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downloads:sphire_beta_20161216 [2017/06/14 17:44] 127.0.0.1 external edit |
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- | ====== SPHIRE beta 2016/12/16 ====== | ||
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- | ===== Download ===== | ||
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- | * [[https:// | ||
- | * [[https:// | ||
- | * [[https:// | ||
- | * [[https:// | ||
- | * [[https:// | ||
- | * [[https:// | ||
- | |||
- | |||
- | ===== Installation instructions ===== | ||
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- | After downloading the binaries, the package must be uncompressed in its final directory. For example, to install SPHIRE in $HOME/ | ||
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- | cd $HOME/ | ||
- | tar xvf sphire_beta_20161216.tar.gz | ||
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- | This will create a folder called EMAN2. You need to go inside the folder and run the eman2-installer | ||
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- | cd EMAN2 | ||
- | ./ | ||
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- | \\ | ||
- | **Important**: | ||
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- | cat eman2.bashrc >> ~/.bashrc | ||
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- | will do the trick. Congratulations, | ||
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- | \\ | ||
- | Most programs within SPHIRE require MPI to run properly. SPHIRE uses the MyMPI package to parallelize many routines. To install this you need a working MPI enviroment and pydusa. A specifically modified version of pydusa needs to be downloaded for SPHIRE (You can find it at the top of the page). Most clusters will already have a working MPI environment. If you want to install this on a workstation you can download openmpi and compile like: | ||
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- | tar xvf openmpi.2.0.1.tar.gz | ||
- | cd openmpi-2.0.1 | ||
- | ./configure --prefix=/ | ||
- | make -j 4 | ||
- | make install | ||
- | | ||
- | The --disable-dlopen flag is necessary, otherwise SPHIRE will have issues with mpirun. | ||
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- | \\ | ||
- | After the MPI and EMAN2 environments are properly set up, you need to uncompress pydusa and install MyMPI. For instance if you downloaded pydusa into the EMAN2 folder you should | ||
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- | cd $EMAN2DIR | ||
- | tar xvf pydusa-1.15es-fftmpi-6__2016_09_07.tgz | ||
- | cd pydusa-1.15es-fftmpi-6 | ||
- | ./ | ||
- | | ||
- | This will create all the necessary files, and append the new environmental setting to the eman2.bashrc file. To test the installation start a fresh terminal and source the eman2.bashrc file. | ||
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- | In case you do not have a working mpi environment and also you do not want to compile one from scratch, pydusa can perform a local installation for you with the command | ||
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- | ./ | ||
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- | Finally source again the eman2.bashrc file and run | ||
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- | sx.py | ||
- | import mpi | ||
- | quit | ||
- | | ||
- | If no error occur while importing mpi then, congratulations your MPI version of SPHIRE is working. Happy processing! | ||
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- | \\ | ||
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- | ===== Known Issues ===== | ||
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- | A list of the known issues can be found here: [[known_issues: | ||