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Editor: TunayDurmaz
Comment: recover broken cmake and ccmake
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 1. Download and install [[https://conda.io/miniconda.html | Miniconda2]] or [[https://www.continuum.io/downloads | Anaconda2]].
   a. '''Miniconda2 (<30MB)''': Minimal installer that contains conda and Python. Ideal for cluster installations and if you need conda only for EMAN2.
   a. '''Anaconda2 (270-350 MB)''': Entire Anaconda distribution, open data science platform powered by Python. Includes packages like Jupyter, Spyder, Anaconda Navigator.		 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. Checkout EMAN2 code from [[https://github.com/cryoem/eman2 | GitHub:cryoem/eman2]]. {{{

cd <some-path-to-keep-eman2-source>		 === Miniconda2 ===
 1. Download and install [[https://conda.io/miniconda.html | Miniconda2]] - make sure you don't get the Python3 version
 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-to-eman2-source>
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 }}}
 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="*"="np18*" -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="*"="np18*" -c cryoem -c defaults -c conda-forge # Linux
 }}}
 1. Create a build directory (out-of-source builds are recommended).
 {{{
cd <build-directory>
cmake -DENABLE_CONDA=ON <path-to-eman2-source>
# on linux, also add -DENABLE_OPTIMIZE_MACHINE=ON
 }}}
  * If conda is not found in PATH, set CONDA_ROOT 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_ROOT to an environment, make sure to delete any cmake variables that cmake already found, variables like EMAN_INSTALL_PREFIX, EMAN_PREFIX, *_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
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 1. Install dependencies. Follow only one of the steps below:
   a. This option installs EMAN2 dependencies into a conda environment. It requires running the second command in each shell before trying to run EMAN2/SPARX/SPHIRE commands. {{{
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 don't get the 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-to-eman2-source>
git clone https://github.com/cryoem/eman2.git
 }}}
 1. Install dependencies
 {{{
conda install cmake=3.8 -c conda-forge
conda create -n eman-env eman-deps -c cryoem -c defaults -c conda-forge # Mac
conda create -n eman-env eman-deps="*"="np18*" -c cryoem -c defaults -c conda-forge # Linux
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}}}
   a. This option is easier, and doesn't use an environment. It will work with Miniconda, but will not work with Anaconda versions 4.2.0 (2016-09-28) and newer, because the bundled Qt version was upgraded from version 4 to 5. {{{
conda install eman-deps -c cryoem -c defaults -c conda-forge # Mac OSX
conda install eman-deps=*=np18* -c cryoem -c defaults -c conda-forge # Linux
}}} 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 a recommended practice in general, 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="*"="np18*" -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).
 {{{
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cmake <some-path-to-keep-eman2-source>
}}}
 1. If conda is not found in PATH, set CONDA_ROOT 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'''.
   a. If you set CONDA_ROOT to an environment, make sure to delete any cmake variables that cmake already found, variables like EMAN_INSTALL_PREFIX, EMAN_PREFIX, *_LIBRARY or similar, *_INCLUDE_PATH or similar.
   a. Rerun cmake.
 1. Continue with '''make'''. {{{
make -j                     # "make" should pick up the number of available processors,
make -j4 # but you may specify the number if you like
make install && make test
make test-verbose # verbose test output to help to identify failures
}}}		 cmake -DENABLE_CONDA=ON <path-to-eman2-source>
# on linux, also add -DENABLE_OPTIMIZE_MACHINE=ON
 }}}
  * If conda is not found in PATH, set CONDA_ROOT 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_ROOT to an environment, make sure to delete any cmake variables that cmake already found, variables like EMAN_INSTALL_PREFIX, EMAN_PREFIX, *_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
 }}}

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.

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.

Miniconda2

  1. Download and install Miniconda2 - make sure you don't get the Python3 version

  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-to-eman2-source>
git clone https://github.com/cryoem/eman2.git
  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="*"="np18*" -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="*"="np18*" -c cryoem -c defaults -c conda-forge  # Linux
  5. Create a build directory (out-of-source builds are recommended). 
    cd <build-directory>
cmake -DENABLE_CONDA=ON <path-to-eman2-source>
# on linux, also add -DENABLE_OPTIMIZE_MACHINE=ON

    • If conda is not found in PATH, set CONDA_ROOT 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_ROOT to an environment, make sure to delete any cmake variables that cmake already found, variables like EMAN_INSTALL_PREFIX, EMAN_PREFIX, *_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 don't get the 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-to-eman2-source>
git clone https://github.com/cryoem/eman2.git
  4. Install dependencies 
    conda install cmake=3.8 -c conda-forge
conda create -n eman-env eman-deps -c cryoem -c defaults -c conda-forge              # Mac
conda create -n eman-env eman-deps="*"="np18*" -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="*"="np18*" -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). 
    cd <build-directory>
cmake -DENABLE_CONDA=ON <path-to-eman2-source>
# on linux, also add -DENABLE_OPTIMIZE_MACHINE=ON

    • If conda is not found in PATH, set CONDA_ROOT 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_ROOT to an environment, make sure to delete any cmake variables that cmake already found, variables like EMAN_INSTALL_PREFIX, EMAN_PREFIX, *_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)