.

docs/Installation/Standlone-installation/index.rst → docs/Installation/Installation/index.rst

@@ -1,3 +1,14 @@
+Installation with Scipion
+================================
+
+The recommended way for users (not developers) to install and use Xmipp is via the 
+`Scipion framework <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_, 
+where you can use Xmipp with other Cryo-EM-related software. 
+
+Xmipp will be installed during Scipion installation (pay attention to not include the flag *-noXmipp*).
+You can also install Xmipp from the `plugin manager of Scipion <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html#installing-other-plugins>`_
+
+
 Standlone-installation
 ====================================
 

docs/Installation/Troubleshooting/index.rst

@@ -0,0 +1,88 @@
+Troubleshooting
+====================================
+
+
+General error while installing/compiling Xmipp (non-development installations)
+==============================================================================
+
+If you are getting an error during the Xmipp compilation, consider to read compilationLog.txt file located in the xmipp floder (by default in scipion2/software/em) and review the `Xmipp's configuration page <https://i2pc.github.io/docs/Utils/ConfigurationF/index.html#configuration-file>`_.
+
+Alternatively, you can go with the plugin manager or by running
+
+::
+
+    scipion3 installb xmippSrc 
+
+If ``ERROR: Could not find target xmippSrc`` is gotten, try to run
+
+::
+
+    scipion3 installp -p scipion-em-xmipp 
+
+
+If the problem persist, don't hesitate to `contact us <https://scipion-em.github.io/docs/release-3.0.0/docs/misc/contact-us.html#contact-us>`__.
+
+
+Compiling Xmipp to be used in both Intel and AMD cores
+======================================================
+
+Xmipp is optimizing the compilation to the architecture found in the compilation
+time. However, this is not a good idea if it must run on both AMD and Intel cores
+at once (e.g. in a cluster or so). To make more flexible the optimization on the
+compilation, then the ``CXXFLAGS`` can be set properly.
+
+Please, just
+
+::
+
+    export CXXFLAGS="-mfma -mavx2 -m3dnow -fomit-frame-pointer -std=c++11 -O3"
+
+before running the Scipion3 installer.
+
+Please, check `Xmipp's configuration page <https://i2pc.github.io/docs/Utils/ConfigurationF/index.html#configuration-file>`_ for more details.
+
+
+Xmipp dependencies
+======================
+
+HDF5
+--------
+
+We sometimes see issues regarding the HDF5 dependency.
+We recommend removing all hdf5 versions and install just hdf5-devel. To do that:
+```
+sudo apt remove hdf5
+sudo apt remove hdf5-devel
+pip uninstall h5py
+```
+Remove all files related to hdf5 in /usr/lib64/libhdf5*, /usr/include/hdf5* and .../anaconda3/include/hdf5*. 
+
+We strongy recommend you to install it via your default package manager:
+`sudo apt-get install libhdf5-dev` 
+If you install it using other package management system (such as Conda), it might lead to compile/link time issues caused by incompatible version being fetched.
+
+
+
+Cannot compile with Java
+-------------------------
+
+::
+
+    Checking Java configuration...
+    /usr/lib/jvm/java-11-openjdk-amd64/bin/javac Xmipp.java
+    /bin/sh: 1: /usr/lib/jvm/java-11-openjdk-amd64/bin/javac: not found
+    Check the JAVAC
+    Cannot compile with Java
+
+Java compiler is missing. Needs to install the jdk-devel version.
+In ubuntu would be like:
+
+::
+
+    sudo apt-get install default-jdk
+
+or activate a jdk with javac using alternatives.  
+
+If this is not the case, and you have <SCIPION_HOME>/config/scipion.conf (optional),
+review the JAVA_XXX variables there. They might be pointing to a non existing JAVA home.
+

docs/index.rst

@@ -32,9 +32,10 @@ the main repository is required and also the installation of the plugins.
     :caption: Installing Xmipp
 
     Installation/Requirements/index
-    Installation/Installation-with-Scipion/index
-    Installation/Standlone-installation/index
-    Installation/InstallationNotes/index
+    Installation/Installation/index
+    Installation/Optionals/index
+    Installation/troubleshooting/index
+
 
 
 .. _Releases-docs: