Differences between revisions 12 and 20 (spanning 8 versions)
⇤ ← Revision 12 as of 2019-10-04 14:53:26 →
Size: 8458
Editor: TunayDurmaz
Comment: conda-init, activate links
← Revision 20 as of 2019-10-22 01:45:26 → ⇥
Size: 7362
Editor: TunayDurmaz
Comment:
Deletions are marked like this. Additions are marked like this.
Line 12: Line 12:
For features which support the GPU, please complete the source install instructions below, then follow the [[EMAN2/Install/BinaryInstallAnaconda#GPU|GPU instructions]] from the binary installation page. For features which support the GPU, please complete the source install instructions below, then follow the [[EMAN2/Install/BinaryInstallAnaconda/2.31#Using_the_GPU|GPU instructions]] from the binary installation page.
Line 17: Line 17:
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 [[https://www.anaconda.com/distribution/|Anaconda]]. 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 and Anaconda are similar, the only difference is the installer used.
Line 19: Line 19:
== Initial Setup ==
Line 20: Line 21:
=== 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 [[EMAN2/Install/BinaryInstallAnaconda|binary install page]]. Those instructions should also work with either of the source-based installations below.



== Setup Development Environment with Conda ==

{{{#!wiki caution
'''TODO'''

 1. Review how to install new vs existing installations. How do you use conda-init, if conda is not on PATH?
  1. If you have an existing '''Miniconda2/Anaconda2''' installation which is used by adding it to PATH in shell initialization files, remove that export command that looks like
 {{{#!highlight bash
export PATH=<Miniconda-installation-path>/bin:$PATH
Line 35: Line 26:
 1. If you have an existing '''Miniconda2/Anaconda2''' installation,
  a. '''Remove miniconda/anaconda entries from PATH'''.
  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		  1. Download and install '''Miniconda''' 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]].
Line 42: Line 28:
mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cache-directory>
mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cache-directory>		  {{{#!highlight bash
bash <Miniconda-installer>

# See command help for supported options
bash <Miniconda-installer> --help
}}}
 and follow the prompts.

 1. Make sure that:
  a. You do '''not''' have any <miniconda/anaconda>/bin entries in '''PATH''' added by your shell initialization files.
  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. At this point, if you have cleaned up your shell initialization files and started a new terminal session, you shouldn't be able to use conda. If that is not the case and you have a working conda, run the following

 {{{#!highlight bash
conda init
Line 46: Line 48:
 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.  If you can't run conda, run
Line 48: Line 50:
 1. Download '''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]].  {{{#!highlight bash
source <miniconda-path>/etc/profile.d/conda.sh
conda init
}}}
Line 50: Line 55:
 1. Install '''Miniconda3'''.
 {{{#!highlight bash
bash <Miniconda3-installer>		  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.
Line 54: Line 57:
# See command help for supported options
bash <Miniconda3-installer> --help		  {{{#!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/.
Line 57: Line 64:
 and follow the prompts.
Line 64: Line 71:
  a. If you don't want conda's base environment to be activated automatically. '''(Optional)'''   This is to prevent automatic upgrades of conda which sometimes introduce breaking changes. The latest version known to work with EMAN is '''conda 4.6.14'''.
 a. If you don't want conda's '''base''' environment to be activated automatically. '''(Optional)'''
Line 68: Line 76:
  The current default behavior is to automatically activate the base environment. This adds the base environment to PATH and the shell prompt displays the name of the environment. If these are not desired, turn the auto activation off.
Line 69: Line 78:
 1. Install '''conda 4.6.14'''.  1. Create a new environment with the dependencies. For the [[https://github.com/cryoem/eman-deps-feedstock/blob/v15.1/recipe/meta.yaml#L9-L53|list of conda dependencies]] that '''eman-deps''' is built from, click [[https://github.com/cryoem/eman-deps-feedstock/blob/v15.1/recipe/meta.yaml#L9-L53|here]].
Line 71: Line 80:
conda install conda=4.6.14 -c defaults conda create -n eman eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
Line 74: Line 83:
 1. Initialize conda for shell interaction, if you haven't done it during installation. 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.  1. '''Get EMAN code''' from [[https://github.com/cryoem/eman2|GitHub:cryoem/eman2]].
 {{{#!highlight bash
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
}}}
Line 76: Line 89:
 1. '''Create a build directory''' (out-of-source builds are recommended).
Line 77: Line 91:
conda init bash

# See command help for supported shells
conda init --help
}}}
 {{{#!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/.		 mkdir <build-directory> # eg- $HOME/src/eman2-build
Line 89: Line 95:
 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. == EMAN Daily Development ==

 1. '''Activate''' your environment.
Line 91: Line 99:
  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
}}}



== 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.
}}}


 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
}}}


 1. '''Activate''' the environment.
 {{{#!highlight bash
conda activate eman-deps-15.1
}}}
 OR
 {{{#!highlight bash
conda activate eman-env
}}}


 1. '''Get EMAN code if you don't have it''' from [[https://github.com/cryoem/eman2|GitHub:cryoem/eman2]].
 {{{#!highlight bash
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		 conda activate eman
Line 144: Line 109:
 1. '''Create a build directory''' (out-of-source builds are recommended).  1. '''Build EMAN'''
Line 146: Line 111:
mkdir <build-directory> # eg- $HOME/src/eman2-build
Line 150: Line 114:
{{{#!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.
Line 158: Line 118:

 1. '''Build EMAN'''
Line 175: Line 133:


== Linux Clusters ==

The approach above 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/2.31#Linux_Clusters|binary install page]]. Those instructions should also work with either of the source-based installations below.

Contents

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

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 and Anaconda are similar, the only difference is the installer used.

Initial Setup

  1. If you have an existing Miniconda2/Anaconda2 installation which is used by adding it to PATH in shell initialization files, remove that export command that looks like 

       1 export PATH=<Miniconda-installation-path>/bin:$PATH

  2. Download and install Miniconda for Linux or MacOSX. 

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

    1. You do not have any <miniconda/anaconda>/bin entries in PATH added by your shell initialization files.

    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. At this point, if you have cleaned up your shell initialization files and started a new terminal session, you shouldn't be able to use conda. If that is not the case and you have a working conda, run the following 
       1 conda init
    If you can't run conda, run 
       1 source <miniconda-path>/etc/profile.d/conda.sh
   2 conda init

    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

      This is to prevent automatic upgrades of conda which sometimes introduce breaking changes. The latest version known to work with EMAN is conda 4.6.14.

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

         1 conda config --set auto_activate_base False
      The current default behavior is to automatically activate the base environment. This adds the base environment to PATH and the shell prompt displays the name of the environment. If these are not desired, turn the auto activation off.

  6. Create a new environment with the dependencies. For the list of conda dependencies that eman-deps is built from, click here. 

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

  7. Get EMAN code from GitHub:cryoem/eman2. 

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

  8. Create a build directory (out-of-source builds are recommended). 

       1 mkdir <build-directory> # eg- $HOME/src/eman2-build
   2

EMAN Daily Development

  1. Activate your environment. 

       1 conda activate eman

  2. 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

  3. Build EMAN 

       1 cd <build-directory>
   2 cmake <source-directory>   # - eg $HOME/src/eman2. On linux, also add -DENABLE_OPTIMIZE_MACHINE=ON
   3

    • 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. 
       1 make -j
   2 make install
  4. 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
  5. To switch to another conda environment, first deactivate your current environment. 
       1 conda deactivate

Linux Clusters

The approach above 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.

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