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eman2:install:binaryinstallanaconda_2.99 [2025/07/06 18:08] – steveludtkeeman2:install:binaryinstallanaconda_2.99 [2025/07/06 18:16] (current) – steveludtke
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     * LD_LIBRARY_PATH, DYLD_LIBRARY_PATH, PYTHONPATH and PYTHONHOME are NO LONGER USED, and should be removed if you have them set.     * LD_LIBRARY_PATH, DYLD_LIBRARY_PATH, PYTHONPATH and PYTHONHOME are NO LONGER USED, and should be removed if you have them set.
     * If you have any of these shell variables set for use with other software, it may be necessary to remove those settings as well. If the tests below fail after installation, this is the first thing to check.     * If you have any of these shell variables set for use with other software, it may be necessary to remove those settings as well. If the tests below fail after installation, this is the first thing to check.
 +
  2. **Download:** [[https://cryoem.bcm.edu/cryoem/downloads/view_eman2_version/33|Download EMAN2.99.47]]  2. **Download:** [[https://cryoem.bcm.edu/cryoem/downloads/view_eman2_version/33|Download EMAN2.99.47]]
  
  3. **Install:**  3. **Install:**
- <code>#!highlight bash+ <code bash>
 bash <path-to-EMAN2-installer> bash <path-to-EMAN2-installer>
 </code> </code>
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     * You will be asked if you want to initialize EMAN2 (conda init). Answer yes, or you won't have access to the 'conda' command in your shell.     * You will be asked if you want to initialize EMAN2 (conda init). Answer yes, or you won't have access to the 'conda' command in your shell.
     * EMAN2 initialization will add a block of code to your //.profile/.bashrc/.zshrc// file. You may check this file after installation to make sure an Anaconda block exists.     * EMAN2 initialization will add a block of code to your //.profile/.bashrc/.zshrc// file. You may check this file after installation to make sure an Anaconda block exists.
 +
  4. **Close Shell** After installation, close your current terminal window/tab, and open a new one. The new terminal should have access to the 'conda' command. Depending on your Anaconda settings, you may need to run //conda activate// before using EMAN2 commands and //conda deactivate// to return to your normal shell settings.  4. **Close Shell** After installation, close your current terminal window/tab, and open a new one. The new terminal should have access to the 'conda' command. Depending on your Anaconda settings, you may need to run //conda activate// before using EMAN2 commands and //conda deactivate// to return to your normal shell settings.
 +
  5. **Test:** Run these programs to see if the install worked:  5. **Test:** Run these programs to see if the install worked:
- <code>#!highlight bash+ <code bash>
 # This will display the exact version you have installed. If you ask for help, provide the full output of this command. # This will display the exact version you have installed. If you ask for help, provide the full output of this command.
 e2version.py e2version.py
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     * If you have any of these shell variables set for use with other software, it may be necessary to remove those settings as well. If the tests below fail after installation, this is the first thing to check.     * If you have any of these shell variables set for use with other software, it may be necessary to remove those settings as well. If the tests below fail after installation, this is the first thing to check.
  2. **Download:** [[https://cryoem.bcm.edu/cryoem/downloads/view_eman2_version/33|Download EMAN2.99.47]]  2. **Download:** [[https://cryoem.bcm.edu/cryoem/downloads/view_eman2_version/33|Download EMAN2.99.47]]
 +
  3. **Install:**  3. **Install:**
- <code>#!highlight bash+ <code bash>
 bash <path-to-EMAN2-installer> bash <path-to-EMAN2-installer>
 </code> </code>
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     * EMAN2 initialization will add a block of code to your //.profile/.bashrc/.zshrc// file. You may check this file after installation to make sure an Anaconda block exists.     * EMAN2 initialization will add a block of code to your //.profile/.bashrc/.zshrc// file. You may check this file after installation to make sure an Anaconda block exists.
  4. Close your current terminal window (you may actually want to log out completely), then open a new terminal. The new terminal should have access to the 'conda' command. If you see (base) at the beginning of your command line, then Anaconda is active, and the following tests can be run. If you want to stop using EMAN2, you can run //conda deactivate//.  4. Close your current terminal window (you may actually want to log out completely), then open a new terminal. The new terminal should have access to the 'conda' command. If you see (base) at the beginning of your command line, then Anaconda is active, and the following tests can be run. If you want to stop using EMAN2, you can run //conda deactivate//.
 +
  5. **Test:** Run these programs to see if the install worked:  5. **Test:** Run these programs to see if the install worked:
- <code>#!highlight bash+ <code bash>
 # This will display the exact version you have installed. If you ask for help, provide the full output of this command. # This will display the exact version you have installed. If you ask for help, provide the full output of this command.
 e2version.py e2version.py
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  4. Install OpenGL.  4. Install OpenGL.
- <code>#!highlight bash+ <code bash>
 sudo apt update sudo apt update
 sudo apt install libsm-dev libxrender-dev build-essential libgl1-mesa-dev mesa-utils mesa-common-dev libglu1-mesa libglu1-mesa-dev mesa-utils sudo apt install libsm-dev libxrender-dev build-essential libgl1-mesa-dev mesa-utils mesa-common-dev libglu1-mesa libglu1-mesa-dev mesa-utils
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  7. Start X Server and set environment variables.  7. Start X Server and set environment variables.
- <code>#!highlight bash+ <code bash>
 export DISPLAY=:0 export DISPLAY=:0
 glxinfo | grep OpenGL glxinfo | grep OpenGL
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  8. Run these programs to see if the install worked:  8. Run these programs to see if the install worked:
- <code>#!highlight bash+ <code bash>
 e2version.py e2version.py
 e2speedtest.py e2speedtest.py
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 This support is limited to Linux, and (potentially with some extra effort) Win 11 with an LSW2 installation. This support is limited to Linux, and (potentially with some extra effort) Win 11 with an LSW2 installation.
  
-Many machines will have CUDA installed already, and if CUDA is an appropriate version, this should work fine with the !TensorFlow version shipped with EMAN2. However, if you are running newer versions of CUDA there may be problems. You can test compatibility quickly with:+Many machines will have CUDA installed already, and if CUDA is an appropriate version, this should work fine with the TensorFlow version shipped with EMAN2. However, if you are running newer versions of CUDA there may be problems. You can test compatibility quickly with:
 <code> <code>
 # Make sure you have your environment set to run EMAN2 programs # Make sure you have your environment set to run EMAN2 programs
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       * Installation depends on linux distribution, try your package manager for CUDA and/or CUDA-toolkit, for example, on Ubuntu:       * Installation depends on linux distribution, try your package manager for CUDA and/or CUDA-toolkit, for example, on Ubuntu:
  
-   <code>+<code>
 apt-get install nvidia-cuda-toolkit apt-get install nvidia-cuda-toolkit
 </code> </code>
   * If the version of CUDA you have installed is incompatible, then you will need to get a compatible tensorflow installed in your Anaconda environment. Here is one possible suggestion:   * If the version of CUDA you have installed is incompatible, then you will need to get a compatible tensorflow installed in your Anaconda environment. Here is one possible suggestion:
- <code>+<code>
 conda remove tensorflow-gpu tensorflow-gpu-base conda remove tensorflow-gpu tensorflow-gpu-base
 pip install tensorflow pip install tensorflow
eman2/install/binaryinstallanaconda_2.99.1751825303.txt.gz · Last modified: by steveludtke