Differences between revisions 24 and 25
⇤ ← Revision 24 as of 2019-10-10 04:43:27 →
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Editor: TunayDurmaz
Comment: obsolete environment instructions
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Editor: TunayDurmaz
Comment: no caching
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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

mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cache-directory>
mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cache-directory>
}}}
Line 64: Line 57:
 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
}}}

Python 3 Transition Environments

Phase 1: Upgrade CMake to 3.14

PR: Upgrade CMake to 3.14

Install cmake=3.24 and eman-deps=15.1. 

  •    1 conda install eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge

Phase 2: Test Boost 1.64

PR: Upgrade Boost to 1.64 

  •    1 conda install eman-deps=16.1 cmake=3.14 boost=1.64 -c cryoem -c defaults -c conda-forge

Phase 3: Test Boost 1.66

PR: Build with Boost versions 1.65-1.66 

  •    1 conda install eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge

Python 3 Environments (Coming Soon!)

Coming soon!

The following sections were written with conda environments in mind, but will not be used. Keeping here for future reference.

Setup Development Environment with Conda

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

    1. Remove miniconda/anaconda entries from PATH.

  2. Download Miniconda3 for Linux or MacOSX.

  3. Install Miniconda3. 

       1 bash <Miniconda3-installer>
    and follow the prompts.
  4. 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

  5. Install conda 4.6.14. 

       1 conda install conda=4.6.14 -c defaults
  6. 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

Python 3 Transition Environments

Phase 1: Upgrade CMake to 3.14

PR: Upgrade CMake to 3.14

  1. Create a new environment and activate it. 
       1 conda create -n eman-deps-15.1 eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
   2 conda activate eman-deps-15.1

  2. Navigate to your source directory. Checkout branch cmake-upgrade and pull updates from the remote. 

       1 cd <source-directory>
   2 git checkout cmake-upgrade
   3 git pull --rebase
  3. Navigate to your build directory, build and install. 
       1 cd <build-directory>
   2 cmake <eman2-source-directory>
   3 make
   4 make install
  4. To switch to another conda environment, first deactivate your current environment. 
       1 conda deactivate

Phase 2: Test Boost 1.64

PR: Upgrade Boost to 1.64

  1. Create a new environment and activate it. 
       1 conda create -n eman-deps-16.1 eman-deps=16.1 cmake=3.14 boost=1.64 -c cryoem -c defaults -c conda-forge
   2 conda activate eman-deps-16.1

  2. Navigate to your source directory. Checkout branch py2-boost-164 and pull updates from the remote. 

       1 cd <source-directory>
   2 git checkout py2-boost-164
   3 git pull --rebase
  3. Navigate to your build directory, build and install. 
       1 cd <build-directory>
   2 cmake <eman2-source-directory>
   3 make
   4 make install
  4. To switch to another conda environment, first deactivate your current environment. 
       1 conda deactivate

Phase 3: Test Boost 1.66

PR: Build with Boost versions 1.65-1.66

  1. Create a new environment and activate it. 
       1 conda create -n eman-deps-16.1 eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge
   2 conda activate eman-deps-16.1

  2. Navigate to your source directory. Checkout branch py2-boost-166 and pull updates from the remote. 

       1 cd <source-directory>
   2 git checkout py2-boost-166
   3 git pull --rebase
  3. Navigate to your build directory, build and install. 
       1 cd <build-directory>
   2 cmake <eman2-source-directory>
   3 make
   4 make install
  4. To switch to another conda environment, first deactivate your current environment. 
       1 conda deactivate

Python 3 Environments (Coming Soon!)

Coming soon!