.

Author: albertmena

docs/Installation/Troubleshooting/index.rst

@@ -2,9 +2,9 @@ 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>`_.
+If you are getting an error during the Xmipp compilation, consider to read compilationLog.txt file located in the xmipp folder (by default in scipion3/software/em)/xmippSrc). You can also review the  `requirements of Xmipp <https://i2pc.github.io/docs/Installation/Requirements/index.html>`_.
 
 Alternatively, you can go with the plugin manager or by running
 
@@ -22,39 +22,27 @@ If ``ERROR: Could not find target xmippSrc`` is gotten, try to run
 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.
+HDF5
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Please, just
+We sometimes see issues regarding the HDF5 dependency.
+We recommend removing all hdf5 versions and install just hdf5-devel. To do that:
 
-::
 
-    export CXXFLAGS="-mfma -mavx2 -m3dnow -fomit-frame-pointer -std=c++11 -O3"
+.. code-block:: bash
 
-before running the Scipion3 installer.
+    sudo apt remove hdf5
+    sudo apt remove hdf5-devel
+    pip uninstall h5py
 
-Please, check `Xmipp's configuration page <https://i2pc.github.io/docs/Utils/ConfigurationF/index.html#configuration-file>`_ for more details.
+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:
 
-HDF5
-^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. code-block:: bash
 
-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*. 
+    sudo apt-get install libhdf5-dev
 
-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.