Differences between revisions 1 and 82 (spanning 81 versions)

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

Download and install Miniconda2-4.4.10 for Linux or Mac OSX.
1. For existing installations install conda 4.5.
```
conda install "conda>=4.5.2" -c defaults
```
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.

Install dependencies

conda install cmake=3.9 -c defaults
conda install eman-deps=12 -c cryoem -c defaults -c conda-forge

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

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.
Build EMAN2
```
make -j
make install
```

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

Download and install Anaconda2-5.1.0 for Linux or Mac OSX.
1. For existing installations install conda 4.5.
```
conda install "conda>=4.5.2" -c defaults
```
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 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.

Install dependencies

conda create -n eman-env cmake=3.9 -c defaults
conda install -n eman-env eman-deps=12 -c cryoem -c defaults -c conda-forge

source activate eman-env

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

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

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.
Build EMAN2
```
make -j
make install
```

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)

-  ⇤ ← Revision 1 as of 2017-05-15 18:25:40 → 
  Size: 716
  Editor: TunayDurmaz
  Comment: incomplete draft
+   ← Revision 82 as of 2018-07-30 16:51:41 → ⇥
  Size: 6149
  Editor: TunayDurmaz
  Comment: eman-deps=12
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= !!! UNDER CONSTRUCTION !!! =
+= Anaconda based Build, All Platforms =
These instructions are for building with '''!NumPy v1.13'''.
-Line 3:
+Line 4:
-= 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.
-Line 5:
+Line 6:
-The following instructions will work with cmake changes introduced in https://github.com/cryoem/eman2/pull/65.
+== 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 8:
+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 9:
+Line 12:
-. Download and install Anaconda/Miniconda (:TODO: links).
+=== 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.
-Line 11:
+Line 15:
-. Optionally, activate an existing conda environment, i.e. `source activate eman-env`.

3. Checkout EMAN2 code from GitHub, (link here). {{{

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 4.5.
  {{{
conda install "conda>=4.5.2" -c defaults
-Line 19:
+Line 22:
-. Out-of-source builds are recommended, so work in a directory outside of eman2 source. {{{
+. 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.
-Line 21:
+Line 24:
+. '''Install dependencies'''
 {{{
conda install cmake=3.9 -c defaults
conda install eman-deps=12 -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 22:
+Line 41:
-cmake <some-path-to-keep-eman2-source>
+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'''
 {{{
-Line 27:
+Line 53:
-# == Linux ==
+. 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 29:
+Line 59:
+=== Anaconda2 ===
-Line 30:
+Line 61:
-== Windows ==
+. 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 4.5.
  {{{
conda install "conda>=4.5.2" -c defaults
}}}

 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 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=12 -c cryoem -c defaults -c conda-forge

source activate eman-env
}}}

 1. Note that you will need to run {{{ source 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
}}}