Binary Installation Instructions

Mac OS X

1. Download eman2.X.MacOS.sh
2. Run:

   bash <path to EMAN2 installer>

   • You will be prompted for a location to install EMAN2. Note that you cannot rename this folder after installation! You must reinstall if you wish to move the installation

   • You will be asked if you want to add  export PATH=...  to your .profile file.

   • If you use a different shell, such as tcsh or zsh, you may need to edit the appropriate file yourself.
   • You should not normally need to run the OpenMPI reinstallation scripts. The copy of OpenMPI/Pydusa now distributed with the binaries should work on Macs in most cases.
   • Don't forget to restart your shell if you changed the .profile or other scripts
3. Run these programs to see if the install worked:

   e2version.py
   e2speedtest.py
   e2display.py
   e2proc2d.py :64:64:1 test.hdf --process mask.sharp:outer_radius=24

4. If you have problems with any of these programs, the first thing to check is whether you have PYTHONPATH, LD_LIBRARY_PATH or DYLD_LIBRARY_PATH set in your shell. While used in previous versions of EMAN, these variables are no longer necessary. If they are set to make some other software package work, but they interfere with the programs above, you will have to unset them, and set them only when you need the other software.

Linux Workstations (not clusters)

1. There are two linux binaries available: eman2.X.centos6.sh and eman2.X.centos7.sh
   • See release specific notes below. If you are using a distribution other than CentOS, which version you need will depend on how old your OS is. We suggest starting with centos7, and going back to centos6 if it fails.
2. Run:

   bash <path to EMAN2 installer>

   • You will be prompted for a location to install EMAN2. Note that you cannot rename this folder after installation! You must reinstall if you wish to move the installation

   • You will be asked if you want to add  export PATH=...  to your .profile file.

   • If you use a different shell, such as tcsh or zsh, you may need to edit the appropriate file yourself.
   • You should not normally need to run the OpenMPI reinstallation scripts. The copy of OpenMPI/Pydusa now distributed with the binaries should work on Linux workstations in most cases.
   • Don't forget to restart your shell if you changed the .profile or other scripts
3. Run these programs to see if the install worked:

   e2version.py
   e2speedtest.py
   e2display.py
   e2proc2d.py :64:64:1 test.hdf --process mask.sharp:outer_radius=24

4. If you have problems with any of these programs, the first thing to check is whether you have PYTHONPATH or LD_LIBRARY_PATH set in your shell. While used in previous versions of EMAN, these variables are no longer used, and in some cases may interfere with Anaconda. If they have been set to make some other software package work, but they interfere with the programs above, you will have to unset them, and set them only when you need the other software.

release specific notes

• Ubuntu 16.10 - centos7
• Arch (if kept reasonably current) - centos7

Linux Clusters

• Follow the Linux workstation instructions above.
• When using EMAN2/SPARX/SPHIRE on a cluster, the version of OpenMPI provided with the EMAN2.2 binaries may not be aware of the batch queuing system used to launch jobs on the cluster, and may only be able to run on one node at a time unless you follow the OpenMPI reinstallation instructions below. Follow only ONE of the sets of instructions below.

Use system OpenMPI and NumPy v1.8

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'
3. Rebuild and install Pydusa using the system installed OpenMPI.

   bash <path to EMAN2 directory>/utils/build_pydusa_numpy.sh 1.8
   bash <path to EMAN2 directory>/utils/install_pydusa_numpy.sh 1.8

Rebuild your own OpenMPI, use NumPy v1.8

This option insures that --disable-dlopen is used when compiling OpenMPI, but may lack some system-specific optimizations provided by your sysadmin.

1. Remove the OpenMPI we provided:

   bash <path to EMAN2 directory>/utils/uninstall_openmpi.sh

2. Rebuild OpenMPI.

   bash <path to EMAN2 directory>/utils/build_and_install_openmpi.sh

3. Rebuild and install Pydusa using the system installed OpenMPI:

   bash <path to EMAN2 directory>/utils/build_pydusa_numpy.sh 1.8
   bash <path to EMAN2 directory>/utils/install_pydusa_numpy.sh 1.8

Build against a version of NumPy other than the bundled version (NOT RECOMMENDED)

OpenMPI doesn't depend on NumPy, so changing to a different NumPy version doesn't require OpenMPI to be rebuilt. However, Pydusa and EMAN2 need to be rebuilt.

1. Rebuild and install Pydusa against the desired NumPy version.

   bash <path to EMAN2 directory>/utils/build_pydusa_numpy.sh   <list of NumPy version(s)>
   bash <path to EMAN2 directory>/utils/install_pydusa_numpy.sh <NumPy version>
   bash <path to EMAN2 directory>/utils/build_eman_numpy.sh     <list of NumPy version(s)>
   bash <path to EMAN2 directory>/utils/install_pydusa_numpy.sh <NumPy version>

Windows

We are finally able to provide 64 bit Windows binaries for EMAN2. Notes:

• SPARX/SPHIRE are not supported.
• EMAN2 functionality may not be complete using this first approach. You may get more complete functionality, but with some additional effort using the Linux/Bash shell approach below.
• Even for EMAN2, Windows support remains somewhat marginal, and is provided primarily for utility functions and basic GUI tools, like micrograph evaluation and particle picking. Complete refinements may not work well under Windows. You are welcome to ask questions in the mailing list, but there may be limited help we can provide because we simply don't have Windows machines around for testing.

Native Win7/10 64 bit

1. Download eman2.X.win64.exe
2. Launch the installer, and answer any security questions you are prompted for.

3. In most cases you will want to install: Python Launcher.

Windows 10 - Linux/Bash shell

Windows 10 includes an embeded Ubuntu Linux environment. It is possible to run the EMAN2 Linux binaries within this environment, but you will need to install some additional dependencies to do so.

1. Install "Bash on Windows 10", https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/.

2. When prompted to set a user name, enter root. This should give you an account without a password.

Install OpenGL and X Server, set environment variables

1. Install OpenGL.

   sudo apt-get update
   sudo apt-get install libsm-dev libxrender-dev build-essential libgl1-mesa-dev mesa-utils mesa-common-dev
   sudo apt-get autoremove

2. Install Xming X Server for Windows.

3. Set environment variables.

   export DISPLAY=:0
   glxinfo | grep OpenGL
   export KMP_AFFINITY=disabled # per https://github.com/Microsoft/BashOnWindows/issues/785#issuecomment-238079769

4. Download and install eman2.2.linux64.centos7.sh.

5. Start X Server before running eman2 programs
6. Run these programs to see if the install worked:

   e2version.py
   e2speedtest.py
   e2display.py
   e2proc2d.py :64:64:1 test.hdf --process mask.sharp:outer_radius=24