Differences between revisions 10 and 12 (spanning 2 versions)
⇤ ← Revision 10 as of 2019-07-15 05:24:40 →
Size: 4514
Editor: TunayDurmaz
Comment: todo
← Revision 12 as of 2019-08-18 02:05:22 → ⇥
Size: 6033
Editor: TunayDurmaz
Comment: bash parser
Deletions are marked like this. Additions are marked like this.
Line 8: Line 8:
  {{{
  mkdir -p <path-to-conda-cahe-directory>		   {{{#!highlight bash
  mkdir -p <path-to-conda-cache-directory>
Line 12: Line 12:
mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cahe-directory>
mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cahe-directory>		 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 17: Line 17:
 {{{  {{{#!highlight bash
Line 21: Line 21:
 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.
 {{{
  conda config --set pkgs_dirs <path-to-conda-cahe-directory>/pkgs		  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 --set pkgs_dirs <path-to-conda-cache-directory>/pkgs
Line 26: Line 29:
  conda config --set envs_dirs <path-to-conda-cahe-directory>/envs   conda config --set envs_dirs <path-to-conda-cache-directory>/envs
Line 31: Line 34:
  {{{   {{{#!highlight bash
Line 35: Line 38:
  {{{   {{{#!highlight bash
Line 39: Line 42:
 {{{  {{{#!highlight bash
Line 43: Line 46:
 {{{  {{{#!highlight bash
Line 57: Line 60:
 {{{  {{{#!highlight bash
Line 61: Line 64:
 {{{  {{{#!highlight bash
Line 65: Line 68:
 {{{  {{{#!highlight bash
Line 69: Line 72:
 {{{  {{{#!highlight bash
Line 73: Line 76:
 {{{  {{{#!highlight bash
Line 79: Line 82:
 {{{  {{{#!highlight bash
Line 91: Line 94:
 1. Add mkdir build-eman-deps-14 steps, maybe, after activation.
Line 94: Line 96:
'''END TODO'''
Line 95: Line 98:
== Upgrade CMake to 3.14 == == Phase 1: Upgrade CMake to 3.14 ==
Line 99: Line 102:
 {{{  {{{#!highlight bash
Line 103: Line 106:
 1. Navigate to your source directory. Checkout branch '''cmake-upgrade''' and pull updates from the remote.
 {{{#!highlight bash
cd <source directory>
git checkout cmake-upgrade
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{#!highlight bash
cd <build directory>
cmake <eman2 source directory>
make
make install
}}}
Line 104: Line 120:
 {{{  {{{#!highlight bash
Line 108: Line 124:
== Test Boost 1.64 == == Phase 2: Test Boost 1.64 ==
Line 112: Line 128:
 {{{  {{{#!highlight bash
Line 116: Line 132:
 1. Navigate to your source directory. Checkout branch '''py2-boost-164''' and pull updates from the remote.
 {{{#!highlight bash
cd <source directory>
git checkout py2-boost-164
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{#!highlight bash
cd <build directory>
cmake <eman2 source directory>
make
make install
}}}
Line 117: Line 146:
 {{{  {{{#!highlight bash
Line 122: Line 151:
== Test Boost 1.66 == == Phase 3: Test Boost 1.66 ==
Line 126: Line 155:
 {{{  {{{#!highlight bash
Line 130: Line 159:
 1. Navigate to your source directory. Checkout branch '''py2-boost-166''' and pull updates from the remote.
 {{{#!highlight bash
cd <source directory>
git checkout py2-boost-166
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{#!highlight bash
cd <build directory>
cmake <eman2 source directory>
make
make install
}}}
Line 131: Line 173:
 {{{  {{{#!highlight bash

Under Construction

Setup Development Environment with Conda

  1. If you have an existing Miniconda2 installation,

    1. Remove miniconda 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. Download Miniconda3 for Linux or MacOSX.

  3. Install Miniconda3. 

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

  4. 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 --set pkgs_dirs <path-to-conda-cache-directory>/pkgs
   5 # conda config --set pkgs_dirs ~/conda-global-cache/pkgs
   6 
   7   conda config --set envs_dirs <path-to-conda-cache-directory>/envs
   8 # conda config --set pkgs_dirs ~/conda-global-cache/envs
   9
  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. 
       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 <eman2 source directory>
   3 make
   4 make install

Python 3 Transition Environments

TODO

  1. Fix eman-deps versions in the PR envs.
  2. Add new env for new compilers, maybe, for boost 1.67 and update eman-deps-feedstock.

END TODO

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-14.2 eman-deps=14.2 cmake=3.14 -c cryoem/label/dev -c cryoem -c defaults -c conda-forge
   2 conda activate eman-deps-14.2

  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-14.2 eman-deps=14.3 cmake=3.14 boost=1.64 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge
   2 conda activate eman-deps-14.3

  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-14.2 eman-deps=14.3 cmake=3.14 boost=1.66 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge
   2 conda activate eman-deps-14.3

  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