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= !!! UNDER CONSTRUCTION !!! = = NOTE =
Due to recent version upgrades of some packages, build instructions may be broken. Assessing the situation and applying fixes if necessary...
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= All platforms = = Anaconda based Build, All Platforms =
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 6-7 years old. Please report any problems.

== GPU Support ==
For features which support the GPU, please complete the source install instructions below, then follow the [[EMAN2/Install/BinaryInstallAnaconda#GPU|GPU instructions]] from the binary installation page.
Line 6: Line 11:
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, but will require the use of a conda environment to make EMAN2 work properly at present.
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 1. Download and install [[https://www.continuum.io/downloads | Anaconda2]] or [[https://conda.io/miniconda.html | Miniconda2]].

 1. Checkout EMAN2 code from [[https://github.com/cryoem/eman2 | GitHub:cryoem/eman2]]. {{{

cd <some-path-to-keep-eman2-source>		 === Linux Clusters ===
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.
https://github.com/cryoem/eman2/pull/167
=== Miniconda2 ===
 1. Download and install [[https://conda.io/miniconda.html|Miniconda2]] - make sure you get the '''Python2''' version, not --(Python3)-- version.
  a. '''Linux''': Latest version known to work with Linux is [[https://repo.continuum.io/miniconda/Miniconda2-4.3.21-Linux-x86_64.sh|here]].
 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. Checkout EMAN2 code from [[https://github.com/cryoem/eman2|GitHub:cryoem/eman2]].
 {{{
cd <path-where-you-want-eman2-source> # eg - $HOME/src
Line 13: Line 24:
# this will create an eman2 folder containing the current source code from the master branch
}}}
 1. Install dependencies
 {{{
conda install cmake=3.8 -c conda-forge
conda install eman-deps -c cryoem -c defaults -c conda-forge # Mac OSX
conda install eman-deps="*"="np19*" -c cryoem -c defaults -c conda-forge # Linux
}}}
  a. If you have a broken cmake or ccmake, try the following sequence of commands.
  {{{
conda remove cmake bzip2 expat jsoncpp ncurses
conda install cmake=3.8 -c conda-forge
conda install eman-deps -c cryoem -c defaults -c conda-forge # Mac OSX
conda install eman-deps="*"="np19*" -c cryoem -c defaults -c conda-forge # Linux
}}}
 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
Line 15: Line 59:
 1. Optionally, activate an existing conda environment, e.g. `source activate eman-env`. Skip this step, if you don't understand this statement. However, if you already use anaconda, you may get package conflicts when you install eman dependencies in the next step. In that case, you need to install eman and its dependencies in its own conda environment and skip the next step, "Install dependencies".{{{
conda create -n eman-env eman-deps -c cryoem -c defaults -c conda-forge		 === Anaconda2 ===
 1. Download and install [[https://www.continuum.io/downloads|Anaconda2]] - make sure you get the '''Python2''' version, not --(Python3)-- version.
 1. Make sure that you have added anaconda2/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. 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. Install dependencies
 {{{
conda create -n eman-env cmake=3.8 -c conda-forge
conda install -n eman-env eman-deps -c cryoem -c defaults -c conda-forge # Mac
conda install -n eman-env eman-deps="*"="np19*" -c cryoem -c defaults -c conda-forge # Linux
Line 19: Line 75:

 1. Install dependencies {{{
conda install eman-deps -c cryoem -c defaults -c conda-forge
}}} Listing the channels explicitly can be avoided by specifying them in $HOME/.condarc, see conda documentation for more details, https://conda.io/docs/using/index.html.

 1. Out-of-source builds are recommended, so work in a directory outside of eman2 source (this is generally true, not EMAN2-specific). Note '''cmake''', not '''--( ccmake )--'''. CMake will automatically find the dependencies. If you want to change any of the CMake values, then use '''cmake-gui''' or '''ccmake'''. {{{
   a. If you have a broken cmake or ccmake, try the following sequence of commands.
  {{{
conda remove cmake bzip2 expat jsoncpp ncurses
conda install cmake=3.8 -c conda-forge
conda install eman-deps -c cryoem -c defaults -c conda-forge # Mac OSX
conda install eman-deps="*"="np19*" -c cryoem -c defaults -c conda-forge # Linux
}}}
 1. Note that you will need to run {{{ source activate eman-env }}} once in each shell before being able to run EMAN2 commands.
 1. Create a build directory (out-of-source builds are recommended).
 {{{
mkdir <build-directory> # eg- $HOME/src/eman2-build
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rm -f CMakeCache.txt # This is needed to ensure cmake doesn't have any leftovers from previous runs
cmake <some-path-to-keep-eman2-source> -DENABLE_CONDA=ON \
                                       -DEMAN_CXX_FLAGS="-D_GLIBCXX_USE_CXX11_ABI=0" # This flag will be set in cmake with https://github.com/cryoem/eman2/pull/80
make -j # "make" should pick up the number of available processors,
make -j4 # but you may specify the number if you like		 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
Line 34: Line 97:
 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
}}}

NOTE

Due to recent version upgrades of some packages, build instructions may be broken. Assessing the situation and applying fixes if necessary...

Anaconda based Build, All Platforms

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 6-7 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 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, but will require the use of a conda environment to make EMAN2 work properly at present.

Linux Clusters

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 binary install page. Those instructions should also work with either of the source-based installations below. https://github.com/cryoem/eman2/pull/167

Miniconda2

  1. Download and install Miniconda2 - make sure you get the Python2 version, not Python3 version.

    1. Linux: Latest version known to work with Linux is here.

  2. 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.

  3. Checkout EMAN2 code from 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
  4. Install dependencies 
    conda install cmake=3.8 -c conda-forge
conda install eman-deps -c cryoem -c defaults -c conda-forge              # Mac OSX
conda install eman-deps="*"="np19*" -c cryoem -c defaults -c conda-forge  # Linux
    1. If you have a broken cmake or ccmake, try the following sequence of commands. 
      conda remove cmake bzip2 expat jsoncpp ncurses
conda install cmake=3.8 -c conda-forge
conda install eman-deps -c cryoem -c defaults -c conda-forge              # Mac OSX
conda install eman-deps="*"="np19*" -c cryoem -c defaults -c conda-forge  # Linux
  5. 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.
  6. Build EMAN2 
    make -j
make install
  7. 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

Anaconda2

  1. Download and install Anaconda2 - make sure you get the Python2 version, not Python3 version.

  2. Make sure that you have added anaconda2/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.

  3. Checkout EMAN2 code from 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
  4. Install dependencies 
    conda create -n eman-env cmake=3.8 -c conda-forge
conda install -n eman-env eman-deps -c cryoem -c defaults -c conda-forge              # Mac
conda install -n eman-env eman-deps="*"="np19*" -c cryoem -c defaults -c conda-forge  # Linux
source activate eman-env
    1. If you have a broken cmake or ccmake, try the following sequence of commands. 
      conda remove cmake bzip2 expat jsoncpp ncurses
conda install cmake=3.8 -c conda-forge
conda install eman-deps -c cryoem -c defaults -c conda-forge              # Mac OSX
conda install eman-deps="*"="np19*" -c cryoem -c defaults -c conda-forge  # Linux

  5. Note that you will need to run  source activate eman-env  once in each shell before being able to run EMAN2 commands.

  6. 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.
  7. Build EMAN2 
    make -j
make install
  8. 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

EMAN2/COMPILE_EMAN2_ANACONDA-PRE-CONDA-ENVIRONMENTS (last edited 2019-11-01 14:27:54 by TunayDurmaz)