Main features added in this release:
We are currently updating the tutorial to comply with the most recent version. In the meantime, links to the SPHIRE 1.0 tutorial and data sets are included below:
The installer uses Anaconda, which should install independently of the choice of Linux distribution. The Mac installer is experimental. SPHIRE does not support Windows.
Libraries that needs to be installed in advance:
- OpenGL
In order to avoid conflicts with existing installations, we recommend to use a system environment that does not contain any environment variables related to OpenMPI, EMAN2, EMAN, and SPHIRE installations.
Especially, the output of
echo $PATH
should not contain paths to any existing OpenMPI, EMAN2, EMAN, and SPARX installations and
which ompi_info
should output
ompi_info not found.
In case ompi_info is still present, contact your system administrator and ask him/her to remove those PATH variables from the system wide environment settings.
The following installation describes the installation of binary packages. (You can find additional information about the installation at the Installing EMAN2 page.)
Download the installer, run it by typing
cd <Download directory> bash sphire_1_2a_linux.sh # or for Mac: bash sphire_1_2a_mac.sh
and follow the instructions given by the installer.
This creates the directory you specified during installation (default ${HOME}/EMAN2).
Now restart your terminal (log out & log in) and make sure that the path to the <path to EMAN2 directory>/bin folder is present in your PATH variable afterwards.
echo $PATH <path to EMAN2 directory>/bin:<more PATH content>
Continue with reinstalling Pydusa.
The following installation describes the installation from source code. (You can find additional information about the installation at the Installing EMAN2 page.)
Clone the git repository for this release:
mkdir <path-where-you-want-eman2-source> # e.g., $HOME/src cd <path-where-you-want-eman2-source> git clone https://github.com/cryoem/eman2.git # this will create an eman2 folder containing the current source code from the master branch cd eman2 git checkout tags/v2.3 # this will checkout the source code from the v2.3 tag cd ..
Check if it has been successful:
cd eman2
git log | head -n 4
commit 6aaac88e2763318efb61ae5a06681e9357f81adf
Author: Pawel Penczek <pawelpap@att.net>
Date: Thu Apr 25 14:03:56 2019 -0500
cd ..
Create a new virtual environment with python 2.7.
which conda
PATH/TO/YOUR/ANACONDA/conda
conda create -n sphire_1_2a python=2.7
Install dependencies:
source activate sphire_1_2a or conda activate sphire_1_2a # The 'conda create' command above should tell you which conda install cmake=3.9 -c conda-forge conda install eman-deps=14 -c cryoem -c defaults -c conda-forge conda install -n root conda-build -c conda-forge
Create a <build-directory> (out-of-source builds are recommended) and prepare the installation process.
mkdir <build-directory> # e.g., $HOME/src/eman2-build cd <build-directory> cmake <path-to-eman2-source> -DENABLE_OPTIMIZE_MACHINE=ON -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON # e.g, $HOME/src/eman2
Install SPHIRE from source.
make -j make install
Continue with reinstalling Pydusa.
The following installation describes the installation from source code. (You can find additional information about the installation at the Installing EMAN2 page.)
Clone the git repository for this release:
mkdir <path-where-you-want-eman2-source> # e.g., $HOME/src cd <path-where-you-want-eman2-source> git clone https://github.com/cryoem/eman2.git # this will create an eman2 folder containing the current source code from the master branch cd eman2 git checkout tags/v2.3 # this will checkout the source code from the v2.3 tag cd ..
Check if it has been successful:
cd eman2
git log | head -n 4
commit 6aaac88e2763318efb61ae5a06681e9357f81adf
Author: Pawel Penczek <pawelpap@att.net>
Date: Thu Apr 25 14:03:56 2019 -0500
cd ..
Install Miniconda version 4.5 for python 2.7.
wget https://repo.continuum.io/miniconda/Miniconda2-4.5.4-Linux-x86_64.sh bash Miniconda2-4.5.4-Linux-x86_64.sh -b -p <path-where-you-want-SPHIRE-installation> # e.g., $HOME/SPHIRE_1_2a
Add the bin folder of the installation (e.g., $HOME/SPHIRE_1_2a/bin) to your PATH variable and, if possible, make sure to remove the variables LD_LIBRARY_PATH, DYLD_LIBRARY_PATH and PYTHONPATH for the installation process.
