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⇤ ← Revision 74 as of 2018-02-28 03:03:38 →
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Editor: TunayDurmaz
Comment: WIP
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Editor: TunayDurmaz
Comment: NumPy 1.13 instructions with setting PATH
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'''Note:''' Along with upgrading '''!NumPy''' to 1.13, we are also upgrading '''conda''' to 4.4 and '''conda-build''' to 3. Please, pay attention to PATH related instructions as there is no need to manipulate PATH anymore. These instructions are for building with '''!NumPy v1.13'''.
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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 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.
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 1. '''Remove''' any miniconda2/bin entries from your PATH and run
 {{{
. <miniconda2-path>/etc/profile.d/conda.sh # Note the dot in the beginning of the line
conda activate base
}}}
  . or, if you have a line reading
 {{{
 export PATH=<miniconda2-path>/bin:$PATH
}}}
 in your .bashrc or .profile, replace it with
 {{{
. <miniconda2-path>/etc/profile.d/conda.sh # Note the dot in the beginning of the line
conda activate base
}}}

 1. Make sure 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. 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.
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'''Currently, building EMAN with Anaconda is not possible without unsetting some environment variables that are set by Anaconda's new compilers.'''
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 1. '''Remove''' any anaconda2/bin entries from your PATH and run
 {{{
. <anaconda2-path>/etc/profile.d/conda.sh
}}}
  . or,  if you have a line reading
 {{{
 export PATH=<anaconda2-path>/bin:$PATH
}}}
 in your .bashrc or .profile, replace it with
 {{{
. <anaconda2-path>/etc/profile.d/conda.sh # Note the dot in the beginning of the line
}}}

 1. Make sure 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 Anaconda. Alternatively, you may set up a shell script or alias to make these environment changes on demand when you want to use EMAN2/anaconda.		  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.

THESE INSTRUCTIONS ARE STILL WORK-IN-PROGRESS

Anaconda based Build, All Platforms

These instructions are for building with NumPy v1.13.

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.

Miniconda2

  1. Download and install Miniconda2-4.4.10 for Linux or Mac OSX.

    1. For existing installations install conda 4.4. 
      conda install conda=4.4 -c defaults

  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. Install dependencies 

    conda install cmake=3.9 -c defaults
conda install eman-deps=8 -c cryoem -c defaults -c conda-forge

  4. 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

  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

Currently, building EMAN with Anaconda is not possible without unsetting some environment variables that are set by Anaconda's new compilers.

  1. Download and install Anaconda2-5.1.0 for Linux or Mac OSX.

    1. For existing installations install conda 4.4. 
      conda install conda=4.4 -c defaults
  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. Install dependencies 

    conda create -n eman-env cmake=3.9 -c defaults
conda install -n eman-env eman-deps=8 -c cryoem -c defaults -c conda-forge

conda activate eman-env

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

  5. 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

  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)