Differences between revisions 46 and 73 (spanning 27 versions)
Revision 46 as of 2017-07-26 22:22:20
Size: 2429
Editor: SteveLudtke
Comment:
Revision 73 as of 2018-02-27 18:54:00
Size: 6759
Editor: TunayDurmaz
Comment:
Deletions are marked like this. Additions are marked like this.
Line 2: Line 2:
'''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.
Line 5: Line 6:
== 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 10:
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.
Line 7: Line 12:
 1. Download and install [[https://www.continuum.io/downloads | Anaconda2]] or [[https://conda.io/miniconda.html | Miniconda2]]. === 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
Line 9: Line 15:
 1. Checkout EMAN2 code from [[https://github.com/cryoem/eman2 | GitHub:cryoem/eman2]]. {{{

cd <some-path-to-keep-eman2-source>
git clone https://github.com/cryoem/eman2.git
=== Miniconda2 ===
 1. Download and install '''Miniconda2-4.4.10''' for [[https://repo.continuum.io/miniconda/Miniconda2-4.4.10-Linux-x86_64.sh|Linux]] or [[https://repo.continuum.io/miniconda/Miniconda2-4.4.10-MacOSX-x86_64.sh|Mac OSX]].
  1. For existing installations install conda 4.4.
  {{{
conda install conda=4.4 -c defaults
Line 15: Line 22:
 1. Install dependencies. Follow only one of the steps below:
   a. This option installs Anaconda and sets up a specific environment for EMAN2. 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
source activate eman-env
 1. '''Remove''' any miniconda2/bin entries from your PATH and run
 {{{
. <miniconda2-path>/etc/profile.d/conda.sh
Line 20: Line 26:
   a. This option is easier, and doesn't use an environment, but may be broken (July 2017) due to recent Qt changes in Anaconda {{{
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 $HOME/.condarc, see conda documentation for more details, https://conda.io/docs/using/index.html.
  . or, if you have a line reading
 {{{
 export PATH=<miniconda2-path>/bin:$PATH
}}}
 in your .bashrc or .profile, replace it with
 {{{
. <miniconda2-path>/etc/profile.d/conda.sh
}}}
Line 25: Line 35:
 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'''. {{{  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.
Line 27: Line 37:
 1. '''Install dependencies'''
 {{{
conda install cmake=3.9 -c defaults
conda install eman-deps=8 -c cryoem -c defaults -c conda-forge
}}}

 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. '''Create a build directory''' (out-of-source builds are recommended).
 {{{
mkdir <build-directory> # eg- $HOME/src/eman2-build
Line 28: Line 54:
cmake <some-path-to-keep-eman2-source> cmake <path-to-eman2-source> # - eg $HOME/src/eman2. On linux, also add -DENABLE_OPTIMIZE_MACHINE=ON
Line 30: Line 56:
 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.
 1. 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.
 1. Rerun cmake and continue with make. {{{
cmake <some-path-to-keep-eman2-source>
make -j # "make" should pick up the number of available processors,
make -j4 # but you may specify the number if you like
  * 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 38: Line 65:

 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
}}}

=== Anaconda2 ===
 1. Download and install '''Anaconda2-5.1.0''' for [[https://repo.continuum.io/archive/Anaconda2-5.1.0-Linux-x86_64.sh|Linux]] or [[https://repo.continuum.io/archive/Anaconda2-5.1.0-MacOSX-x86_64.sh|Mac OSX]].
  1. For existing installations install conda 4.4.
  {{{
conda install conda=4.4 -c defaults
}}}

 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
}}}

 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. '''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
}}}

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

 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. '''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
}}}

Anaconda based Build, All Platforms

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.

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 Miniconda2-4.4.10 for Linux or Mac OSX.

    1. For existing installations install conda 4.4.
      conda install conda=4.4 -c defaults
  2. Remove any miniconda2/bin entries from your PATH and run

    . <miniconda2-path>/etc/profile.d/conda.sh
    • 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
  3. 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.
  4. Install dependencies

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

Anaconda2

  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. 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
  3. 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.
  4. 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
  5. Note that you will need to run  conda activate eman-env  once in each shell before being able to run EMAN2 commands.

  6. 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
  7. 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.
  8. Build EMAN2

    make -j
    make install
  9. 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)