Check:
which conda
$HOME/SPHIRE_1_2a/bin/conda
Install conda dependencies.
conda install cmake=3.9 -c conda-forge conda install eman-deps=14 -c cryoem -c defaults -c conda-forge conda install -n root conda-build -c conda-forge
Create a <build-directory> (out-of-source builds are recommended) and prepare the installation process.
mkdir <build-directory> # e.g., $HOME/src/eman2-build cd <build-directory> cmake <path-to-eman2-source> -DENABLE_OPTIMIZE_MACHINE=ON -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON # e.g., $HOME/src/eman2
Install SPHIRE from source.
make -j make install
Continue with reinstalling Pydusa.
0. Install pytz
python -m pip install pytz
The shipped version of OpenMPI and system wide OpenMPI installations might not work most of the time. That is why we recommend following the reinstallation process below (If you wish to install your own version of OpenMPI, you can find information below existing OpenMPI installation.)
Please check the information on our prepare submission installation site first, if there is already information about your queuing system.
1. Change to the installation directory you specified during installation
cd <path to EMAN2 directory> # e.g., $HOME/SPHIRE_1_2a (binary, source with own anaconda) or $ANACONDA_INSTALL/envs/SPHIRE_1_2a (source within existing anaconda)
2. Remove the OpenMPI provided:
bash utils/uninstall_openmpi.sh
3. Rebuild OpenMPI:
bash utils/build_and_install_openmpi.sh
Most Linux clusters will have at least one OpenMPI installation on the cluster. In some cases there may be more than one, and you may have to select a “module” to get the correct one. It is also critical that OpenMPI be compiled with the –disable-dlopen option. If you don't understand this statement, please consult with your cluster sysadmin.
1. Remove the OpenMPI we provided:
bash <path to EMAN2 directory>/utils/uninstall_openmpi.sh
2. Make sure that the correct OpenMPI for your cluster is in your path.
You should be able to run 'mpicc' and get a message like 'gcc: no input files'.
1. Rebuild Pydusa:
bash utils/build_pydusa_numpy.sh 1.13 --no-test --python=2.7
Note 2018/02/15: With the current version of the installer, the “no-test” option is necessary to avoid installation errors. It is a known issue to be fixed in the future.
2. Install Pydusa:
bash utils/install_pydusa_numpy.sh 1.13
Now restart your terminal (log out & log in).
If the following commands do not throw any errors, the installation is successful.
Binary installation
sparx
In [1]: import mpi
In [2]: Util.version()
Source modification date: 02/05/2018 10:55 AM
In [3]: quit
e2version.py
EMAN 2.22 final (GITHUB: 2018-08-22 11:59 - commit: v2.22 )
Your EMAN2 is running on: Linux-2.6.32-431.23.3.el6.x86_64-x86_64-with-redhat-6.5-Santiago 2.6.32-431.23.3.el6.x86_64
Your Python version is: 2.7.14
Source code installation
» sparx Python 2.7.14 |Anaconda, Inc.| (default, Mar 27 2018, 17:29:31) Type "copyright", "credits" or "license" for more information. IPython 5.8.0 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object', use 'object??' for extra details. libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast Welcome to the interactive SPARX-GUI Python interface, provided by ipython SPHIRE v1.2 (GitHub: 2019-04-25 09:34) In [1]: import mpi In [2]: Util.version() Source modification date: 03/02/2019 In [3]: quit » e2version.py EMAN 2.3 final (GITHUB: 2019-04-25 09:34 - commit: 67c1712 ) Your EMAN2 is running on: XXX XXX Your Python version is: 2.7.14
Congratulations! You installed SPHIRE!
During rebuild step 4, an error might occur.
Can't build /home/stevel/EMAN2/recipes/fftw-mpi due to environment creation error: Downloaded bytes did not match Content-Length url: http://www.fftw.org/fftw-3.3.6-pl1.tar.gz target_path: /home/stevel/EMAN2/conda-bld/src_cache/fftw-3.3.6.tar.gz Content-Length: 4179807 downloaded bytes: 208916 If you encounter this error, please do the following: rm conda-bld/src_cache/fftw-3.3.6.tar.gz bash utils/build_pydusa_numpy.sh 1.13 --no-test