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--- eman2:install:sourceinstall [2026/03/06 16:21] – steveludtke
+++ eman2:install:sourceinstall [2026/03/07 00:23] (current) – steveludtke
@@ Line 38: / Line 38: @@
     * Install:
- <code>#!highlight bash
+ <code bash>
 bash <MiniForge-installer>
 </code>
@@ Line 82: / Line 82: @@
- <code>#!highlight bash
+ <code bash>
-conda create -n eman2 eman-dev --only-deps -c cryoem -c conda-forge
+conda create -n eman2 eman-dev --only-deps -c conda-forge -c cryoem
 </code>
  If, and ONLY if, you are installing on a headless machine without graphics, you can alternatively set up the **non-GUI** variant which will not have pyqt and pyopengl. Doing this will severely limit EMAN2's capabilities:
- <code>#!highlight bash
+ <code bash>
-conda create -n eman2 'eman-dev=*=nogui_*' --only-deps -c cryoem -c conda-forge
+conda create -n eman2 'eman-dev=*=nogui_*' --only-deps -c conda-forge -c cryoem
 </code>
@@ Line 99: / Line 99: @@
  Linux + NVidia GPU:
- <code>#!highlight bash
+ <code bash>
 conda activate eman2
 pip install "jax[cuda12]" optax
@@ Line 105: / Line 105: @@
  Mac or other non-Nvidia:
- <code>#!highlight bash
+ <code bash>
 conda activate eman2>
 pip install jax optax
@@ Line 194: / Line 194: @@
 Solutions to potential known problems will be listed here. If these don't help, please report your problem (http://groups.google.com/group/eman2):
+  * **Linux**
+    * On recent linux installs (2025+) when running a tensorflow program you may encounter an error like **ImportError: libtensorflow_cc.so.2: cannot enable executable stack as shared object requires: Invalid argument**. This is a problem with the way conda-forge is compiling tensorflow conflicting with Linux security settings, and has nothing directly to do with EMAN2. It is easy to fix, but the specific method depends on your linux variant. I suggest pasting the exact error you're getting into one of the LLMs (ChatGPT, etc.) and get it to advise you.
+    * This command may help in some situations: //patchelf --clear-execstack $CONDA_PREFIX/lib/libtensorflow_cc.so.2//
   *  **macOS** Users (bash only)
     * On macOS, installation modifies //~/.bash_profile//. If you have a //~/.profile// startup file, creation of //~/.bash_profile// will prevent //~/.profile// from being read. A simple solution is to //source .profile// within //.bash_profile//.