Differences between revisions 36 and 57 (spanning 21 versions)

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

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

Checkout EMAN2 code from GitHub:cryoem/eman2.

cd <path-to-eman2-source>
git clone https://github.com/cryoem/eman2.git

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

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

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.
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 - make sure you don't get the Python3 version
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.

Checkout EMAN2 code from GitHub:cryoem/eman2.

cd <path-to-eman2-source>
git clone https://github.com/cryoem/eman2.git

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

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

Note that you will need to run source activate eman-env once in each shell before being able to run EMAN2 commands.
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.
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 36 as of 2017-06-14 20:46:35 → 
  Size: 1857
  Editor: TunayDurmaz
  Comment:
+   ← Revision 57 as of 2017-08-06 00:15:18 → ⇥
  Size: 5409
  Editor: TunayDurmaz
  Comment: recover broken cmake and ccmake
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= !!! UNDER CONSTRUCTION !!! =
+= Anaconda based Build, All Platforms =
 Line 3:
-= 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 7:
-. Download and install [[https://www.continuum.io/downloads | Anaconda2]] or [[https://conda.io/miniconda.html | Miniconda2]].
+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:
-. 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>
-Line 13:
+Line 16:
+ }}}
 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
-Line 15:
+Line 48:
-. 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.

 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'''. {{{
+=== 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
source activate eman-env
 }}}
   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). 
 {{{
-Line 24:
+Line 73:
-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 -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
-Line 30:
+Line 82:
-}}}
+ }}}
 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
 }}}