Diff for "EMAN2/Install/CondaInstall"

Differences between revisions 2 and 4 (spanning 2 versions)

Install into an existing Anaconda setup (all platforms)

To use this approach, you must already have Miniconda or Anaconda installed.
On M1/M2 Macs, make sure you have the ARM64 Anaconda/Miniconda, not Intel.
On Windows 11 machines, you may not use a native Windows Anaconda install, but rather need a Linux Anaconda install within a WSL2 environment!
Update (optional): You may wish to consider updating Anaconda before installing:
```
conda update --all
```
but consider possible impact on other Anaconda environments you may have configured.
Install mamba (optional): We had been recommending that everyone install 'mamba', a MUCH faster alternative to the 'conda' command. However, mamba no longer seems to be installing properly itself with the current (as of Mar 2023) release of Anaconda. So, if you are using a somewhat older Anaconda installation, you may want to consider installing mamba, then using 'mamba' instead of 'conda' when installing packages. If you try to install mamba and it gets stuck for a long time or fails, then just use 'conda' for the EMAN2 install. Conda may take a long time to solve the install. If you want to try installing mamba:
```
conda install mamba -c conda-forge
```
Install: We strongly recommend installing EMAN2 within its own Anaconda/Miniconda environment:
```
conda create -n eman2 eman-dev -c cryoem -c conda-forge
```
Current version:
M1/M2 Macs (Optional): initial support for Tensorflow on the GPU is available via PyPi, but not conda.
```
# with the eman2 environment activated
pip install tensorflow-metal
```
Linux: see the GPU section below.
Activate to Use: Any time you want to use EMAN2 you will need to first activate the correct environment. You can deactivate when done.
```
conda activate eman2
```
Run these programs to see if the install worked:
```
   1 # This will display the exact version you have installed. If you ask for help, provide the full output of this command.
   2 e2version.py
   3 # Relative speed factor of a single core on your computer, 2-3 typ.
   4 e2speedtest.py
   5 # Opens a browser window you can use to view any EMAN2 compatible file in various ways
   6 e2display.py
   7 # Creates a small image with a circle in the middle of it
   8 e2proc2d.py :64:64:1 test.hdf --process mask.sharp:outer_radius=24
   9 # Displays the file you just created
  10 e2display.py test.hdf
```

-  ⇤ ← Revision 2 as of 2023-02-03 08:28:03 → 
  Size: 260
  Editor: TunayDurmaz
  Comment:
+   ← Revision 4 as of 2024-06-06 01:37:27 → ⇥
  Size: 3001
  Editor: TunayDurmaz
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-=== Conda Installation of eman-dev ===
 1. [[EMAN2/Install/SourceInstall#Initial_Setup_.28one_time.29|Install Miniconda and mamba]].
 1. Run
+<<Anchor(Anaconda)>>

=== Install into an existing Anaconda setup (all platforms) ===
 * ''To use this approach, you must already have [[https://docs.conda.io/en/main/miniconda.html|Miniconda]] or [[https://anaconda.com|Anaconda]] installed.''
 * On M1/M2 Macs, make sure you have the ARM64 Anaconda/Miniconda, not Intel.
 * On Windows 11 machines, you may not use a native Windows Anaconda install, but rather need a Linux Anaconda install within a [[https://learn.microsoft.com/en-us/windows/wsl/install|WSL2]] environment!

 1. '''Update (optional):''' You may wish to consider updating Anaconda before installing:
 {{{
conda update --all
}}}
 but consider possible impact on other Anaconda environments you may have configured.
 1. '''Install mamba (optional):''' We had been recommending that everyone install 'mamba', a MUCH faster alternative to the 'conda' command. However, mamba no longer seems to be installing properly itself with the current (as of Mar 2023) release of Anaconda. So, if you are using a somewhat older Anaconda installation, you may want to consider installing mamba, then using 'mamba' instead of 'conda' when installing packages. If you try to install mamba and it gets stuck for a long time or fails, then just use 'conda' for the EMAN2 install. Conda may take a long time to solve the install. If you want to try installing mamba:
 {{{
conda install mamba -c conda-forge
}}}
 1. '''Install:''' We strongly recommend installing EMAN2 within its own Anaconda/Miniconda [[https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html|environment]]:
 {{{
conda create -n eman2 eman-dev -c cryoem -c conda-forge
}}}
 ||Current version: || {{https://anaconda.org/cryoem/eman-dev/badges/version.svg}} {{https://anaconda.org/cryoem/eman-dev/badges/latest_release_date.svg}} {{https://anaconda.org/cryoem/eman-dev/badges/downloads.svg}} ||
 || ||{{https://anaconda.org/cryoem/eman-dev/badges/platforms.svg}}||


 1. '''M1/M2 Macs (Optional):''' initial support for Tensorflow on the GPU is available via PyPi, but not conda.
 {{{
# with the eman2 environment activated
pip install tensorflow-metal
}}}
 1. '''Linux:''' see the [[#GPU|GPU]] section below.
 1. '''Activate to Use:''' Any time you want to use EMAN2 you will need to first activate the correct environment. You can deactivate when done.
 {{{
conda activate eman2
}}}
 1. Run these programs to see if the install worked:
-Line 5:
+Line 37:
-  mamba create -n eman-dev eman-dev -c cryoem -c conda-forge
  conda activate eman-dev
+# This will display the exact version you have installed. If you ask for help, provide the full output of this command.
e2version.py
# Relative speed factor of a single core on your computer, 2-3 typ.
e2speedtest.py
# Opens a browser window you can use to view any EMAN2 compatible file in various ways
e2display.py
# Creates a small image with a circle in the middle of it
e2proc2d.py :64:64:1 test.hdf --process mask.sharp:outer_radius=24
# Displays the file you just created
e2display.py test.hdf

Current version: