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Editor: TunayDurmaz
Comment: remove anaconda
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Editor: TunayDurmaz
Comment: shell startup file on mac
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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! 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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 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/
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{{{#!wiki caution
'''???'''}}}
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 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. Make sure 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 EMAN.
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{{{#!wiki caution
'''???'''}}}
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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.
 {{{#!highlight bash
  mkdir -p <path-to-conda-cache-directory>
# mkdir -p ~/conda-global-cache

  conda config --add pkgs_dirs <path-to-conda-cache-directory>/pkgs
# conda config --add pkgs_dirs ~/conda-global-cache/pkgs

  conda config --add envs_dirs <path-to-conda-cache-directory>/envs
# conda config --add pkgs_dirs ~/conda-global-cache/envs
}}}
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 1. Initialize conda for shell interaction.  1. Initialize conda for shell interaction, if you haven't done it during installation.
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 {{{#!wiki caution
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 difference between login- and non-login shells, order of reading the startup files on Mac OSX, see, https://www.anintegratedworld.com/basics-of-osx-bashrc-v-profile-v-bash_profile/.
}}}


 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.
 {{{#!highlight bash
  mkdir -p <path-to-conda-cache-directory>
# mkdir -p ~/conda-global-cache

  conda config --add pkgs_dirs <path-to-conda-cache-directory>/pkgs
# conda config --add pkgs_dirs ~/conda-global-cache/pkgs

  conda config --add envs_dirs <path-to-conda-cache-directory>/envs
# conda config --add pkgs_dirs ~/conda-global-cache/envs
}}}
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== Development Environments ==
{{{#!wiki caution
'''???'''}}}		 == EMAN Development Environment ==
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Do not install anything into the '''base''' environment, do not use the '''base''' environment for development, use '''non-base''' environments. {{{#!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.
 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.
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conda create -n eman-deps-14.1 eman-deps=14.1 -c cryoem -c defaults -c conda-forge conda create -n eman-deps-15.1 eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
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conda create -n eman-env eman-deps=14.1 -c cryoem -c defaults -c conda-forge conda create -n eman-env eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
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 1. Activate the environment.
1. '''Activate''' the environment.
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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.
 1. '''Get EMAN code if you don't have it''' from [[https://github.com/cryoem/eman2|GitHub:cryoem/eman2]].
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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
}}}



== 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.
 {{{#!highlight bash
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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 1. '''Build EMAN2'''
 {{{
1. '''Build EMAN'''
 {{{#!highlight bash
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 {{{  {{{#!highlight bash
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=== 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.

 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 Development Environment with 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 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

TODO

  1. Review how to install new vs existing installations. How do you use conda-init, if conda is not on PATH?
    1. The installer seems to take care of it, if it is not used in batch mode.
    2. How do we handle it manually, if the installation was done in batch mode.

  2. Activation, conda init ... https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment

  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>

  2. Make sure 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 EMAN.

  3. Download Miniconda3 for Linux or MacOSX.

  4. Install Miniconda3. 

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

  6. Install conda 4.6.14. 

       1 conda install conda=4.6.14 -c defaults
  7. 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

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

  8. 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

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 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 EMAN 

       1 make -j
   2 make install
  2. 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
  3. 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)