into the '''base''' environment, do not use the '''base''' environment for development, use '''non-base''' environments.
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 1. Create a new environment with the dependencies, if it doesn't exist. Click [[https://github.com/cryoem/eman-deps-feedstock/blob/v15.1/recipe/meta.yaml#L9-L53|here]] for the list of conda dependencies that '''eman-deps''' is built from.
 {{{#!highlight bash
conda create -n eman-deps-15.1 eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
}}}
 OR
 choose a simpler name for the environment, '''eman-env''' or '''eman'''.
 {{{#!highlight bash
conda create -n eman-env eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
}}}
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== Development Environments ==
{{{#!wiki caution
'''???'''}}}
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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. '''Activate''' the environment.
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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'''.
 {{{#!highlight bash
conda create -n eman-env eman-deps=14.1 -c cryoem -c defaults -c conda-forge
}}}
 1. Activate the environment.
 {{{#!highlight bash
conda activate eman-deps-14.1		 conda activate eman-deps-15.1
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 1. Navigate to your source directory. Checkout a branch and pull updates from the remote.
 {{{#!highlight bash
cd <source-directory>
git checkout <branch>
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{#!highlight bash
cd <build-directory>
cmake <eman-source-directory>
make
make install
}}}
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== Current Development Environment ==
'''After [[https://github.com/cryoem/eman2/pull/407|PR: Upgrade CMake to 3.14]] is merged.'''

 1. Create a new environment, if it doesn't exist.		  1. '''Get EMAN code if you don't have it''' from [[https://github.com/cryoem/eman2|GitHub:cryoem/eman2]].
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conda create -n eman-deps-15.1 eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
}}}

 1. Activate your environment.
 {{{#!highlight bash
conda activate eman-deps-15.1
}}}

 1. '''Get EMAN2 code if you don't have it''' from [[https://github.com/cryoem/eman2|GitHub:cryoem/eman2]].
 {{{
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 1. '''Checkout branch'''. Navigate to your source directory. Checkout a branch and pull updates from the remote.  1. '''Checkout source code''' and pull from the remote.
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cd <source-directory>
git checkout master		 cd <source-directory>  # <path-where-you-want-eman2-source>/eman2
git checkout <branch>
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{{{#!wiki caution
'''???'''}}}
  * '''???''' 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'''.
{{{#!wiki caution
'''???'''}}}
   * '''???''' 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.		   * 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.
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 1. '''Build EMAN2'''
 {{{
1. '''Build EMAN'''
 {{{#!highlight bash
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 {{{  {{{#!highlight bash
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=== Miniconda2 ===
 1. Download and install '''Miniconda2-4.4.10''' for [[https://repo.continuum.io/miniconda/Miniconda2-4.4.10-Linux-x86_64.sh|Linux]] or [[https://repo.continuum.io/miniconda/Miniconda2-4.4.10-MacOSX-x86_64.sh|Mac OSX]].

 1. Download and install '''Anaconda2-5.1.0''' for [[https://repo.continuum.io/archive/Anaconda2-5.1.0-Linux-x86_64.sh|Linux]] or [[https://repo.continuum.io/archive/Anaconda2-5.1.0-MacOSX-x86_64.sh|Mac OSX]].



 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.

 1. '''Install dependencies''', click [[https://github.com/cryoem/eman-deps-feedstock/blob/e8c31645c2e263efeeff232a7aa8a1e7eea65479/recipe/meta.yaml#L11-L42|here]] for conda dependencies
 {{{
conda install cmake=3.9 -c defaults
conda install eman-deps=14 -c cryoem -c defaults -c conda-forge
}}}

 1. '''Checkout EMAN2 code''' from [[https://github.com/cryoem/eman2|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
}}}

 1. '''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.

 1. '''Build EMAN2'''
 {{{
make -j
make install
}}}

 1. 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
}}}

Contents

  1. Anaconda based Build, All Platforms (except Windows)
    1. GPU Support
    2. Mac OS X, Linux
      1. Linux Clusters
    3. Setup Conda
    4. EMAN Development Environment

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 to 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 Conda

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

    1. Remove miniconda/anaconda entries from PATH.

  2. Download and install Miniconda3 for Linux or MacOSX. 

       1 bash <Miniconda3-installer>
   2 
   3 # See command help for supported options
   4 bash <Miniconda3-installer> --help
    and follow the prompts.
  3. Make sure that:

    1. You do not have any miniconda/anaconda entries in PATH.

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

    If you can't run conda, because it is not in PATH, run 

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

    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

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

         1 conda config --set auto_activate_base False

EMAN Development Environment

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

  1. Create a new environment with the dependencies, if it doesn't exist. Click here for the list of conda dependencies that eman-deps is built from. 

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

  2. Activate the environment. 

       1 conda activate eman-deps-15.1
    OR 
       1 conda activate eman-env

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

       1 cd <path-where-you-want-eman2-source>   # eg - $HOME/src
   2 git clone https://github.com/cryoem/eman2.git
   3 # this will create an eman2 folder containing the current source code from the master branch
   4

  4. 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

  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 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.

  6. Build EMAN 

       1 make -j
   2 make install
  7. 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
  8. To switch to another conda environment, first deactivate your current environment. 
       1 conda deactivate

EMAN2/Install/SourceInstall (last edited 2024-09-13 17:55:35 by TunayDurmaz)